Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. - Sanjay Joshua Swamidass; Jonathan H. Chen; Jocelyne Bruand; Peter Phung; Liva Ralaivola; Pierre Baldi (ISMB (Supplement of Bioinformatics), 2005)

Statistical Distribution of Chemical Fingerprints. - Sanjay Joshua Swamidass; Pierre Baldi (WILF, 2005)

ChemDB: a public database of small molecules and related chemoinformatics resources. - Jonathan H. Chen; Sanjay Joshua Swamidass; Yimeng Dou; Jocelyne Bruand; Pierre Baldi (Bioinform., 2005)

Graph kernels for chemical informatics. - Liva Ralaivola; Sanjay Joshua Swamidass; Hiroto Saigo; Pierre Baldi (Neural Networks, 2005)

Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants. - Samuel A. Danziger; Sanjay Joshua Swamidass; Jue Zeng; Lawrence R. Dearth; Qiang Lu; Jonathan H. Chen; Jianlin Cheng; Vinh P. Hoang; Hiroto Saigo; Ray Luo 001; Pierre Baldi; Rainer K. Brachmann; et al. (IEEE ACM Trans. Comput. Biol. Bioinform., 2006)

ChemDB update - full-text search and virtual chemical space. - Jonathan H. Chen; Erik Linstead; Sanjay Joshua Swamidass; Dennis Wang; Pierre Baldi (Bioinform., 2007)

One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties. - Chloé-Agathe Azencott; Alexandre Ksikes; S. Joshua Swamidass; Jonathan H. Chen; Liva Ralaivola; Pierre Baldi (J. Chem. Inf. Model., 2007)

Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval. - Pierre Baldi; Ryan W. Benz; Daniel S. Hirschberg; S. Joshua Swamidass (J. Chem. Inf. Model., 2007)

Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time. - S. Joshua Swamidass; Pierre Baldi (J. Chem. Inf. Model., 2007)

Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval. - S. Joshua Swamidass; Pierre Baldi (J. Chem. Inf. Model., 2007)

Discovery of Power-Laws in Chemical Space. - Ryan W. Benz; S. Joshua Swamidass; Pierre Baldi (J. Chem. Inf. Model., 2008)

Large scale study of multiple-molecule queries. - Ramzi Nasr; Sanjay Joshua Swamidass; Pierre Baldi (J. Cheminformatics, 2009)

Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method. - S. Joshua Swamidass; Chloé-Agathe Azencott; Ting-Wan Lin; Hugo Gramajo; Shiou-Chuan Tsai; Pierre Baldi (J. Chem. Inf. Model., 2009)

Bridging the Gap Between Neural Network and Kernel Methods: Applications to Drug Discovery. - Pierre Baldi; Chloé-Agathe Azencott; Sanjay Joshua Swamidass (WIRN, 2010)

A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. - Sanjay Joshua Swamidass; Chloé-Agathe Azencott; Kenny Daily; Pierre Baldi (Bioinform., 2010)

Mining small-molecule screens to repurpose drugs. - Sanjay Joshua Swamidass (Briefings Bioinform., 2011)

Enhancing the rate of scaffold discovery with diversity-oriented prioritization. - Sanjay Joshua Swamidass; Bradley T. Calhoun; Joshua A. Bittker; Nicole E. Bodycombe; Paul A. Clemons (Bioinform., 2011)

Utility-Aware Screening with Clique-Oriented Prioritization. - S. Joshua Swamidass; Bradley T. Calhoun; Joshua A. Bittker; Nicole E. Bodycombe; Paul A. Clemons (J. Chem. Inf. Model., 2012)

Accounting for noise when clustering biological data. - Roman Sloutsky; Nicolas Jimenez; S. Joshua Swamidass; Kristen M. Naegle (Briefings Bioinform., 2013)

Scaffold network generator: a tool for mining molecular structures. - Matthew K. Matlock; Jed Zaretzki; S. Joshua Swamidass (Bioinform., 2013)

RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules. - Jed Zaretzki; Charles Bergeron; Tao-wei Huang; Patrik Rydberg; S. Joshua Swamidass; Curt M. Breneman (Bioinform., 2013)

Managing missing measurements in small-molecule screens. - Michael R. Browning; Bradley T. Calhoun; Sanjay Joshua Swamidass (J. Comput. Aided Mol. Des., 2013)

XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks. - Jed Zaretzki; Matthew K. Matlock; S. Joshua Swamidass (J. Chem. Inf. Model., 2013)

Session Introduction. - S. Joshua Swamidass; Zhiyong Lu; Pankaj Agarwal; Atul J. Butte (Pacific Symposium on Biocomputing, 2014)

Bigger data, collaborative tools and the future of predictive drug discovery. - Sean Ekins; Alex M. Clark; S. Joshua Swamidass; Nadia K. Litterman; Antony J. Williams (J. Comput. Aided Mol. Des., 2014)

Sharing Chemical Relationships Does Not Reveal Structures. - Matthew K. Matlock; S. Joshua Swamidass (J. Chem. Inf. Model., 2014)

Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data. - Runjun D. Kumar; Adam C. Searleman; S. Joshua Swamidass; Obi L. Griffith; Ron Bose (Bioinform., 2015)

XenoSite server: a web-available site of metabolism prediction tool. - Matthew K. Matlock; Tyler B. Hughes; Sanjay Joshua Swamidass (Bioinform., 2015)

Extending P450 site-of-metabolism models with region-resolution data. - Jed M. Zaretzki; Michael R. Browning; Tyler B. Hughes; S. Joshua Swamidass (Bioinform., 2015)

Accurate and efficient target prediction using a potency-sensitive influence-relevance voter. - Alessandro Lusci; Michael R. Browning; David Fooshee; S. Joshua Swamidass; Pierre Baldi (J. Cheminformatics, 2015)

Improved Prediction of CYP-Mediated Metabolism with Chemical Fingerprints. - Jed Zaretzki; Kevin Michael Boehm; Sanjay Joshua Swamidass (J. Chem. Inf. Model., 2015)

A survey of current trends in computational drug repositioning. - Jiao Li 001; Si Zheng 001; Bin Chen; Atul J. Butte; S. Joshua Swamidass; Zhiyong Lu (Briefings Bioinform., 2016)

A simple model predicts UGT-mediated metabolism. - Na Le Dang; Tyler B. Hughes; Varun Krishnamurthy; S. Joshua Swamidass (Bioinform., 2016)

BEESEM: estimation of binding energy models using HT-SELEX data. - Shuxiang Ruan; S. Joshua Swamidass; Gary D. Stormo (Bioinform., 2017)

The diversity and disparity in biomedical informatics (DDBI) workshop. - William M. Southerland; S. Joshua Swamidass; Philip R. O. Payne; Laura K. Wiley; ClarLynda R. Williams-DeVane (PSB, 2018)

Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive Compounds. - Matthew K. Matlock; Tyler B. Hughes; Jayme L. Dahlin; S. Joshua Swamidass (J. Chem. Inf. Model., 2018)

Deep Learning Global Glomerulosclerosis in Transplant Kidney Frozen Sections. - Jon N. Marsh; Matthew K. Matlock; Satoru Kudose; Ta-Chiang Liu; Thaddeus S. Stappenbeck; Joseph P. Gaut; S. Joshua Swamidass (IEEE Trans. Medical Imaging, 2018)

Deep learning long-range information in undirected graphs with wave networks. - Matthew K. Matlock; Arghya Datta; Na Le Dang; Kevin Jiang; S. Joshua Swamidass (IJCNN, 2019)

The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five Colors. - Na Le Dang; Matthew K. Matlock; Tyler B. Hughes; S. Joshua Swamidass (J. Chem. Inf. Model., 2020)

XenoNet: Inference and Likelihood of Intermediate Metabolite Formation. - Noah R. Flynn; Na Le Dang; Michael D. Ward; S. Joshua Swamidass (J. Chem. Inf. Model., 2020)

Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites. - Tyler B. Hughes; Na Le Dang; Ayush Kumar; Noah R. Flynn; S. Joshua Swamidass (J. Chem. Inf. Model., 2020)

Cal-Net: Jointly Learning Classification and Calibration On Imbalanced Binary Classification Tasks. - Arghya Datta; Noah R. Flynn; S. Joshua Swamidass (IJCNN, 2021)

Machine learning liver-injuring drug interactions with non-steroidal anti-inflammatory drugs (NSAIDs) from a retrospective electronic health record (EHR) cohort. - Arghya Datta; Noah R. Flynn; Dustyn A. Barnette; Keith F. Woeltje; Grover P. Miller; S. Joshua Swamidass (PLoS Comput. Biol., 2021)

'Black Box' to 'Conversational' Machine Learning: Ondansetron Reduces Risk of Hospital-Acquired Venous Thromboembolism. - Arghya Datta; Matthew K. Matlock; Na Le Dang; Thiago C. Moulin; Keith F. Woeltje; Elizabeth L. Yanik; Sanjay Joshua Swamidass (IEEE J. Biomed. Health Informatics, 2021)

Fair-Net: A Network Architecture for Reducing Performance Disparity between Identifiable Sub-populations. - Arghya Datta; S. Joshua Swamidass (ICAART (3), 2022)

Message Passing Neural Networks Improve Prediction of Metabolite Authenticity. - Noah R. Flynn; S. Joshua Swamidass (J. Chem. Inf. Model., 2023)

sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets. - Luiz Irber; N. Tessa Pierce-Ward; Mohamed Abuelanin; Harriet Alexander; Abhishek Anant; Keya Barve; Colton Baumler; Olga B. Botvinnik; Phillip Brooks; Daniel Dsouza; Gautier Laurent; Mahmudur Rahman Hera; et al. (J. Open Source Softw., 2024)

GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysis. - Michael R. Waters; Matthew Inkman; Kay Jayachandran; Roman M. Kowalchuk; Clifford Robinson; Julie K. Schwarz; S. Joshua Swamidass; Obi L. Griffith; Jeffrey J. Szymanski; Jin Zhang 038 (Patterns, 2024)