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Items: 6

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.

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.

3.

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.

4.

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.

5.

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.

Circ Res. 2015 Feb 27;116(5):804-15. doi: 10.1161/CIRCRESAHA.116.304269. Epub 2014 Dec 4.

6.

Dynamic and coordinated epigenetic regulation of developmental transitions in the cardiac lineage.

Wamstad JA, Alexander JM, Truty RM, Shrikumar A, Li F, Eilertson KE, Ding H, Wylie JN, Pico AR, Capra JA, Erwin G, Kattman SJ, Keller GM, Srivastava D, Levine SS, Pollard KS, Holloway AK, Boyer LA, Bruneau BG.

Cell. 2012 Sep 28;151(1):206-20. doi: 10.1016/j.cell.2012.07.035. Epub 2012 Sep 12.

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