Year |
Citation |
Score |
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
2016 |
Brady JJ, Chuang CH, Greenside PG, Rogers ZN, Murray CW, Caswell DR, Hartmann U, Connolly AJ, Sweet-Cordero EA, Kundaje A, Winslow MM. An Arntl2-Driven Secretome Enables Lung Adenocarcinoma Metastatic Self-Sufficiency. Cancer Cell. PMID 27150038 DOI: 10.1016/j.ccell.2016.03.003 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
2015 |
Lin H, Chen M, Kundaje A, Valouev A, Yin H, Liu N, Neuenkirchen N, Zhong M, Snyder M. Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution. Developmental Cell. 32: 772-4. PMID 25805139 DOI: 10.1016/j.devcel.2015.03.004 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
2014 |
Marinov GK, Kundaje A, Park PJ, Wold BJ. Large-scale quality analysis of published ChIP-seq data. G3 (Bethesda, Md.). 4: 209-23. PMID 24347632 DOI: 10.1534/g3.113.008680 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
2012 |
. An integrated encyclopedia of DNA elements in the human genome. Nature. 489: 57-74. PMID 22955616 DOI: 10.1038/nature11247 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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 |
0.56 |
|
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. |
0.56 |
|
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. |
0.56 |
|
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 |
0.56 |
|
2004 |
Sussillo D, Kundaje A, Anastassiou D. Spectrogram Analysis of Genomes Eurasip Journal On Applied Signal Processing. 2004: 29-42. DOI: 10.1155/S1110865704310048 |
0.56 |
|
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