Shawn M. Gomez

Publication Activity (10 Years)

Years Active: 2000-2024
Publications (10 Years): 7

Top Topics

Dimensionality Reduction

Chemical Reactions

Gaussian Process Latent Variable Models

Top Venues

Nucleic Acids Res.

Publications

Kathryn E. Kirchoff, James Wellnitz, Joshua E. Hochuli, Travis Maxfield, Konstantin I. Popov, Shawn M. Gomez, Alexander Tropsha
Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search. ECIR (2) (2024)
Kathryn E. Kirchoff, Travis Maxfield, Alexander Tropsha, Shawn M. Gomez
SALSA: Semantically-Aware Latent Space Autoencoder. AAAI (2024)
Kathryn E. Kirchoff, James Wellnitz, Joshua E. Hochuli, Travis Maxfield, Konstantin I. Popov, Shawn M. Gomez, Alexander Tropsha
Utilizing Low-Dimensional Molecular Embeddings for Rapid Chemical Similarity Search. CoRR (2024)
Matthew E. Berginski, Chinmaya U. Joisa, Brian T. Golitz, Shawn M. Gomez
Kinome inhibition states and multiomics data enable prediction of cell viability in diverse cancer types. PLoS Comput. Biol. 19 (2) (2023)
Kathryn E. Kirchoff, Travis Maxfield, Alexander Tropsha, Shawn M. Gomez
SALSA: Semantically-Aware Latent Space Autoencoder. CoRR (2023)
Kathryn E. Kirchoff, Shawn M. Gomez
EMBER: multi-label prediction of kinase-substrate phosphorylation events through deep learning. Bioinform. 38 (8) (2022)
Matthew E. Berginski, Nienke Moret, Changchang Liu, Dennis Goldfarb, Peter K. Sorger, Shawn M. Gomez
The Dark Kinase Knowledgebase: an online compendium of knowledge and experimental results of understudied kinases. Nucleic Acids Res. 49 (Database-Issue) (2021)
Matthew E. Berginski, Shawn M. Gomez
The Focal Adhesion Analysis Server: a web tool for analyzing focal adhesion dynamics. F1000Research 2 (2013)
Ke Xu, Kevin T. Morgan, Abby Todd Gehris, Timothy C. Elston, Shawn M. Gomez
A Whole-Body Model for Glycogen Regulation Reveals a Critical Role for Substrate Cycling in Maintaining Blood Glucose Homeostasis. PLoS Comput. Biol. 7 (12) (2011)
Jennifer M. Staab, Thomas M. O'Connell, Shawn M. Gomez
Enhancing metabolomic data analysis with Progressive Consensus Alignment of NMR Spectra (PCANS). BMC Bioinform. 11 (2010)
Kwangbom Choi, Shawn M. Gomez
Comparison of phylogenetic trees through alignment of embedded evolutionary distances. BMC Bioinform. 10 (2009)
Shawn M. Gomez, William Stafford Noble, Andrey Rzhetsky
Learning to predict protein-protein interactions from protein sequences. Bioinform. 19 (15) (2003)
Michael Krauthammer, Pauline Kra, Ivan Iossifov, Shawn M. Gomez, George Hripcsak, Vasileios Hatzivassiloglou, Carol Friedman, Andrey Rzhetsky
Of truth and pathways: chasing bits of information through myriads of articles. ISMB (2002)
Shawn M. Gomez, Andrey Rzhetsky
Towards the Prediction of Complete Protein-Protein Interaction Networks. Pacific Symposium on Biocomputing (2002)
Andrey Rzhetsky, Michael Krauthammer, Tomohiro Koike, Pauline Kra, Shawn M. Gomez, Hong Yu, Pablo Ariel Duboué, Wubin Weng, Stephen B. Johnson, Vasileios Hatzivassiloglou, Carol Friedman
GeneWays: A System for Mining Text and for Integrating Data on Molecular Pathways. German Conference on Bioinformatics (2001)
Andrey Rzhetsky, Shawn M. Gomez
Birth of scale-free molecular networks and the number of distinct DNA and protein domains per genome. Bioinform. 17 (10) (2001)
Andrey Rzhetsky, Tomohiro Koike, Sergey Kalachikov, Shawn M. Gomez, Michael Krauthammer, Sabina H. Kaplan, Pauline Kra, James J. Russo, Carol Friedman
A knowledge model for analysis and simulation of regulatory networks. Bioinform. 16 (12) (2000)