Shrikumar A - Search Results

1

Short tandem repeats bind transcription factors to tune eukaryotic gene expression.

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. Horton CA, et al. Among authors: shrikumar a. Science. 2023 Sep 22;381(6664):eadd1250. doi: 10.1126/science.add1250. Epub 2023 Sep 22. Science. 2023. PMID: 37733848

2

De novo distillation of thermodynamic affinity from deep learning regulatory sequence models of in vivo protein-DNA binding.

Alexandari AM, Horton CA, Shrikumar A, Shah N, Li E, Weilert M, Pufall MA, Zeitlinger J, Fordyce PM, Kundaje A. Alexandari AM, et al. Among authors: shrikumar a. bioRxiv [Preprint]. 2023 May 11:2023.05.11.540401. doi: 10.1101/2023.05.11.540401. bioRxiv. 2023. PMID: 37214836 Free PMC article. Preprint.

3

fastISM: performant in silico saturation mutagenesis for convolutional neural networks.

Nair S, Shrikumar A, Schreiber J, Kundaje A. Nair S, et al. Among authors: shrikumar a. Bioinformatics. 2022 Apr 28;38(9):2397-2403. doi: 10.1093/bioinformatics/btac135. Bioinformatics. 2022. PMID: 35238376 Free PMC article.

4

Domain-adaptive neural networks improve cross-species prediction of transcription factor binding.

Cochran K, Srivastava D, Shrikumar A, Balsubramani A, Hardison RC, Kundaje A, Mahony S. Cochran K, et al. Among authors: shrikumar a. Genome Res. 2022 Mar;32(3):512-523. doi: 10.1101/gr.275394.121. Epub 2022 Jan 18. Genome Res. 2022. PMID: 35042722 Free PMC article.

5

Base-resolution models of transcription-factor binding reveal soft motif syntax.

Avsec Ž, Weilert M, Shrikumar A, Krueger S, Alexandari A, Dalal K, Fropf R, McAnany C, Gagneur J, Kundaje A, Zeitlinger J. Avsec Ž, et al. Among authors: shrikumar a. Nat Genet. 2021 Mar;53(3):354-366. doi: 10.1038/s41588-021-00782-6. Epub 2021 Feb 18. Nat Genet. 2021. PMID: 33603233 Free PMC article.

6

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

Shrikumar A, Prakash E, Kundaje A. Shrikumar A, et al. Bioinformatics. 2019 Jul 15;35(14):i173-i182. doi: 10.1093/bioinformatics/btz322. Bioinformatics. 2019. PMID: 31510661 Free PMC article.

7

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. Movva R, et al. Among authors: shrikumar a. PLoS One. 2019 Jun 17;14(6):e0218073. doi: 10.1371/journal.pone.0218073. eCollection 2019. PLoS One. 2019. PMID: 31206543 Free PMC article.

8

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. Avsec Ž, et al. Among authors: shrikumar a. Nat Biotechnol. 2019 Jun;37(6):592-600. doi: 10.1038/s41587-019-0140-0. Nat Biotechnol. 2019. PMID: 31138913 Free PMC article. No abstract available.

9

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. Ching T, et al. Among authors: shrikumar a. J R Soc Interface. 2018 Apr;15(141):20170387. doi: 10.1098/rsif.2017.0387. J R Soc Interface. 2018. PMID: 29618526 Free PMC article. Review.

10

Transcriptional reversion of cardiac myocyte fate during mammalian cardiac regeneration.

O'Meara CC, Wamstad JA, Gladstone RA, Fomovsky GM, Butty VL, Shrikumar A, Gannon JB, Boyer LA, Lee RT. O'Meara CC, et al. Among authors: shrikumar a. Circ Res. 2015 Feb 27;116(5):804-15. doi: 10.1161/CIRCRESAHA.116.304269. Epub 2014 Dec 4. Circ Res. 2015. PMID: 25477501 Free PMC article.

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