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Items: 1 to 50 of 79

1.

GkmExplain: fast and accurate interpretation of nonlinear gapped k-mer SVMs.

Shrikumar A, Prakash E, Kundaje A.

Bioinformatics. 2019 Jul 15;35(14):i173-i182. doi: 10.1093/bioinformatics/btz322.

2.

Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts.

Nair S, Kim DS, Perricone J, Kundaje A.

Bioinformatics. 2019 Jul 15;35(14):i108-i116. doi: 10.1093/bioinformatics/btz352.

3.

Mitigation of off-target toxicity in CRISPR-Cas9 screens for essential non-coding elements.

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, Phanstiel DH, Snyder MP, Bintu L, Greenleaf WJ, Kundaje A, Bassik MC.

Nat Commun. 2019 Sep 6;10(1):4063. doi: 10.1038/s41467-019-11955-7.

4.

Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility.

Stowers RS, Shcherbina A, Israeli J, Gruber JJ, Chang J, Nam S, Rabiee A, Teruel MN, Snyder MP, Kundaje A, Chaudhuri O.

Nat Biomed Eng. 2019 Jul 8. doi: 10.1038/s41551-019-0420-5. [Epub ahead of print]

PMID:
31285581
5.

The ENCODE Blacklist: Identification of Problematic Regions of the Genome.

Amemiya HM, Kundaje A, Boyle AP.

Sci Rep. 2019 Jun 27;9(1):9354. doi: 10.1038/s41598-019-45839-z.

6.

Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays.

Movva R, Greenside P, Marinov GK, Nair S, Shrikumar A, Kundaje A.

PLoS One. 2019 Jun 17;14(6):e0218073. doi: 10.1371/journal.pone.0218073. eCollection 2019.

7.

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.

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.

Nat Biotechnol. 2019 Jun;37(6):592-600. doi: 10.1038/s41587-019-0140-0. No abstract available.

PMID:
31138913
8.

Brief Report: Cell Cycle Dynamics of Human Pluripotent Stem Cells Primed for Differentiation.

Shcherbina A, Li J, Narayanan C, Greenleaf W, Kundaje A, Chetty S.

Stem Cells. 2019 Sep;37(9):1151-1157. doi: 10.1002/stem.3041. Epub 2019 Jun 10.

PMID:
31135093
9.

Corrigendum: Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution.

Blumberg A, Rice EJ, Kundaje A, Danko CG, Mishmar D.

Genome Res. 2019 Apr;29(4):710.1. doi: 10.1101/gr.248971.119. No abstract available.

10.

Opportunities and challenges for transcriptome-wide association studies.

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.

Nat Genet. 2019 Apr;51(4):592-599. doi: 10.1038/s41588-019-0385-z. Epub 2019 Mar 29. Review.

PMID:
30926968
11.

Measuring the reproducibility and quality of Hi-C data.

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, Taylor J, Yue F, Dekker J, Noble WS.

Genome Biol. 2019 Mar 19;20(1):57. doi: 10.1186/s13059-019-1658-7.

12.

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses.

Benayoun BA, Pollina EA, Singh PP, Mahmoudi S, Harel I, Casey KM, Dulken BW, Kundaje A, Brunet A.

Genome Res. 2019 Apr;29(4):697-709. doi: 10.1101/gr.240093.118. Epub 2019 Mar 11.

13.

mtDNA Chromatin-like Organization Is Gradually Established during Mammalian Embryogenesis.

Marom S, Blumberg A, Kundaje A, Mishmar D.

iScience. 2019 Feb 22;12:141-151. doi: 10.1016/j.isci.2018.12.032. Epub 2019 Jan 8.

14.

Discovery of common and rare genetic risk variants for colorectal cancer.

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, Nelson SC, Sinnott-Armstrong NA, Albanes D, Alonso MH, Anderson K, Arnau-Collell C, Arndt V, Bamia C, Banbury BL, Baron JA, Berndt SI, Bézieau S, Bishop DT, Boehm J, Boeing H, Brenner H, Brezina S, Buch S, Buchanan DD, Burnett-Hartman A, Butterbach K, Caan BJ, Campbell PT, Carlson CS, Castellví-Bel S, Chan AT, Chang-Claude J, Chanock SJ, Chirlaque MD, Cho SH, Connolly CM, Cross AJ, Cuk K, Curtis KR, de la Chapelle A, Doheny KF, Duggan D, Easton DF, Elias SG, Elliott F, English DR, Feskens EJM, Figueiredo JC, Fischer R, FitzGerald LM, Forman D, Gala M, Gallinger S, Gauderman WJ, Giles GG, Gillanders E, Gong J, Goodman PJ, Grady WM, Grove JS, Gsur A, Gunter MJ, Haile RW, Hampe J, Hampel H, Harlid S, Hayes RB, Hofer P, Hoffmeister M, Hopper JL, Hsu WL, Huang WY, Hudson TJ, Hunter DJ, Ibañez-Sanz G, Idos GE, Ingersoll R, Jackson RD, Jacobs EJ, Jenkins MA, Joshi AD, Joshu CE, Keku TO, Key TJ, Kim HR, Kobayashi E, Kolonel LN, Kooperberg C, Kühn T, Küry S, Kweon SS, Larsson SC, Laurie CA, Le Marchand L, Leal SM, Lee SC, Lejbkowicz F, Lemire M, Li CI, Li L, Lieb W, Lin Y, Lindblom A, Lindor NM, Ling H, Louie TL, Männistö S, Markowitz SD, Martín V, Masala G, McNeil CE, Melas M, Milne RL, Moreno L, Murphy N, Myte R, Naccarati A, Newcomb PA, Offit K, Ogino S, Onland-Moret NC, Pardini B, Parfrey PS, Pearlman R, Perduca V, Pharoah PDP, Pinchev M, Platz EA, Prentice RL, Pugh E, Raskin L, Rennert G, Rennert HS, Riboli E, Rodríguez-Barranco M, Romm J, Sakoda LC, Schafmayer C, Schoen RE, Seminara D, Shah M, Shelford T, Shin MH, Shulman K, Sieri S, Slattery ML, Southey MC, Stadler ZK, Stegmaier C, Su YR, Tangen CM, Thibodeau SN, Thomas DC, Thomas SS, Toland AE, Trichopoulou A, Ulrich CM, Van Den Berg DJ, van Duijnhoven FJB, Van Guelpen B, van Kranen H, Vijai J, Visvanathan K, Vodicka P, Vodickova L, Vymetalkova V, Weigl K, Weinstein SJ, White E, Win AK, Wolf CR, Wolk A, Woods MO, Wu AH, Zaidi SH, Zanke BW, Zhang Q, Zheng W, Scacheri PC, Potter JD, Bassik MC, Kundaje A, Casey G, Moreno V, Abecasis GR, Nickerson DA, Gruber SB, Hsu L, Peters U.

Nat Genet. 2019 Jan;51(1):76-87. doi: 10.1038/s41588-018-0286-6. Epub 2018 Dec 3.

15.

Discovering epistatic feature interactions from neural network models of regulatory DNA sequences.

Greenside P, Shimko T, Fordyce P, Kundaje A.

Bioinformatics. 2018 Sep 1;34(17):i629-i637. doi: 10.1093/bioinformatics/bty575.

16.

Intertumoral Heterogeneity in SCLC Is Influenced by the Cell Type of Origin.

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, Preusser M, Kundaje A, Greenleaf WJ, Sage J, Winslow MM.

Cancer Discov. 2018 Oct;8(10):1316-1331. doi: 10.1158/2159-8290.CD-17-0987. Epub 2018 Sep 18.

PMID:
30228179
17.

Umap and Bismap: quantifying genome and methylome mappability.

Karimzadeh M, Ernst C, Kundaje A, Hoffman MM.

Nucleic Acids Res. 2018 Nov 16;46(20):e120. doi: 10.1093/nar/gky677.

18.

Differential analysis of chromatin accessibility and histone modifications for predicting mouse developmental enhancers.

Fu S, Wang Q, Moore JE, Purcaro MJ, Pratt HE, Fan K, Gu C, Jiang C, Zhu R, Kundaje A, Lu A, Weng Z.

Nucleic Acids Res. 2018 Nov 30;46(21):11184-11201. doi: 10.1093/nar/gky753.

19.

A common pattern of DNase I footprinting throughout the human mtDNA unveils clues for a chromatin-like organization.

Blumberg A, Danko CG, Kundaje A, Mishmar D.

Genome Res. 2018 Aug;28(8):1158-1168. doi: 10.1101/gr.230409.117. Epub 2018 Jul 12.

20.

Opportunities and obstacles for deep learning in biology and medicine.

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow PM, Zietz M, Hoffman MM, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Lavender CA, Turaga SC, Alexandari AM, Lu Z, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass SJ, Huang A, Gitter A, Greene CS.

J R Soc Interface. 2018 Apr;15(141). pii: 20170387. doi: 10.1098/rsif.2017.0387. Review.

21.

GenomeDISCO: a concordance score for chromosome conformation capture experiments using random walks on contact map graphs.

Ursu O, Boley N, Taranova M, Wang YXR, Yardimci GG, Stafford Noble W, Kundaje A.

Bioinformatics. 2018 Aug 15;34(16):2701-2707. doi: 10.1093/bioinformatics/bty164.

22.

ChIP-ping the branches of the tree: functional genomics and the evolution of eukaryotic gene regulation.

Marinov GK, Kundaje A.

Brief Funct Genomics. 2018 Mar 1;17(2):116-137. doi: 10.1093/bfgp/ely004. Review.

23.

Challenges and recommendations for epigenomics in precision health.

Carter AC, Chang HY, Church G, Dombkowski A, Ecker JR, Gil E, Giresi PG, Greely H, Greenleaf WJ, Hacohen N, He C, Hill D, Ko J, Kohane I, Kundaje A, Palmer M, Snyder MP, Tung J, Urban A, Vidal M, Wong W.

Nat Biotechnol. 2017 Dec 8;35(12):1128-1132. doi: 10.1038/nbt.4030. No abstract available.

24.
25.

Impact of regulatory variation across human iPSCs and differentiated cells.

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, Gilad Y.

Genome Res. 2018 Jan;28(1):122-131. doi: 10.1101/gr.224436.117. Epub 2017 Dec 5.

26.

Enrichment of colorectal cancer associations in functional regions: Insight for using epigenomics data in the analysis of whole genome sequence-imputed GWAS data.

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, Banbury BL, Chang-Claude J, Chanock SJ, Haile RW, Hoffmeister M, Fuchsberger C, Jenkins MA, Leal SM, Lemire M, Newcomb PA, Gallinger S, Potter JD, Schoen RE, Slattery ML, Smith JD, Le Marchand L, White E, Zanke BW, Abeçasis GR, Carlson CS, Peters U, Nickerson DA, Kundaje A, Hsu L; GECCO and CCFR.

PLoS One. 2017 Nov 21;12(11):e0186518. doi: 10.1371/journal.pone.0186518. eCollection 2017.

27.

Chromatin accessibility dynamics reveal novel functional enhancers in C. elegans.

Daugherty AC, Yeo RW, Buenrostro JD, Greenleaf WJ, Kundaje A, Brunet A.

Genome Res. 2017 Dec;27(12):2096-2107. doi: 10.1101/gr.226233.117. Epub 2017 Nov 15.

28.

Vicus: Exploiting local structures to improve network-based analysis of biological data.

Wang B, Huang L, Zhu Y, Kundaje A, Batzoglou S, Goldenberg A.

PLoS Comput Biol. 2017 Oct 12;13(10):e1005621. doi: 10.1371/journal.pcbi.1005621. eCollection 2017 Oct.

29.

Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements.

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, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY.

Nat Genet. 2017 Nov;49(11):1602-1612. doi: 10.1038/ng.3963. Epub 2017 Sep 25.

30.

Denoising genome-wide histone ChIP-seq with convolutional neural networks.

Koh PW, Pierson E, Kundaje A.

Bioinformatics. 2017 Jul 15;33(14):i225-i233. doi: 10.1093/bioinformatics/btx243.

31.

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues.

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, Orloff LA, Risca VI, Kundaje A, Khavari PA, Montine TJ, Greenleaf WJ, Chang HY.

Nat Methods. 2017 Oct;14(10):959-962. doi: 10.1038/nmeth.4396. Epub 2017 Aug 28.

32.

Lineage-specific dynamic and pre-established enhancer-promoter contacts cooperate in terminal differentiation.

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, Snyder M, Chang HY, Fraser P, Khavari PA.

Nat Genet. 2017 Oct;49(10):1522-1528. doi: 10.1038/ng.3935. Epub 2017 Aug 14.

33.

High-Throughput Characterization of Cascade type I-E CRISPR Guide Efficacy Reveals Unexpected PAM Diversity and Target Sequence Preferences.

Fu BX, Wainberg M, Kundaje A, Fire AZ.

Genetics. 2017 Aug;206(4):1727-1738. doi: 10.1534/genetics.117.202580. Epub 2017 Jun 20.

34.

Genome-scale measurement of off-target activity using Cas9 toxicity in high-throughput screens.

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.

Nat Commun. 2017 May 5;8:15178. doi: 10.1038/ncomms15178.

35.

Predicting gene expression in massively parallel reporter assays: A comparative study.

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, Tewhey R, Sabeti PC, Goke J, Mueller NS, Kellis M, Kundaje A, Beer MA, Keles S, Gifford DK, Yosef N.

Hum Mutat. 2017 Sep;38(9):1240-1250. doi: 10.1002/humu.23197. Epub 2017 Mar 9.

36.

Molecular definition of a metastatic lung cancer state reveals a targetable CD109-Janus kinase-Stat axis.

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, Li JB, Kundaje A, Winslow MM.

Nat Med. 2017 Mar;23(3):291-300. doi: 10.1038/nm.4285. Epub 2017 Feb 13.

37.

Initiation of mtDNA transcription is followed by pausing, and diverges across human cell types and during evolution.

Blumberg A, Rice EJ, Kundaje A, Danko CG, Mishmar D.

Genome Res. 2017 Mar;27(3):362-373. doi: 10.1101/gr.209924.116. Epub 2017 Jan 3. Erratum in: Genome Res. 2019 Apr;29(4):710.1.

38.

An atlas of transcriptional, chromatin accessibility, and surface marker changes in human mesoderm development.

Koh PW, Sinha R, Barkal AA, Morganti RM, Chen A, Weissman IL, Ang LT, Kundaje A, Loh KM.

Sci Data. 2016 Dec 20;3:160109. doi: 10.1038/sdata.2016.109.

39.

Lineage-specific and single-cell chromatin accessibility charts human hematopoiesis and leukemia evolution.

Corces MR, Buenrostro JD, Wu B, Greenside PG, Chan SM, Koenig JL, Snyder MP, Pritchard JK, Kundaje A, Greenleaf WJ, Majeti R, Chang HY.

Nat Genet. 2016 Oct;48(10):1193-203. doi: 10.1038/ng.3646. Epub 2016 Aug 15.

40.

Mapping the Pairwise Choices Leading from Pluripotency to Human Bone, Heart, and Other Mesoderm Cell Types.

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 REA, Chen Z, Vogel H, Epstein JA, Kundaje A, Talbot WS, Beachy PA, Ang LT, Weissman IL.

Cell. 2016 Jul 14;166(2):451-467. doi: 10.1016/j.cell.2016.06.011.

41.

Impact of the X Chromosome and sex on regulatory variation.

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, Awadalla P, Mostafavi S, Battle A, Montgomery SB.

Genome Res. 2016 Jun;26(6):768-77. doi: 10.1101/gr.197897.115. Epub 2016 Apr 21.

42.

An Arntl2-Driven Secretome Enables Lung Adenocarcinoma Metastatic Self-Sufficiency.

Brady JJ, Chuang CH, Greenside PG, Rogers ZN, Murray CW, Caswell DR, Hartmann U, Connolly AJ, Sweet-Cordero EA, Kundaje A, Winslow MM.

Cancer Cell. 2016 May 9;29(5):697-710. doi: 10.1016/j.ccell.2016.03.003. Epub 2016 Apr 14.

43.

Characterization of the direct targets of FOXO transcription factors throughout evolution.

Webb AE, Kundaje A, Brunet A.

Aging Cell. 2016 Aug;15(4):673-85. doi: 10.1111/acel.12479. Epub 2016 Apr 8.

44.

H3K4me3 Breadth Is Linked to Cell Identity and Transcriptional Consistency.

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, Cherry JM, Brunet A.

Cell. 2015 Nov 19;163(5):1281-1286. doi: 10.1016/j.cell.2015.10.051. Epub 2015 Nov 19. No abstract available.

45.

Corrigendum: Regulatory analysis of the C. elegans genome with spatiotemporal resolution.

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, Reinke V, Waterston RH, Snyder M.

Nature. 2015 Dec 3;528(7580):152. doi: 10.1038/nature16075. Epub 2015 Nov 11. No abstract available.

PMID:
26560031
46.

Genetic Control of Chromatin States in Humans Involves Local and Distal Chromosomal Interactions.

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, Steinmetz LM, Kundaje A, Snyder M.

Cell. 2015 Aug 27;162(5):1051-65. doi: 10.1016/j.cell.2015.07.048. Epub 2015 Aug 20.

47.

Characterization of TCF21 Downstream Target Regions Identifies a Transcriptional Network Linking Multiple Independent Coronary Artery Disease Loci.

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.

PLoS Genet. 2015 May 28;11(5):e1005202. doi: 10.1371/journal.pgen.1005202. eCollection 2015 May.

48.

Reassessment of Piwi binding to the genome and Piwi impact on RNA polymerase II distribution.

Lin H, Chen M, Kundaje A, Valouev A, Yin H, Liu N, Neuenkirchen N, Zhong M, Snyder M.

Dev Cell. 2015 Mar 23;32(6):772-4. doi: 10.1016/j.devcel.2015.03.004.

49.

Fine mapping of type 1 diabetes susceptibility loci and evidence for colocalization of causal variants with lymphoid gene enhancers.

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, Ward LD, Kundaje A, Kellis M, Daly MJ, Barrett JC, Cooper JD, Deloukas P; Type 1 Diabetes Genetics Consortium, Todd JA, Wallace C, Concannon P, Rich SS.

Nat Genet. 2015 Apr;47(4):381-6. doi: 10.1038/ng.3245. Epub 2015 Mar 9.

50.

Conserved epigenomic signals in mice and humans reveal immune basis of Alzheimer's disease.

Gjoneska E, Pfenning AR, Mathys H, Quon G, Kundaje A, Tsai LH, Kellis M.

Nature. 2015 Feb 19;518(7539):365-9. doi: 10.1038/nature14252.

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