J
Johnny Israeli
Researcher at Stanford University
Publications - 10
Citations - 1854
Johnny Israeli is an academic researcher from Stanford University. The author has contributed to research in topics: Computer science & Biology. The author has an hindex of 5, co-authored 6 publications receiving 1268 citations.
Papers
More filters
Journal ArticleDOI
Opportunities and obstacles for deep learning in biology and medicine.
Travers Ching,Daniel Himmelstein,Brett K. Beaulieu-Jones,Alexandr A. Kalinin,Brian T. Do,Gregory P. Way,Enrico Ferrero,Paul-Michael Agapow,Michael Zietz,Michael M. Hoffman,Michael M. Hoffman,Wei Xie,Gail L. Rosen,Benjamin J. Lengerich,Johnny Israeli,Jack Lanchantin,Stephen Woloszynek,Anne E. Carpenter,Avanti Shrikumar,Jinbo Xu,Evan M. Cofer,Evan M. Cofer,Christopher A. Lavender,Srinivas C. Turaga,Amr Alexandari,Zhiyong Lu,David J. Harris,Dave DeCaprio,Yanjun Qi,Anshul Kundaje,Yifan Peng,Laura K. Wiley,Marwin H. S. Segler,Simina M. Boca,S. Joshua Swamidass,Austin Huang,Anthony Gitter,Anthony Gitter,Casey S. Greene +38 more
TL;DR: It is found that deep learning has yet to revolutionize biomedicine or definitively resolve any of the most pressing challenges in the field, but promising advances have been made on the prior state of the art.
Journal ArticleDOI
Matrix stiffness induces a tumorigenic phenotype in mammary epithelium through changes in chromatin accessibility.
Ryan S. Stowers,Anna Shcherbina,Johnny Israeli,Joshua J. Gruber,Julie Chang,Sungmin Nam,Atefeh Rabiee,Mary N. Teruel,Michael Snyder,Anshul Kundaje,Ovijit Chaudhuri +10 more
TL;DR: 3D model of breast cancer shows that a stiff extracellular matrix promotes a tumorigenic phenotype through broad changes in chromatin accessibility and in the activity of histone deacetylases and the transcription factor Sp1, and reveals that chromatin state is a critical mediator of mechanotransduction.
Journal ArticleDOI
The Kipoi repository accelerates community exchange and reuse of predictive models for genomics.
Žiga Avsec,Žiga Avsec,Roman Kreuzhuber,Roman Kreuzhuber,Johnny Israeli,Nancy Xu,Jun Cheng,Jun Cheng,Avanti Shrikumar,Abhimanyu Banerjee,Daniel S Kim,Thorsten Beier,Lara Urban,Anshul Kundaje,Oliver Stegle,Oliver Stegle,Julien Gagneur +16 more
TL;DR: It is argued here that it is a quirk of history that both MRT and gene editing have come to the forefront of public attention at roughly the same time and to best protect citizens from harm, limited regulatory pathways that can be monitored and carefully delineated are preferable to shadowy practices and a potential regulatory race to the bottom.
Posted ContentDOI
Opportunities And Obstacles For Deep Learning In Biology And Medicine
Travers Ching,Daniel Himmelstein,Brett K. Beaulieu-Jones,Alexandr A. Kalinin,Brian T. Do,Gregory P. Way,Enrico Ferrero,Paul-Michael Agapow,Wei Xie,Gail L. Rosen,Benjamin J. Lengerich,Johnny Israeli,Jack Lanchantin,Stephen Woloszynek,Anne E. Carpenter,Avanti Shrikumar,Jinbo Xu,Evan M. Cofer,David J. Harris,Dave DeCaprio,Yanjun Qi,Anshul Kundaje,Yifan Peng,Laura K. Wiley,Marwin H. S. Segler,Anthony Gitter,Casey S. Greene +26 more
TL;DR: This work examines applications of deep learning to a variety of biomedical problems -- patient classification, fundamental biological processes, and treatment of patients -- to predict whether deep learning will transform these tasks or if the biomedical sphere poses unique challenges.
Posted ContentDOI
Kipoi: accelerating the community exchange and reuse of predictive models for genomics
Ziga Avsec,Roman Kreuzhuber,Johnny Israeli,Nancy Xu,Jun Cheng,Avanti Shrikumar,Abhimanyu Banerjee,Daniel S Kim,Lara Urban,Anshul Kundaje,Oliver Stegle,Julien Gagneur +11 more
TL;DR: Kipoi, a collaborative initiative to define standards and to foster reuse of trained models in genomics, is presented, providing a unified framework to archive, share, access, use, and build on models developed by the community.