Michael A. Beer

ScholarGPS® ID: 89035309674218

Affiliation

Johns Hopkins University, Baltimore, United States

Affiliation History

Field

Engineering and Computer Science

Discipline

Biomedical Engineering

Top Specialties

Regulatory Sequence | Genomics | DNA

Metrics Summary

Publication Count

Predicted Citations

5,964

Predicted h-index

Ranking

Publications and Citation History

Publications based on Top Specialties

Types of Publication

Publications
Books
Patents
NIH/NSF

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Machine learning identifies activation of RUNX/AP-1 as drivers of mesenchymal and fibrotic regulatory programs in gastric cancer (journal article) Razavi-Mohseni, Milad \| Huang, Weitai \| Guo, Yu A. \| Shigaki, Dustin \| Ho, Shamaine Wei Ting \| Tan, Patrick \| Skanderup, Anders J. \| Beer, Michael A. Genome Research, volume 34, issue 5, pages 680-695 (2024). 10.1101/gr.278565.123 Cite \| Source
Machine Learning Sequence Modeling Identifies Gene Regulatory Responses to Bone Marrow Stromal Interactions in Multiple Myeloma (journal article) Razavi-Mohseni, Milad \| Shigaki, Dustin \| Beer, Michael A Blood, volume 142, issue Supplement 1, pages 4144-4144 (2023). 10.1182/blood-2023-186981 Cite \| Source
Indicators of Successful Career Transitions from Physical Sciences and Engineering to Biomedical Research (journal article) Beer, Michael A. Current Genomics, volume 22, issue 4, pages 301-305 (2021). 10.2174/138920292204211203162041 Cite \| Source
Sequence-based correction of barcode bias in massively parallel reporter assays (journal article) Lee, Dongwon \| Kapoor, Ashish \| Lee, Changhee \| Mudgett, Michael \| Beer, Michael A. \| Chakravarti, Aravinda Genome Research, volume 31, issue 9, pages 1638-1645 (2021). 10.1101/gr.268599.120 Cited by (3) \| Cite \| Source
Loop competition and extrusion model predicts CTCF interaction specificity (journal article) Xi, Wang \| Beer, Michael A. Nature Communications, volume 12, issue 1 (2021). 10.1038/s41467-021-21368-0 Cited by (21) \| Cite \| Source
Enhancer Predictions and Genome-Wide Regulatory Circuits (journal article) Beer, Michael A. \| Shigaki, Dustin \| Huangfu, Danwei Annual Review of Genomics and Human Genetics, volume 21, issue 1, pages 37-54 (2020). 10.1146/annurev-genom-121719-010946 Cited by (12) \| Cite \| Source
Epigenetic activation and memory at a TGFB2 enhancer in systemic sclerosis (journal article) Shin, Joseph Yusup \| Beckett, James Daniel \| Bagirzadeh, Rustam \| Creamer, Tyler J. \| Shah, Ami A. \| McMahan, Zsuzsanna \| Paik, Julie J. \| Sampedro, Margaret M. \| MacFarlane, Elena G. \| Beer, Michael A. \| ... \| Dietz, Harry C. Science Translational Medicine, volume 11, issue 497 (2019). 10.1126/scitranslmed.aaw0790 Cited by (49) \| Cite \| Source
Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy (journal article) Xi, Wang \| Beer, Michael A. PLOS Computational Biology, volume 14, issue 12, pages e1006625- (2018). 10.1371/journal.pcbi.1006625 Cited by (33) \| Cite \| Source
Local epigenomic state cannot discriminate interacting and non-interacting enhancer-promoter pairs with high accuracy (journal article) Xi, Wang \| Beer, Michael bioRxiv (2018). 10.1101/420372 Cited by (1) \| Cite \| Source
Predicting enhancer activity and variant impact using gkm‐SVM (journal article) Beer, Michael A. Human Mutation, volume 38, issue 9, pages 1251-1258 (2017). 10.1002/humu.23185 Cited by (37) \| Cite \| Source \| Open Access
Embryonic loss of human females with partial trisomy 19 identifies region critical for the single active X (journal article) Migeon, Barbara R. \| Beer, Michael A. \| Bjornsson, Hans T. PLOS ONE, volume 12, issue 4, pages e0170403- (2017). 10.1371/journal.pone.0170403 Cited by (15) \| Cite \| Source \| Open Access
gkmSVM: an R package for gapped-kmer SVM (journal article) Ghandi, Mahmoud \| Mohammad-Noori, Morteza \| Ghareghani, Narges \| Lee, Dongwon \| Garraway, Levi \| Beer, Michael A. Bioinformatics, volume 32, issue 14, pages 2205-2207 (2016). 10.1093/bioinformatics/btw203 Cited by (118) \| Cite \| Source \| Open Access
Epigenomic landscapes of retinal rods and cones (journal article) Mo, Alisa \| Luo, Chongyuan \| Davis, Fred P \| Mukamel, Eran A \| Henry, Gilbert L \| Nery, Joseph R \| Urich, Mark A \| Picard, Serge \| Lister, Ryan \| Eddy, Sean R \| ... \| Nathans, Jeremy eLife, volume 5 (2016). 10.7554/eLife.11613 Cited by (133) \| Cite \| Source \| Open Access
Identification of Predictive Cis-Regulatory Elements Using a Discriminative Objective Function and a Dynamic Search Space (journal article) Karnik, Rahul \| Beer, Michael A. PLOS ONE, volume 10, issue 10, pages e0140557- (2015). 10.1371/journal.pone.0140557 Cited by (5) \| Cite \| Source \| Open Access
A method to predict the impact of regulatory variants from DNA sequence (journal article) Lee, Dongwon \| Gorkin, David U \| Baker, Maggie \| Strober, Benjamin J \| Asoni, Alessandro L \| McCallion, Andrew S \| Beer, Michael A Nature Genetics, volume 47, issue 8, pages 955-961 (2015). 10.1038/ng.3331 Cited by (328) \| Cite \| Source \| Open Access
Comparison of the transcriptional landscapes between human and mouse tissues (journal article) Lin, Shin \| Lin, Yiing \| Nery, Joseph R. \| Urich, Mark A. \| Breschi, Alessandra \| Davis, Carrie A. \| Dobin, Alexander \| Zaleski, Christopher \| Beer, Michael A. \| Chapman, William C. \| ... \| Snyder, Michael P. Proceedings of the National Academy of Sciences, volume 111, issue 48, pages 17224-17229 (2014). 10.1073/pnas.1413624111 Cited by (288) \| Cite \| Source \| Open Access
Divergent functions of hematopoietic transcription factors in lineage priming and differentiation during erythro-megakaryopoiesis (journal article) Pimkin, Maxim \| Kossenkov, Andrew V. \| Mishra, Tejaswini \| Morrissey, Christapher S. \| Wu, Weisheng \| Keller, Cheryl A. \| Blobel, Gerd A. \| Lee, Dongwon \| Beer, Michael A. \| Hardison, Ross C. \| Weiss, Mitchell J. Genome Research, volume 24, issue 12, pages 1932-1944 (2014). 10.1101/gr.164178.113 Cited by (78) \| Cite \| Source \| Open Access
Robust $$k$$ k -mer frequency estimation using gapped $$k$$ k -mers (journal article) Ghandi, Mahmoud \| Mohammad-Noori, Morteza \| Beer, Michael A. Journal of Mathematical Biology, volume 69, issue 2, pages 469-500 (2014). 10.1007/s00285-013-0705-3 Cited by (37) \| Cite \| Source \| Open Access
Enhanced Regulatory Sequence Prediction Using Gapped k-mer Features (journal article) Ghandi, Mahmoud \| Lee, Dongwon \| Mohammad-Noori, Morteza \| Beer, Michael A. PLoS Computational Biology, volume 10, issue 7, pages e1003711- (2014). 10.1371/journal.pcbi.1003711 Cited by (354) \| Cite \| Source \| Open Access
kmer-SVM: a web server for identifying predictive regulatory sequence features in genomic data sets (journal article) Fletez-Brant, Christopher \| Lee, Dongwon \| McCallion, Andrew S. \| Beer, Michael A. Nucleic Acids Research, volume 41, issue W1, pages W544-W556 (2013). 10.1093/nar/gkt519 Cited by (110) \| Cite \| Source \| Open Access

Title	Investigators	Year	Cost	Agency
SVM-based Analysis of the Fine Scale Structure of Regulatory Elements	Beer, Michael A	2017	$469,721	NATIONAL HUMAN GENOME RESEARCH INSTITUTE
SVM-based Analysis of the Fine Scale Structure of Regulatory Elements	Beer, Michael A.	2016	$471,140	NATIONAL HUMAN GENOME RESEARCH INSTITUTE
SVM-based Analysis of the Fine Scale Structure of Regulatory Elements	Beer, Michael A.	2015	$459,169	NATIONAL HUMAN GENOME RESEARCH INSTITUTE
SVM-based Analysis of the Fine Scale Structure of Regulatory Elements	Beer, Michael A.	2014	$461,332	NATIONAL HUMAN GENOME RESEARCH INSTITUTE
SVM-based Analysis of the Fine Scale Structure of Regulatory Elements	Beer, Michael A.	2013	$460,570	NATIONAL HUMAN GENOME RESEARCH INSTITUTE