| Year |
Citation |
Score |
| 2023 |
Martyn GE, Montgomery MT, Jones H, Guo K, Doughty BR, Linder J, Chen Z, Cochran K, Lawrence KA, Munson G, Pampari A, Fulco CP, Kelley DR, Lander ES, Kundaje A, et al. Rewriting regulatory DNA to dissect and reprogram gene expression. Biorxiv : the Preprint Server For Biology. PMID 38187584 DOI: 10.1101/2023.12.20.572268 |
0.399 |
|
| 2023 |
Kuderna LFK, Ulirsch JC, Rashid S, Ameen M, Sundaram L, Hickey G, Cox AJ, Gao H, Kumar A, Aguet F, Christmas MJ, Clawson H, Haeussler M, Janiak MC, Kuhlwilm M, ... ... Kundaje A, et al. Identification of constrained sequence elements across 239 primate genomes. Nature. PMID 38030727 DOI: 10.1038/s41586-023-06798-8 |
0.391 |
|
| 2023 |
Gschwind AR, Mualim KS, Karbalayghareh A, Sheth MU, Dey KK, Jagoda E, Nurtdinov RN, Xi W, Tan AS, Jones H, Ma XR, Yao D, Nasser J, Avsec Ž, James BT, ... ... Kundaje A, et al. An encyclopedia of enhancer-gene regulatory interactions in the human genome. Biorxiv : the Preprint Server For Biology. PMID 38014075 DOI: 10.1101/2023.11.09.563812 |
0.699 |
|
| 2023 |
DeGorter MK, Goddard PC, Karakoc E, Kundu S, Yan SM, Nachun D, Abell N, Aguirre M, Carstensen T, Chen Z, Durrant M, Dwaracherla VR, Feng K, Gloudemans MJ, Hunter N, ... ... Kundaje A, et al. Transcriptomics and chromatin accessibility in multiple African population samples. Biorxiv : the Preprint Server For Biology. PMID 37986808 DOI: 10.1101/2023.11.04.564839 |
0.371 |
|
| 2023 |
Marinov GK, Doughty B, Kundaje A, Greenleaf WJ. The landscape of the histone-organized chromatin of Bdellovibrionota bacteria. Biorxiv : the Preprint Server For Biology. PMID 37961278 DOI: 10.1101/2023.10.30.564843 |
0.328 |
|
| 2023 |
Nair S, Ameen M, Sundaram L, Pampari A, Schreiber J, Balsubramani A, Wang YX, Burns D, Blau HM, Karakikes I, Wang KC, Kundaje A. Transcription factor stoichiometry, motif affinity and syntax regulate single-cell chromatin dynamics during fibroblast reprogramming to pluripotency. Biorxiv : the Preprint Server For Biology. PMID 37873116 DOI: 10.1101/2023.10.04.560808 |
0.366 |
|
| 2023 |
Horton CA, Alexandari AM, Hayes MGB, Marklund E, Schaepe JM, Aditham AK, Shah N, Suzuki PH, Shrikumar A, Afek A, Greenleaf WJ, Gordân R, Zeitlinger J, Kundaje A, Fordyce PM. Short tandem repeats bind transcription factors to tune eukaryotic gene expression. Science (New York, N.Y.). 381: eadd1250. PMID 37733848 DOI: 10.1126/science.add1250 |
0.343 |
|
| 2023 |
Brennan KJ, Weilert M, Krueger S, Pampari A, Liu HY, Yang AWH, Morrison JA, Hughes TR, Rushlow CA, Kundaje A, Zeitlinger J. Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation. Developmental Cell. PMID 37557175 DOI: 10.1016/j.devcel.2023.07.007 |
0.351 |
|
| 2023 |
Hitz B, Lee JW, Jolanki O, Kagda M, Graham K, Sud P, Gabdank I, Strattan JS, Sloan C, Dreszer T, Rowe L, Podduturi N, Malladi V, Chan E, Davidson J, ... ... Kundaje A, et al. The ENCODE Uniform Analysis Pipelines. Research Square. PMID 37503119 DOI: 10.21203/rs.3.rs-3111932/v1 |
0.301 |
|
| 2023 |
Alexandari AM, Horton CA, Shrikumar A, Shah N, Li E, Weilert M, Pufall MA, Zeitlinger J, Fordyce PM, Kundaje A. distillation of thermodynamic affinity from deep learning regulatory sequence models of protein-DNA binding. Biorxiv : the Preprint Server For Biology. PMID 37214836 DOI: 10.1101/2023.05.11.540401 |
0.312 |
|
| 2023 |
Schreiber J, Boix C, Wook Lee J, Li H, Guan Y, Chang CC, Chang JC, Hawkins-Hooker A, Schölkopf B, Schweikert G, Carulla MR, Canakoglu A, Guzzo F, Nanni L, Masseroli M, ... ... Kundaje A, et al. The ENCODE Imputation Challenge: a critical assessment of methods for cross-cell type imputation of epigenomic profiles. Genome Biology. 24: 79. PMID 37072822 DOI: 10.1186/s13059-023-02915-y |
0.483 |
|
| 2023 |
Hitz BC, Lee JW, Jolanki O, Kagda MS, Graham K, Sud P, Gabdank I, Seth Strattan J, Sloan CA, Dreszer T, Rowe LD, Podduturi NR, Malladi VS, Chan ET, Davidson JM, ... ... Kundaje A, et al. The ENCODE Uniform Analysis Pipelines. Biorxiv : the Preprint Server For Biology. PMID 37066421 DOI: 10.1101/2023.04.04.535623 |
0.301 |
|
| 2023 |
Marinov GK, Shipony Z, Kundaje A, Greenleaf WJ. Genome-Wide Mapping of Active Regulatory Elements Using ATAC-seq. Methods in Molecular Biology (Clifton, N.J.). 2611: 3-19. PMID 36807060 DOI: 10.1007/978-1-0716-2899-7_1 |
0.341 |
|
| 2023 |
Kowalski MH, Wessels HH, Linder J, Choudhary S, Hartman A, Hao Y, Mascio I, Dalgarno C, Kundaje A, Satija R. CPA-Perturb-seq: Multiplexed single-cell characterization of alternative polyadenylation regulators. Biorxiv : the Preprint Server For Biology. PMID 36798324 DOI: 10.1101/2023.02.09.527751 |
0.326 |
|
| 2022 |
Frankish A, Carbonell-Sala S, Diekhans M, Jungreis I, Loveland JE, Mudge JM, Sisu C, Wright JC, Arnan C, Barnes I, Banerjee A, Bennett R, Berry A, Bignell A, Boix C, ... ... Kundaje A, et al. GENCODE: reference annotation for the human and mouse genomes in 2023. Nucleic Acids Research. PMID 36420896 DOI: 10.1093/nar/gkac1071 |
0.591 |
|
| 2022 |
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, Shen Y, ... ... Kundaje A, et al. Author Correction: Expanded encyclopaedias of DNA elements in the human and mouse genomes. Nature. PMID 35474001 DOI: 10.1038/s41586-021-04226-3 |
0.518 |
|
| 2022 |
Marinov GK, Shipony Z, Kundaje A, Greenleaf WJ. Single-Molecule Multikilobase-Scale Profiling of Chromatin Accessibility Using m6A-SMAC-Seq and m6A-CpG-GpC-SMAC-Seq. Methods in Molecular Biology (Clifton, N.J.). 2458: 269-298. PMID 35103973 DOI: 10.1007/978-1-0716-2140-0_15 |
0.314 |
|
| 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 |
0.334 |
|
| 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 |
0.382 |
|
| 2021 |
Markov GJ, Mai T, Nair S, Shcherbina A, Wang YX, Burns DM, Kundaje A, Blau HM. AP-1 is a temporally regulated dual gatekeeper of reprogramming to pluripotency. Proceedings of the National Academy of Sciences of the United States of America. 118. PMID 34088849 DOI: 10.1073/pnas.2104841118 |
0.315 |
|
| 2021 |
Marinov GK, Trevino AE, Xiang T, Kundaje A, Grossman AR, Greenleaf WJ. Transcription-dependent domain-scale three-dimensional genome organization in the dinoflagellate Breviolum minutum. Nature Genetics. PMID 33927397 DOI: 10.1038/s41588-021-00848-5 |
0.324 |
|
| 2021 |
Wainberg M, Kamber RA, Balsubramani A, Meyers RM, Sinnott-Armstrong N, Hornburg D, Jiang L, Chan J, Jian R, Gu M, Shcherbina A, Dubreuil MM, Spees K, Meuleman W, Snyder MP, ... ... Kundaje A, et al. A genome-wide atlas of co-essential modules assigns function to uncharacterized genes. Nature Genetics. PMID 33859415 DOI: 10.1038/s41588-021-00840-z |
0.308 |
|
| 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 |
0.357 |
|
| 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 |
0.317 |
|
| 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 |
0.636 |
|
| 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 |
0.473 |
|
| 2020 |
Shipony Z, Marinov GK, Swaffer MP, Sinnott-Armstrong NA, Skotheim JM, Kundaje A, Greenleaf WJ. Long-range single-molecule mapping of chromatin accessibility in eukaryotes. Nature Methods. PMID 32042188 DOI: 10.1038/S41592-019-0730-2 |
0.425 |
|
| 2019 |
Wang YXR, Sarkar P, Ursu O, Kundaje A, Bickel PJ. NETWORK MODELLING OF TOPOLOGICAL DOMAINS USING HI-C DATA. The Annals of Applied Statistics. 13: 1511-1536. PMID 32968472 DOI: 10.1214/19-Aoas1244 |
0.362 |
|
| 2019 |
Shrikumar A, Prakash E, Kundaje A. GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs. Bioinformatics (Oxford, England). 35: i173-i182. PMID 31510661 DOI: 10.1093/Bioinformatics/Btz322 |
0.398 |
|
| 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 |
0.503 |
|
| 2019 |
Tycko J, Wainberg M, Marinov GK, Ursu O, Hess GT, Ego BK, Aradhana, Li A, Truong A, Trevino AE, Spees K, Yao D, Kaplow IM, Greenside PG, Morgens DW, ... ... Kundaje A, et al. Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements. Nature Communications. 10: 4063. PMID 31492858 DOI: 10.1038/S41467-019-11955-7 |
0.361 |
|
| 2019 |
Stowers RS, Shcherbina A, Israeli J, Gruber JJ, Chang J, Nam S, Rabiee A, Teruel MN, Snyder MP, Kundaje A, Chaudhuri O. Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility. Nature Biomedical Engineering. PMID 31285581 DOI: 10.1038/S41551-019-0420-5 |
0.319 |
|
| 2019 |
Amemiya HM, Kundaje A, Boyle AP. The ENCODE Blacklist: Identification of Problematic Regions of the Genome. Scientific Reports. 9: 9354. PMID 31249361 DOI: 10.1038/S41598-019-45839-Z |
0.411 |
|
| 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 |
0.463 |
|
| 2019 |
Avsec Ž, Kreuzhuber R, Israeli J, Xu N, Cheng J, Shrikumar A, Banerjee A, Kim DS, Beier T, Urban L, Kundaje A, Stegle O, Gagneur J. The Kipoi repository accelerates community exchange and reuse of predictive models for genomics. Nature Biotechnology. PMID 31138913 DOI: 10.1038/S41587-019-0140-0 |
0.312 |
|
| 2019 |
Shcherbina A, Li J, Narayanan C, Greenleaf W, Kundaje A, Chetty S. Cell cycle dynamics of human pluripotent stem cells primed for differentiation. Stem Cells (Dayton, Ohio). PMID 31135093 DOI: 10.1002/Stem.3041 |
0.365 |
|
| 2019 |
Wainberg M, Sinnott-Armstrong N, Mancuso N, Barbeira AN, Knowles DA, Golan D, Ermel R, Ruusalepp A, Quertermous T, Hao K, Björkegren JLM, Im HK, Pasaniuc B, Rivas MA, Kundaje A. Opportunities and challenges for transcriptome-wide association studies. Nature Genetics. 51: 592-599. PMID 30926968 DOI: 10.1038/S41588-019-0385-Z |
0.409 |
|
| 2019 |
Yardımcı GG, Ozadam H, Sauria MEG, Ursu O, Yan KK, Yang T, Chakraborty A, Kaul A, Lajoie BR, Song F, Zhan Y, Ay F, Gerstein M, Kundaje A, Li Q, et al. Measuring the reproducibility and quality of Hi-C data. Genome Biology. 20: 57. PMID 30890172 DOI: 10.1186/S13059-019-1658-7 |
0.347 |
|
| 2019 |
Benayoun BA, Pollina EA, Singh PP, Mahmoudi S, Harel I, Casey KM, Dulken BW, Kundaje A, Brunet A. Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses. Genome Research. PMID 30858345 DOI: 10.1101/Gr.240093.118 |
0.364 |
|
| 2019 |
Marom S, Blumberg A, Kundaje A, Mishmar D. mtDNA Chromatin-like Organization Is Gradually Established during Mammalian Embryogenesis. Iscience. 12: 141-151. PMID 30684873 DOI: 10.1016/J.Isci.2018.12.032 |
0.406 |
|
| 2019 |
John JAS, Gafni E, White B, Kannan A, Hansen L, Jaroszewicz A, Kundaje A, Boley N. Abstract 4349: Predicting gene expression from plasma cell-free DNA using both the fragment length and fragment position Cancer Research. 79: 4349-4349. DOI: 10.1158/1538-7445.Sabcs18-4349 |
0.42 |
|
| 2018 |
Huyghe JR, Bien SA, Harrison TA, Kang HM, Chen S, Schmit SL, Conti DV, Qu C, Jeon J, Edlund CK, Greenside P, Wainberg M, Schumacher FR, Smith JD, Levine DM, ... ... Kundaje A, et al. Discovery of common and rare genetic risk variants for colorectal cancer. Nature Genetics. PMID 30510241 DOI: 10.1038/S41588-018-0286-6 |
0.334 |
|
| 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 |
0.431 |
|
| 2018 |
Yang D, Denny SK, Greenside PG, Chaikovsky AC, Brady JJ, Ouadah Y, Granja JM, Jahchan NS, Lim JS, Kwok S, Kong CS, Berghoff AS, Schmitt A, Reinhardt HC, Park KS, ... ... Kundaje A, et al. Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin. Cancer Discovery. PMID 30228179 DOI: 10.1158/2159-8290.Cd-17-0987 |
0.316 |
|
| 2018 |
Karimzadeh M, Ernst C, Kundaje A, Hoffman MM. Umap and Bismap: quantifying genome and methylome mappability. Nucleic Acids Research. PMID 30169659 DOI: 10.1093/Nar/Gky677 |
0.406 |
|
| 2018 |
Fu S, Wang Q, Moore JE, Purcaro MJ, Pratt HE, Fan K, Gu C, Jiang C, Zhu R, Kundaje A, Lu A, Weng Z. Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers. Nucleic Acids Research. PMID 30137428 DOI: 10.1093/Nar/Gky753 |
0.367 |
|
| 2018 |
Blumberg A, Danko CG, Kundaje A, Mishmar D. A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization. Genome Research. 28: 1158-1168. PMID 30002158 DOI: 10.1101/Gr.230409.117 |
0.432 |
|
| 2018 |
Ursu O, Boley N, Taranova M, Wang YXR, Yardimci GG, Noble WS, Kundaje A. GenomeDISCO: A concordance score for chromosome conformation capture experiments using random walks on contact map graphs. Bioinformatics (Oxford, England). PMID 29554289 DOI: 10.1093/Bioinformatics/Bty164 |
0.356 |
|
| 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 |
0.459 |
|
| 2017 |
Banovich NE, Li YI, Raj A, Ward MC, Greenside P, Calderon D, Tung PY, Burnett JE, Myrthil M, Thomas SM, Burrows CK, Romero IG, Pavlovic BJ, Kundaje A, Pritchard JK, et al. Impact of regulatory variation across human iPSCs and differentiated cells. Genome Research. PMID 29208628 DOI: 10.1101/Gr.224436.117 |
0.42 |
|
| 2017 |
Bien SA, Auer PL, Harrison TA, Qu C, Connolly CM, Greenside PG, Chen S, Berndt SI, Bézieau S, Kang HM, Huyghe J, Brenner H, Casey G, Chan AT, Hopper JL, ... ... Kundaje A, et al. Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data. Plos One. 12: e0186518. PMID 29161273 DOI: 10.1371/Journal.Pone.0186518 |
0.385 |
|
| 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 |
0.432 |
|
| 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 |
0.574 |
|
| 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 |
0.415 |
|
| 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 |
0.443 |
|
| 2017 |
Corces MR, Trevino AE, Hamilton EG, Greenside PG, Sinnott-Armstrong NA, Vesuna S, Satpathy AT, Rubin AJ, Montine KS, Wu B, Kathiria A, Cho SW, Mumbach MR, Carter AC, Kasowski M, ... ... Kundaje A, et al. An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues. Nature Methods. PMID 28846090 DOI: 10.1038/Nmeth.4396 |
0.336 |
|
| 2017 |
Rubin AJ, Barajas BC, Furlan-Magaril M, Lopez-Pajares V, Mumbach MR, Howard I, Kim DS, Boxer LD, Cairns J, Spivakov M, Wingett SW, Shi M, Zhao Z, Greenleaf WJ, Kundaje A, et al. Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation. Nature Genetics. PMID 28805829 DOI: 10.1038/Ng.3935 |
0.41 |
|
| 2017 |
Fu BXH, Wainberg M, Kundaje A, Fire AZ. High-Throughput Characterization of Cascade Type I-E CRISPR Guide Efficacy Reveals Unexpected PAM Diversity and Target Sequence Preferences. Genetics. PMID 28634160 DOI: 10.1534/Genetics.117.202580 |
0.319 |
|
| 2017 |
Morgens DW, Wainberg M, Boyle EA, Ursu O, Araya CL, Tsui CK, Haney MS, Hess GT, Han K, Jeng EE, Li A, Snyder MP, Greenleaf WJ, Kundaje A, Bassik MC. Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens. Nature Communications. 8: 15178. PMID 28474669 DOI: 10.1038/Ncomms15178 |
0.317 |
|
| 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 |
0.633 |
|
| 2017 |
Chuang CH, Greenside PG, Rogers ZN, Brady JJ, Yang D, Ma RK, Caswell DR, Chiou SH, Winters AF, Grüner BM, Ramaswami G, Spencley AL, Kopecky KE, Sayles LC, Sweet-Cordero EA, ... ... Kundaje A, et al. Molecular definition of a metastatic lung cancer state reveals a targetable CD109-Janus kinase-Stat axis. Nature Medicine. PMID 28191885 DOI: 10.1038/Nm.4285 |
0.329 |
|
| 2017 |
Blumberg A, Rice EJ, Kundaje A, Danko CG, Mishmar D. Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution. Genome Research. 27: 362-373. PMID 28049628 DOI: 10.1101/Gr.209924.116 |
0.441 |
|
| 2017 |
Strattan JS, Dreszer TR, Hitz BC, Chan ET, Davidson JM, Gabdank I, Hilton JA, Sloan CA, Weng Z, Kundaje A, Cherry JM. The ENCODE Annotation Pipeline: Standard analyses for ChIP-seq, RNA-seq, DNase-seq, and whole-genome bisulfite experiments F1000research. 6. DOI: 10.7490/F1000Research.1113977.1 |
0.353 |
|
| 2017 |
Lopez-Pajares V, Rubin A, Barajas B, Furlan-Magaril M, Mumbach M, Greenleaf W, Kundaje A, Snyder M, Chang H, Fraser P, Khavari P. 464 Dynamic and stable enhancer-promoter contacts regulate epidermal terminal differentiation Journal of Investigative Dermatology. 137: S80. DOI: 10.1016/J.Jid.2017.02.483 |
0.302 |
|
| 2016 |
Koh PW, Sinha R, Barkal AA, Morganti RM, Chen A, Weissman IL, Ang LT, Kundaje A, Loh KM. An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development. Scientific Data. 3: 160109. PMID 27996962 DOI: 10.1038/Sdata.2016.109 |
0.363 |
|
| 2016 |
Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY. Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution. Nature Genetics. PMID 27526324 DOI: 10.1038/Ng.3646 |
0.405 |
|
| 2016 |
Loh KM, Chen A, Koh PW, Deng TZ, Sinha R, Tsai JM, Barkal AA, Shen KY, Jain R, Morganti RM, Shyh-Chang N, Fernhoff NB, George BM, Wernig G, Salomon RE, ... ... Kundaje A, et al. Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types. Cell. 166: 451-467. PMID 27419872 DOI: 10.1016/J.Cell.2016.06.011 |
0.315 |
|
| 2016 |
Kukurba KR, Parsana P, Balliu B, Smith KS, Zappala Z, Knowles DA, Favé MJ, Davis JR, Li X, Zhu X, Potash JB, Weissman MM, Shi J, Kundaje A, Levinson DF, et al. Impact of the X Chromosome and sex on regulatory variation. Genome Research. PMID 27197214 DOI: 10.1101/Gr.197897.115 |
0.382 |
|
| 2016 |
Webb AE, Kundaje A, Brunet A. Characterization of the direct targets of FOXO transcription factors throughout evolution. Aging Cell. PMID 27061590 DOI: 10.1111/Acel.12479 |
0.377 |
|
| 2016 |
Bien SA, Harrison TA, Auer PL, Qu F, Huyghe J, Banbury B, Greenside P, Abecasis GR, Berndt SI, Bézieau S, Brenner H, Casey G, Chan AT, Chang-Claude J, Chen S, ... ... Kundaje A, et al. Abstract 4489: Using functional data from Roadmap Epigenomics to inform analysis of rare variants linked to gene expression in a large colorectal cancer study Cancer Research. 76: 4489-4489. DOI: 10.1158/1538-7445.Am2016-4489 |
0.329 |
|
| 2015 |
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. Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution. Nature. PMID 26560031 DOI: 10.1038/Nature16075 |
0.323 |
|
| 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 |
0.449 |
|
| 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 |
0.341 |
|
| 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 |
0.56 |
|
| 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 |
0.561 |
|
| 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 |
0.62 |
|
| 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 |
0.51 |
|
| 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 |
0.665 |
|
| 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 |
0.568 |
|
| 2014 |
Blumberg A, Sri Sailaja B, Kundaje A, Levin L, Dadon S, Shmorak S, Shaulian E, Meshorer E, Mishmar D. Transcription factors bind negatively selected sites within human mtDNA genes. Genome Biology and Evolution. 6: 2634-46. PMID 25245407 DOI: 10.1093/Gbe/Evu210 |
0.446 |
|
| 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 |
0.634 |
|
| 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 |
0.608 |
|
| 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 |
0.474 |
|
| 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 |
0.324 |
|
| 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 |
0.642 |
|
| 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 |
0.644 |
|
| 2013 |
Hardee J, Ouyang Z, Zhang Y, Kundaje A, Lacroute P, Snyder M. STAT3 targets suggest mechanisms of aggressive tumorigenesis in diffuse large B-cell lymphoma. G3 (Bethesda, Md.). 3: 2173-85. PMID 24142927 DOI: 10.1534/G3.113.007674 |
0.344 |
|
| 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 |
0.704 |
|
| 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 |
0.64 |
|
| 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 |
0.698 |
|
| 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 |
0.465 |
|
| 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 |
0.559 |
|
| 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 |
0.654 |
|
| 2012 |
Bánfai B, Jia H, Khatun J, Wood E, Risk B, Gundling WE, Kundaje A, Gunawardena HP, Yu Y, Xie L, Krajewski K, Strahl BD, Chen X, Bickel P, Giddings MC, et al. Long noncoding RNAs are rarely translated in two human cell lines. Genome Research. 22: 1646-57. PMID 22955977 DOI: 10.1101/Gr.134767.111 |
0.34 |
|
| 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 |
0.673 |
|
| 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 |
0.384 |
|
| 2012 |
Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z. Modeling gene expression using chromatin features in various cellular contexts. Genome Biology. 13: R53. PMID 22950368 DOI: 10.1186/Gb-2012-13-9-R53 |
0.375 |
|
| 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 |
0.642 |
|
| 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 |
0.621 |
|
| 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 |
0.628 |
|
| 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 |
0.623 |
|
| 2005 |
Stolovitzky GA, Kundaje A, Held GA, Duggar KH, Haudenschild CD, Zhou D, Vasicek TJ, Smith KD, Aderem A, Roach JC. Statistical analysis of MPSS measurements: application to the study of LPS-activated macrophage gene expression. Proceedings of the National Academy of Sciences of the United States of America. 102: 1402-7. PMID 15668391 DOI: 10.1073/Pnas.0406555102 |
0.376 |
|
| 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. |
0.452 |
|
| 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. |
0.529 |
|
| 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 |
0.584 |
|
| 2004 |
Sussillo D, Kundaje A, Anastassiou D. Spectrogram Analysis of Genomes Eurasip Journal On Applied Signal Processing. 2004: 29-42. DOI: 10.1155/S1110865704310048 |
0.342 |
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