Anshul Kundaje - Publications

Affiliations: 
Computer Science Stanford University, Palo Alto, CA 

47 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2022 Ludwig L, Lareau CA, Bao EL, Liu N, Utsugisawa T, Tseng AM, Myers SA, Verboon JM, Ulirsch JC, Luo W, Muus C, Fiorini C, Olive ME, Vockley CM, Munschauer M, ... ... Kundaje A, et al. A Congenital Anemia Reveals Distinct Targeting Mechanisms for Master Transcription Factor GATA1. Blood. PMID 35030251 DOI: 10.1182/blood.2021013753  0.338
2022 Cheng P, Wirka RC, Clarke LS, Zhao Q, Kundu R, Nguyen T, Nair S, Sharma D, Kim HJ, Shi H, Assimes T, Kim JB, Kundaje A, Quertermous T. ZEB2 Shapes the Epigenetic Landscape of Atherosclerosis. Circulation. PMID 34990206 DOI: 10.1161/CIRCULATIONAHA.121.057789  0.308
2021 Kim DS, Risca VI, Reynolds DL, Chappell J, Rubin AJ, Jung N, Donohue LKH, Lopez-Pajares V, Kathiria A, Shi M, Zhao Z, Deep H, Sharmin M, Rao D, Lin S, ... ... Kundaje A, et al. The dynamic, combinatorial cis-regulatory lexicon of epidermal differentiation. Nature Genetics. PMID 34650237 DOI: 10.1038/s41588-021-00947-3  0.321
2021 Trevino AE, Müller F, Andersen J, Sundaram L, Kathiria A, Shcherbina A, Farh K, Chang HY, Pașca AM, Kundaje A, Pașca SP, Greenleaf WJ. Chromatin and gene-regulatory dynamics of the developing human cerebral cortex at single-cell resolution. Cell. PMID 34390642 DOI: 10.1016/j.cell.2021.07.039  0.34
2021 Nasser J, Bergman DT, Fulco CP, Guckelberger P, Doughty BR, Patwardhan TA, Jones TR, Nguyen TH, Ulirsch JC, Lekschas F, Mualim K, Natri HM, Weeks EM, Munson G, Kane M, ... ... Kundaje A, et al. Genome-wide enhancer maps link risk variants to disease genes. Nature. PMID 33828297 DOI: 10.1038/s41586-021-03446-x  0.337
2021 Avsec Ž, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J. Base-resolution models of transcription-factor binding reveal soft motif syntax. Nature Genetics. PMID 33603233 DOI: 10.1038/s41588-021-00782-6  0.31
2020 Corces MR, Shcherbina A, Kundu S, Gloudemans MJ, Frésard L, Granja JM, Louie BH, Eulalio T, Shams S, Bagdatli ST, Mumbach MR, Liu B, Montine KS, Greenleaf WJ, Kundaje A, et al. Single-cell epigenomic analyses implicate candidate causal variants at inherited risk loci for Alzheimer's and Parkinson's diseases. Nature Genetics. PMID 33106633 DOI: 10.1038/s41588-020-00721-x  0.303
2020 Moore JE, Purcaro MJ, Pratt HE, Epstein CB, Shoresh N, Adrian J, Kawli T, Davis CA, Dobin A, Kaul R, Halow J, Van Nostrand EL, Freese P, Gorkin DU, ... ... Kundaje A, et al. Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. 583: 699-710. PMID 32728249 DOI: 10.1038/S41586-020-2493-4  0.709
2020 Grubert F, Srivas R, Spacek DV, Kasowski M, Ruiz-Velasco M, Sinnott-Armstrong N, Greenside P, Narasimha A, Liu Q, Geller B, Sanghi A, Kulik M, Sa S, Rabinovitch M, Kundaje A, et al. Landscape of cohesin-mediated chromatin loops in the human genome. Nature. 583: 737-743. PMID 32728247 DOI: 10.1038/S41586-020-2151-X  0.338
2019 Nair S, Kim DS, Perricone J, Kundaje A. Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts. Bioinformatics (Oxford, England). 35: i108-i116. PMID 31510655 DOI: 10.1093/Bioinformatics/Btz352  0.366
2019 Movva R, Greenside P, Marinov GK, Nair S, Shrikumar A, Kundaje A. Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays. Plos One. 14: e0218073. PMID 31206543 DOI: 10.1371/Journal.Pone.0218073  0.343
2018 Greenside P, Shimko T, Fordyce P, Kundaje A. Discovering epistatic feature interactions from neural network models of regulatory DNA sequences. Bioinformatics (Oxford, England). 34: i629-i637. PMID 30423062 DOI: 10.1093/Bioinformatics/Bty575  0.326
2018 Marinov GK, Kundaje A. ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation. Briefings in Functional Genomics. 17: 116-137. PMID 29529131 DOI: 10.1093/Bfgp/Ely004  0.335
2017 Daugherty AC, Yeo RW, Buenrostro JD, Greenleaf WJ, Kundaje A, Brunet A. Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans. Genome Research. PMID 29141961 DOI: 10.1101/Gr.226233.117  0.335
2017 Wang B, Huang L, Zhu Y, Kundaje A, Batzoglou S, Goldenberg A. Vicus: Exploiting local structures to improve network-based analysis of biological data. Plos Computational Biology. 13: e1005621. PMID 29023470 DOI: 10.1371/Journal.Pcbi.1005621  0.553
2017 Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, ... ... Kundaje A, et al. Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nature Genetics. PMID 28945252 DOI: 10.1038/Ng.3963  0.303
2017 Koh PW, Pierson E, Kundaje A. Denoising genome-wide histone ChIP-seq with convolutional neural networks. Bioinformatics (Oxford, England). 33: i225-i233. PMID 28881977 DOI: 10.1093/Bioinformatics/Btx243  0.304
2017 Kreimer A, Zeng H, Edwards MD, Guo Y, Tian K, Shin S, Welch R, Wainberg M, Mohan R, Sinnott-Armstrong NA, Li Y, Eraslan G, Amin TB, Goke J, Mueller NS, ... ... Kundaje A, et al. Predicting gene expression in massively parallel reporter assays: a comparative study. Human Mutation. PMID 28220625 DOI: 10.1002/Humu.23197  0.601
2015 Grubert F, Zaugg JB, Kasowski M, Ursu O, Spacek DV, Martin AR, Greenside P, Srivas R, Phanstiel DH, Pekowska A, Heidari N, Euskirchen G, Huber W, Pritchard JK, Bustamante CD, ... ... Kundaje A, et al. Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions. Cell. PMID 26300125 DOI: 10.1016/J.Cell.2015.07.048  0.32
2015 Sazonova O, Zhao Y, Nürnberg S, Miller C, Pjanic M, Castano VG, Kim JB, Salfati EL, Kundaje AB, Bejerano G, Assimes T, Yang X, Quertermous T. Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci. Plos Genetics. 11: e1005202. PMID 26020271 DOI: 10.1371/Journal.Pgen.1005202  0.348
2015 Onengut-Gumuscu S, Chen WM, Burren O, Cooper NJ, Quinlan AR, Mychaleckyj JC, Farber E, Bonnie JK, Szpak M, Schofield E, Achuthan P, Guo H, Fortune MD, Stevens H, Walker NM, ... ... Kundaje A, et al. Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers. Nature Genetics. 47: 381-6. PMID 25751624 DOI: 10.1038/Ng.3245  0.53
2015 Gjoneska E, Pfenning AR, Mathys H, Quon G, Kundaje A, Tsai LH, Kellis M. Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease. Nature. 518: 365-9. PMID 25693568 DOI: 10.1038/Nature14252  0.543
2015 Kundaje A, Meuleman W, Ernst J, Bilenky M, Yen A, Heravi-Moussavi A, Kheradpour P, Zhang Z, Wang J, Ziller MJ, Amin V, Whitaker JW, Schultz MD, Ward LD, et al. Integrative analysis of 111 reference human epigenomes. Nature. 518: 317-30. PMID 25693563 DOI: 10.1038/Nature14248  0.577
2014 Cheng Y, Ma Z, Kim BH, Wu W, Cayting P, Boyle AP, Sundaram V, Xing X, Dogan N, Li J, Euskirchen G, Lin S, Lin Y, Visel A, Kawli T, ... ... Kundaje A, et al. Principles of regulatory information conservation between mouse and human. Nature. 515: 371-5. PMID 25409826 DOI: 10.1038/Nature13985  0.382
2014 Yue F, Cheng Y, Breschi A, Vierstra J, Wu W, Ryba T, Sandstrom R, Ma Z, Davis C, Pope BD, Shen Y, Pervouchine DD, Djebali S, Thurman RE, Kaul R, ... ... Kundaje A, et al. A comparative encyclopedia of DNA elements in the mouse genome. Nature. 515: 355-64. PMID 25409824 DOI: 10.1038/Nature13992  0.616
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Reply to Brunet and Doolittle: Both selected effect and causal role elements can influence human biology and disease. Proceedings of the National Academy of Sciences of the United States of America. 111: E3366. PMID 25275169 DOI: 10.1073/Pnas.1410434111  0.519
2014 Boyle AP, Araya CL, Brdlik C, Cayting P, Cheng C, Cheng Y, Gardner K, Hillier LW, Janette J, Jiang L, Kasper D, Kawli T, Kheradpour P, Kundaje A, Li JJ, et al. Comparative analysis of regulatory information and circuits across distant species. Nature. 512: 453-6. PMID 25164757 DOI: 10.1038/Nature13668  0.594
2014 Ho JW, Jung YL, Liu T, Alver BH, Lee S, Ikegami K, Sohn KA, Minoda A, Tolstorukov MY, Appert A, Parker SC, Gu T, Kundaje A, Riddle NC, Bishop E, et al. Comparative analysis of metazoan chromatin organization. Nature. 512: 449-52. PMID 25164756 DOI: 10.1038/Nature13415  0.552
2014 Araya CL, Kawli T, Kundaje A, Jiang L, Wu B, Vafeados D, Terrell R, Weissdepp P, Gevirtzman L, Mace D, Niu W, Boyle AP, Xie D, Ma L, Murray JI, et al. Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. 512: 400-5. PMID 25164749 DOI: 10.1038/Nature13497  0.345
2014 Benayoun BA, Pollina EA, Ucar D, Mahmoudi S, Karra K, Wong ED, Devarajan K, Daugherty AC, Kundaje AB, Mancini E, Hitz BC, Gupta R, Rando TA, Baker JC, Snyder MP, et al. H3K4me3 breadth is linked to cell identity and transcriptional consistency. Cell. 158: 673-88. PMID 25083876 DOI: 10.1016/J.Cell.2014.06.027  0.309
2014 Slattery M, Ma L, Spokony RF, Arthur RK, Kheradpour P, Kundaje A, Nègre N, Crofts A, Ptashkin R, Zieba J, Ostapenko A, Suchy S, Victorsen A, Jameel N, Grundstad AJ, et al. Diverse patterns of genomic targeting by transcriptional regulators in Drosophila melanogaster. Genome Research. 24: 1224-35. PMID 24985916 DOI: 10.1101/Gr.168807.113  0.589
2014 Kellis M, Wold B, Snyder MP, Bernstein BE, Kundaje A, Marinov GK, Ward LD, Birney E, Crawford GE, Dekker J, Dunham I, Elnitski LL, Farnham PJ, Feingold EA, Gerstein M, et al. Defining functional DNA elements in the human genome. Proceedings of the National Academy of Sciences of the United States of America. 111: 6131-8. PMID 24753594 DOI: 10.1073/Pnas.1318948111  0.597
2013 Kasowski M, Kyriazopoulou-Panagiotopoulou S, Grubert F, Zaugg JB, Kundaje A, Liu Y, Boyle AP, Zhang QC, Zakharia F, Spacek DV, Li J, Xie D, Olarerin-George A, Steinmetz LM, Hogenesch JB, et al. Extensive variation in chromatin states across humans. Science (New York, N.Y.). 342: 750-2. PMID 24136358 DOI: 10.1126/Science.1242510  0.721
2013 Hoffman MM, Ernst J, Wilder SP, Kundaje A, Harris RS, Libbrecht M, Giardine B, Ellenbogen PM, Bilmes JA, Birney E, Hardison RC, Dunham I, Kellis M, Noble WS. Integrative annotation of chromatin elements from ENCODE data. Nucleic Acids Research. 41: 827-41. PMID 23221638 DOI: 10.1093/Nar/Gks1284  0.605
2012 Landt SG, Marinov GK, Kundaje A, Kheradpour P, Pauli F, Batzoglou S, Bernstein BE, Bickel P, Brown JB, Cayting P, Chen Y, DeSalvo G, Epstein C, Fisher-Aylor KI, Euskirchen G, et al. ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia. Genome Research. 22: 1813-31. PMID 22955991 DOI: 10.1101/Gr.136184.111  0.711
2012 Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, et al. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Research. 22: 1798-812. PMID 22955990 DOI: 10.1101/Gr.139105.112  0.346
2012 Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Research. 22: 1748-59. PMID 22955986 DOI: 10.1101/gr.136127.111  0.568
2012 Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A. Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements. Genome Research. 22: 1735-47. PMID 22955985 DOI: 10.1101/Gr.136366.111  0.616
2012 Gerstein MB, Kundaje A, Hariharan M, Landt SG, Yan KK, Cheng C, Mu XJ, Khurana E, Rozowsky J, Alexander R, Min R, Alves P, Abyzov A, Addleman N, Bhardwaj N, et al. Architecture of the human regulatory network derived from ENCODE data. Nature. 489: 91-100. PMID 22955619 DOI: 10.1038/Nature11245  0.648
2012 Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M. Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors. Genome Biology. 13: R48. PMID 22950945 DOI: 10.1186/Gb-2012-13-9-R48  0.367
2008 Kundaje A, Xin X, Lan C, Lianoglou S, Zhou M, Zhang L, Leslie C. A predictive model of the oxygen and heme regulatory network in yeast. Plos Computational Biology. 4: e1000224. PMID 19008939 DOI: 10.1371/Journal.Pcbi.1000224  0.611
2007 Kundaje A, Lianoglou S, Li X, Quigley D, Arias M, Wiggins CH, Zhang L, Leslie C. Learning regulatory programs that accurately predict differential expression with MEDUSA. Annals of the New York Academy of Sciences. 1115: 178-202. PMID 17934055 DOI: 10.1196/Annals.1407.020  0.597
2006 Kundaje A, Middendorf M, Shah M, Wiggins CH, Freund Y, Leslie C. A classification-based framework for predicting and analyzing gene regulatory response. Bmc Bioinformatics. 7: S5. PMID 16723008 DOI: 10.1186/1471-2105-7-S1-S5  0.594
2005 Kundaje A, Middendorf M, Gao F, Wiggins C, Leslie C. Combining sequence and time series expression data to learn transcriptional modules. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 2: 194-202. PMID 17044183 DOI: 10.1109/Tcbb.2005.34  0.598
2005 Middendorf M, Kundaje A, Shah M, Freund Y, Wiggins CH, Leslie C. Motif discovery through predictive modeling of gene regulation Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 3500: 538-552.  0.482
2005 Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C. Predicting genetic regulatory response using classification: Yeast stress response Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 3318: 1-13.  0.482
2004 Middendorf M, Kundaje A, Wiggins C, Freund Y, Leslie C. Predicting genetic regulatory response using classification. Bioinformatics (Oxford, England). 20: i232-40. PMID 15262804 DOI: 10.1093/bioinformatics/bth923  0.588
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