Visualizing the effects of filtering chaotic signals. - Michael T. Rosenstein; James J. Collins (Comput. Graph., 1994)

Robust Identification of Large Genetic Networks. - Diego di Bernardo; Timothy S. Gardner; James J. Collins (Pacific Symposium on Biocomputing, 2004)

Engineering Gene Regulatory Networks: A Reductionist Approach to Systems Biology. - James J. Collins (RECOMB, 2005)

Epigenetic Landscapes Explain Partially Reprogrammed Cells and Identify Key Reprogramming Genes. - Alex H. Lang; Hu Li; James J. Collins; Pankaj Mehta (PLoS Comput. Biol., 2014)

Ribocomputing devices for sophisticated in vivo logic computation. - Alexander A. Green; Jongmin Kim 001; Duo Ma; Pamela A. Silver; James J. Collins; Peng Yin (NANOCOM, 2016)

Deep learning identifies synergistic drug combinations for treating COVID-19. - Wengong Jin; Jonathan M. Stokes; Richard T. Eastman; Zina Itkin; Alexey V. Zakharov; James J. Collins; Tommi S. Jaakkola; Regina Barzilay (Proc. Natl. Acad. Sci. USA, 2021)

Discovery of a structural class of antibiotics with explainable deep learning. - Felix Wong; Erica J. Zheng; Jacqueline A. Valeri; Nina M. Donghia; Melis N. Anahtar; Satotaka Omori; Alicia Li; Andres Cubillos-Ruiz; Aarti Krishnan; Wengong Jin; Abigail L. Manson; Jens Friedrichs; et al. (Nat., 2024)

Deep generative design of RNA aptamers using structural predictions. - Felix Wong; Dongchen He; Aarti Krishnan; Liang Hong; Alexander Z. Wang; Jiuming Wang; Zhihang Hu; Satotaka Omori; Alicia Li; Jiahua Rao; Qinze Yu; Wengong Jin; et al. (Nat. Comput. Sci., 2024)