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

por Shrikumar, Avanti, Prakash, Eva, Kundaje, Anshul
Publicado 2019

Deciphering regulatory DNA sequences and noncoding genetic variants using neural network models of massively parallel reporter assays

por Movva, Rajiv, Greenside, Peyton, Marinov, Georgi K., Nair, Surag, Shrikumar, Avanti, Kundaje, Anshul
Publicado 2019

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

por Cochran, Kelly, Srivastava, Divyanshi, Shrikumar, Avanti, Balsubramani, Akshay, Hardison, Ross C., Kundaje, Anshul, Mahony, Shaun
Publicado 2022

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

por Avsec, Žiga, Weilert, Melanie, Shrikumar, Avanti, Krueger, Sabrina, Alexandari, Amr, Dalal, Khyati, Fropf, Robin, McAnany, Charles, Gagneur, Julien, Kundaje, Anshul, Zeitlinger, Julia
Publicado 2021

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

por Alexandari, Amr M., Horton, Connor A., Shrikumar, Avanti, Shah, Nilay, Li, Eileen, Weilert, Melanie, Pufall, Miles A., Zeitlinger, Julia, Fordyce, Polly M., Kundaje, Anshul
Publicado 2023

The Kipoi repository accelerates community exchange and reuse of predictive models for genomics

por Avsec, Žiga, Kreuzhuber, Roman, Israeli, Johnny, Xu, Nancy, Cheng, Jun, Shrikumar, Avanti, Banerjee, Abhimanyu, Kim, Daniel S., Beier, Thorsten, Urban, Lara, Kundaje, Anshul, Stegle, Oliver, Gagneur, Julien
Publicado 2019

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