Publications


Chen KM*, Cofer EM*, Zhou J, and Troyanskaya OG. Selene: a PyTorch-based deep learning library for sequence data. Nature Methods, March 2019. [GitHub] (*Equal contribution)

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P, 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, Zhiyong L, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Boca SM, Swamidass J, Huang A, Gitter A*, and Greene CS*. Opportunities and obstacles for deep learning in biology and medicine. Journal of the Royal Society Interface, April 2018. doi:10.1098/rsif.2017.0387. [GitHub] (Randomized ordering where not marked by *)

Luber JM, Tierney BT, Cofer EM, Patel CJ, and Kostic AD. Aether: leveraging linear programming for optimal cloud computing in genomics. Bioinformatics, December 2017. doi:10.1093/bioinformatics/btx787. [GitHub]


Preprints


Chen KM*, Cofer EM*, Zhou J, and Troyanskaya OG. Selene: a PyTorch-based deep learning library for biological sequence-level data. bioRxiv, October 2018. doi:10.1101/438291. [GitHub] (*Equal contribution)

Luber JM, Tierney BT, Cofer EM, Patel CJ, and Kostic AD. Aether: leveraging linear programming for optimal cloud computing in genomics. bioRxiv, July 2017. doi:10.1101/162883. [GitHub]

Ching T, Himmelstein DS, Beaulieu-Jones BK, Kalinin AA, Do BT, Way GP, Ferrero E, Agapow P, Xie W, Rosen GL, Lengerich BJ, Israeli J, Lanchantin J, Woloszynek S, Carpenter AE, Shrikumar A, Xu J, Cofer EM, Harris DJ, DeCaprio D, Qi Y, Kundaje A, Peng Y, Wiley LK, Segler MHS, Gitter A, and Greene CS. Opportunities and obstacles for deep learning in biology and medicine. bioRxiv, May 2017. doi:10.1101/142760. [GitHub] (Randomized ordering where not marked by )