Selene: a PyTorch-based deep learning library for sequence data

por Chen, Kathleen M., Cofer, Evan M., Zhou, Jian, Troyanskaya, Olga G.
Publicado 2019

Aether: leveraging linear programming for optimal cloud computing in genomics

por Luber, Jacob M, Tierney, Braden T, Cofer, Evan M, Patel, Chirag J, Kostic, Aleksandar D
Publicado 2018

A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type

por Le Goallec, Alan, Tierney, Braden T., Luber, Jacob M., Cofer, Evan M., Kostic, Aleksandar D., Patel, Chirag J.
Publicado 2020

Modeling transcriptional regulation of model species with deep learning

por Cofer, Evan M., Raimundo, João, Tadych, Alicja, Yamazaki, Yuji, Wong, Aaron K., Theesfeld, Chandra L., Levine, Michael S., Troyanskaya, Olga G.
Publicado 2021

Ten quick tips for deep learning in biology

por Lee, Benjamin D., Gitter, Anthony, Greene, Casey S., Raschka, Sebastian, Maguire, Finlay, Titus, Alexander J., Kessler, Michael D., Lee, Alexandra J., Chevrette, Marc G., Stewart, Paul Allen, Britto-Borges, Thiago, Cofer, Evan M., Yu, Kun-Hsing, Carmona, Juan Jose, Fertig, Elana J., Kalinin, Alexandr A., Signal, Brandon, Lengerich, Benjamin J., Triche, Timothy J., Boca, Simina M.
Publicado 2022

Opportunities and obstacles for deep learning in biology and medicine

por Ching, Travers, Himmelstein, Daniel S., Beaulieu-Jones, Brett K., Kalinin, Alexandr A., Do, Brian T., Way, Gregory P., Ferrero, Enrico, Agapow, Paul-Michael, Zietz, Michael, Hoffman, Michael M., Xie, Wei, Rosen, Gail L., Lengerich, Benjamin J., Israeli, Johnny, Lanchantin, Jack, Woloszynek, Stephen, Carpenter, Anne E., Shrikumar, Avanti, Xu, Jinbo, Cofer, Evan M., Lavender, Christopher A., Turaga, Srinivas C., Alexandari, Amr M., Lu, Zhiyong, Harris, David J., DeCaprio, Dave, Qi, Yanjun, Kundaje, Anshul, Peng, Yifan, Wiley, Laura K., Segler, Marwin H. S., Boca, Simina M., Swamidass, S. Joshua, Huang, Austin, Gitter, Anthony, Greene, Casey S.
Publicado 2018