http://beerlab.org/api.php?action=feedcontributions&feedformat=atom&user=MBeer 2026-05-26T03:49:36Z User contributions MediaWiki 1.35.2 http://beerlab.org/index.php?title=Lab_Members&diff=19681 2026-05-20T11:52:37Z

<p>MBeer: </p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:Duke_IGVF_Lab_Pic.jpg|350px]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]]<br /> [[File:Jinwoo_dustin.png|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary2.png|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.png|100px]]<br /> * Matias Lee<br /> [[File:Matias.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.png|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.kaist.ac.kr/en/ KAIST] independent research fellow)<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19680 2025-11-25T00:53:19Z

<p>MBeer: </p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:Duke_IGVF_Lab_Pic.jpg|350px]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]]<br /> [[File:Jinwoo_dustin.png|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary2.png|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.png|100px]]<br /> * Matias Lee<br /> [[File:Matias.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.png|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=File:Jinwoo_dustin.png&diff=19679 2025-11-25T00:50:07Z

<p>MBeer: </p> <hr /> <div></div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19678 2025-11-25T00:49:45Z

<p>MBeer: </p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:Duke_IGVF_Lab_Pic.jpg|350px]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]]<br /> [[File:jinwoo_dustin.png|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary2.png|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.png|100px]]<br /> * Matias Lee<br /> [[File:Matias.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.png|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=File:Matias.jpg&diff=19677 2025-11-17T05:32:16Z

<p>MBeer: </p> <hr /> <div></div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19676 2025-11-17T05:31:47Z

<p>MBeer: </p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:Duke_IGVF_Lab_Pic.jpg|350px]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary2.png|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.png|100px]]<br /> * Matias Lee<br /> [[File:Matias.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.png|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=File:Duke_IGVF_Lab_Pic.jpg&diff=19675 2025-11-17T04:43:42Z

<p>MBeer: </p> <hr /> <div></div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19674 2025-11-17T04:43:21Z

<p>MBeer: /* PI */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:Duke_IGVF_Lab_Pic.jpg|350px]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary2.png|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.png|100px]]<br /> * Sky Li<br /> [[File:Sky.png|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.png|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=Publications&diff=19673 2025-11-09T05:53:02Z

<p>MBeer: </p> <hr /> <div>Full publication list on '''[https://scholar.google.com/citations?hl=en&amp;user=9aH8_eEAAAAJ google scholar]''' or '''[https://orcid.org/0000-0001-9955-3809 Orcid]'''. My student '''[https://beerlab.org/dissertations PhD dissertations]'''.<br /> <br /> * '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''<br /> <br /> * '''[https://www.nature.com/articles/s41467-024-50708-z Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals.]''' Oh JW and Beer MA. Nature Communications 2024.<br /> <br /> * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023 '''[https://beerlab.org/papers/2023%20NG.pdf pdf]'''<br /> <br /> * '''[https://www.nature.com/articles/s41467-021-21368-0 Loop competition and extrusion model predicts CTCF interaction specificity.]''' Xi W, Beer MA. Nature Comms. 2021.<br /> <br /> * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.<br /> <br /> * '''[https://www.nature.com/articles/s41586-020-2493-4 Expanded encyclopaedias of DNA elements in the human and mouse genomes.]''' ENCODE Project Consortium. Nature 2020.<br /> <br /> * '''[https://www.jci.org/articles/view/126726 Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer.]''' Xing M, Ooi WF, Tan J, Qamra A, Lee PH, Li Z, Xu C, Padmanabhan N, Lim JQ, Guo YA, Yao X, Amit M, Ng LM, Sheng T, Wang J, Huang KK, Anene-Nzelu CG, Ho SWT, Ray M, Ma L, Fazzi G, Lim KJ, Wijaya GC, Zhang S, Nandi T, Yan T, Chang MM, Das K, Isa ZFA, Wu J, Yean PPS, Lam YN, Lin JS, Tay ST, Lee M, Keng ATL, Ong X, White K, Rozen SG, Beer MA, Foo RSY, Grabsch H, Skanderup AJ, Li S, Teh BT, Tan P. J. Clin. Invest. 2020<br /> <br /> * '''[https://www.nature.com/articles/s41588-019-0408-9 Genome-scale screens uncover JNK/JUN signaling as a key barrier from pluripotency to human endoderm differentiation.]''' Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh C-L, Yang D, Crespo M, Shukla A, Xiang Q, Dundar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massague J, Garippa R, Evans T, Beer MA, and Huangfu D. Nature Genetics 2019. <br /> <br /> * '''[https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, Adato O, Adhikar A, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar D, Schubach M, Xiong C, Yan Z, Boyle A, Kreimer A, Kulakovskiy IV, Reid J, Unger R, Yosef N, Shendure J, Ahituv N, Kircher M, and Beer MA. Human Mutation 2019. [http://www.beerlab.org/deltasvm_models (models)]<br /> <br /> * '''[https://stm.sciencemag.org/content/11/497/eaaw0790.abstract Epigenetic activation and memory at a novel TGFβ2 enhancer in systemic sclerosis fibroblasts.]''' Shin JY, Beckett JD, Shah A, McMahan Z, Paik J, Sampedro MM, MacFarlane EG, Beer MA, Warren D, Wigley FM, and Dietz HC. Science Translational Medicine 2019.<br /> <br /> * '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy.]''' Xi, W and Beer, MA. PLOS Comp Biol 2018.<br /> <br /> * '''[https://www.sciencedirect.com/science/article/pii/S0002929718303707 Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons.]''' McClymont SA, Hook PW, Soto AI, Reed X, Law WD, Kerans SJ, Waite EL, Briceno NJ, Thole JF, Heckman MG, Diehl NN, Wszolek ZK, Moore CD, Zhu H, Akiyama JA, Dickel DE, Visel A, Pennacchio LA, Ross OA, Beer MA, &amp; McCallion AS. Am. Jour. Human Genetics 2018<br /> <br /> * '''[https://www.nature.com/articles/s41588-018-0156-2 Genetic determinants of co-accessible chromatin regions in activated T cells across humans.]''' Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang S-C, Durand NC, Feng T, De Jager PL, Chang HY, Lieberman Aiden E, Benoist C, Beer MA, Ye CJ &amp; Regev A. Nature Genetics 2018. <br /> <br /> * '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23185/full Predicting enhancer activity and variant impact using gkm-SVM.]''' Beer, MA. Human Mutation 2017.<br /> <br /> * '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23197/full Predicting gene expression in massively parallel reporter assays: A comparative study.]''' Kreimer A, Zeng H, Edwards M, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong N, Li Y, Amin T, Goke J, Mueller N, Kellis, M, Kundaje A, Beer MA, Keles S, Gifford D, and Yosef, N. Human Mutation 2017.<br /> <br /> * '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170403 Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X.]''' Migeon BR, Beer MA, and Bjornsson HT. Plos ONE 2017.<br /> <br /> * '''[http://bioinformatics.oxfordjournals.org/content/early/2016/05/05/bioinformatics.btw203 gkmSVM: an R package for gapped-kmer SVM.]''' [[Media:Bioinformatics-2016-Ghandi-bioinformatics-btw203.pdf|pdf]] [[tutorial]] Ghandi, M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, and Beer MA. Bioinformatics 2016.<br /> <br /> * '''[http://elifesciences.org/content/5/e11613v1 Epigenomic landscapes of retinal rods and cones.]''' Mo, A, Luo, C, Davis, FP, Mukamel, EA, Henry, GL, Nery JR, Urich, MA, Picard, S, Lister, R, Eddy, SR, Beer, MA, Ecker, JR, and Nathans, J. eLife 2016.<br /> <br /> * '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25582907 Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.]''' Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin, A, Tanzer A, Lagarde J, Zaleski C, See L-H, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Nat. Comm 2015.<br /> <br /> * '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140557 Identification of predictive cis-regulatory elements using a discriminative objective function and dynamic search spaces.]''' Karnik, R, and Beer MA. PLOS One 2015.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25413365 Comparison of the transcriptional landscapes between human and mouse tissues.]''' Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP. PNAS 2014.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25409824 A comparative encyclopedia of DNA elements in the mouse genome.]''' Mouse ENCODE Consortium (includes Lee D and Beer MA). 2014. Nature 515:355–364.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25319996 Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis.]''' Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ. 2014. Genome Research.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25033408 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M*, Lee D*, Mohammad-Noori M, and Beer MA. 2014. PLoS Computational Biology 10(7):e1003711.<br /> <br /> * '''[http://www.horizonpress.com/genomeanalysis Mammalian Enhancer Prediction.]''' Lee D, Beer MA. 2014. Genome Analysis: Current Procedures and Applications. Horizon Press. [[Media:book.pdf|pdf]]<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23861010 Robust k-mer Frequency Estimation Using Gapped k-mers.]''' Ghandi M, Mohammad-Noori M, and Beer MA. 2013. Journal of Mathematical Biology. (Epub ahead of print)<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23771147 kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic datasets.]''' Fletez-Brant C*, Lee D*, McCallion AS and Beer MA. 2013. Nucleic Acids Research 41: W544–W556.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23019145 Integration of ChIP-seq and Machine Learning Reveals Enhancers and a Predictive Regulatory Sequence Vocabulary in Melanocytes.]''' Gorkin DU, Lee D, Reed X, Fletez-Brant C, Blessling SL, Loftus SK, Beer MA, Pavan WJ, and McCallion AS. 2012. Genome Research 22:2290-2301.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/22912661 Group Normalization for Genomic Data.]''' Ghandi M, and Beer MA. 2012. PLoS ONE 7:e38695.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/21875935 Discriminative prediction of mammalian enhancers from DNA sequence.]''' Lee D, Karchin R, and Beer MA. 2011. Genome Research 21:2167-2180.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/21720494 Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome.]''' Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon WH, Joore J, Beer MA, Cope L, Pandey A. 2011. J Proteomics Bioinform 4:22-35.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19430481 A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies.]''' Khanna H, Davis EE, Murga-Zamalloa CA, Estrada-Cuzcano A, Lopez I, den Hollander AI, Zonneveld MN, Othman MI, Waseem N, Chakarova CF, Maubaret C, Diaz-Font A, MacDonald I, Muzny DM, Wheeler DA, Morgan M, Lewis LR, Logan CV, Tan PL, Beer MA, Inglehearn CF, Lewis RA, Jacobson SG, Bergmann C, Beales PL, Attié-Bitach T, Johnson CA, Otto EA, Bhattacharya SS, Hildebrandt F, Gibbs RA, Koenekoop RK, Swaroop A, Katsanis N. 2009. Nat Genet. 41:739-45.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19253296 Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach.]''' Yang Y, Chaerkady R, Beer MA, Mendell JT, and Pandey A. 2009. Proteomics 9:1374-1384.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19211792 Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation.]''' Chang T-C, Zeitels LR, Hwang H-W, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, and Mendell JT. 2009. PNAS 106:3384-3389.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/18071029 Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b.]''' McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, and McCallion AS. 2008. Genome Research 18:252-260.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/17540599 Transactivation of miR-34a by p53 Broadly Influences Gene Expression and Promotes Apoptosis.]''' Chang T-C, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, and Mendell JT. 2007. Molecular Cell 26: 745-752.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/15870260 Functional Characterization of a Novel Ku70/80 Pause Site at the H19/Igf2 Imprinting Control Region.]''' Katz DJ, Beer MA, Levorse JM, and Tilghman SM. 2005. Mol Cell Biol 25:3855-3863.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/14672978 Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation.]''' Pritsker M, Liu Y-C, Beer MA, and Tavazoie S. 2004. Genome Research 14:99-108.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence.]''' Beer MA and Tavazoie S. 2004. Cell 117:185-198.<br /> <br /> <br /> ----<br /> <br /> For a full list including my prior work in simulations of plasma turbulence, see '''[https://scholar.google.com/citations?user=9aH8_eEAAAAJ&amp;hl=en&amp;oi=ao my google scholar page.]'''</div>

MBeer http://beerlab.org/index.php?title=Publications&diff=19672 2025-11-09T05:52:26Z

<p>MBeer: </p> <hr /> <div>Full publication list on '''[https://scholar.google.com/citations?hl=en&amp;user=9aH8_eEAAAAJ google scholar]''' or ''https://orcid.org/0000-0001-9955-3809 Orcid'''.<br /> My student '''[https://beerlab.org/dissertations PhD dissertations]'''.<br /> <br /> * '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''<br /> <br /> * '''[https://www.nature.com/articles/s41467-024-50708-z Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals.]''' Oh JW and Beer MA. Nature Communications 2024.<br /> <br /> * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023 '''[https://beerlab.org/papers/2023%20NG.pdf pdf]'''<br /> <br /> * '''[https://www.nature.com/articles/s41467-021-21368-0 Loop competition and extrusion model predicts CTCF interaction specificity.]''' Xi W, Beer MA. Nature Comms. 2021.<br /> <br /> * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.<br /> <br /> * '''[https://www.nature.com/articles/s41586-020-2493-4 Expanded encyclopaedias of DNA elements in the human and mouse genomes.]''' ENCODE Project Consortium. Nature 2020.<br /> <br /> * '''[https://www.jci.org/articles/view/126726 Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer.]''' Xing M, Ooi WF, Tan J, Qamra A, Lee PH, Li Z, Xu C, Padmanabhan N, Lim JQ, Guo YA, Yao X, Amit M, Ng LM, Sheng T, Wang J, Huang KK, Anene-Nzelu CG, Ho SWT, Ray M, Ma L, Fazzi G, Lim KJ, Wijaya GC, Zhang S, Nandi T, Yan T, Chang MM, Das K, Isa ZFA, Wu J, Yean PPS, Lam YN, Lin JS, Tay ST, Lee M, Keng ATL, Ong X, White K, Rozen SG, Beer MA, Foo RSY, Grabsch H, Skanderup AJ, Li S, Teh BT, Tan P. J. Clin. Invest. 2020<br /> <br /> * '''[https://www.nature.com/articles/s41588-019-0408-9 Genome-scale screens uncover JNK/JUN signaling as a key barrier from pluripotency to human endoderm differentiation.]''' Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh C-L, Yang D, Crespo M, Shukla A, Xiang Q, Dundar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massague J, Garippa R, Evans T, Beer MA, and Huangfu D. Nature Genetics 2019. <br /> <br /> * '''[https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, Adato O, Adhikar A, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar D, Schubach M, Xiong C, Yan Z, Boyle A, Kreimer A, Kulakovskiy IV, Reid J, Unger R, Yosef N, Shendure J, Ahituv N, Kircher M, and Beer MA. Human Mutation 2019. [http://www.beerlab.org/deltasvm_models (models)]<br /> <br /> * '''[https://stm.sciencemag.org/content/11/497/eaaw0790.abstract Epigenetic activation and memory at a novel TGFβ2 enhancer in systemic sclerosis fibroblasts.]''' Shin JY, Beckett JD, Shah A, McMahan Z, Paik J, Sampedro MM, MacFarlane EG, Beer MA, Warren D, Wigley FM, and Dietz HC. Science Translational Medicine 2019.<br /> <br /> * '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy.]''' Xi, W and Beer, MA. PLOS Comp Biol 2018.<br /> <br /> * '''[https://www.sciencedirect.com/science/article/pii/S0002929718303707 Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons.]''' McClymont SA, Hook PW, Soto AI, Reed X, Law WD, Kerans SJ, Waite EL, Briceno NJ, Thole JF, Heckman MG, Diehl NN, Wszolek ZK, Moore CD, Zhu H, Akiyama JA, Dickel DE, Visel A, Pennacchio LA, Ross OA, Beer MA, &amp; McCallion AS. Am. Jour. Human Genetics 2018<br /> <br /> * '''[https://www.nature.com/articles/s41588-018-0156-2 Genetic determinants of co-accessible chromatin regions in activated T cells across humans.]''' Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang S-C, Durand NC, Feng T, De Jager PL, Chang HY, Lieberman Aiden E, Benoist C, Beer MA, Ye CJ &amp; Regev A. Nature Genetics 2018. <br /> <br /> * '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23185/full Predicting enhancer activity and variant impact using gkm-SVM.]''' Beer, MA. Human Mutation 2017.<br /> <br /> * '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23197/full Predicting gene expression in massively parallel reporter assays: A comparative study.]''' Kreimer A, Zeng H, Edwards M, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong N, Li Y, Amin T, Goke J, Mueller N, Kellis, M, Kundaje A, Beer MA, Keles S, Gifford D, and Yosef, N. Human Mutation 2017.<br /> <br /> * '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170403 Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X.]''' Migeon BR, Beer MA, and Bjornsson HT. Plos ONE 2017.<br /> <br /> * '''[http://bioinformatics.oxfordjournals.org/content/early/2016/05/05/bioinformatics.btw203 gkmSVM: an R package for gapped-kmer SVM.]''' [[Media:Bioinformatics-2016-Ghandi-bioinformatics-btw203.pdf|pdf]] [[tutorial]] Ghandi, M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, and Beer MA. Bioinformatics 2016.<br /> <br /> * '''[http://elifesciences.org/content/5/e11613v1 Epigenomic landscapes of retinal rods and cones.]''' Mo, A, Luo, C, Davis, FP, Mukamel, EA, Henry, GL, Nery JR, Urich, MA, Picard, S, Lister, R, Eddy, SR, Beer, MA, Ecker, JR, and Nathans, J. eLife 2016.<br /> <br /> * '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25582907 Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.]''' Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin, A, Tanzer A, Lagarde J, Zaleski C, See L-H, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Nat. Comm 2015.<br /> <br /> * '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140557 Identification of predictive cis-regulatory elements using a discriminative objective function and dynamic search spaces.]''' Karnik, R, and Beer MA. PLOS One 2015.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25413365 Comparison of the transcriptional landscapes between human and mouse tissues.]''' Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP. PNAS 2014.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25409824 A comparative encyclopedia of DNA elements in the mouse genome.]''' Mouse ENCODE Consortium (includes Lee D and Beer MA). 2014. Nature 515:355–364.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25319996 Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis.]''' Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ. 2014. Genome Research.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25033408 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M*, Lee D*, Mohammad-Noori M, and Beer MA. 2014. PLoS Computational Biology 10(7):e1003711.<br /> <br /> * '''[http://www.horizonpress.com/genomeanalysis Mammalian Enhancer Prediction.]''' Lee D, Beer MA. 2014. Genome Analysis: Current Procedures and Applications. Horizon Press. [[Media:book.pdf|pdf]]<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23861010 Robust k-mer Frequency Estimation Using Gapped k-mers.]''' Ghandi M, Mohammad-Noori M, and Beer MA. 2013. Journal of Mathematical Biology. (Epub ahead of print)<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23771147 kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic datasets.]''' Fletez-Brant C*, Lee D*, McCallion AS and Beer MA. 2013. Nucleic Acids Research 41: W544–W556.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23019145 Integration of ChIP-seq and Machine Learning Reveals Enhancers and a Predictive Regulatory Sequence Vocabulary in Melanocytes.]''' Gorkin DU, Lee D, Reed X, Fletez-Brant C, Blessling SL, Loftus SK, Beer MA, Pavan WJ, and McCallion AS. 2012. Genome Research 22:2290-2301.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/22912661 Group Normalization for Genomic Data.]''' Ghandi M, and Beer MA. 2012. PLoS ONE 7:e38695.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/21875935 Discriminative prediction of mammalian enhancers from DNA sequence.]''' Lee D, Karchin R, and Beer MA. 2011. Genome Research 21:2167-2180.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/21720494 Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome.]''' Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon WH, Joore J, Beer MA, Cope L, Pandey A. 2011. J Proteomics Bioinform 4:22-35.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19430481 A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies.]''' Khanna H, Davis EE, Murga-Zamalloa CA, Estrada-Cuzcano A, Lopez I, den Hollander AI, Zonneveld MN, Othman MI, Waseem N, Chakarova CF, Maubaret C, Diaz-Font A, MacDonald I, Muzny DM, Wheeler DA, Morgan M, Lewis LR, Logan CV, Tan PL, Beer MA, Inglehearn CF, Lewis RA, Jacobson SG, Bergmann C, Beales PL, Attié-Bitach T, Johnson CA, Otto EA, Bhattacharya SS, Hildebrandt F, Gibbs RA, Koenekoop RK, Swaroop A, Katsanis N. 2009. Nat Genet. 41:739-45.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19253296 Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach.]''' Yang Y, Chaerkady R, Beer MA, Mendell JT, and Pandey A. 2009. Proteomics 9:1374-1384.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19211792 Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation.]''' Chang T-C, Zeitels LR, Hwang H-W, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, and Mendell JT. 2009. PNAS 106:3384-3389.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/18071029 Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b.]''' McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, and McCallion AS. 2008. Genome Research 18:252-260.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/17540599 Transactivation of miR-34a by p53 Broadly Influences Gene Expression and Promotes Apoptosis.]''' Chang T-C, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, and Mendell JT. 2007. Molecular Cell 26: 745-752.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/15870260 Functional Characterization of a Novel Ku70/80 Pause Site at the H19/Igf2 Imprinting Control Region.]''' Katz DJ, Beer MA, Levorse JM, and Tilghman SM. 2005. Mol Cell Biol 25:3855-3863.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/14672978 Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation.]''' Pritsker M, Liu Y-C, Beer MA, and Tavazoie S. 2004. Genome Research 14:99-108.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence.]''' Beer MA and Tavazoie S. 2004. Cell 117:185-198.<br /> <br /> <br /> ----<br /> <br /> For a full list including my prior work in simulations of plasma turbulence, see '''[https://scholar.google.com/citations?user=9aH8_eEAAAAJ&amp;hl=en&amp;oi=ao my google scholar page.]'''</div>

MBeer http://beerlab.org/index.php?title=Publications&diff=19671 2025-11-09T05:51:04Z

<p>MBeer: </p> <hr /> <div>Full publication list on '''[https://scholar.google.com/citations?hl=en&amp;user=9aH8_eEAAAAJ google scholar]''' or ''https://orcid.org/0000-0001-9955-3809 Orcid'''.<br /> <br /> * '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''<br /> <br /> * '''[https://www.nature.com/articles/s41467-024-50708-z Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals.]''' Oh JW and Beer MA. Nature Communications 2024.<br /> <br /> * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023 '''[https://beerlab.org/papers/2023%20NG.pdf pdf]'''<br /> <br /> * '''[https://www.nature.com/articles/s41467-021-21368-0 Loop competition and extrusion model predicts CTCF interaction specificity.]''' Xi W, Beer MA. Nature Comms. 2021.<br /> <br /> * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.<br /> <br /> * '''[https://www.nature.com/articles/s41586-020-2493-4 Expanded encyclopaedias of DNA elements in the human and mouse genomes.]''' ENCODE Project Consortium. Nature 2020.<br /> <br /> * '''[https://www.jci.org/articles/view/126726 Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer.]''' Xing M, Ooi WF, Tan J, Qamra A, Lee PH, Li Z, Xu C, Padmanabhan N, Lim JQ, Guo YA, Yao X, Amit M, Ng LM, Sheng T, Wang J, Huang KK, Anene-Nzelu CG, Ho SWT, Ray M, Ma L, Fazzi G, Lim KJ, Wijaya GC, Zhang S, Nandi T, Yan T, Chang MM, Das K, Isa ZFA, Wu J, Yean PPS, Lam YN, Lin JS, Tay ST, Lee M, Keng ATL, Ong X, White K, Rozen SG, Beer MA, Foo RSY, Grabsch H, Skanderup AJ, Li S, Teh BT, Tan P. J. Clin. Invest. 2020<br /> <br /> * '''[https://www.nature.com/articles/s41588-019-0408-9 Genome-scale screens uncover JNK/JUN signaling as a key barrier from pluripotency to human endoderm differentiation.]''' Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh C-L, Yang D, Crespo M, Shukla A, Xiang Q, Dundar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massague J, Garippa R, Evans T, Beer MA, and Huangfu D. Nature Genetics 2019. <br /> <br /> * '''[https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, Adato O, Adhikar A, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar D, Schubach M, Xiong C, Yan Z, Boyle A, Kreimer A, Kulakovskiy IV, Reid J, Unger R, Yosef N, Shendure J, Ahituv N, Kircher M, and Beer MA. Human Mutation 2019. [http://www.beerlab.org/deltasvm_models (models)]<br /> <br /> * '''[https://stm.sciencemag.org/content/11/497/eaaw0790.abstract Epigenetic activation and memory at a novel TGFβ2 enhancer in systemic sclerosis fibroblasts.]''' Shin JY, Beckett JD, Shah A, McMahan Z, Paik J, Sampedro MM, MacFarlane EG, Beer MA, Warren D, Wigley FM, and Dietz HC. Science Translational Medicine 2019.<br /> <br /> * '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy.]''' Xi, W and Beer, MA. PLOS Comp Biol 2018.<br /> <br /> * '''[https://www.sciencedirect.com/science/article/pii/S0002929718303707 Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons.]''' McClymont SA, Hook PW, Soto AI, Reed X, Law WD, Kerans SJ, Waite EL, Briceno NJ, Thole JF, Heckman MG, Diehl NN, Wszolek ZK, Moore CD, Zhu H, Akiyama JA, Dickel DE, Visel A, Pennacchio LA, Ross OA, Beer MA, &amp; McCallion AS. Am. Jour. Human Genetics 2018<br /> <br /> * '''[https://www.nature.com/articles/s41588-018-0156-2 Genetic determinants of co-accessible chromatin regions in activated T cells across humans.]''' Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang S-C, Durand NC, Feng T, De Jager PL, Chang HY, Lieberman Aiden E, Benoist C, Beer MA, Ye CJ &amp; Regev A. Nature Genetics 2018. <br /> <br /> * '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23185/full Predicting enhancer activity and variant impact using gkm-SVM.]''' Beer, MA. Human Mutation 2017.<br /> <br /> * '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23197/full Predicting gene expression in massively parallel reporter assays: A comparative study.]''' Kreimer A, Zeng H, Edwards M, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong N, Li Y, Amin T, Goke J, Mueller N, Kellis, M, Kundaje A, Beer MA, Keles S, Gifford D, and Yosef, N. Human Mutation 2017.<br /> <br /> * '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170403 Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X.]''' Migeon BR, Beer MA, and Bjornsson HT. Plos ONE 2017.<br /> <br /> * '''[http://bioinformatics.oxfordjournals.org/content/early/2016/05/05/bioinformatics.btw203 gkmSVM: an R package for gapped-kmer SVM.]''' [[Media:Bioinformatics-2016-Ghandi-bioinformatics-btw203.pdf|pdf]] [[tutorial]] Ghandi, M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, and Beer MA. Bioinformatics 2016.<br /> <br /> * '''[http://elifesciences.org/content/5/e11613v1 Epigenomic landscapes of retinal rods and cones.]''' Mo, A, Luo, C, Davis, FP, Mukamel, EA, Henry, GL, Nery JR, Urich, MA, Picard, S, Lister, R, Eddy, SR, Beer, MA, Ecker, JR, and Nathans, J. eLife 2016.<br /> <br /> * '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25582907 Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.]''' Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin, A, Tanzer A, Lagarde J, Zaleski C, See L-H, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Nat. Comm 2015.<br /> <br /> * '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140557 Identification of predictive cis-regulatory elements using a discriminative objective function and dynamic search spaces.]''' Karnik, R, and Beer MA. PLOS One 2015.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25413365 Comparison of the transcriptional landscapes between human and mouse tissues.]''' Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP. PNAS 2014.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25409824 A comparative encyclopedia of DNA elements in the mouse genome.]''' Mouse ENCODE Consortium (includes Lee D and Beer MA). 2014. Nature 515:355–364.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25319996 Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis.]''' Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ. 2014. Genome Research.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25033408 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M*, Lee D*, Mohammad-Noori M, and Beer MA. 2014. PLoS Computational Biology 10(7):e1003711.<br /> <br /> * '''[http://www.horizonpress.com/genomeanalysis Mammalian Enhancer Prediction.]''' Lee D, Beer MA. 2014. Genome Analysis: Current Procedures and Applications. Horizon Press. [[Media:book.pdf|pdf]]<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23861010 Robust k-mer Frequency Estimation Using Gapped k-mers.]''' Ghandi M, Mohammad-Noori M, and Beer MA. 2013. Journal of Mathematical Biology. (Epub ahead of print)<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23771147 kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic datasets.]''' Fletez-Brant C*, Lee D*, McCallion AS and Beer MA. 2013. Nucleic Acids Research 41: W544–W556.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23019145 Integration of ChIP-seq and Machine Learning Reveals Enhancers and a Predictive Regulatory Sequence Vocabulary in Melanocytes.]''' Gorkin DU, Lee D, Reed X, Fletez-Brant C, Blessling SL, Loftus SK, Beer MA, Pavan WJ, and McCallion AS. 2012. Genome Research 22:2290-2301.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/22912661 Group Normalization for Genomic Data.]''' Ghandi M, and Beer MA. 2012. PLoS ONE 7:e38695.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/21875935 Discriminative prediction of mammalian enhancers from DNA sequence.]''' Lee D, Karchin R, and Beer MA. 2011. Genome Research 21:2167-2180.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/21720494 Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome.]''' Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon WH, Joore J, Beer MA, Cope L, Pandey A. 2011. J Proteomics Bioinform 4:22-35.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19430481 A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies.]''' Khanna H, Davis EE, Murga-Zamalloa CA, Estrada-Cuzcano A, Lopez I, den Hollander AI, Zonneveld MN, Othman MI, Waseem N, Chakarova CF, Maubaret C, Diaz-Font A, MacDonald I, Muzny DM, Wheeler DA, Morgan M, Lewis LR, Logan CV, Tan PL, Beer MA, Inglehearn CF, Lewis RA, Jacobson SG, Bergmann C, Beales PL, Attié-Bitach T, Johnson CA, Otto EA, Bhattacharya SS, Hildebrandt F, Gibbs RA, Koenekoop RK, Swaroop A, Katsanis N. 2009. Nat Genet. 41:739-45.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19253296 Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach.]''' Yang Y, Chaerkady R, Beer MA, Mendell JT, and Pandey A. 2009. Proteomics 9:1374-1384.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19211792 Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation.]''' Chang T-C, Zeitels LR, Hwang H-W, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, and Mendell JT. 2009. PNAS 106:3384-3389.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/18071029 Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b.]''' McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, and McCallion AS. 2008. Genome Research 18:252-260.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/17540599 Transactivation of miR-34a by p53 Broadly Influences Gene Expression and Promotes Apoptosis.]''' Chang T-C, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, and Mendell JT. 2007. Molecular Cell 26: 745-752.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/15870260 Functional Characterization of a Novel Ku70/80 Pause Site at the H19/Igf2 Imprinting Control Region.]''' Katz DJ, Beer MA, Levorse JM, and Tilghman SM. 2005. Mol Cell Biol 25:3855-3863.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/14672978 Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation.]''' Pritsker M, Liu Y-C, Beer MA, and Tavazoie S. 2004. Genome Research 14:99-108.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence.]''' Beer MA and Tavazoie S. 2004. Cell 117:185-198.<br /> <br /> <br /> ----<br /> <br /> For a full list including my prior work in simulations of plasma turbulence, see '''[https://scholar.google.com/citations?user=9aH8_eEAAAAJ&amp;hl=en&amp;oi=ao my google scholar page.]'''</div>

MBeer http://beerlab.org/index.php?title=Resources&diff=19670 2025-10-28T02:28:15Z

<p>MBeer: </p> <hr /> <div>[http://www.beerlab.org/dissertations PhD Dissertations from Beer lab]<br /> <br /> [http://www.beerlab.org/gkmsvm gkm-SVM software (PLOS Computational Biology 2014, Bioinformatics 2016)]<br /> <br /> [http://www.beerlab.org/deltasvm deltaSVM software (Nature Genetics 2015)]<br /> <br /> [https://github.com/Dongwon-Lee/lsgkm ls-gkm software (Bioinformatics 2016)]<br /> <br /> [http://www.beerlab.org/deltasvm_models deltaSVM ENCODE models (Human Mutation 2019)]<br /> <br /> [http://www.beerlab.org/kmersvm kmer-SVM server (Nucleic Acids Research 2013) (out of date, use gkm-SVM)]<br /> <br /> [http://www.beerlab.org/p300enhancer P300 enhancers (Genome Research 2011) (out of date, use gkm-SVM)]<br /> <br /> [http://www.ee.surrey.ac.uk/Teaching/Unix/ Unix Tutorial 1]<br /> <br /> [https://www.unixtutorial.org/basic-unix-commands Unix Tutorial 2]<br /> <br /> [http://www.rgrjr.com/emacs/emacs_cheat.html Emacs Summary]<br /> <br /> [https://www.atmos.albany.edu/daes/atmclasses/atm350/vi_cheat_sheet.pdf Vi Command Summary]<br /> <br /> [[useful textbooks]]<br /> <br /> [[useful JHU graduate courses]]<br /> <br /> [[useful review articles]]<br /> <br /> [[Twelve Things I Wish They Taught in School]]<br /> <br /> [https://www.youtube.com/watch?app=desktop&amp;v=hV41QEKiMlM&amp;list=PLVV0r6CmEsFzDA6mtmKQEgWfcIu49J4nN&amp;index=94&amp;fbclid=IwAR2N6Pu7bJID4ys_G9UlsYZSzT6RQeeGU188FcB2HVKKGJZ-W968gnhP-24&amp;ab_channel=WebofStories-LifeStoriesofRemarkablePeople Freeman Dyson discussing how to respond positively to criticism]<br /> <br /> [[Max Planck on how science progresses]]<br /> <br /> [http://www.beerlab.org/SCHWARZENEGGER_5_RULES_FOR_SUCCESS.mp3 Five rules for success]<br /> <br /> [[important information for recommendations]]<br /> <br /> [[important information for PhD program applicants]]</div>

MBeer http://beerlab.org/index.php?title=Computational_Regulatory_Genomics&diff=19669 2025-08-31T01:24:28Z

<p>MBeer: </p> <hr /> <div>&lt;h2&gt;Computational Regulatory Genomics, Gene Regulatory Networks, and Transcriptional Regulation &lt;br&gt; Beer Lab&lt;/h2&gt; __NOTOC__ __NOTITLE__<br /> &lt;metadesc&gt;Computational Regulatory Genomics, Gene Regulatory Networks, and Transcriptional Regulation in the Beer Lab for graduate PhD and postdoctoral research in BME and IGM at Johns Hopkins, top ranking programs modeling DNA and systems biology.&lt;/metadesc&gt;<br /> &lt;h3&gt;[[Recent News ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;[[Lab Members ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Publications]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Postdoctoral Positions Available]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Resources]]&lt;/h3&gt;<br /> <br /> [[File:Beer_Michael_small.jpg|link=http://www.bme.jhu.edu/people/faculty/michael-beer/]] [[File:EncodeNatureGraphic_small.png]] [[File:dyn_net.gif]]<br /> <br /> [[File:Igvf_logo.png|150px]] &amp;nbsp;&amp;nbsp; [[File:Encode_logo.png]] &amp;nbsp;&amp;nbsp; [[File:Nhgri_logo.jpg|250px]] &amp;nbsp;&amp;nbsp;[[File:hopkins_logo.jpg|200px]]<br /> <br /> We are in the '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ Department of Biomedical Engineering]''' and the '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer McKusick-Nathans Department of Genetic Medicine]''' at Johns Hopkins University. You can apply for graduate study in my lab through '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ BME]''' or the Ph.D. program in '''[https://www.hopkinsmedicine.org/genetic-medicine/education-training/human-genetics-genomics-graduate-program Human Genetics and Genomics.]'''<br /> <br /> &lt;h3&gt;Research Interests: &lt;/h3&gt; The ultimate goal of our research is to understand how gene regulatory information is encoded in genomic DNA sequence.<br /> <br /> We have recently made significant progress using AI/ML to understand how DNA sequence specifies cell-type specific enhancer activity, target gene activation through looping constraints, and how dynamic enhancer-gene regulatory networks control cell-fate decisions and contribute to human disease. For details, see:<br /> <br /> * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023<br /> <br /> * '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 <br /> <br /> * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.<br /> <br /> * '''[https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, et al. Human Mutation 2019. <br /> <br /> * '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.<br /> <br /> * '''[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003711 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M, Lee D, Mohammad-Noori M, and Beer MA. 2014. PLOS Computational Biology. July 17, 2014.<br /> <br /> and other [[Publications]].<br /> <br /> Our work uses functional genomics DNase-seq, ATAC-seq, ChIP-seq, RNA-seq, CRISPR, MPRA, Hi-C, and chromatin state data to computationally identify combinations of transcription factor binding sites which operate to define the activity of cell-type specific enhancers and their activation of target genes. We are currently focused on:<br /> <br /> * improving AI/ML methods to build more accurate models of enhancer activity<br /> <br /> * predicting the impact of mutations on enhancer activity and their contributions to disease <br /> <br /> * using AI/ML models to build and test dynamic gene regulatory networks with targeted CRISPR perturbation<br /> <br /> * using large scale datasets (ENCODE/IGVF) and CRISPR to constrain models of enhancer-promoter interactions and DNA looping mechanisms<br /> <br /> * using this sequence based regulatory code to understand mechanisms of gene regulatory network disruption in cancer and develop therapeutic strategies<br /> <br /> We are located in the McKusick-Nathans Institute of Genetic Medicine, and the Department of Biomedical Engineering, which has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Genomics, Bioinformatics, and Computational Biology at Johns Hopkins, including research in Systems Biology, AI, Machine Learning, and Dynamic Gene Regulatory Network Modeling.<br /> <br /> &lt;h3&gt;About Computational Biology in JHU Biomedical Engineering:&lt;/h3&gt;<br /> <br /> The Department of Biomedical Engineering has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Bioinformatics and Computational Biology at Johns Hopkins. Students with backgrounds in Physics, Mathematics, Computer Science and Engineering are encouraged to apply. Opportunities for research include: Computational Medicine, Genomics, Systems Biology, Machine Learning, and Network Modeling. Graduate students in Johns Hopkins' Biomedical Engineering programs can select research advisors from throughout Johns Hopkins' Medical Institutions, Whiting School of Engineering, and Krieger School of Arts and Sciences.<br /> <br /> &lt;!--&lt;h3&gt;[http://karchinlab.org/bme-compbio-jhu Visit Some Computational Labs at Johns Hopkins]&lt;/h3&gt;<br /> <br /> &lt;h3&gt;[http://ccb.jhu.edu/ Center for Computational Biology at Johns Hopkins]&lt;/h3&gt; --&gt;<br /> <br /> [[File:bmesmall.png]]</div>

MBeer http://beerlab.org/index.php?title=Computational_Regulatory_Genomics&diff=19668 2025-08-31T01:23:38Z

<p>MBeer: </p> <hr /> <div>&lt;h2&gt;Computational Regulatory Genomics, Gene Regulatory Networks, and Transcriptional Regulation in the Beer Lab&lt;/h2&gt; __NOTOC__ __NOTITLE__<br /> &lt;metadesc&gt;Computational Regulatory Genomics, Gene Regulatory Networks, and Transcriptional Regulation in the Beer Lab for graduate PhD and postdoctoral research in BME and IGM at Johns Hopkins, top ranking programs modeling DNA and systems biology.&lt;/metadesc&gt;<br /> &lt;h3&gt;[[Recent News ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;[[Lab Members ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Publications]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Postdoctoral Positions Available]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Resources]]&lt;/h3&gt;<br /> <br /> [[File:Beer_Michael_small.jpg|link=http://www.bme.jhu.edu/people/faculty/michael-beer/]] [[File:EncodeNatureGraphic_small.png]] [[File:dyn_net.gif]]<br /> <br /> [[File:Igvf_logo.png|150px]] &amp;nbsp;&amp;nbsp; [[File:Encode_logo.png]] &amp;nbsp;&amp;nbsp; [[File:Nhgri_logo.jpg|250px]] &amp;nbsp;&amp;nbsp;[[File:hopkins_logo.jpg|200px]]<br /> <br /> We are in the '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ Department of Biomedical Engineering]''' and the '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer McKusick-Nathans Department of Genetic Medicine]''' at Johns Hopkins University. You can apply for graduate study in my lab through '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ BME]''' or the Ph.D. program in '''[https://www.hopkinsmedicine.org/genetic-medicine/education-training/human-genetics-genomics-graduate-program Human Genetics and Genomics.]'''<br /> <br /> &lt;h3&gt;Research Interests: &lt;/h3&gt; The ultimate goal of our research is to understand how gene regulatory information is encoded in genomic DNA sequence.<br /> <br /> We have recently made significant progress using AI/ML to understand how DNA sequence specifies cell-type specific enhancer activity, target gene activation through looping constraints, and how dynamic enhancer-gene regulatory networks control cell-fate decisions and contribute to human disease. For details, see:<br /> <br /> * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023<br /> <br /> * '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 <br /> <br /> * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.<br /> <br /> * '''[https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, et al. Human Mutation 2019. <br /> <br /> * '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.<br /> <br /> * '''[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003711 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M, Lee D, Mohammad-Noori M, and Beer MA. 2014. PLOS Computational Biology. July 17, 2014.<br /> <br /> and other [[Publications]].<br /> <br /> Our work uses functional genomics DNase-seq, ATAC-seq, ChIP-seq, RNA-seq, CRISPR, MPRA, Hi-C, and chromatin state data to computationally identify combinations of transcription factor binding sites which operate to define the activity of cell-type specific enhancers and their activation of target genes. We are currently focused on:<br /> <br /> * improving AI/ML methods to build more accurate models of enhancer activity<br /> <br /> * predicting the impact of mutations on enhancer activity and their contributions to disease <br /> <br /> * using AI/ML models to build and test dynamic gene regulatory networks with targeted CRISPR perturbation<br /> <br /> * using large scale datasets (ENCODE/IGVF) and CRISPR to constrain models of enhancer-promoter interactions and DNA looping mechanisms<br /> <br /> * using this sequence based regulatory code to understand mechanisms of gene regulatory network disruption in cancer and develop therapeutic strategies<br /> <br /> We are located in the McKusick-Nathans Institute of Genetic Medicine, and the Department of Biomedical Engineering, which has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Genomics, Bioinformatics, and Computational Biology at Johns Hopkins, including research in Systems Biology, AI, Machine Learning, and Dynamic Gene Regulatory Network Modeling.<br /> <br /> &lt;h3&gt;About Computational Biology in JHU Biomedical Engineering:&lt;/h3&gt;<br /> <br /> The Department of Biomedical Engineering has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Bioinformatics and Computational Biology at Johns Hopkins. Students with backgrounds in Physics, Mathematics, Computer Science and Engineering are encouraged to apply. Opportunities for research include: Computational Medicine, Genomics, Systems Biology, Machine Learning, and Network Modeling. Graduate students in Johns Hopkins' Biomedical Engineering programs can select research advisors from throughout Johns Hopkins' Medical Institutions, Whiting School of Engineering, and Krieger School of Arts and Sciences.<br /> <br /> &lt;!--&lt;h3&gt;[http://karchinlab.org/bme-compbio-jhu Visit Some Computational Labs at Johns Hopkins]&lt;/h3&gt;<br /> <br /> &lt;h3&gt;[http://ccb.jhu.edu/ Center for Computational Biology at Johns Hopkins]&lt;/h3&gt; --&gt;<br /> <br /> [[File:bmesmall.png]]</div>

MBeer http://beerlab.org/index.php?title=Recent_News&diff=19667 2025-08-18T20:28:52Z

<p>MBeer: </p> <hr /> <div>'''[https://substack.com/app-link/post?publication_id=5291662&amp;post_id=171276375&amp;utm_source=post-email-title&amp;utm_campaign=email-post-title&amp;isFreemail=true&amp;r=87ovy&amp;token=eyJ1c2VyX2lkIjoxMzc5NTc3NCwicG9zdF9pZCI6MTcxMjc2Mzc1LCJpYXQiOjE3NTU1MjYxNzYsImV4cCI6MTc1ODExODE3NiwiaXNzIjoicHViLTUyOTE2NjIiLCJzdWIiOiJwb3N0LXJlYWN0aW9uIn0.QlvDHMclEvRyA3Qu5_RS60R_AN4vT45_eY_j_w6B0w0 Terence Tao on Republican War on Science.]''' The new administration, in just its first six months, has deliberately attacked and weakened almost all the supporting pillars of this ecosystem. '''[https://beerlab.org/papers/disengagement_is_no_longer_a_viable_option.pdf pdf]'''<br /> <br /> '''[https://engineering.jhu.edu/magazine/2024/06/delivering-on-the-promise-of-personalized-medicine/ Delivering on the Promise of Personalized Medicine.]''' JHU Engineering magazine news article on AI with a bit on our CRISPR enhancer modeling in cell-state transitions.<br /> <br /> '''[https://physicsworld.com/a/iter-fusion-reactor-hit-by-massive-decade-long-delay-and-e5bn-price-hike/ ITER fusion project decade long delay and massive cost increase.]''' This is the closest thing to a feasible fusion power plant, and there is more bad news for economic feasibility. It was a great education, but I have no regrets leaving that field over 20 years ago.<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2024 Jin Woo awarded Mette Strand JHU Young Investigator Day Award.]'''<br /> <br /> '''[https://hub.jhu.edu/2023/08/10/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ JHU HUB News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]''' I would add that this work was an equal collaboration between our lab and Danwei Huangfu's lab at MSKCC, which was underplayed in the JHU articles.<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ BME News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]'''<br /> <br /> '''[https://mlbbs.bme.jhu.edu Applications are now open for the Machine Learning in the Basic Biomedical Sciences Postdoctoral Program.]'''<br /> <br /> '''[https://thanhnien.vn/hanh-trinh-tro-thanh-nha-nghien-cuu-ung-thu-hang-dau-the-gioi-post1423871.html?fbclid=IwAR0MRKXdjyduDtZYyS3Rf5QZgzCReUY3IP-mMi2ru1TnzaApDx54-RLKXko My first interview in a Vietnamese newspaper.]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/Impact-of-Genomic-Variation-on-Function-Consortium#awardees Beer Lab awarded IGVF Consortium Grant.]'''<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2021/ Wang awarded Bae Gyo Jung JHU Young Investigator Day Award.]''' '''[https://www.bme.jhu.edu/news-events/news/three-from-hopkins-bme-recognized-at-young-investigators-day/ also here.]'''<br /> <br /> '''[https://med.stanford.edu/genetics/events/encode-2021.html Jin-Woo, Wang, and Dustin selected for talks at 2021 ENCODE Consortium Meeting.]'''<br /> <br /> '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Wang discovered Enhancer-Promoter interaction prediction is harder than it looks.]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi5-regulation-saturation.html Dustin leads integrative analysis of CAGI5 regulation saturation challenge.]'''<br /> <br /> '''[https://www.nature.com/articles/d41586-020-00335-7 Highly cited researcher banned from journal board for citation abuse.]''' I put this here because K-C Chou wrote &lt;b&gt;many&lt;/b&gt; papers with and appears to have been a mentor to Bin Liu, who plagiarized our gkm-SVM paper as described in the several items below. Eleven papers co-authored by Bin Liu and K-C Chou were (self-)cited in the paper which plagiarized our gkm-SVM paper. See also the original reporting from '''[https://academic.oup.com/bioinformatics/article/35/18/3217/5304360 Bioinformatics]''' and '''[https://www.sciencedirect.com/science/article/pii/S0022519320300278?via%3Dihub Journal of Theoretical Biology.]''' I'm glad K-C Chou finally got called out on his gross citation manipulation, but the problem is broader than just these two journals. Although K-C Chou was removed, his proteges were and still are on the boards of many other journals and continue their citation inflation through mechanisms not discussed in these articles. For example, these articles do not mention that the authors who added the ~30 citations to K-C Chou during the review process may have been explicitly promised future citations from K-C Chou in return. The group of authors who cite K-C Chou is small, but they all cite each other multiple times in each paper, exponentially inflating citations of all members of the group.<br /> The scientific publishing industry has been manipulated by their lack of attention to these problems. If they want to investigate, all they have to do is look at who continues to cite '''[https://academic.oup.com/nar/article/43/W1/W65/2467922 this useless paper]''' over '''[https://scholar.google.com/scholar?hl=en&amp;as_sdt=0%2C21&amp;q=Pse-in-One%3A+a+web+server+for+generating+various+modes+of+pseudo+components+of+DNA%2C+RNA%2C+and+protein+sequences&amp;btnG= 600 times]'''. You may notice a pattern. None of these papers are real and each of these journals allowed it to happen for some unknown reasons. The list of these journals is clear from the citation patterns.<br /> <br /> '''[https://retractionwatch.com/2018/03/20/over-a-dozen-board-members-resigned-after-a-journal-refused-to-retract-a-paper-today-its-retracted/ Scientific Reports finally retracts paper plagiarizing our gkm-SVM paper.]''' '''[http://www.bmj.com/content/360/bmj.k1386 related article]'''<br /> <br /> Don't do this: '''[http://www.sixthtone.com/news/1001156/19-academics-resign-from-journal-over-alleged-plagiarism/ plagiarism1]'''<br /> '''[http://retractionwatch.com/2017/10/17/21-faculty-johns-hopkins-threaten-resign-board-journal-doesnt-retract-paper/ plagiarism2]'''<br /> '''[http://retractionwatch.com/2017/10/10/board-member-resigns-journal-handling-paper-accused-plagiarism/ plagiarism3]'''<br /> '''[http://retractionwatch.com/2017/11/07/17-johns-hopkins-researchers-resign-protest-ed-board-nature-journal/ plagiarism4]'''<br /> '''[http://www.the-scientist.com/?articles.view/articleNo/50888/title/Mass-Resignation-from-Scientific-Reports-s-Editorial-Board/ plagiarism5]'''<br /> <br /> '''[http://www.jhunewsletter.com/2017/02/16/professor-beer-awarded-1-8-million-nih-grant/ JHU Newsletter article on our ENCODE grant by Anna Chen]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements NHGRI on next phase of ENCODE project consortium]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-awarded-1-8-million-grant-from-nih/ Beer Lab awarded NIH ENCODE grant]'''<br /> <br /> '''[http://www.nature.com/nature/journal/v538/n7624/full/538275a.html Our computational work featured in Nature news article on &quot;The Dark Side of the Human Genome&quot;]'''<br /> <br /> '''[http://www.beerlab.org/gkmsvm New R package for gkmSVM and deltaSVM released]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi4-2eqtl.html gkmSVM among top-scoring methods for CAGI4 eQTL prediction challenge] '''<br /> <br /> '''[http://www.iscb.org/recomb-regsysgen2015-submissions/recomb-regsysgen2015-top-papers-reading-papers deltaSVM paper voted Top 10 in Regulatory Genomics 2015] '''<br /> <br /> '''[http://www.nature.com/ng/journal/v47/n8/full/ng.3364.html Nature Genetics News &amp; Views article on our deltaSVM paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/vulnerabilities_in_genomes_dimmer_switches_should_shed_light_on_hundreds_of_complex_diseases Nature Genetics paper on impact of regulatory variants]'''<br /> <br /> '''[http://www.newsweek.com/humans-and-mice-are-both-more-similar-and-different-previously-thought-285635 Newsweek article on Mouse ENCODE paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/scientists_map_mouse_genomes_mission_control_centers Mouse ENCODE Consortium paper in Nature]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/unraveling-the-genetic-underpinning-of-disease/ Beer Lab awarded NIH grant for regulatory contributions to disease. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-improves-methodology-for-predicting-disease-enabling-genetic-mutations/ Beer Lab improves methodology for predicting disease enabling genetic mutations. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/dongwon-lee-paper-voted-top-10-of-2011/ kmer-SVM Genome Research paper voted Top 10 in Regulatory Genomics.] '''<br /> <br /> '''[http://www.hopkinsmedicine.org/institute_basic_biomedical_sciences/news_events/Announcements/2013_04_YID.html Dongwon Lee awarded Young Investigator Day Award.] '''</div>

MBeer http://beerlab.org/index.php?title=Recent_News&diff=19666 2025-08-18T20:23:29Z

<p>MBeer: </p> <hr /> <div>'''[https://substack.com/app-link/post?publication_id=5291662&amp;post_id=171276375&amp;utm_source=post-email-title&amp;utm_campaign=email-post-title&amp;isFreemail=true&amp;r=87ovy&amp;token=eyJ1c2VyX2lkIjoxMzc5NTc3NCwicG9zdF9pZCI6MTcxMjc2Mzc1LCJpYXQiOjE3NTU1MjYxNzYsImV4cCI6MTc1ODExODE3NiwiaXNzIjoicHViLTUyOTE2NjIiLCJzdWIiOiJwb3N0LXJlYWN0aW9uIn0.QlvDHMclEvRyA3Qu5_RS60R_AN4vT45_eY_j_w6B0w0 Terence Tao on Republican War on Science.]''' The luxury of disengagement is no longer a viable option. '''[https://beerlab.org/papers/disengagement_is_no_longer_a_viable_option.pdf pdf]'''<br /> <br /> '''[https://engineering.jhu.edu/magazine/2024/06/delivering-on-the-promise-of-personalized-medicine/ Delivering on the Promise of Personalized Medicine.]''' JHU Engineering magazine news article on AI with a bit on our CRISPR enhancer modeling in cell-state transitions.<br /> <br /> '''[https://physicsworld.com/a/iter-fusion-reactor-hit-by-massive-decade-long-delay-and-e5bn-price-hike/ ITER fusion project decade long delay and massive cost increase.]''' This is the closest thing to a feasible fusion power plant, and there is more bad news for economic feasibility. It was a great education, but I have no regrets leaving that field over 20 years ago.<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2024 Jin Woo awarded Mette Strand JHU Young Investigator Day Award.]'''<br /> <br /> '''[https://hub.jhu.edu/2023/08/10/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ JHU HUB News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]''' I would add that this work was an equal collaboration between our lab and Danwei Huangfu's lab at MSKCC, which was underplayed in the JHU articles.<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ BME News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]'''<br /> <br /> '''[https://mlbbs.bme.jhu.edu Applications are now open for the Machine Learning in the Basic Biomedical Sciences Postdoctoral Program.]'''<br /> <br /> '''[https://thanhnien.vn/hanh-trinh-tro-thanh-nha-nghien-cuu-ung-thu-hang-dau-the-gioi-post1423871.html?fbclid=IwAR0MRKXdjyduDtZYyS3Rf5QZgzCReUY3IP-mMi2ru1TnzaApDx54-RLKXko My first interview in a Vietnamese newspaper.]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/Impact-of-Genomic-Variation-on-Function-Consortium#awardees Beer Lab awarded IGVF Consortium Grant.]'''<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2021/ Wang awarded Bae Gyo Jung JHU Young Investigator Day Award.]''' '''[https://www.bme.jhu.edu/news-events/news/three-from-hopkins-bme-recognized-at-young-investigators-day/ also here.]'''<br /> <br /> '''[https://med.stanford.edu/genetics/events/encode-2021.html Jin-Woo, Wang, and Dustin selected for talks at 2021 ENCODE Consortium Meeting.]'''<br /> <br /> '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Wang discovered Enhancer-Promoter interaction prediction is harder than it looks.]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi5-regulation-saturation.html Dustin leads integrative analysis of CAGI5 regulation saturation challenge.]'''<br /> <br /> '''[https://www.nature.com/articles/d41586-020-00335-7 Highly cited researcher banned from journal board for citation abuse.]''' I put this here because K-C Chou wrote &lt;b&gt;many&lt;/b&gt; papers with and appears to have been a mentor to Bin Liu, who plagiarized our gkm-SVM paper as described in the several items below. Eleven papers co-authored by Bin Liu and K-C Chou were (self-)cited in the paper which plagiarized our gkm-SVM paper. See also the original reporting from '''[https://academic.oup.com/bioinformatics/article/35/18/3217/5304360 Bioinformatics]''' and '''[https://www.sciencedirect.com/science/article/pii/S0022519320300278?via%3Dihub Journal of Theoretical Biology.]''' I'm glad K-C Chou finally got called out on his gross citation manipulation, but the problem is broader than just these two journals. Although K-C Chou was removed, his proteges were and still are on the boards of many other journals and continue their citation inflation through mechanisms not discussed in these articles. For example, these articles do not mention that the authors who added the ~30 citations to K-C Chou during the review process may have been explicitly promised future citations from K-C Chou in return. The group of authors who cite K-C Chou is small, but they all cite each other multiple times in each paper, exponentially inflating citations of all members of the group.<br /> The scientific publishing industry has been manipulated by their lack of attention to these problems. If they want to investigate, all they have to do is look at who continues to cite '''[https://academic.oup.com/nar/article/43/W1/W65/2467922 this useless paper]''' over '''[https://scholar.google.com/scholar?hl=en&amp;as_sdt=0%2C21&amp;q=Pse-in-One%3A+a+web+server+for+generating+various+modes+of+pseudo+components+of+DNA%2C+RNA%2C+and+protein+sequences&amp;btnG= 600 times]'''. You may notice a pattern. None of these papers are real and each of these journals allowed it to happen for some unknown reasons. The list of these journals is clear from the citation patterns.<br /> <br /> '''[https://retractionwatch.com/2018/03/20/over-a-dozen-board-members-resigned-after-a-journal-refused-to-retract-a-paper-today-its-retracted/ Scientific Reports finally retracts paper plagiarizing our gkm-SVM paper.]''' '''[http://www.bmj.com/content/360/bmj.k1386 related article]'''<br /> <br /> Don't do this: '''[http://www.sixthtone.com/news/1001156/19-academics-resign-from-journal-over-alleged-plagiarism/ plagiarism1]'''<br /> '''[http://retractionwatch.com/2017/10/17/21-faculty-johns-hopkins-threaten-resign-board-journal-doesnt-retract-paper/ plagiarism2]'''<br /> '''[http://retractionwatch.com/2017/10/10/board-member-resigns-journal-handling-paper-accused-plagiarism/ plagiarism3]'''<br /> '''[http://retractionwatch.com/2017/11/07/17-johns-hopkins-researchers-resign-protest-ed-board-nature-journal/ plagiarism4]'''<br /> '''[http://www.the-scientist.com/?articles.view/articleNo/50888/title/Mass-Resignation-from-Scientific-Reports-s-Editorial-Board/ plagiarism5]'''<br /> <br /> '''[http://www.jhunewsletter.com/2017/02/16/professor-beer-awarded-1-8-million-nih-grant/ JHU Newsletter article on our ENCODE grant by Anna Chen]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements NHGRI on next phase of ENCODE project consortium]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-awarded-1-8-million-grant-from-nih/ Beer Lab awarded NIH ENCODE grant]'''<br /> <br /> '''[http://www.nature.com/nature/journal/v538/n7624/full/538275a.html Our computational work featured in Nature news article on &quot;The Dark Side of the Human Genome&quot;]'''<br /> <br /> '''[http://www.beerlab.org/gkmsvm New R package for gkmSVM and deltaSVM released]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi4-2eqtl.html gkmSVM among top-scoring methods for CAGI4 eQTL prediction challenge] '''<br /> <br /> '''[http://www.iscb.org/recomb-regsysgen2015-submissions/recomb-regsysgen2015-top-papers-reading-papers deltaSVM paper voted Top 10 in Regulatory Genomics 2015] '''<br /> <br /> '''[http://www.nature.com/ng/journal/v47/n8/full/ng.3364.html Nature Genetics News &amp; Views article on our deltaSVM paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/vulnerabilities_in_genomes_dimmer_switches_should_shed_light_on_hundreds_of_complex_diseases Nature Genetics paper on impact of regulatory variants]'''<br /> <br /> '''[http://www.newsweek.com/humans-and-mice-are-both-more-similar-and-different-previously-thought-285635 Newsweek article on Mouse ENCODE paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/scientists_map_mouse_genomes_mission_control_centers Mouse ENCODE Consortium paper in Nature]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/unraveling-the-genetic-underpinning-of-disease/ Beer Lab awarded NIH grant for regulatory contributions to disease. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-improves-methodology-for-predicting-disease-enabling-genetic-mutations/ Beer Lab improves methodology for predicting disease enabling genetic mutations. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/dongwon-lee-paper-voted-top-10-of-2011/ kmer-SVM Genome Research paper voted Top 10 in Regulatory Genomics.] '''<br /> <br /> '''[http://www.hopkinsmedicine.org/institute_basic_biomedical_sciences/news_events/Announcements/2013_04_YID.html Dongwon Lee awarded Young Investigator Day Award.] '''</div>

MBeer http://beerlab.org/index.php?title=Recent_News&diff=19665 2025-08-18T20:22:39Z

<p>MBeer: </p> <hr /> <div>'''[https://substack.com/app-link/post?publication_id=5291662&amp;post_id=171276375&amp;utm_source=post-email-title&amp;utm_campaign=email-post-title&amp;isFreemail=true&amp;r=87ovy&amp;token=eyJ1c2VyX2lkIjoxMzc5NTc3NCwicG9zdF9pZCI6MTcxMjc2Mzc1LCJpYXQiOjE3NTU1MjYxNzYsImV4cCI6MTc1ODExODE3NiwiaXNzIjoicHViLTUyOTE2NjIiLCJzdWIiOiJwb3N0LXJlYWN0aW9uIn0.QlvDHMclEvRyA3Qu5_RS60R_AN4vT45_eY_j_w6B0w0 Terrance Tao on Republican War on Science.]''' The luxury of disengagement is no longer a viable option. '''[https://beerlab.org/papers/disengagement_is_no_longer_a_viable_option.pdf pdf]'''<br /> <br /> '''[https://engineering.jhu.edu/magazine/2024/06/delivering-on-the-promise-of-personalized-medicine/ Delivering on the Promise of Personalized Medicine.]''' JHU Engineering magazine news article on AI with a bit on our CRISPR enhancer modeling in cell-state transitions.<br /> <br /> '''[https://physicsworld.com/a/iter-fusion-reactor-hit-by-massive-decade-long-delay-and-e5bn-price-hike/ ITER fusion project decade long delay and massive cost increase.]''' This is the closest thing to a feasible fusion power plant, and there is more bad news for economic feasibility. It was a great education, but I have no regrets leaving that field over 20 years ago.<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2024 Jin Woo awarded Mette Strand JHU Young Investigator Day Award.]'''<br /> <br /> '''[https://hub.jhu.edu/2023/08/10/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ JHU HUB News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]''' I would add that this work was an equal collaboration between our lab and Danwei Huangfu's lab at MSKCC, which was underplayed in the JHU articles.<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ BME News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]'''<br /> <br /> '''[https://mlbbs.bme.jhu.edu Applications are now open for the Machine Learning in the Basic Biomedical Sciences Postdoctoral Program.]'''<br /> <br /> '''[https://thanhnien.vn/hanh-trinh-tro-thanh-nha-nghien-cuu-ung-thu-hang-dau-the-gioi-post1423871.html?fbclid=IwAR0MRKXdjyduDtZYyS3Rf5QZgzCReUY3IP-mMi2ru1TnzaApDx54-RLKXko My first interview in a Vietnamese newspaper.]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/Impact-of-Genomic-Variation-on-Function-Consortium#awardees Beer Lab awarded IGVF Consortium Grant.]'''<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2021/ Wang awarded Bae Gyo Jung JHU Young Investigator Day Award.]''' '''[https://www.bme.jhu.edu/news-events/news/three-from-hopkins-bme-recognized-at-young-investigators-day/ also here.]'''<br /> <br /> '''[https://med.stanford.edu/genetics/events/encode-2021.html Jin-Woo, Wang, and Dustin selected for talks at 2021 ENCODE Consortium Meeting.]'''<br /> <br /> '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Wang discovered Enhancer-Promoter interaction prediction is harder than it looks.]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi5-regulation-saturation.html Dustin leads integrative analysis of CAGI5 regulation saturation challenge.]'''<br /> <br /> '''[https://www.nature.com/articles/d41586-020-00335-7 Highly cited researcher banned from journal board for citation abuse.]''' I put this here because K-C Chou wrote &lt;b&gt;many&lt;/b&gt; papers with and appears to have been a mentor to Bin Liu, who plagiarized our gkm-SVM paper as described in the several items below. Eleven papers co-authored by Bin Liu and K-C Chou were (self-)cited in the paper which plagiarized our gkm-SVM paper. See also the original reporting from '''[https://academic.oup.com/bioinformatics/article/35/18/3217/5304360 Bioinformatics]''' and '''[https://www.sciencedirect.com/science/article/pii/S0022519320300278?via%3Dihub Journal of Theoretical Biology.]''' I'm glad K-C Chou finally got called out on his gross citation manipulation, but the problem is broader than just these two journals. Although K-C Chou was removed, his proteges were and still are on the boards of many other journals and continue their citation inflation through mechanisms not discussed in these articles. For example, these articles do not mention that the authors who added the ~30 citations to K-C Chou during the review process may have been explicitly promised future citations from K-C Chou in return. The group of authors who cite K-C Chou is small, but they all cite each other multiple times in each paper, exponentially inflating citations of all members of the group.<br /> The scientific publishing industry has been manipulated by their lack of attention to these problems. If they want to investigate, all they have to do is look at who continues to cite '''[https://academic.oup.com/nar/article/43/W1/W65/2467922 this useless paper]''' over '''[https://scholar.google.com/scholar?hl=en&amp;as_sdt=0%2C21&amp;q=Pse-in-One%3A+a+web+server+for+generating+various+modes+of+pseudo+components+of+DNA%2C+RNA%2C+and+protein+sequences&amp;btnG= 600 times]'''. You may notice a pattern. None of these papers are real and each of these journals allowed it to happen for some unknown reasons. The list of these journals is clear from the citation patterns.<br /> <br /> '''[https://retractionwatch.com/2018/03/20/over-a-dozen-board-members-resigned-after-a-journal-refused-to-retract-a-paper-today-its-retracted/ Scientific Reports finally retracts paper plagiarizing our gkm-SVM paper.]''' '''[http://www.bmj.com/content/360/bmj.k1386 related article]'''<br /> <br /> Don't do this: '''[http://www.sixthtone.com/news/1001156/19-academics-resign-from-journal-over-alleged-plagiarism/ plagiarism1]'''<br /> '''[http://retractionwatch.com/2017/10/17/21-faculty-johns-hopkins-threaten-resign-board-journal-doesnt-retract-paper/ plagiarism2]'''<br /> '''[http://retractionwatch.com/2017/10/10/board-member-resigns-journal-handling-paper-accused-plagiarism/ plagiarism3]'''<br /> '''[http://retractionwatch.com/2017/11/07/17-johns-hopkins-researchers-resign-protest-ed-board-nature-journal/ plagiarism4]'''<br /> '''[http://www.the-scientist.com/?articles.view/articleNo/50888/title/Mass-Resignation-from-Scientific-Reports-s-Editorial-Board/ plagiarism5]'''<br /> <br /> '''[http://www.jhunewsletter.com/2017/02/16/professor-beer-awarded-1-8-million-nih-grant/ JHU Newsletter article on our ENCODE grant by Anna Chen]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements NHGRI on next phase of ENCODE project consortium]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-awarded-1-8-million-grant-from-nih/ Beer Lab awarded NIH ENCODE grant]'''<br /> <br /> '''[http://www.nature.com/nature/journal/v538/n7624/full/538275a.html Our computational work featured in Nature news article on &quot;The Dark Side of the Human Genome&quot;]'''<br /> <br /> '''[http://www.beerlab.org/gkmsvm New R package for gkmSVM and deltaSVM released]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi4-2eqtl.html gkmSVM among top-scoring methods for CAGI4 eQTL prediction challenge] '''<br /> <br /> '''[http://www.iscb.org/recomb-regsysgen2015-submissions/recomb-regsysgen2015-top-papers-reading-papers deltaSVM paper voted Top 10 in Regulatory Genomics 2015] '''<br /> <br /> '''[http://www.nature.com/ng/journal/v47/n8/full/ng.3364.html Nature Genetics News &amp; Views article on our deltaSVM paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/vulnerabilities_in_genomes_dimmer_switches_should_shed_light_on_hundreds_of_complex_diseases Nature Genetics paper on impact of regulatory variants]'''<br /> <br /> '''[http://www.newsweek.com/humans-and-mice-are-both-more-similar-and-different-previously-thought-285635 Newsweek article on Mouse ENCODE paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/scientists_map_mouse_genomes_mission_control_centers Mouse ENCODE Consortium paper in Nature]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/unraveling-the-genetic-underpinning-of-disease/ Beer Lab awarded NIH grant for regulatory contributions to disease. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-improves-methodology-for-predicting-disease-enabling-genetic-mutations/ Beer Lab improves methodology for predicting disease enabling genetic mutations. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/dongwon-lee-paper-voted-top-10-of-2011/ kmer-SVM Genome Research paper voted Top 10 in Regulatory Genomics.] '''<br /> <br /> '''[http://www.hopkinsmedicine.org/institute_basic_biomedical_sciences/news_events/Announcements/2013_04_YID.html Dongwon Lee awarded Young Investigator Day Award.] '''</div>

MBeer http://beerlab.org/index.php?title=Recent_News&diff=19664 2025-08-18T20:21:33Z

<p>MBeer: </p> <hr /> <div>'''[https://substack.com/app-link/post?publication_id=5291662&amp;post_id=171276375&amp;utm_source=post-email-title&amp;utm_campaign=email-post-title&amp;isFreemail=true&amp;r=87ovy&amp;token=eyJ1c2VyX2lkIjoxMzc5NTc3NCwicG9zdF9pZCI6MTcxMjc2Mzc1LCJpYXQiOjE3NTU1MjYxNzYsImV4cCI6MTc1ODExODE3NiwiaXNzIjoicHViLTUyOTE2NjIiLCJzdWIiOiJwb3N0LXJlYWN0aW9uIn0.QlvDHMclEvRyA3Qu5_RS60R_AN4vT45_eY_j_w6B0w0 Terrance Tao on Republican War on Science.]''' , The luxury of disengagement is no longer a viable option. '''[https://beerlab.org/papers/papers/disengagement_is_no_longer_a_viable_option.pdf pdf]'''<br /> <br /> '''[https://engineering.jhu.edu/magazine/2024/06/delivering-on-the-promise-of-personalized-medicine/ Delivering on the Promise of Personalized Medicine.]''' JHU Engineering magazine news article on AI with a bit on our CRISPR enhancer modeling in cell-state transitions.<br /> <br /> '''[https://physicsworld.com/a/iter-fusion-reactor-hit-by-massive-decade-long-delay-and-e5bn-price-hike/ ITER fusion project decade long delay and massive cost increase.]''' This is the closest thing to a feasible fusion power plant, and there is more bad news for economic feasibility. It was a great education, but I have no regrets leaving that field over 20 years ago.<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2024 Jin Woo awarded Mette Strand JHU Young Investigator Day Award.]'''<br /> <br /> '''[https://hub.jhu.edu/2023/08/10/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ JHU HUB News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]''' I would add that this work was an equal collaboration between our lab and Danwei Huangfu's lab at MSKCC, which was underplayed in the JHU articles.<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ BME News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]'''<br /> <br /> '''[https://mlbbs.bme.jhu.edu Applications are now open for the Machine Learning in the Basic Biomedical Sciences Postdoctoral Program.]'''<br /> <br /> '''[https://thanhnien.vn/hanh-trinh-tro-thanh-nha-nghien-cuu-ung-thu-hang-dau-the-gioi-post1423871.html?fbclid=IwAR0MRKXdjyduDtZYyS3Rf5QZgzCReUY3IP-mMi2ru1TnzaApDx54-RLKXko My first interview in a Vietnamese newspaper.]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/Impact-of-Genomic-Variation-on-Function-Consortium#awardees Beer Lab awarded IGVF Consortium Grant.]'''<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2021/ Wang awarded Bae Gyo Jung JHU Young Investigator Day Award.]''' '''[https://www.bme.jhu.edu/news-events/news/three-from-hopkins-bme-recognized-at-young-investigators-day/ also here.]'''<br /> <br /> '''[https://med.stanford.edu/genetics/events/encode-2021.html Jin-Woo, Wang, and Dustin selected for talks at 2021 ENCODE Consortium Meeting.]'''<br /> <br /> '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Wang discovered Enhancer-Promoter interaction prediction is harder than it looks.]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi5-regulation-saturation.html Dustin leads integrative analysis of CAGI5 regulation saturation challenge.]'''<br /> <br /> '''[https://www.nature.com/articles/d41586-020-00335-7 Highly cited researcher banned from journal board for citation abuse.]''' I put this here because K-C Chou wrote &lt;b&gt;many&lt;/b&gt; papers with and appears to have been a mentor to Bin Liu, who plagiarized our gkm-SVM paper as described in the several items below. Eleven papers co-authored by Bin Liu and K-C Chou were (self-)cited in the paper which plagiarized our gkm-SVM paper. See also the original reporting from '''[https://academic.oup.com/bioinformatics/article/35/18/3217/5304360 Bioinformatics]''' and '''[https://www.sciencedirect.com/science/article/pii/S0022519320300278?via%3Dihub Journal of Theoretical Biology.]''' I'm glad K-C Chou finally got called out on his gross citation manipulation, but the problem is broader than just these two journals. Although K-C Chou was removed, his proteges were and still are on the boards of many other journals and continue their citation inflation through mechanisms not discussed in these articles. For example, these articles do not mention that the authors who added the ~30 citations to K-C Chou during the review process may have been explicitly promised future citations from K-C Chou in return. The group of authors who cite K-C Chou is small, but they all cite each other multiple times in each paper, exponentially inflating citations of all members of the group.<br /> The scientific publishing industry has been manipulated by their lack of attention to these problems. If they want to investigate, all they have to do is look at who continues to cite '''[https://academic.oup.com/nar/article/43/W1/W65/2467922 this useless paper]''' over '''[https://scholar.google.com/scholar?hl=en&amp;as_sdt=0%2C21&amp;q=Pse-in-One%3A+a+web+server+for+generating+various+modes+of+pseudo+components+of+DNA%2C+RNA%2C+and+protein+sequences&amp;btnG= 600 times]'''. You may notice a pattern. None of these papers are real and each of these journals allowed it to happen for some unknown reasons. The list of these journals is clear from the citation patterns.<br /> <br /> '''[https://retractionwatch.com/2018/03/20/over-a-dozen-board-members-resigned-after-a-journal-refused-to-retract-a-paper-today-its-retracted/ Scientific Reports finally retracts paper plagiarizing our gkm-SVM paper.]''' '''[http://www.bmj.com/content/360/bmj.k1386 related article]'''<br /> <br /> Don't do this: '''[http://www.sixthtone.com/news/1001156/19-academics-resign-from-journal-over-alleged-plagiarism/ plagiarism1]'''<br /> '''[http://retractionwatch.com/2017/10/17/21-faculty-johns-hopkins-threaten-resign-board-journal-doesnt-retract-paper/ plagiarism2]'''<br /> '''[http://retractionwatch.com/2017/10/10/board-member-resigns-journal-handling-paper-accused-plagiarism/ plagiarism3]'''<br /> '''[http://retractionwatch.com/2017/11/07/17-johns-hopkins-researchers-resign-protest-ed-board-nature-journal/ plagiarism4]'''<br /> '''[http://www.the-scientist.com/?articles.view/articleNo/50888/title/Mass-Resignation-from-Scientific-Reports-s-Editorial-Board/ plagiarism5]'''<br /> <br /> '''[http://www.jhunewsletter.com/2017/02/16/professor-beer-awarded-1-8-million-nih-grant/ JHU Newsletter article on our ENCODE grant by Anna Chen]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements NHGRI on next phase of ENCODE project consortium]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-awarded-1-8-million-grant-from-nih/ Beer Lab awarded NIH ENCODE grant]'''<br /> <br /> '''[http://www.nature.com/nature/journal/v538/n7624/full/538275a.html Our computational work featured in Nature news article on &quot;The Dark Side of the Human Genome&quot;]'''<br /> <br /> '''[http://www.beerlab.org/gkmsvm New R package for gkmSVM and deltaSVM released]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi4-2eqtl.html gkmSVM among top-scoring methods for CAGI4 eQTL prediction challenge] '''<br /> <br /> '''[http://www.iscb.org/recomb-regsysgen2015-submissions/recomb-regsysgen2015-top-papers-reading-papers deltaSVM paper voted Top 10 in Regulatory Genomics 2015] '''<br /> <br /> '''[http://www.nature.com/ng/journal/v47/n8/full/ng.3364.html Nature Genetics News &amp; Views article on our deltaSVM paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/vulnerabilities_in_genomes_dimmer_switches_should_shed_light_on_hundreds_of_complex_diseases Nature Genetics paper on impact of regulatory variants]'''<br /> <br /> '''[http://www.newsweek.com/humans-and-mice-are-both-more-similar-and-different-previously-thought-285635 Newsweek article on Mouse ENCODE paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/scientists_map_mouse_genomes_mission_control_centers Mouse ENCODE Consortium paper in Nature]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/unraveling-the-genetic-underpinning-of-disease/ Beer Lab awarded NIH grant for regulatory contributions to disease. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-improves-methodology-for-predicting-disease-enabling-genetic-mutations/ Beer Lab improves methodology for predicting disease enabling genetic mutations. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/dongwon-lee-paper-voted-top-10-of-2011/ kmer-SVM Genome Research paper voted Top 10 in Regulatory Genomics.] '''<br /> <br /> '''[http://www.hopkinsmedicine.org/institute_basic_biomedical_sciences/news_events/Announcements/2013_04_YID.html Dongwon Lee awarded Young Investigator Day Award.] '''</div>

MBeer http://beerlab.org/index.php?title=File:Sky.png&diff=19663 2024-12-03T04:16:54Z

<p>MBeer: </p> <hr /> <div></div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19662 2024-12-03T04:16:39Z

<p>MBeer: /* Graduate students */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary2.png|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.png|100px]]<br /> * Sky Li<br /> [[File:Sky.png|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.png|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=File:Andrew.png&diff=19661 2024-12-03T04:12:22Z

<p>MBeer: </p> <hr /> <div></div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19660 2024-12-03T04:11:14Z

<p>MBeer: /* Graduate students */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary2.png|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.png|100px]]<br /> * Sky Li<br /> [[File:Sky.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.png|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19659 2024-12-03T04:10:54Z

<p>MBeer: /* Graduate students */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary2.png|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.jpeg|100px]]<br /> * Sky Li<br /> [[File:Sky.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.png|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=File:Gary2.png&diff=19658 2024-12-03T04:07:56Z

<p>MBeer: </p> <hr /> <div></div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19657 2024-12-03T04:06:57Z

<p>MBeer: /* Graduate students */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary2.png|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.jpg|100px]]<br /> * Sky Li<br /> [[File:Sky.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.png|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=File:Jason.png&diff=19656 2024-12-03T04:03:51Z

<p>MBeer: </p> <hr /> <div></div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19655 2024-12-03T04:02:27Z

<p>MBeer: /* Current Undergraduates */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary.jpg|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.jpg|100px]]<br /> * Sky Li<br /> [[File:Sky.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.png|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=File:Jason.pdf&diff=19654 2024-12-03T04:00:47Z

<p>MBeer: </p> <hr /> <div></div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19653 2024-12-03T04:00:30Z

<p>MBeer: /* Current Undergraduates */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary.jpg|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.jpg|100px]]<br /> * Sky Li<br /> [[File:Sky.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.pdf|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=File:Daniel.jpg&diff=19652 2024-12-03T03:53:38Z

<p>MBeer: </p> <hr /> <div></div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19651 2024-12-03T03:53:28Z

<p>MBeer: /* Current Undergraduates */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary.jpg|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.jpg|100px]]<br /> * Sky Li<br /> [[File:Sky.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.jpg|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19650 2024-12-03T03:52:48Z

<p>MBeer: /* Current Undergraduates */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary.jpg|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.jpg|100px]]<br /> * Sky Li<br /> [[File:Sky.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.jpg|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.png|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=File:Brooke.png&diff=19649 2024-12-03T03:50:17Z

<p>MBeer: </p> <hr /> <div></div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19648 2024-12-03T03:50:02Z

<p>MBeer: /* Graduate students */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary.jpg|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.jpg|100px]]<br /> * Sky Li<br /> [[File:Sky.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.png|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.jpg|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19647 2024-12-03T03:46:59Z

<p>MBeer: /* Current Undergraduates */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary.jpg|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.jpg|100px]]<br /> * Sky Li<br /> [[File:Sky.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.jpg|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> [[File:Jason.jpg|100px]]<br /> * Daniel Chen<br /> [[File:Daniel.jpg|100px]]<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19646 2024-12-03T03:46:32Z

<p>MBeer: /* Graduate students */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary.jpg|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Andrew.jpg|100px]]<br /> * Sky Li<br /> [[File:Sky.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.jpg|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> * Daniel Chen<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19645 2024-12-03T03:46:07Z

<p>MBeer: /* Graduate students */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> [[File:Gary.jpg|100px]]<br /> * Andrew Rojnuckarin<br /> [[File:Gary.jpg|100px]]<br /> * Sky Li<br /> [[File:Sky.jpg|100px]]<br /> * Brooke Szczesny (HGG rotation)<br /> [[File:Brooke.jpg|100px]]<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> * Daniel Chen<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19644 2024-12-03T03:32:12Z

<p>MBeer: /* Former graduate students */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Dustin Shigaki<br /> [[File:Dustin.jpg|100px]]<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> * Andrew Rojnuckarin<br /> * Sky Li<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> * Daniel Chen<br /> <br /> ==Former graduate students==<br /> * [https://scholar.google.com/citations?user=vPWtY18AAAAJ&amp;hl=en&amp;oi=ao Dustin Shigaki] (MLBBS Postdoctoral Fellow, JHU)<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer http://beerlab.org/index.php?title=Recent_News&diff=19643 2024-09-24T16:43:56Z

<p>MBeer: </p> <hr /> <div>'''[https://engineering.jhu.edu/magazine/2024/06/delivering-on-the-promise-of-personalized-medicine/ Delivering on the Promise of Personalized Medicine.]''' JHU Engineering magazine news article on AI with a bit on our CRISPR enhancer modeling in cell-state transitions.<br /> <br /> '''[https://physicsworld.com/a/iter-fusion-reactor-hit-by-massive-decade-long-delay-and-e5bn-price-hike/ ITER fusion project decade long delay and massive cost increase.]''' This is the closest thing to a feasible fusion power plant, and there is more bad news for economic feasibility. It was a great education, but I have no regrets leaving that field over 20 years ago.<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2024 Jin Woo awarded Mette Strand JHU Young Investigator Day Award.]'''<br /> <br /> '''[https://hub.jhu.edu/2023/08/10/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ JHU HUB News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]''' I would add that this work was an equal collaboration between our lab and Danwei Huangfu's lab at MSKCC, which was underplayed in the JHU articles.<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ BME News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]'''<br /> <br /> '''[https://mlbbs.bme.jhu.edu Applications are now open for the Machine Learning in the Basic Biomedical Sciences Postdoctoral Program.]'''<br /> <br /> '''[https://thanhnien.vn/hanh-trinh-tro-thanh-nha-nghien-cuu-ung-thu-hang-dau-the-gioi-post1423871.html?fbclid=IwAR0MRKXdjyduDtZYyS3Rf5QZgzCReUY3IP-mMi2ru1TnzaApDx54-RLKXko My first interview in a Vietnamese newspaper.]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/Impact-of-Genomic-Variation-on-Function-Consortium#awardees Beer Lab awarded IGVF Consortium Grant.]'''<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2021/ Wang awarded Bae Gyo Jung JHU Young Investigator Day Award.]''' '''[https://www.bme.jhu.edu/news-events/news/three-from-hopkins-bme-recognized-at-young-investigators-day/ also here.]'''<br /> <br /> '''[https://med.stanford.edu/genetics/events/encode-2021.html Jin-Woo, Wang, and Dustin selected for talks at 2021 ENCODE Consortium Meeting.]'''<br /> <br /> '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Wang discovered Enhancer-Promoter interaction prediction is harder than it looks.]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi5-regulation-saturation.html Dustin leads integrative analysis of CAGI5 regulation saturation challenge.]'''<br /> <br /> '''[https://www.nature.com/articles/d41586-020-00335-7 Highly cited researcher banned from journal board for citation abuse.]''' I put this here because K-C Chou wrote &lt;b&gt;many&lt;/b&gt; papers with and appears to have been a mentor to Bin Liu, who plagiarized our gkm-SVM paper as described in the several items below. Eleven papers co-authored by Bin Liu and K-C Chou were (self-)cited in the paper which plagiarized our gkm-SVM paper. See also the original reporting from '''[https://academic.oup.com/bioinformatics/article/35/18/3217/5304360 Bioinformatics]''' and '''[https://www.sciencedirect.com/science/article/pii/S0022519320300278?via%3Dihub Journal of Theoretical Biology.]''' I'm glad K-C Chou finally got called out on his gross citation manipulation, but the problem is broader than just these two journals. Although K-C Chou was removed, his proteges were and still are on the boards of many other journals and continue their citation inflation through mechanisms not discussed in these articles. For example, these articles do not mention that the authors who added the ~30 citations to K-C Chou during the review process may have been explicitly promised future citations from K-C Chou in return. The group of authors who cite K-C Chou is small, but they all cite each other multiple times in each paper, exponentially inflating citations of all members of the group.<br /> The scientific publishing industry has been manipulated by their lack of attention to these problems. If they want to investigate, all they have to do is look at who continues to cite '''[https://academic.oup.com/nar/article/43/W1/W65/2467922 this useless paper]''' over '''[https://scholar.google.com/scholar?hl=en&amp;as_sdt=0%2C21&amp;q=Pse-in-One%3A+a+web+server+for+generating+various+modes+of+pseudo+components+of+DNA%2C+RNA%2C+and+protein+sequences&amp;btnG= 600 times]'''. You may notice a pattern. None of these papers are real and each of these journals allowed it to happen for some unknown reasons. The list of these journals is clear from the citation patterns.<br /> <br /> '''[https://retractionwatch.com/2018/03/20/over-a-dozen-board-members-resigned-after-a-journal-refused-to-retract-a-paper-today-its-retracted/ Scientific Reports finally retracts paper plagiarizing our gkm-SVM paper.]''' '''[http://www.bmj.com/content/360/bmj.k1386 related article]'''<br /> <br /> Don't do this: '''[http://www.sixthtone.com/news/1001156/19-academics-resign-from-journal-over-alleged-plagiarism/ plagiarism1]'''<br /> '''[http://retractionwatch.com/2017/10/17/21-faculty-johns-hopkins-threaten-resign-board-journal-doesnt-retract-paper/ plagiarism2]'''<br /> '''[http://retractionwatch.com/2017/10/10/board-member-resigns-journal-handling-paper-accused-plagiarism/ plagiarism3]'''<br /> '''[http://retractionwatch.com/2017/11/07/17-johns-hopkins-researchers-resign-protest-ed-board-nature-journal/ plagiarism4]'''<br /> '''[http://www.the-scientist.com/?articles.view/articleNo/50888/title/Mass-Resignation-from-Scientific-Reports-s-Editorial-Board/ plagiarism5]'''<br /> <br /> '''[http://www.jhunewsletter.com/2017/02/16/professor-beer-awarded-1-8-million-nih-grant/ JHU Newsletter article on our ENCODE grant by Anna Chen]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements NHGRI on next phase of ENCODE project consortium]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-awarded-1-8-million-grant-from-nih/ Beer Lab awarded NIH ENCODE grant]'''<br /> <br /> '''[http://www.nature.com/nature/journal/v538/n7624/full/538275a.html Our computational work featured in Nature news article on &quot;The Dark Side of the Human Genome&quot;]'''<br /> <br /> '''[http://www.beerlab.org/gkmsvm New R package for gkmSVM and deltaSVM released]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi4-2eqtl.html gkmSVM among top-scoring methods for CAGI4 eQTL prediction challenge] '''<br /> <br /> '''[http://www.iscb.org/recomb-regsysgen2015-submissions/recomb-regsysgen2015-top-papers-reading-papers deltaSVM paper voted Top 10 in Regulatory Genomics 2015] '''<br /> <br /> '''[http://www.nature.com/ng/journal/v47/n8/full/ng.3364.html Nature Genetics News &amp; Views article on our deltaSVM paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/vulnerabilities_in_genomes_dimmer_switches_should_shed_light_on_hundreds_of_complex_diseases Nature Genetics paper on impact of regulatory variants]'''<br /> <br /> '''[http://www.newsweek.com/humans-and-mice-are-both-more-similar-and-different-previously-thought-285635 Newsweek article on Mouse ENCODE paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/scientists_map_mouse_genomes_mission_control_centers Mouse ENCODE Consortium paper in Nature]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/unraveling-the-genetic-underpinning-of-disease/ Beer Lab awarded NIH grant for regulatory contributions to disease. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-improves-methodology-for-predicting-disease-enabling-genetic-mutations/ Beer Lab improves methodology for predicting disease enabling genetic mutations. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/dongwon-lee-paper-voted-top-10-of-2011/ kmer-SVM Genome Research paper voted Top 10 in Regulatory Genomics.] '''<br /> <br /> '''[http://www.hopkinsmedicine.org/institute_basic_biomedical_sciences/news_events/Announcements/2013_04_YID.html Dongwon Lee awarded Young Investigator Day Award.] '''</div>

MBeer http://beerlab.org/index.php?title=Recent_News&diff=19642 2024-09-24T16:42:58Z

<p>MBeer: </p> <hr /> <div>'''[https://engineering.jhu.edu/magazine/2024/06/delivering-on-the-promise-of-personalized-medicine/ Delivering on the Promise of Personalized Medicine.]''' JHU Engineering magazine news article on AI.<br /> <br /> '''[https://physicsworld.com/a/iter-fusion-reactor-hit-by-massive-decade-long-delay-and-e5bn-price-hike/ ITER fusion project decade long delay and massive cost increase.]''' This is the closest thing to a feasible fusion power plant, and there is more bad news for economic feasibility. It was a great education, but I have no regrets leaving that field over 20 years ago.<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2024 Jin Woo awarded Mette Strand JHU Young Investigator Day Award.]'''<br /> <br /> '''[https://hub.jhu.edu/2023/08/10/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ JHU HUB News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]''' I would add that this work was an equal collaboration between our lab and Danwei Huangfu's lab at MSKCC, which was underplayed in the JHU articles.<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ BME News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]'''<br /> <br /> '''[https://mlbbs.bme.jhu.edu Applications are now open for the Machine Learning in the Basic Biomedical Sciences Postdoctoral Program.]'''<br /> <br /> '''[https://thanhnien.vn/hanh-trinh-tro-thanh-nha-nghien-cuu-ung-thu-hang-dau-the-gioi-post1423871.html?fbclid=IwAR0MRKXdjyduDtZYyS3Rf5QZgzCReUY3IP-mMi2ru1TnzaApDx54-RLKXko My first interview in a Vietnamese newspaper.]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/Impact-of-Genomic-Variation-on-Function-Consortium#awardees Beer Lab awarded IGVF Consortium Grant.]'''<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2021/ Wang awarded Bae Gyo Jung JHU Young Investigator Day Award.]''' '''[https://www.bme.jhu.edu/news-events/news/three-from-hopkins-bme-recognized-at-young-investigators-day/ also here.]'''<br /> <br /> '''[https://med.stanford.edu/genetics/events/encode-2021.html Jin-Woo, Wang, and Dustin selected for talks at 2021 ENCODE Consortium Meeting.]'''<br /> <br /> '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Wang discovered Enhancer-Promoter interaction prediction is harder than it looks.]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi5-regulation-saturation.html Dustin leads integrative analysis of CAGI5 regulation saturation challenge.]'''<br /> <br /> '''[https://www.nature.com/articles/d41586-020-00335-7 Highly cited researcher banned from journal board for citation abuse.]''' I put this here because K-C Chou wrote &lt;b&gt;many&lt;/b&gt; papers with and appears to have been a mentor to Bin Liu, who plagiarized our gkm-SVM paper as described in the several items below. Eleven papers co-authored by Bin Liu and K-C Chou were (self-)cited in the paper which plagiarized our gkm-SVM paper. See also the original reporting from '''[https://academic.oup.com/bioinformatics/article/35/18/3217/5304360 Bioinformatics]''' and '''[https://www.sciencedirect.com/science/article/pii/S0022519320300278?via%3Dihub Journal of Theoretical Biology.]''' I'm glad K-C Chou finally got called out on his gross citation manipulation, but the problem is broader than just these two journals. Although K-C Chou was removed, his proteges were and still are on the boards of many other journals and continue their citation inflation through mechanisms not discussed in these articles. For example, these articles do not mention that the authors who added the ~30 citations to K-C Chou during the review process may have been explicitly promised future citations from K-C Chou in return. The group of authors who cite K-C Chou is small, but they all cite each other multiple times in each paper, exponentially inflating citations of all members of the group.<br /> The scientific publishing industry has been manipulated by their lack of attention to these problems. If they want to investigate, all they have to do is look at who continues to cite '''[https://academic.oup.com/nar/article/43/W1/W65/2467922 this useless paper]''' over '''[https://scholar.google.com/scholar?hl=en&amp;as_sdt=0%2C21&amp;q=Pse-in-One%3A+a+web+server+for+generating+various+modes+of+pseudo+components+of+DNA%2C+RNA%2C+and+protein+sequences&amp;btnG= 600 times]'''. You may notice a pattern. None of these papers are real and each of these journals allowed it to happen for some unknown reasons. The list of these journals is clear from the citation patterns.<br /> <br /> '''[https://retractionwatch.com/2018/03/20/over-a-dozen-board-members-resigned-after-a-journal-refused-to-retract-a-paper-today-its-retracted/ Scientific Reports finally retracts paper plagiarizing our gkm-SVM paper.]''' '''[http://www.bmj.com/content/360/bmj.k1386 related article]'''<br /> <br /> Don't do this: '''[http://www.sixthtone.com/news/1001156/19-academics-resign-from-journal-over-alleged-plagiarism/ plagiarism1]'''<br /> '''[http://retractionwatch.com/2017/10/17/21-faculty-johns-hopkins-threaten-resign-board-journal-doesnt-retract-paper/ plagiarism2]'''<br /> '''[http://retractionwatch.com/2017/10/10/board-member-resigns-journal-handling-paper-accused-plagiarism/ plagiarism3]'''<br /> '''[http://retractionwatch.com/2017/11/07/17-johns-hopkins-researchers-resign-protest-ed-board-nature-journal/ plagiarism4]'''<br /> '''[http://www.the-scientist.com/?articles.view/articleNo/50888/title/Mass-Resignation-from-Scientific-Reports-s-Editorial-Board/ plagiarism5]'''<br /> <br /> '''[http://www.jhunewsletter.com/2017/02/16/professor-beer-awarded-1-8-million-nih-grant/ JHU Newsletter article on our ENCODE grant by Anna Chen]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements NHGRI on next phase of ENCODE project consortium]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-awarded-1-8-million-grant-from-nih/ Beer Lab awarded NIH ENCODE grant]'''<br /> <br /> '''[http://www.nature.com/nature/journal/v538/n7624/full/538275a.html Our computational work featured in Nature news article on &quot;The Dark Side of the Human Genome&quot;]'''<br /> <br /> '''[http://www.beerlab.org/gkmsvm New R package for gkmSVM and deltaSVM released]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi4-2eqtl.html gkmSVM among top-scoring methods for CAGI4 eQTL prediction challenge] '''<br /> <br /> '''[http://www.iscb.org/recomb-regsysgen2015-submissions/recomb-regsysgen2015-top-papers-reading-papers deltaSVM paper voted Top 10 in Regulatory Genomics 2015] '''<br /> <br /> '''[http://www.nature.com/ng/journal/v47/n8/full/ng.3364.html Nature Genetics News &amp; Views article on our deltaSVM paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/vulnerabilities_in_genomes_dimmer_switches_should_shed_light_on_hundreds_of_complex_diseases Nature Genetics paper on impact of regulatory variants]'''<br /> <br /> '''[http://www.newsweek.com/humans-and-mice-are-both-more-similar-and-different-previously-thought-285635 Newsweek article on Mouse ENCODE paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/scientists_map_mouse_genomes_mission_control_centers Mouse ENCODE Consortium paper in Nature]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/unraveling-the-genetic-underpinning-of-disease/ Beer Lab awarded NIH grant for regulatory contributions to disease. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-improves-methodology-for-predicting-disease-enabling-genetic-mutations/ Beer Lab improves methodology for predicting disease enabling genetic mutations. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/dongwon-lee-paper-voted-top-10-of-2011/ kmer-SVM Genome Research paper voted Top 10 in Regulatory Genomics.] '''<br /> <br /> '''[http://www.hopkinsmedicine.org/institute_basic_biomedical_sciences/news_events/Announcements/2013_04_YID.html Dongwon Lee awarded Young Investigator Day Award.] '''</div>

MBeer http://beerlab.org/index.php?title=Publications&diff=19641 2024-08-01T15:19:38Z

<p>MBeer: </p> <hr /> <div>Full publication list on '''[https://scholar.google.com/citations?hl=en&amp;user=9aH8_eEAAAAJ google scholar]'''.<br /> <br /> * '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''<br /> <br /> * '''[https://www.nature.com/articles/s41467-024-50708-z Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals.]''' Oh JW and Beer MA. Nature Communications 2024.<br /> <br /> * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023 '''[https://beerlab.org/papers/2023%20NG.pdf pdf]'''<br /> <br /> * '''[https://www.nature.com/articles/s41467-021-21368-0 Loop competition and extrusion model predicts CTCF interaction specificity.]''' Xi W, Beer MA. Nature Comms. 2021.<br /> <br /> * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.<br /> <br /> * '''[https://www.nature.com/articles/s41586-020-2493-4 Expanded encyclopaedias of DNA elements in the human and mouse genomes.]''' ENCODE Project Consortium. Nature 2020.<br /> <br /> * '''[https://www.jci.org/articles/view/126726 Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer.]''' Xing M, Ooi WF, Tan J, Qamra A, Lee PH, Li Z, Xu C, Padmanabhan N, Lim JQ, Guo YA, Yao X, Amit M, Ng LM, Sheng T, Wang J, Huang KK, Anene-Nzelu CG, Ho SWT, Ray M, Ma L, Fazzi G, Lim KJ, Wijaya GC, Zhang S, Nandi T, Yan T, Chang MM, Das K, Isa ZFA, Wu J, Yean PPS, Lam YN, Lin JS, Tay ST, Lee M, Keng ATL, Ong X, White K, Rozen SG, Beer MA, Foo RSY, Grabsch H, Skanderup AJ, Li S, Teh BT, Tan P. J. Clin. Invest. 2020<br /> <br /> * '''[https://www.nature.com/articles/s41588-019-0408-9 Genome-scale screens uncover JNK/JUN signaling as a key barrier from pluripotency to human endoderm differentiation.]''' Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh C-L, Yang D, Crespo M, Shukla A, Xiang Q, Dundar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massague J, Garippa R, Evans T, Beer MA, and Huangfu D. Nature Genetics 2019. <br /> <br /> * '''[https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, Adato O, Adhikar A, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar D, Schubach M, Xiong C, Yan Z, Boyle A, Kreimer A, Kulakovskiy IV, Reid J, Unger R, Yosef N, Shendure J, Ahituv N, Kircher M, and Beer MA. Human Mutation 2019. [http://www.beerlab.org/deltasvm_models (models)]<br /> <br /> * '''[https://stm.sciencemag.org/content/11/497/eaaw0790.abstract Epigenetic activation and memory at a novel TGFβ2 enhancer in systemic sclerosis fibroblasts.]''' Shin JY, Beckett JD, Shah A, McMahan Z, Paik J, Sampedro MM, MacFarlane EG, Beer MA, Warren D, Wigley FM, and Dietz HC. Science Translational Medicine 2019.<br /> <br /> * '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy.]''' Xi, W and Beer, MA. PLOS Comp Biol 2018.<br /> <br /> * '''[https://www.sciencedirect.com/science/article/pii/S0002929718303707 Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons.]''' McClymont SA, Hook PW, Soto AI, Reed X, Law WD, Kerans SJ, Waite EL, Briceno NJ, Thole JF, Heckman MG, Diehl NN, Wszolek ZK, Moore CD, Zhu H, Akiyama JA, Dickel DE, Visel A, Pennacchio LA, Ross OA, Beer MA, &amp; McCallion AS. Am. Jour. Human Genetics 2018<br /> <br /> * '''[https://www.nature.com/articles/s41588-018-0156-2 Genetic determinants of co-accessible chromatin regions in activated T cells across humans.]''' Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang S-C, Durand NC, Feng T, De Jager PL, Chang HY, Lieberman Aiden E, Benoist C, Beer MA, Ye CJ &amp; Regev A. Nature Genetics 2018. <br /> <br /> * '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23185/full Predicting enhancer activity and variant impact using gkm-SVM.]''' Beer, MA. Human Mutation 2017.<br /> <br /> * '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23197/full Predicting gene expression in massively parallel reporter assays: A comparative study.]''' Kreimer A, Zeng H, Edwards M, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong N, Li Y, Amin T, Goke J, Mueller N, Kellis, M, Kundaje A, Beer MA, Keles S, Gifford D, and Yosef, N. Human Mutation 2017.<br /> <br /> * '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170403 Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X.]''' Migeon BR, Beer MA, and Bjornsson HT. Plos ONE 2017.<br /> <br /> * '''[http://bioinformatics.oxfordjournals.org/content/early/2016/05/05/bioinformatics.btw203 gkmSVM: an R package for gapped-kmer SVM.]''' [[Media:Bioinformatics-2016-Ghandi-bioinformatics-btw203.pdf|pdf]] [[tutorial]] Ghandi, M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, and Beer MA. Bioinformatics 2016.<br /> <br /> * '''[http://elifesciences.org/content/5/e11613v1 Epigenomic landscapes of retinal rods and cones.]''' Mo, A, Luo, C, Davis, FP, Mukamel, EA, Henry, GL, Nery JR, Urich, MA, Picard, S, Lister, R, Eddy, SR, Beer, MA, Ecker, JR, and Nathans, J. eLife 2016.<br /> <br /> * '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25582907 Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.]''' Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin, A, Tanzer A, Lagarde J, Zaleski C, See L-H, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Nat. Comm 2015.<br /> <br /> * '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140557 Identification of predictive cis-regulatory elements using a discriminative objective function and dynamic search spaces.]''' Karnik, R, and Beer MA. PLOS One 2015.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25413365 Comparison of the transcriptional landscapes between human and mouse tissues.]''' Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP. PNAS 2014.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25409824 A comparative encyclopedia of DNA elements in the mouse genome.]''' Mouse ENCODE Consortium (includes Lee D and Beer MA). 2014. Nature 515:355–364.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25319996 Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis.]''' Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ. 2014. Genome Research.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25033408 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M*, Lee D*, Mohammad-Noori M, and Beer MA. 2014. PLoS Computational Biology 10(7):e1003711.<br /> <br /> * '''[http://www.horizonpress.com/genomeanalysis Mammalian Enhancer Prediction.]''' Lee D, Beer MA. 2014. Genome Analysis: Current Procedures and Applications. Horizon Press. [[Media:book.pdf|pdf]]<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23861010 Robust k-mer Frequency Estimation Using Gapped k-mers.]''' Ghandi M, Mohammad-Noori M, and Beer MA. 2013. Journal of Mathematical Biology. (Epub ahead of print)<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23771147 kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic datasets.]''' Fletez-Brant C*, Lee D*, McCallion AS and Beer MA. 2013. Nucleic Acids Research 41: W544–W556.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23019145 Integration of ChIP-seq and Machine Learning Reveals Enhancers and a Predictive Regulatory Sequence Vocabulary in Melanocytes.]''' Gorkin DU, Lee D, Reed X, Fletez-Brant C, Blessling SL, Loftus SK, Beer MA, Pavan WJ, and McCallion AS. 2012. Genome Research 22:2290-2301.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/22912661 Group Normalization for Genomic Data.]''' Ghandi M, and Beer MA. 2012. PLoS ONE 7:e38695.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/21875935 Discriminative prediction of mammalian enhancers from DNA sequence.]''' Lee D, Karchin R, and Beer MA. 2011. Genome Research 21:2167-2180.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/21720494 Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome.]''' Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon WH, Joore J, Beer MA, Cope L, Pandey A. 2011. J Proteomics Bioinform 4:22-35.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19430481 A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies.]''' Khanna H, Davis EE, Murga-Zamalloa CA, Estrada-Cuzcano A, Lopez I, den Hollander AI, Zonneveld MN, Othman MI, Waseem N, Chakarova CF, Maubaret C, Diaz-Font A, MacDonald I, Muzny DM, Wheeler DA, Morgan M, Lewis LR, Logan CV, Tan PL, Beer MA, Inglehearn CF, Lewis RA, Jacobson SG, Bergmann C, Beales PL, Attié-Bitach T, Johnson CA, Otto EA, Bhattacharya SS, Hildebrandt F, Gibbs RA, Koenekoop RK, Swaroop A, Katsanis N. 2009. Nat Genet. 41:739-45.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19253296 Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach.]''' Yang Y, Chaerkady R, Beer MA, Mendell JT, and Pandey A. 2009. Proteomics 9:1374-1384.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19211792 Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation.]''' Chang T-C, Zeitels LR, Hwang H-W, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, and Mendell JT. 2009. PNAS 106:3384-3389.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/18071029 Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b.]''' McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, and McCallion AS. 2008. Genome Research 18:252-260.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/17540599 Transactivation of miR-34a by p53 Broadly Influences Gene Expression and Promotes Apoptosis.]''' Chang T-C, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, and Mendell JT. 2007. Molecular Cell 26: 745-752.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/15870260 Functional Characterization of a Novel Ku70/80 Pause Site at the H19/Igf2 Imprinting Control Region.]''' Katz DJ, Beer MA, Levorse JM, and Tilghman SM. 2005. Mol Cell Biol 25:3855-3863.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/14672978 Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation.]''' Pritsker M, Liu Y-C, Beer MA, and Tavazoie S. 2004. Genome Research 14:99-108.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence.]''' Beer MA and Tavazoie S. 2004. Cell 117:185-198.<br /> <br /> <br /> ----<br /> <br /> For a full list including my prior work in simulations of plasma turbulence, see '''[https://scholar.google.com/citations?user=9aH8_eEAAAAJ&amp;hl=en&amp;oi=ao my google scholar page.]'''</div>

MBeer http://beerlab.org/index.php?title=Publications&diff=19640 2024-08-01T15:18:24Z

<p>MBeer: </p> <hr /> <div>Full publication list on '''[https://scholar.google.com/citations?hl=en&amp;user=9aH8_eEAAAAJ google scholar]'''.<br /> <br /> * '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''<br /> <br /> * '''https://www.nature.com/articles/s41467-024-50708-z Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals.]''' Oh JW and Beer MA. Nature Communications 2024.<br /> <br /> * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023 '''[https://beerlab.org/papers/2023%20NG.pdf pdf]'''<br /> <br /> * '''[https://www.nature.com/articles/s41467-021-21368-0 Loop competition and extrusion model predicts CTCF interaction specificity.]''' Xi W, Beer MA. Nature Comms. 2021.<br /> <br /> * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.<br /> <br /> * '''[https://www.nature.com/articles/s41586-020-2493-4 Expanded encyclopaedias of DNA elements in the human and mouse genomes.]''' ENCODE Project Consortium. Nature 2020.<br /> <br /> * '''[https://www.jci.org/articles/view/126726 Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer.]''' Xing M, Ooi WF, Tan J, Qamra A, Lee PH, Li Z, Xu C, Padmanabhan N, Lim JQ, Guo YA, Yao X, Amit M, Ng LM, Sheng T, Wang J, Huang KK, Anene-Nzelu CG, Ho SWT, Ray M, Ma L, Fazzi G, Lim KJ, Wijaya GC, Zhang S, Nandi T, Yan T, Chang MM, Das K, Isa ZFA, Wu J, Yean PPS, Lam YN, Lin JS, Tay ST, Lee M, Keng ATL, Ong X, White K, Rozen SG, Beer MA, Foo RSY, Grabsch H, Skanderup AJ, Li S, Teh BT, Tan P. J. Clin. Invest. 2020<br /> <br /> * '''[https://www.nature.com/articles/s41588-019-0408-9 Genome-scale screens uncover JNK/JUN signaling as a key barrier from pluripotency to human endoderm differentiation.]''' Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh C-L, Yang D, Crespo M, Shukla A, Xiang Q, Dundar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massague J, Garippa R, Evans T, Beer MA, and Huangfu D. Nature Genetics 2019. <br /> <br /> * '''[https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, Adato O, Adhikar A, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar D, Schubach M, Xiong C, Yan Z, Boyle A, Kreimer A, Kulakovskiy IV, Reid J, Unger R, Yosef N, Shendure J, Ahituv N, Kircher M, and Beer MA. Human Mutation 2019. [http://www.beerlab.org/deltasvm_models (models)]<br /> <br /> * '''[https://stm.sciencemag.org/content/11/497/eaaw0790.abstract Epigenetic activation and memory at a novel TGFβ2 enhancer in systemic sclerosis fibroblasts.]''' Shin JY, Beckett JD, Shah A, McMahan Z, Paik J, Sampedro MM, MacFarlane EG, Beer MA, Warren D, Wigley FM, and Dietz HC. Science Translational Medicine 2019.<br /> <br /> * '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy.]''' Xi, W and Beer, MA. PLOS Comp Biol 2018.<br /> <br /> * '''[https://www.sciencedirect.com/science/article/pii/S0002929718303707 Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons.]''' McClymont SA, Hook PW, Soto AI, Reed X, Law WD, Kerans SJ, Waite EL, Briceno NJ, Thole JF, Heckman MG, Diehl NN, Wszolek ZK, Moore CD, Zhu H, Akiyama JA, Dickel DE, Visel A, Pennacchio LA, Ross OA, Beer MA, &amp; McCallion AS. Am. Jour. Human Genetics 2018<br /> <br /> * '''[https://www.nature.com/articles/s41588-018-0156-2 Genetic determinants of co-accessible chromatin regions in activated T cells across humans.]''' Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang S-C, Durand NC, Feng T, De Jager PL, Chang HY, Lieberman Aiden E, Benoist C, Beer MA, Ye CJ &amp; Regev A. Nature Genetics 2018. <br /> <br /> * '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23185/full Predicting enhancer activity and variant impact using gkm-SVM.]''' Beer, MA. Human Mutation 2017.<br /> <br /> * '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23197/full Predicting gene expression in massively parallel reporter assays: A comparative study.]''' Kreimer A, Zeng H, Edwards M, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong N, Li Y, Amin T, Goke J, Mueller N, Kellis, M, Kundaje A, Beer MA, Keles S, Gifford D, and Yosef, N. Human Mutation 2017.<br /> <br /> * '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170403 Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X.]''' Migeon BR, Beer MA, and Bjornsson HT. Plos ONE 2017.<br /> <br /> * '''[http://bioinformatics.oxfordjournals.org/content/early/2016/05/05/bioinformatics.btw203 gkmSVM: an R package for gapped-kmer SVM.]''' [[Media:Bioinformatics-2016-Ghandi-bioinformatics-btw203.pdf|pdf]] [[tutorial]] Ghandi, M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, and Beer MA. Bioinformatics 2016.<br /> <br /> * '''[http://elifesciences.org/content/5/e11613v1 Epigenomic landscapes of retinal rods and cones.]''' Mo, A, Luo, C, Davis, FP, Mukamel, EA, Henry, GL, Nery JR, Urich, MA, Picard, S, Lister, R, Eddy, SR, Beer, MA, Ecker, JR, and Nathans, J. eLife 2016.<br /> <br /> * '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25582907 Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.]''' Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin, A, Tanzer A, Lagarde J, Zaleski C, See L-H, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Nat. Comm 2015.<br /> <br /> * '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140557 Identification of predictive cis-regulatory elements using a discriminative objective function and dynamic search spaces.]''' Karnik, R, and Beer MA. PLOS One 2015.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25413365 Comparison of the transcriptional landscapes between human and mouse tissues.]''' Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP. PNAS 2014.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25409824 A comparative encyclopedia of DNA elements in the mouse genome.]''' Mouse ENCODE Consortium (includes Lee D and Beer MA). 2014. Nature 515:355–364.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25319996 Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis.]''' Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ. 2014. Genome Research.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25033408 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M*, Lee D*, Mohammad-Noori M, and Beer MA. 2014. PLoS Computational Biology 10(7):e1003711.<br /> <br /> * '''[http://www.horizonpress.com/genomeanalysis Mammalian Enhancer Prediction.]''' Lee D, Beer MA. 2014. Genome Analysis: Current Procedures and Applications. Horizon Press. [[Media:book.pdf|pdf]]<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23861010 Robust k-mer Frequency Estimation Using Gapped k-mers.]''' Ghandi M, Mohammad-Noori M, and Beer MA. 2013. Journal of Mathematical Biology. (Epub ahead of print)<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23771147 kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic datasets.]''' Fletez-Brant C*, Lee D*, McCallion AS and Beer MA. 2013. Nucleic Acids Research 41: W544–W556.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23019145 Integration of ChIP-seq and Machine Learning Reveals Enhancers and a Predictive Regulatory Sequence Vocabulary in Melanocytes.]''' Gorkin DU, Lee D, Reed X, Fletez-Brant C, Blessling SL, Loftus SK, Beer MA, Pavan WJ, and McCallion AS. 2012. Genome Research 22:2290-2301.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/22912661 Group Normalization for Genomic Data.]''' Ghandi M, and Beer MA. 2012. PLoS ONE 7:e38695.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/21875935 Discriminative prediction of mammalian enhancers from DNA sequence.]''' Lee D, Karchin R, and Beer MA. 2011. Genome Research 21:2167-2180.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/21720494 Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome.]''' Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon WH, Joore J, Beer MA, Cope L, Pandey A. 2011. J Proteomics Bioinform 4:22-35.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19430481 A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies.]''' Khanna H, Davis EE, Murga-Zamalloa CA, Estrada-Cuzcano A, Lopez I, den Hollander AI, Zonneveld MN, Othman MI, Waseem N, Chakarova CF, Maubaret C, Diaz-Font A, MacDonald I, Muzny DM, Wheeler DA, Morgan M, Lewis LR, Logan CV, Tan PL, Beer MA, Inglehearn CF, Lewis RA, Jacobson SG, Bergmann C, Beales PL, Attié-Bitach T, Johnson CA, Otto EA, Bhattacharya SS, Hildebrandt F, Gibbs RA, Koenekoop RK, Swaroop A, Katsanis N. 2009. Nat Genet. 41:739-45.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19253296 Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach.]''' Yang Y, Chaerkady R, Beer MA, Mendell JT, and Pandey A. 2009. Proteomics 9:1374-1384.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19211792 Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation.]''' Chang T-C, Zeitels LR, Hwang H-W, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, and Mendell JT. 2009. PNAS 106:3384-3389.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/18071029 Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b.]''' McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, and McCallion AS. 2008. Genome Research 18:252-260.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/17540599 Transactivation of miR-34a by p53 Broadly Influences Gene Expression and Promotes Apoptosis.]''' Chang T-C, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, and Mendell JT. 2007. Molecular Cell 26: 745-752.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/15870260 Functional Characterization of a Novel Ku70/80 Pause Site at the H19/Igf2 Imprinting Control Region.]''' Katz DJ, Beer MA, Levorse JM, and Tilghman SM. 2005. Mol Cell Biol 25:3855-3863.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/14672978 Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation.]''' Pritsker M, Liu Y-C, Beer MA, and Tavazoie S. 2004. Genome Research 14:99-108.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence.]''' Beer MA and Tavazoie S. 2004. Cell 117:185-198.<br /> <br /> <br /> ----<br /> <br /> For a full list including my prior work in simulations of plasma turbulence, see '''[https://scholar.google.com/citations?user=9aH8_eEAAAAJ&amp;hl=en&amp;oi=ao my google scholar page.]'''</div>

MBeer http://beerlab.org/index.php?title=Publications&diff=19639 2024-07-23T01:36:41Z

<p>MBeer: </p> <hr /> <div>Full publication list on '''[https://scholar.google.com/citations?hl=en&amp;user=9aH8_eEAAAAJ google scholar]'''.<br /> <br /> * '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 '''[https://beerlab.org/papers/gr.278565.123.full.pdf pdf]'''<br /> <br /> * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023 '''[https://beerlab.org/papers/2023%20NG.pdf pdf]'''<br /> <br /> * '''[https://www.nature.com/articles/s41467-021-21368-0 Loop competition and extrusion model predicts CTCF interaction specificity.]''' Xi W, Beer MA. Nature Comms. 2021.<br /> <br /> * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.<br /> <br /> * '''[https://www.nature.com/articles/s41586-020-2493-4 Expanded encyclopaedias of DNA elements in the human and mouse genomes.]''' ENCODE Project Consortium. Nature 2020.<br /> <br /> * '''[https://www.jci.org/articles/view/126726 Genomic and epigenomic EBF1 alterations modulate TERT expression in gastric cancer.]''' Xing M, Ooi WF, Tan J, Qamra A, Lee PH, Li Z, Xu C, Padmanabhan N, Lim JQ, Guo YA, Yao X, Amit M, Ng LM, Sheng T, Wang J, Huang KK, Anene-Nzelu CG, Ho SWT, Ray M, Ma L, Fazzi G, Lim KJ, Wijaya GC, Zhang S, Nandi T, Yan T, Chang MM, Das K, Isa ZFA, Wu J, Yean PPS, Lam YN, Lin JS, Tay ST, Lee M, Keng ATL, Ong X, White K, Rozen SG, Beer MA, Foo RSY, Grabsch H, Skanderup AJ, Li S, Teh BT, Tan P. J. Clin. Invest. 2020<br /> <br /> * '''[https://www.nature.com/articles/s41588-019-0408-9 Genome-scale screens uncover JNK/JUN signaling as a key barrier from pluripotency to human endoderm differentiation.]''' Li QV, Dixon G, Verma N, Rosen BP, Gordillo M, Luo R, Xu C, Wang Q, Soh C-L, Yang D, Crespo M, Shukla A, Xiang Q, Dundar F, Zumbo P, Witkin M, Koche R, Betel D, Chen S, Massague J, Garippa R, Evans T, Beer MA, and Huangfu D. Nature Genetics 2019. <br /> <br /> * '''[https://onlinelibrary.wiley.com/doi/full/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, Adato O, Adhikar A, Dong S, Hawkins-Hooker A, Inoue F, Juven-Gershon T, Kenlay H, Martin B, Patra A, Penzar D, Schubach M, Xiong C, Yan Z, Boyle A, Kreimer A, Kulakovskiy IV, Reid J, Unger R, Yosef N, Shendure J, Ahituv N, Kircher M, and Beer MA. Human Mutation 2019. [http://www.beerlab.org/deltasvm_models (models)]<br /> <br /> * '''[https://stm.sciencemag.org/content/11/497/eaaw0790.abstract Epigenetic activation and memory at a novel TGFβ2 enhancer in systemic sclerosis fibroblasts.]''' Shin JY, Beckett JD, Shah A, McMahan Z, Paik J, Sampedro MM, MacFarlane EG, Beer MA, Warren D, Wigley FM, and Dietz HC. Science Translational Medicine 2019.<br /> <br /> * '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy.]''' Xi, W and Beer, MA. PLOS Comp Biol 2018.<br /> <br /> * '''[https://www.sciencedirect.com/science/article/pii/S0002929718303707 Parkinson-Associated SNCA Enhancer Variants Revealed by Open Chromatin in Mouse Dopamine Neurons.]''' McClymont SA, Hook PW, Soto AI, Reed X, Law WD, Kerans SJ, Waite EL, Briceno NJ, Thole JF, Heckman MG, Diehl NN, Wszolek ZK, Moore CD, Zhu H, Akiyama JA, Dickel DE, Visel A, Pennacchio LA, Ross OA, Beer MA, &amp; McCallion AS. Am. Jour. Human Genetics 2018<br /> <br /> * '''[https://www.nature.com/articles/s41588-018-0156-2 Genetic determinants of co-accessible chromatin regions in activated T cells across humans.]''' Gate RE, Cheng CS, Aiden AP, Siba A, Tabaka M, Lituiev D, Machol I, Gordon MG, Subramaniam M, Shamim M, Hougen KL, Wortman I, Huang S-C, Durand NC, Feng T, De Jager PL, Chang HY, Lieberman Aiden E, Benoist C, Beer MA, Ye CJ &amp; Regev A. Nature Genetics 2018. <br /> <br /> * '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23185/full Predicting enhancer activity and variant impact using gkm-SVM.]''' Beer, MA. Human Mutation 2017.<br /> <br /> * '''[http://onlinelibrary.wiley.com/doi/10.1002/humu.23197/full Predicting gene expression in massively parallel reporter assays: A comparative study.]''' Kreimer A, Zeng H, Edwards M, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong N, Li Y, Amin T, Goke J, Mueller N, Kellis, M, Kundaje A, Beer MA, Keles S, Gifford D, and Yosef, N. Human Mutation 2017.<br /> <br /> * '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0170403 Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X.]''' Migeon BR, Beer MA, and Bjornsson HT. Plos ONE 2017.<br /> <br /> * '''[http://bioinformatics.oxfordjournals.org/content/early/2016/05/05/bioinformatics.btw203 gkmSVM: an R package for gapped-kmer SVM.]''' [[Media:Bioinformatics-2016-Ghandi-bioinformatics-btw203.pdf|pdf]] [[tutorial]] Ghandi, M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, and Beer MA. Bioinformatics 2016.<br /> <br /> * '''[http://elifesciences.org/content/5/e11613v1 Epigenomic landscapes of retinal rods and cones.]''' Mo, A, Luo, C, Davis, FP, Mukamel, EA, Henry, GL, Nery JR, Urich, MA, Picard, S, Lister, R, Eddy, SR, Beer, MA, Ecker, JR, and Nathans, J. eLife 2016.<br /> <br /> * '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25582907 Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression.]''' Pervouchine DD, Djebali S, Breschi A, Davis CA, Barja PP, Dobin, A, Tanzer A, Lagarde J, Zaleski C, See L-H, Fastuca M, Drenkow J, Wang H, Bussotti G, Pei B, Balasubramanian S, Monlong J, Harmanci A, Gerstein M, Beer MA, Notredame C, Guigó R, Gingeras TR. Nat. Comm 2015.<br /> <br /> * '''[http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0140557 Identification of predictive cis-regulatory elements using a discriminative objective function and dynamic search spaces.]''' Karnik, R, and Beer MA. PLOS One 2015.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25413365 Comparison of the transcriptional landscapes between human and mouse tissues.]''' Lin S, Lin Y, Nery JR, Urich MA, Breschi A, Davis CA, Dobin A, Zaleski C, Beer MA, Chapman WC, Gingeras TR, Ecker JR, Snyder MP. PNAS 2014.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25409824 A comparative encyclopedia of DNA elements in the mouse genome.]''' Mouse ENCODE Consortium (includes Lee D and Beer MA). 2014. Nature 515:355–364.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25319996 Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis.]''' Pimkin M, Kossenkov AV, Mishra T, Morrissey CS, Wu W, Keller CA, Blobel GA, Lee D, Beer MA, Hardison RC, Weiss MJ. 2014. Genome Research.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/25033408 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M*, Lee D*, Mohammad-Noori M, and Beer MA. 2014. PLoS Computational Biology 10(7):e1003711.<br /> <br /> * '''[http://www.horizonpress.com/genomeanalysis Mammalian Enhancer Prediction.]''' Lee D, Beer MA. 2014. Genome Analysis: Current Procedures and Applications. Horizon Press. [[Media:book.pdf|pdf]]<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23861010 Robust k-mer Frequency Estimation Using Gapped k-mers.]''' Ghandi M, Mohammad-Noori M, and Beer MA. 2013. Journal of Mathematical Biology. (Epub ahead of print)<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23771147 kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic datasets.]''' Fletez-Brant C*, Lee D*, McCallion AS and Beer MA. 2013. Nucleic Acids Research 41: W544–W556.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/23019145 Integration of ChIP-seq and Machine Learning Reveals Enhancers and a Predictive Regulatory Sequence Vocabulary in Melanocytes.]''' Gorkin DU, Lee D, Reed X, Fletez-Brant C, Blessling SL, Loftus SK, Beer MA, Pavan WJ, and McCallion AS. 2012. Genome Research 22:2290-2301.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/22912661 Group Normalization for Genomic Data.]''' Ghandi M, and Beer MA. 2012. PLoS ONE 7:e38695.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/21875935 Discriminative prediction of mammalian enhancers from DNA sequence.]''' Lee D, Karchin R, and Beer MA. 2011. Genome Research 21:2167-2180.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/21720494 Identification of Novel Phosphorylation Motifs Through an Integrative Computational and Experimental Analysis of the Human Phosphoproteome.]''' Amanchy R, Kandasamy K, Mathivanan S, Periaswamy B, Reddy R, Yoon WH, Joore J, Beer MA, Cope L, Pandey A. 2011. J Proteomics Bioinform 4:22-35.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19430481 A common allele in RPGRIP1L is a modifier of retinal degeneration in ciliopathies.]''' Khanna H, Davis EE, Murga-Zamalloa CA, Estrada-Cuzcano A, Lopez I, den Hollander AI, Zonneveld MN, Othman MI, Waseem N, Chakarova CF, Maubaret C, Diaz-Font A, MacDonald I, Muzny DM, Wheeler DA, Morgan M, Lewis LR, Logan CV, Tan PL, Beer MA, Inglehearn CF, Lewis RA, Jacobson SG, Bergmann C, Beales PL, Attié-Bitach T, Johnson CA, Otto EA, Bhattacharya SS, Hildebrandt F, Gibbs RA, Koenekoop RK, Swaroop A, Katsanis N. 2009. Nat Genet. 41:739-45.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19253296 Identification of miR-21 targets in breast cancer cells using a quantitative proteomic approach.]''' Yang Y, Chaerkady R, Beer MA, Mendell JT, and Pandey A. 2009. Proteomics 9:1374-1384.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/19211792 Lin-28B transactivation is necessary for Myc-mediated let-7 repression and proliferation.]''' Chang T-C, Zeitels LR, Hwang H-W, Chivukula RR, Wentzel EA, Dews M, Jung J, Gao P, Dang CV, Beer MA, Thomas-Tikhonenko A, and Mendell JT. 2009. PNAS 106:3384-3389.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/18071029 Metrics of sequence constraint overlook regulatory sequences in an exhaustive analysis at phox2b.]''' McGaughey DM, Vinton RM, Huynh J, Al-Saif A, Beer MA, and McCallion AS. 2008. Genome Research 18:252-260.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/17540599 Transactivation of miR-34a by p53 Broadly Influences Gene Expression and Promotes Apoptosis.]''' Chang T-C, Wentzel EA, Kent OA, Ramachandran K, Mullendore M, Lee KH, Feldmann G, Yamakuchi M, Ferlito M, Lowenstein CJ, Arking DE, Beer MA, Maitra A, and Mendell JT. 2007. Molecular Cell 26: 745-752.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/15870260 Functional Characterization of a Novel Ku70/80 Pause Site at the H19/Igf2 Imprinting Control Region.]''' Katz DJ, Beer MA, Levorse JM, and Tilghman SM. 2005. Mol Cell Biol 25:3855-3863.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/14672978 Whole-Genome Discovery of Transcription Factor Binding Sites by Network-Level Conservation.]''' Pritsker M, Liu Y-C, Beer MA, and Tavazoie S. 2004. Genome Research 14:99-108.<br /> <br /> * '''[http://www.ncbi.nlm.nih.gov/pubmed/15084257 Predicting Gene Expression from Sequence.]''' Beer MA and Tavazoie S. 2004. Cell 117:185-198.<br /> <br /> <br /> ----<br /> <br /> For a full list including my prior work in simulations of plasma turbulence, see '''[https://scholar.google.com/citations?user=9aH8_eEAAAAJ&amp;hl=en&amp;oi=ao my google scholar page.]'''</div>

MBeer http://beerlab.org/index.php?title=Computational_Regulatory_Genomics&diff=19638 2024-07-20T20:06:08Z

<p>MBeer: </p> <hr /> <div>&lt;h2&gt;Computational Regulatory Genomics&lt;/h2&gt; __NOTOC__ __NOTITLE__<br /> &lt;metadesc&gt;Computational Regulatory Genomics for graduate PhD and postdoctoral research in BME and IGM at Johns Hopkins, top ranking programs modeling DNA and systems biology.&lt;/metadesc&gt;<br /> &lt;h3&gt;[[Recent News ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;[[Lab Members ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Publications]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Postdoctoral Positions Available]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Resources]]&lt;/h3&gt;<br /> <br /> [[File:Beer_Michael_small.jpg|link=http://www.bme.jhu.edu/people/faculty/michael-beer/]] [[File:EncodeNatureGraphic_small.png]] [[File:dyn_net.gif]]<br /> <br /> [[File:Igvf_logo.png|150px]] &amp;nbsp;&amp;nbsp; [[File:Encode_logo.png]] &amp;nbsp;&amp;nbsp; [[File:Nhgri_logo.jpg|250px]] &amp;nbsp;&amp;nbsp;[[File:hopkins_logo.jpg|200px]]<br /> <br /> We are in the '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ Department of Biomedical Engineering]''' and the '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer McKusick-Nathans Department of Genetic Medicine]''' at Johns Hopkins University. You can apply for graduate study in my lab through '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ BME]''' or the Ph.D. program in '''[https://www.hopkinsmedicine.org/genetic-medicine/education-training/human-genetics-genomics-graduate-program Human Genetics and Genomics.]'''<br /> <br /> &lt;h3&gt;Research Interests: &lt;/h3&gt; The ultimate goal of our research is to understand how gene regulatory information is encoded in genomic DNA sequence.<br /> <br /> We have recently made significant progress using AI/ML to understand how DNA sequence specifies cell-type specific enhancer activity, target gene activation through looping constraints, and how dynamic enhancer-gene regulatory networks control cell-fate decisions and contribute to human disease. For details, see:<br /> <br /> * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023<br /> <br /> * '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 <br /> <br /> * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.<br /> <br /> * '''[https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, et al. Human Mutation 2019. <br /> <br /> * '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.<br /> <br /> * '''[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003711 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M, Lee D, Mohammad-Noori M, and Beer MA. 2014. PLOS Computational Biology. July 17, 2014.<br /> <br /> and other [[Publications]].<br /> <br /> Our work uses functional genomics DNase-seq, ATAC-seq, ChIP-seq, RNA-seq, CRISPR, MPRA, Hi-C, and chromatin state data to computationally identify combinations of transcription factor binding sites which operate to define the activity of cell-type specific enhancers and their activation of target genes. We are currently focused on:<br /> <br /> * improving AI/ML methods to build more accurate models of enhancer activity<br /> <br /> * predicting the impact of mutations on enhancer activity and their contributions to disease <br /> <br /> * using AI/ML models to build and test dynamic gene regulatory networks with targeted CRISPR perturbation<br /> <br /> * using large scale datasets (ENCODE/IGVF) and CRISPR to constrain models of enhancer-promoter interactions and DNA looping mechanisms<br /> <br /> * using this sequence based regulatory code to understand mechanisms of gene regulatory network disruption in cancer and develop therapeutic strategies<br /> <br /> We are located in the McKusick-Nathans Institute of Genetic Medicine, and the Department of Biomedical Engineering, which has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Genomics, Bioinformatics, and Computational Biology at Johns Hopkins, including research in Systems Biology, AI, Machine Learning, and Dynamic Gene Regulatory Network Modeling.<br /> <br /> &lt;h3&gt;About Computational Biology in JHU Biomedical Engineering:&lt;/h3&gt;<br /> <br /> The Department of Biomedical Engineering has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Bioinformatics and Computational Biology at Johns Hopkins. Students with backgrounds in Physics, Mathematics, Computer Science and Engineering are encouraged to apply. Opportunities for research include: Computational Medicine, Genomics, Systems Biology, Machine Learning, and Network Modeling. Graduate students in Johns Hopkins' Biomedical Engineering programs can select research advisors from throughout Johns Hopkins' Medical Institutions, Whiting School of Engineering, and Krieger School of Arts and Sciences.<br /> <br /> &lt;!--&lt;h3&gt;[http://karchinlab.org/bme-compbio-jhu Visit Some Computational Labs at Johns Hopkins]&lt;/h3&gt;<br /> <br /> &lt;h3&gt;[http://ccb.jhu.edu/ Center for Computational Biology at Johns Hopkins]&lt;/h3&gt; --&gt;<br /> <br /> [[File:bmesmall.png]]</div>

MBeer http://beerlab.org/index.php?title=Computational_Regulatory_Genomics&diff=19637 2024-07-20T20:01:48Z

<p>MBeer: </p> <hr /> <div>&lt;h2&gt;Computational Regulatory Genomics&lt;/h2&gt; __NOTOC__ __NOTITLE__<br /> &lt;metadesc&gt;Computational Regulatory Genomics for graduate PhD and postdoctoral research in BME and IGM at Johns Hopkins, top ranking programs modeling DNA and systems biology.&lt;/metadesc&gt;<br /> &lt;h3&gt;[[Recent News ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;[[Lab Members ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Publications]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Postdoctoral Positions Available]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Resources]]&lt;/h3&gt;<br /> <br /> [[File:Beer_Michael_small.jpg|link=http://www.bme.jhu.edu/people/faculty/michael-beer/]] [[File:EncodeNatureGraphic_small.png]] [[File:dyn_net.gif]]<br /> <br /> [[File:Igvf_logo.png|150px]] &amp;nbsp;&amp;nbsp; [[File:Encode_logo.png]] &amp;nbsp;&amp;nbsp; [[File:Nhgri_logo.jpg|250px]] &amp;nbsp;&amp;nbsp;[[File:hopkins_logo.jpg|200px]]<br /> <br /> We are in the '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ Department of Biomedical Engineering]''' and the '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer McKusick-Nathans Department of Genetic Medicine]''' at Johns Hopkins University. You can apply for graduate study in my lab through '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ BME]''' or the Ph.D. program in '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer Human Genetics.]'''<br /> <br /> &lt;h3&gt;Research Interests: &lt;/h3&gt; The ultimate goal of our research is to understand how gene regulatory information is encoded in genomic DNA sequence.<br /> <br /> We have recently made significant progress using AI/ML to understand how DNA sequence specifies cell-type specific enhancer activity, target gene activation through looping constraints, and how dynamic enhancer-gene regulatory networks control cell-fate decisions and contribute to human disease. For details, see:<br /> <br /> * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023<br /> <br /> * '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 <br /> <br /> * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.<br /> <br /> * '''[https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, et al. Human Mutation 2019. <br /> <br /> * '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.<br /> <br /> * '''[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003711 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M, Lee D, Mohammad-Noori M, and Beer MA. 2014. PLOS Computational Biology. July 17, 2014.<br /> <br /> and other [[Publications]].<br /> <br /> Our work uses functional genomics DNase-seq, ATAC-seq, ChIP-seq, RNA-seq, CRISPR, MPRA, Hi-C, and chromatin state data to computationally identify combinations of transcription factor binding sites which operate to define the activity of cell-type specific enhancers and their activation of target genes. We are currently focused on:<br /> <br /> * improving AI/ML methods to build more accurate models of enhancer activity<br /> <br /> * predicting the impact of mutations on enhancer activity and their contributions to disease <br /> <br /> * using AI/ML models to build and test dynamic gene regulatory networks with targeted CRISPR perturbation<br /> <br /> * using large scale datasets (ENCODE/IGVF) and CRISPR to constrain models of enhancer-promoter interactions and DNA looping mechanisms<br /> <br /> * using this sequence based regulatory code to understand mechanisms of gene regulatory network disruption in cancer and develop therapeutic strategies<br /> <br /> We are located in the McKusick-Nathans Institute of Genetic Medicine, and the Department of Biomedical Engineering, which has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Genomics, Bioinformatics, and Computational Biology at Johns Hopkins, including research in Systems Biology, AI, Machine Learning, and Dynamic Gene Regulatory Network Modeling.<br /> <br /> &lt;h3&gt;About Computational Biology in JHU Biomedical Engineering:&lt;/h3&gt;<br /> <br /> The Department of Biomedical Engineering has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Bioinformatics and Computational Biology at Johns Hopkins. Students with backgrounds in Physics, Mathematics, Computer Science and Engineering are encouraged to apply. Opportunities for research include: Computational Medicine, Genomics, Systems Biology, Machine Learning, and Network Modeling. Graduate students in Johns Hopkins' Biomedical Engineering programs can select research advisors from throughout Johns Hopkins' Medical Institutions, Whiting School of Engineering, and Krieger School of Arts and Sciences.<br /> <br /> &lt;!--&lt;h3&gt;[http://karchinlab.org/bme-compbio-jhu Visit Some Computational Labs at Johns Hopkins]&lt;/h3&gt;<br /> <br /> &lt;h3&gt;[http://ccb.jhu.edu/ Center for Computational Biology at Johns Hopkins]&lt;/h3&gt; --&gt;<br /> <br /> [[File:bmesmall.png]]</div>

MBeer http://beerlab.org/index.php?title=Computational_Regulatory_Genomics&diff=19636 2024-07-17T02:13:10Z

<p>MBeer: </p> <hr /> <div>&lt;h2&gt;Computational Regulatory Genomics&lt;/h2&gt; __NOTOC__ __NOTITLE__<br /> &lt;metadesc&gt;Computational Regulatory Genomics for graduate PhD and postdoctoral research in BME and IGM at Johns Hopkins, top ranking programs modeling DNA and systems biology.&lt;/metadesc&gt;<br /> &lt;h3&gt;[[Recent News ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;[[Lab Members ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Publications]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Postdoctoral Positions Available]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Resources]]&lt;/h3&gt;<br /> <br /> [[File:Beer_Michael_small.jpg|link=http://www.bme.jhu.edu/people/faculty/michael-beer/]] [[File:EncodeNatureGraphic_small.png]] [[File:dyn_net.gif]]<br /> <br /> [[File:Igvf_logo.png|150px]] &amp;nbsp;&amp;nbsp; [[File:Encode_logo.png]] &amp;nbsp;&amp;nbsp; [[File:Nhgri_logo.jpg|250px]] &amp;nbsp;&amp;nbsp;[[File:hopkins_logo.jpg|200px]]<br /> <br /> We are in the '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ Department of Biomedical Engineering]''' and the '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer McKusick-Nathans Department of Genetic Medicine]''' at Johns Hopkins University. You can apply for graduate study in my lab through '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ BME]''' or the Ph.D. program in '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer Human Genetics.]'''<br /> <br /> &lt;h3&gt;Research Interests: &lt;/h3&gt; The ultimate goal of our research is to understand how gene regulatory information is encoded in genomic DNA sequence.<br /> <br /> We have recently made significant progress using AI/ML to understand how DNA sequence specifies cell-type specific enhancer activity, target gene activation through looping constraints, and how dynamic enhancer-gene regulatory networks control cell-fate decisions and contribute to human disease. For details, see:<br /> <br /> * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023<br /> <br /> * '''[https://genome.cshlp.org/content/34/5/680 Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer.]''' Razavi-Mohseni M, et al. Genome Research 2024 <br /> <br /> * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.<br /> <br /> * '''[https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, et al. Human Mutation 2019. <br /> <br /> * '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.<br /> <br /> * '''[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003711 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M, Lee D, Mohammad-Noori M, and Beer MA. 2014. PLOS Computational Biology. July 17, 2014.<br /> <br /> and other [[Publications]].<br /> <br /> Our work uses functional genomics DNase-seq, ATAC-seq, ChIP-seq, RNA-seq, CRISPR, MPRA, Hi-C, and chromatin state data to computationally identify combinations of transcription factor binding sites which operate to define the activity of cell-type specific enhancers and their activation of target genes. We are currently focused on:<br /> <br /> * improving AI/ML methods to build more accurate models of enhancer activity<br /> <br /> * predicting the impact of mutations on enhancer activity and their contributions to disease <br /> <br /> * using AI/ML models to build and test dynamic gene regulatory networks with targeted CRISPR perturbation<br /> <br /> * using large scale datasets (ENCODE/IGVF) and CRISPR to constrain models of enhancer-promoter interactions and DNA looping mechanisms<br /> <br /> * using this sequence based regulatory code to understand mechanisms of gene regulatory network disruption in cancer and develop therapeutic strategies<br /> <br /> We are located in the McKusick-Nathans Institute of Genetic Medicine, and the Department of Biomedical Engineering, which has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Genomics, Bioinformatics, and Computational Biology at Johns Hopkins, including research in Systems Biology, AI, Machine Learning, and Dynamic Gene Regulatory Network Modeling.<br /> <br /> &lt;h3&gt;About Computational Biology in JHU Biomedical Engineering:&lt;/h3&gt;<br /> <br /> The Department of Biomedical Engineering has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Bioinformatics and Computational Biology at Johns Hopkins. Students with backgrounds in Physics, Mathematics, Computer Science and Engineering are encouraged to apply. Opportunities for research include: Computational Medicine, Genomics, Systems Biology, Machine Learning, and Network Modeling. Graduate students in Johns Hopkins' Biomedical Engineering programs can select research advisors from throughout Johns Hopkins' Medical Institutions, Whiting School of Engineering, and Krieger School of Arts and Sciences.<br /> <br /> &lt;h3&gt;[http://karchinlab.org/bme-compbio-jhu Visit Some Computational Labs at Johns Hopkins]&lt;/h3&gt;<br /> <br /> &lt;h3&gt;[http://ccb.jhu.edu/ Center for Computational Biology at Johns Hopkins]&lt;/h3&gt;<br /> <br /> [[File:bmesmall.png]]</div>

MBeer http://beerlab.org/index.php?title=Computational_Regulatory_Genomics&diff=19635 2024-07-17T02:07:07Z

<p>MBeer: </p> <hr /> <div>&lt;h2&gt;Computational Regulatory Genomics&lt;/h2&gt; __NOTOC__ __NOTITLE__<br /> &lt;metadesc&gt;Computational Regulatory Genomics for graduate PhD and postdoctoral research in BME and IGM at Johns Hopkins, top ranking programs modeling DNA and systems biology.&lt;/metadesc&gt;<br /> &lt;h3&gt;[[Recent News ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;[[Lab Members ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Publications]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Postdoctoral Positions Available]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Resources]]&lt;/h3&gt;<br /> <br /> [[File:Beer_Michael_small.jpg|link=http://www.bme.jhu.edu/people/faculty/michael-beer/]] [[File:EncodeNatureGraphic_small.png]] [[File:dyn_net.gif]]<br /> <br /> [[File:Igvf_logo.png|150px]] &amp;nbsp;&amp;nbsp; [[File:Encode_logo.png]] &amp;nbsp;&amp;nbsp; [[File:Nhgri_logo.jpg|250px]] &amp;nbsp;&amp;nbsp;[[File:hopkins_logo.jpg|200px]]<br /> <br /> We are in the '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ Department of Biomedical Engineering]''' and the '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer McKusick-Nathans Department of Genetic Medicine]''' at Johns Hopkins University. You can apply for graduate study in my lab through '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ BME]''' or the Ph.D. program in '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer Human Genetics.]'''<br /> <br /> &lt;h3&gt;Research Interests: &lt;/h3&gt; The ultimate goal of our research is to understand how gene regulatory information is encoded in genomic DNA sequence.<br /> <br /> We have recently made significant progress using AI/ML to understand how DNA sequence specifies cell-type specific enhancer activity, target gene activation through looping constraints, and how dynamic enhancer-gene regulatory networks control cell-fate decisions and contribute to human disease. For details, see:<br /> <br /> * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023<br /> <br /> * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.<br /> <br /> * '''[https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, et al. Human Mutation 2019. <br /> <br /> * '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.<br /> <br /> * '''[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003711 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M, Lee D, Mohammad-Noori M, and Beer MA. 2014. PLOS Computational Biology. July 17, 2014.<br /> <br /> and other [[Publications]].<br /> <br /> Our work uses functional genomics DNase-seq, ATAC-seq, ChIP-seq, RNA-seq, CRISPR, MPRA, Hi-C, and chromatin state data to computationally identify combinations of transcription factor binding sites which operate to define the activity of cell-type specific enhancers and their activation of target genes. We are currently focused on:<br /> <br /> * improving AI/ML methods to build more accurate models of enhancer activity<br /> <br /> * predicting the impact of mutations on enhancer activity and their contributions to disease <br /> <br /> * using AI/ML models to build and test dynamic gene regulatory networks with targeted CRISPR perturbation<br /> <br /> * using large scale datasets (ENCODE/IGVF) and CRISPR to constrain models of enhancer-promoter interactions and DNA looping mechanisms<br /> <br /> * using this sequence based regulatory code to understand mechanisms of gene regulatory network disruption in cancer and develop therapeutic strategies<br /> <br /> We are located in the McKusick-Nathans Institute of Genetic Medicine, and the Department of Biomedical Engineering, which has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Genomics, Bioinformatics, and Computational Biology at Johns Hopkins, including research in Systems Biology, AI, Machine Learning, and Dynamic Gene Regulatory Network Modeling.<br /> <br /> &lt;h3&gt;About Computational Biology in JHU Biomedical Engineering:&lt;/h3&gt;<br /> <br /> The Department of Biomedical Engineering has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Bioinformatics and Computational Biology at Johns Hopkins. Students with backgrounds in Physics, Mathematics, Computer Science and Engineering are encouraged to apply. Opportunities for research include: Computational Medicine, Genomics, Systems Biology, Machine Learning, and Network Modeling. Graduate students in Johns Hopkins' Biomedical Engineering programs can select research advisors from throughout Johns Hopkins' Medical Institutions, Whiting School of Engineering, and Krieger School of Arts and Sciences.<br /> <br /> &lt;h3&gt;[http://karchinlab.org/bme-compbio-jhu Visit Some Computational Labs at Johns Hopkins]&lt;/h3&gt;<br /> <br /> &lt;h3&gt;[http://ccb.jhu.edu/ Center for Computational Biology at Johns Hopkins]&lt;/h3&gt;<br /> <br /> [[File:bmesmall.png]]</div>

MBeer http://beerlab.org/index.php?title=Computational_Regulatory_Genomics&diff=19634 2024-07-17T02:04:17Z

<p>MBeer: </p> <hr /> <div>&lt;h2&gt;Computational Regulatory Genomics&lt;/h2&gt; __NOTOC__ __NOTITLE__<br /> &lt;metadesc&gt;Computational Regulatory Genomics for graduate PhD and postdoctoral research in BME and IGM at Johns Hopkins, top ranking programs modeling DNA and systems biology.&lt;/metadesc&gt;<br /> &lt;h3&gt;[[Recent News ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;[[Lab Members ]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Publications]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Postdoctoral Positions Available]]&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp;&amp;nbsp; [[Resources]]&lt;/h3&gt;<br /> <br /> [[File:Beer_Michael_small.jpg|link=http://www.bme.jhu.edu/people/faculty/michael-beer/]] [[File:EncodeNatureGraphic_small.png]] [[File:dyn_net.gif]]<br /> <br /> [[File:Igvf_logo.png|150px]] &amp;nbsp;&amp;nbsp; [[File:Encode_logo.png]] &amp;nbsp;&amp;nbsp; [[File:Nhgri_logo.jpg|250px]] &amp;nbsp;&amp;nbsp;[[File:hopkins_logo.jpg|200px]]<br /> <br /> We are in the '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ Department of Biomedical Engineering]''' and the '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer McKusick-Nathans Department of Genetic Medicine]''' at Johns Hopkins University. You can apply for graduate study in my lab through '''[http://www.bme.jhu.edu/people/faculty/michael-beer/ BME]''' or the Ph.D. program in '''[https://www.hopkinsmedicine.org/profiles/results/directory/profile/8377361/michael-beer Human Genetics.]'''<br /> <br /> &lt;h3&gt;Research Interests: &lt;/h3&gt; The ultimate goal of our research is to understand how gene regulatory information is encoded in genomic DNA sequence.<br /> <br /> We have recently made significant progress using AI/ML to understand how DNA sequence specifies cell-type specific enhancer activity, target gene activation through looping constraints, and how dynamic enhancer-gene regulatory networks control cell-fate decisions and contribute to human disease. For details, see:<br /> <br /> * '''[https://rdcu.be/dhCoG Dynamic network-guided CRISPRi screen identifies CTCF-loop-constrained nonlinear enhancer gene regulatory activity during cell state transitions.]''' Luo R, et al. Nature Genetics 2023<br /> <br /> * '''[https://www.annualreviews.org/doi/abs/10.1146/annurev-genom-121719-010946?journalCode=genom Enhancer Predictions and Genome-Wide Regulatory Circuits.]''' Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.<br /> <br /> * '''[https://onlinelibrary.wiley.com/doi/abs/10.1002/humu.23797 Integration of multiple epigenomic marks improves prediction of variant impact in saturation mutagenesis reporter assay.]''' Shigaki D, et al. Human Mutation 2019. <br /> <br /> * '''[https://www.nature.com/articles/ng.3331 A method to predict the impact of regulatory variants from DNA sequence.]''' Lee D, Gorkin DU, Baker M, Strober BJ, Asoni AL, McCallion AS, Beer, MA. Nature Genetics 2015.<br /> <br /> * '''[http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1003711 Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features.]''' Ghandi M, Lee D, Mohammad-Noori M, and Beer MA. 2014. PLOS Computational Biology. July 17, 2014.<br /> <br /> and other [[Publications]].<br /> <br /> Our work uses functional genomics DNase-seq, ATAC-seq, ChIP-seq, RNA-seq, CRISPR, MPRA, Hi-C, and chromatin state data to computationally identify combinations of transcription factor binding sites which operate to define the activity of cell-type specific enhancers and their activation of target genes. We are currently focused on:<br /> <br /> * improving AI/ML methods to build more accurate models of enhancer activity<br /> <br /> * predicting the impact of mutations on enhancer activity and disease impact<br /> <br /> * using AI/ML models to build and test dynamic gene regulatory networks with targeted CRISPR perturbation<br /> <br /> * using large scale datasets (ENCODE/IGVF) and CRISPR to constrain models of enhancer-promoter interactions and DNA looping mechanisms<br /> <br /> * using this sequence based regulatory code to understand mechanisms of gene regulatory network disruption in cancer and develop therapeutic strategies<br /> <br /> We are located in the McKusick-Nathans Institute of Genetic Medicine, and the Department of Biomedical Engineering, which has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Genomics, Bioinformatics, and Computational Biology at Johns Hopkins, including research in Systems Biology, AI, Machine Learning, and Dynamic Gene Regulatory Network Modeling.<br /> <br /> &lt;h3&gt;About Computational Biology in JHU Biomedical Engineering:&lt;/h3&gt;<br /> <br /> The Department of Biomedical Engineering has long been a leader in the development of rigorous quantitative modeling of biological systems, and is a natural home for graduate studies in Bioinformatics and Computational Biology at Johns Hopkins. Students with backgrounds in Physics, Mathematics, Computer Science and Engineering are encouraged to apply. Opportunities for research include: Computational Medicine, Genomics, Systems Biology, Machine Learning, and Network Modeling. Graduate students in Johns Hopkins' Biomedical Engineering programs can select research advisors from throughout Johns Hopkins' Medical Institutions, Whiting School of Engineering, and Krieger School of Arts and Sciences.<br /> <br /> &lt;h3&gt;[http://karchinlab.org/bme-compbio-jhu Visit Some Computational Labs at Johns Hopkins]&lt;/h3&gt;<br /> <br /> &lt;h3&gt;[http://ccb.jhu.edu/ Center for Computational Biology at Johns Hopkins]&lt;/h3&gt;<br /> <br /> [[File:bmesmall.png]]</div>

MBeer http://beerlab.org/index.php?title=Recent_News&diff=19633 2024-07-04T05:16:47Z

<p>MBeer: </p> <hr /> <div>'''[https://physicsworld.com/a/iter-fusion-reactor-hit-by-massive-decade-long-delay-and-e5bn-price-hike/ ITER fusion project decade long delay and massive cost increase.]''' This is the closest thing to a feasible fusion power plant, and there is more bad news for economic feasibility. It was a great education, but I have no regrets leaving that field over 20 years ago.<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2024 Jin Woo awarded Mette Strand JHU Young Investigator Day Award.]'''<br /> <br /> '''[https://hub.jhu.edu/2023/08/10/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ JHU HUB News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]''' I would add that this work was an equal collaboration between our lab and Danwei Huangfu's lab at MSKCC, which was underplayed in the JHU articles.<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/machine-learning-model-could-enable-targeted-gene-therapies-for-genetic-diseases/ BME News Article about our CRISPRi screen and modeling of cell-fate decisions in Nature Genetics.]'''<br /> <br /> '''[https://mlbbs.bme.jhu.edu Applications are now open for the Machine Learning in the Basic Biomedical Sciences Postdoctoral Program.]'''<br /> <br /> '''[https://thanhnien.vn/hanh-trinh-tro-thanh-nha-nghien-cuu-ung-thu-hang-dau-the-gioi-post1423871.html?fbclid=IwAR0MRKXdjyduDtZYyS3Rf5QZgzCReUY3IP-mMi2ru1TnzaApDx54-RLKXko My first interview in a Vietnamese newspaper.]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/Impact-of-Genomic-Variation-on-Function-Consortium#awardees Beer Lab awarded IGVF Consortium Grant.]'''<br /> <br /> '''[https://www.hopkinsmedicine.org/som/kudos/young-investigators-day-2021/ Wang awarded Bae Gyo Jung JHU Young Investigator Day Award.]''' '''[https://www.bme.jhu.edu/news-events/news/three-from-hopkins-bme-recognized-at-young-investigators-day/ also here.]'''<br /> <br /> '''[https://med.stanford.edu/genetics/events/encode-2021.html Jin-Woo, Wang, and Dustin selected for talks at 2021 ENCODE Consortium Meeting.]'''<br /> <br /> '''[https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1006625 Wang discovered Enhancer-Promoter interaction prediction is harder than it looks.]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi5-regulation-saturation.html Dustin leads integrative analysis of CAGI5 regulation saturation challenge.]'''<br /> <br /> '''[https://www.nature.com/articles/d41586-020-00335-7 Highly cited researcher banned from journal board for citation abuse.]''' I put this here because K-C Chou wrote &lt;b&gt;many&lt;/b&gt; papers with and appears to have been a mentor to Bin Liu, who plagiarized our gkm-SVM paper as described in the several items below. Eleven papers co-authored by Bin Liu and K-C Chou were (self-)cited in the paper which plagiarized our gkm-SVM paper. See also the original reporting from '''[https://academic.oup.com/bioinformatics/article/35/18/3217/5304360 Bioinformatics]''' and '''[https://www.sciencedirect.com/science/article/pii/S0022519320300278?via%3Dihub Journal of Theoretical Biology.]''' I'm glad K-C Chou finally got called out on his gross citation manipulation, but the problem is broader than just these two journals. Although K-C Chou was removed, his proteges were and still are on the boards of many other journals and continue their citation inflation through mechanisms not discussed in these articles. For example, these articles do not mention that the authors who added the ~30 citations to K-C Chou during the review process may have been explicitly promised future citations from K-C Chou in return. The group of authors who cite K-C Chou is small, but they all cite each other multiple times in each paper, exponentially inflating citations of all members of the group.<br /> The scientific publishing industry has been manipulated by their lack of attention to these problems. If they want to investigate, all they have to do is look at who continues to cite '''[https://academic.oup.com/nar/article/43/W1/W65/2467922 this useless paper]''' over '''[https://scholar.google.com/scholar?hl=en&amp;as_sdt=0%2C21&amp;q=Pse-in-One%3A+a+web+server+for+generating+various+modes+of+pseudo+components+of+DNA%2C+RNA%2C+and+protein+sequences&amp;btnG= 600 times]'''. You may notice a pattern. None of these papers are real and each of these journals allowed it to happen for some unknown reasons. The list of these journals is clear from the citation patterns.<br /> <br /> '''[https://retractionwatch.com/2018/03/20/over-a-dozen-board-members-resigned-after-a-journal-refused-to-retract-a-paper-today-its-retracted/ Scientific Reports finally retracts paper plagiarizing our gkm-SVM paper.]''' '''[http://www.bmj.com/content/360/bmj.k1386 related article]'''<br /> <br /> Don't do this: '''[http://www.sixthtone.com/news/1001156/19-academics-resign-from-journal-over-alleged-plagiarism/ plagiarism1]'''<br /> '''[http://retractionwatch.com/2017/10/17/21-faculty-johns-hopkins-threaten-resign-board-journal-doesnt-retract-paper/ plagiarism2]'''<br /> '''[http://retractionwatch.com/2017/10/10/board-member-resigns-journal-handling-paper-accused-plagiarism/ plagiarism3]'''<br /> '''[http://retractionwatch.com/2017/11/07/17-johns-hopkins-researchers-resign-protest-ed-board-nature-journal/ plagiarism4]'''<br /> '''[http://www.the-scientist.com/?articles.view/articleNo/50888/title/Mass-Resignation-from-Scientific-Reports-s-Editorial-Board/ plagiarism5]'''<br /> <br /> '''[http://www.jhunewsletter.com/2017/02/16/professor-beer-awarded-1-8-million-nih-grant/ JHU Newsletter article on our ENCODE grant by Anna Chen]'''<br /> <br /> '''[https://www.genome.gov/Funded-Programs-Projects/ENCODE-Project-ENCyclopedia-Of-DNA-Elements NHGRI on next phase of ENCODE project consortium]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-awarded-1-8-million-grant-from-nih/ Beer Lab awarded NIH ENCODE grant]'''<br /> <br /> '''[http://www.nature.com/nature/journal/v538/n7624/full/538275a.html Our computational work featured in Nature news article on &quot;The Dark Side of the Human Genome&quot;]'''<br /> <br /> '''[http://www.beerlab.org/gkmsvm New R package for gkmSVM and deltaSVM released]'''<br /> <br /> '''[https://genomeinterpretation.org/cagi4-2eqtl.html gkmSVM among top-scoring methods for CAGI4 eQTL prediction challenge] '''<br /> <br /> '''[http://www.iscb.org/recomb-regsysgen2015-submissions/recomb-regsysgen2015-top-papers-reading-papers deltaSVM paper voted Top 10 in Regulatory Genomics 2015] '''<br /> <br /> '''[http://www.nature.com/ng/journal/v47/n8/full/ng.3364.html Nature Genetics News &amp; Views article on our deltaSVM paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/vulnerabilities_in_genomes_dimmer_switches_should_shed_light_on_hundreds_of_complex_diseases Nature Genetics paper on impact of regulatory variants]'''<br /> <br /> '''[http://www.newsweek.com/humans-and-mice-are-both-more-similar-and-different-previously-thought-285635 Newsweek article on Mouse ENCODE paper]'''<br /> <br /> '''[http://www.hopkinsmedicine.org/news/media/releases/scientists_map_mouse_genomes_mission_control_centers Mouse ENCODE Consortium paper in Nature]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/unraveling-the-genetic-underpinning-of-disease/ Beer Lab awarded NIH grant for regulatory contributions to disease. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/michael-beer-improves-methodology-for-predicting-disease-enabling-genetic-mutations/ Beer Lab improves methodology for predicting disease enabling genetic mutations. ]'''<br /> <br /> '''[https://www.bme.jhu.edu/news-events/news/dongwon-lee-paper-voted-top-10-of-2011/ kmer-SVM Genome Research paper voted Top 10 in Regulatory Genomics.] '''<br /> <br /> '''[http://www.hopkinsmedicine.org/institute_basic_biomedical_sciences/news_events/Announcements/2013_04_YID.html Dongwon Lee awarded Young Investigator Day Award.] '''</div>

MBeer http://beerlab.org/index.php?title=Lab_Members&diff=19632 2024-05-28T09:30:51Z

<p>MBeer: /* Current Undergraduates */</p> <hr /> <div>__NOTOC__<br /> ==PI== <br /> [[Users:Mbeer|Mike Beer (with short hair)]]<br /> <br /> [[File:Beer_m.gif]] [[File:JinWooPhD.jpeg|350px]] [[File:Lab2022.jpg|350px]] [[File:group_pic.jpg|350px]] <br /> [[File:IGVF Trainee Awards 2022.jpg|350px]] [[File:CSHL.jpg|350px]]<br /> [[File:6C9A6781.jpg|200px]] [[File:Lab_Pic_2021.jpg|350px]]<br /> <br /> ==Postdocs==<br /> * Ayoti Patra (former)<br /> [[File:Ayoti.png|100px]]<br /> <br /> ==Graduate students==<br /> * Dustin Shigaki<br /> [[File:Dustin.jpg|100px]]<br /> * Milad Razavi-Mohseni<br /> [[File:Milad.jpg|100px]]<br /> * Gary Yang<br /> * Andrew Rojnuckarin<br /> * Sky Li<br /> <br /> ==Current Undergraduates==<br /> * Nadia Momtaz<br /> [[File:Nadia.jpg|100px]]<br /> * Jason Han<br /> * Daniel Chen<br /> <br /> ==Former graduate students==<br /> * [https://www.linkedin.com/in/jin-woo-oh-65113b90/ Jin Woo Oh] ([https://www.lunit.io/en Lunit])<br /> * [https://www.linkedin.com/in/wang-xi-145706168/ Wang Xi] (Verve Therapeutics)<br /> * [https://scholar.google.com/citations?user=7oyAkKkAAAAJ&amp;hl=en Dongwon Lee] (Asst. Prof. at Harvard Medical School and Boston Children's Hospital)<br /> * Kipper Fletez-Brant (HG rotation student, now at 23andMe)<br /> * Mahmoud Ghandi (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Monte Rosa Therapeutics)<br /> * [http://www.genebrew.com Rahul Karnik] (postdoc at Broad Institute of MIT and Harvard, now Director of Computational Biology at Kymera Therapeutics)<br /> * Jun Kyu Rhee (now at Korea Institute of Science and Technology)<br /> * Donavan Cheng (now Director, Population Genomics at Illumina)<br /> <br /> ==Former Undergraduates==<br /> * Gary Yang<br /> * Deepak Manda<br /> * Alex Chang<br /> * Richard Liu<br /> * Nico Eng<br /> * Jin Woo Oh<br /> * Michael Mudgett<br /> * Felix Yu<br /> * Amy Xiao<br /> * Sunny Thodupunuri<br /> * Tianyue Ou<br /> * Ganesh Arvapalli<br /> * Zachary Heiman<br /> * Gianluca Silva Croso<br /> * Kendrick Hougen<br /> * Nole Lin<br /> * Ashutosh Jindal<br /> * Kyle Xiong<br /> * Ben Strober<br /> * Alessandro Asoni<br /> * Billy Kang<br /> * John Lee<br /> * Andrew Pao<br /> * Tuo Li <br /> * Peter Li <br /> * Juinting Chiang</div>

MBeer