Publications

Full publication list on google scholar or Orcid. My student PhD dissertations.

• 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 pdf

• Gapped-kmer sequence modeling robustly identifies regulatory vocabularies and distal enhancers conserved between evolutionarily distant mammals. Oh JW and Beer MA. Nature Communications 2024.

• 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 pdf

• Loop competition and extrusion model predicts CTCF interaction specificity. Xi W, Beer MA. Nature Comms. 2021.

• Enhancer Predictions and Genome-Wide Regulatory Circuits. Beer MA, Shigaki D, Huangfu D. Ann. Rev. Genomics and Human Genetics 2020.

• Expanded encyclopaedias of DNA elements in the human and mouse genomes. ENCODE Project Consortium. Nature 2020.

• 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

• 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.

• 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. (models)

• 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.

• Local epigenomic state cannot discriminate interacting and non-interacting enhancer–promoter pairs with high accuracy. Xi, W and Beer, MA. PLOS Comp Biol 2018.

• 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, & McCallion AS. Am. Jour. Human Genetics 2018

• 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 & Regev A. Nature Genetics 2018.

• Predicting enhancer activity and variant impact using gkm-SVM. Beer, MA. Human Mutation 2017.

• 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.

• 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.

• gkmSVM: an R package for gapped-kmer SVM. pdf tutorial Ghandi, M, Mohammad-Noori M, Ghareghani N, Lee D, Garraway L, and Beer MA. Bioinformatics 2016.

• 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.

• 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.

• 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.

• Identification of predictive cis-regulatory elements using a discriminative objective function and dynamic search spaces. Karnik, R, and Beer MA. PLOS One 2015.

• 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.

• A comparative encyclopedia of DNA elements in the mouse genome. Mouse ENCODE Consortium (includes Lee D and Beer MA). 2014. Nature 515:355–364.

• 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.

• 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.

• Mammalian Enhancer Prediction. Lee D, Beer MA. 2014. Genome Analysis: Current Procedures and Applications. Horizon Press. pdf

• 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)

• 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.

• 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.

• Group Normalization for Genomic Data. Ghandi M, and Beer MA. 2012. PLoS ONE 7:e38695.

• Discriminative prediction of mammalian enhancers from DNA sequence. Lee D, Karchin R, and Beer MA. 2011. Genome Research 21:2167-2180.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• 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.

• Predicting Gene Expression from Sequence. Beer MA and Tavazoie S. 2004. Cell 117:185-198.

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For a full list including my prior work in simulations of plasma turbulence, see my google scholar page.