A knowledge model for analysis and simulation of regulatory networks. - Andrey Rzhetsky; Tomohiro Koike; Sergey Kalachikov; Shawn M. Gomez; Michael Krauthammer; Sabina H. Kaplan; Pauline Kra; James J. Russo; Carol Friedman (Bioinform., 2000)

GeneWays: A System for Mining Text and for Integrating Data on Molecular Pathways. - Andrey Rzhetsky; Michael Krauthammer; Tomohiro Koike; Pauline Kra; Shawn M. Gomez; Hong Yu 001; Pablo Ariel Duboué; Wubin Weng; Stephen B. Johnson; Vasileios Hatzivassiloglou; Carol Friedman (German Conference on Bioinformatics, 2001)

Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. - Andrey Rzhetsky; Shawn M. Gomez (Bioinform., 2001)

Of truth and pathways: chasing bits of information through myriads of articles. - Michael Krauthammer; Pauline Kra; Ivan Iossifov; Shawn M. Gomez; George Hripcsak; Vasileios Hatzivassiloglou; Carol Friedman; Andrey Rzhetsky (ISMB, 2002)

Towards the Prediction of Complete Protein-Protein Interaction Networks. - Shawn M. Gomez; Andrey Rzhetsky (Pacific Symposium on Biocomputing, 2002)

Learning to predict protein-protein interactions from protein sequences. - Shawn M. Gomez; William Stafford Noble; Andrey Rzhetsky (Bioinform., 2003)

Comparison of phylogenetic trees through alignment of embedded evolutionary distances. - Kwangbom Choi; Shawn M. Gomez (BMC Bioinform., 2009)

Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS). - Jennifer M. Staab; Thomas M. O'Connell; Shawn M. Gomez (BMC Bioinform., 2010)

A Whole-Body Model for Glycogen Regulation Reveals a Critical Role for Substrate Cycling in Maintaining Blood Glucose Homeostasis. - Ke Xu; Kevin T. Morgan; Abby Todd Gehris; Timothy C. Elston; Shawn M. Gomez (PLoS Comput. Biol., 2011)

The Focal Adhesion Analysis Server: a web tool for analyzing focal adhesion dynamics. - Matthew E. Berginski; Shawn M. Gomez (F1000Research, 2013)

The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. - Matthew E. Berginski; Nienke Moret; Changchang Liu; Dennis Goldfarb; Peter K. Sorger; Shawn M. Gomez (Nucleic Acids Res., 2021)

EMBER: multi-label prediction of kinase-substrate phosphorylation events through deep learning. - Kathryn E. Kirchoff; Shawn M. Gomez (Bioinform., 2022)

Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types. - Matthew E. Berginski; Chinmaya U. Joisa; Brian T. Golitz; Shawn M. Gomez (PLoS Comput. Biol., 2023)

SALSA: Semantically-Aware Latent Space Autoencoder. - Kathryn E. Kirchoff; Travis Maxfield; Alexander Tropsha; Shawn M. Gomez (AAAI, 2024)

Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search. - Kathryn E. Kirchoff; James Wellnitz; Joshua E. Hochuli; Travis Maxfield; Konstantin I. Popov; Shawn M. Gomez; Alexander Tropsha (ECIR (2), 2024)