Kundaje A - Search Results

1

Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors.

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, Weng Z. Wang J, et al. Among authors: kundaje a. Genome Res. 2012 Sep;22(9):1798-812. doi: 10.1101/gr.139105.112. Genome Res. 2012. PMID: 22955990 Free PMC article.

2

Single-cell multiome of the human retina and deep learning nominate causal variants in complex eye diseases.

Wang SK, Nair S, Li R, Kraft K, Pampari A, Patel A, Kang JB, Luong C, Kundaje A, Chang HY. Wang SK, et al. Among authors: kundaje a. Cell Genom. 2022 Aug 10;2(8):100164. doi: 10.1016/j.xgen.2022.100164. Epub 2022 Jul 27. Cell Genom. 2022. PMID: 36277849 Free PMC article.

3

Single-cell multi-omics of mitochondrial DNA disorders reveals dynamics of purifying selection across human immune cells.

Lareau CA, Dubois SM, Buquicchio FA, Hsieh YH, Garg K, Kautz P, Nitsch L, Praktiknjo SD, Maschmeyer P, Verboon JM, Gutierrez JC, Yin Y, Fiskin E, Luo W, Mimitou EP, Muus C, Malhotra R, Parikh S, Fleming MD, Oevermann L, Schulte J, Eckert C, Kundaje A, Smibert P, Vardhana SA, Satpathy AT, Regev A, Sankaran VG, Agarwal S, Ludwig LS. Lareau CA, et al. Among authors: kundaje a. Nat Genet. 2023 Jul;55(7):1198-1209. doi: 10.1038/s41588-023-01433-8. Epub 2023 Jun 29. Nat Genet. 2023. PMID: 37386249 Free PMC article.

4

A user's guide to the encyclopedia of DNA elements (ENCODE).

ENCODE Project Consortium. ENCODE Project Consortium. PLoS Biol. 2011 Apr;9(4):e1001046. doi: 10.1371/journal.pbio.1001046. Epub 2011 Apr 19. PLoS Biol. 2011. PMID: 21526222 Free PMC article.

5

Modeling gene expression using chromatin features in various cellular contexts.

Dong X, Greven MC, Kundaje A, Djebali S, Brown JB, Cheng C, Gingeras TR, Gerstein M, Guigó R, Birney E, Weng Z. Dong X, et al. Among authors: kundaje a. Genome Biol. 2012 Jun 13;13(9):R53. doi: 10.1186/gb-2012-13-9-r53. Genome Biol. 2012. PMID: 22950368 Free PMC article.

6

Classification of human genomic regions based on experimentally determined binding sites of more than 100 transcription-related factors.

Yip KY, Cheng C, Bhardwaj N, Brown JB, Leng J, Kundaje A, Rozowsky J, Birney E, Bickel P, Snyder M, Gerstein M. Yip KY, et al. Among authors: kundaje a. Genome Biol. 2012 Sep 26;13(9):R48. doi: 10.1186/gb-2012-13-9-r48. Genome Biol. 2012. PMID: 22950945 Free PMC article.

7

An integrated encyclopedia of DNA elements in the human genome.

ENCODE Project Consortium. ENCODE Project Consortium. Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247. Nature. 2012. PMID: 22955616 Free PMC article.

8

Architecture of the human regulatory network derived from ENCODE data.

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, Boyle AP, Cayting P, Charos A, Chen DZ, Cheng Y, Clarke D, Eastman C, Euskirchen G, Frietze S, Fu Y, Gertz J, Grubert F, Harmanci A, Jain P, Kasowski M, Lacroute P, Leng JJ, Lian J, Monahan H, O'Geen H, Ouyang Z, Partridge EC, Patacsil D, Pauli F, Raha D, Ramirez L, Reddy TE, Reed B, Shi M, Slifer T, Wang J, Wu L, Yang X, Yip KY, Zilberman-Schapira G, Batzoglou S, Sidow A, Farnham PJ, Myers RM, Weissman SM, Snyder M. Gerstein MB, et al. Among authors: kundaje a. Nature. 2012 Sep 6;489(7414):91-100. doi: 10.1038/nature11245. Nature. 2012. PMID: 22955619 Free PMC article.

9

Ubiquitous heterogeneity and asymmetry of the chromatin environment at regulatory elements.

Kundaje A, Kyriazopoulou-Panagiotopoulou S, Libbrecht M, Smith CL, Raha D, Winters EE, Johnson SM, Snyder M, Batzoglou S, Sidow A. Kundaje A, et al. Genome Res. 2012 Sep;22(9):1735-47. doi: 10.1101/gr.136366.111. Genome Res. 2012. PMID: 22955985 Free PMC article.

10

Linking disease associations with regulatory information in the human genome.

Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Schaub MA, et al. Among authors: kundaje a. Genome Res. 2012 Sep;22(9):1748-59. doi: 10.1101/gr.136127.111. Genome Res. 2012. PMID: 22955986 Free PMC article.

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