S. Joshua Swamidass

35 papers B 2Misc 2Journal 30Unranked 1
YearRankTypeTitle / Venue / Authors
2024 J jnl
GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysis.
Patterns
Michael R. Waters, Matthew Inkman, Kay Jayachandran, Roman M. Kowalchuk, Clifford G. Robinson, Julie K. Schwarz, S. Joshua Swamidass, Obi L. Griffith, Jeffrey J. Szymanski, Jin Zhang
2024 J jnl
sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets.
J. Open Source Softw.
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, Hannah Eve Houts, Lisa K. Johnson, Fabian Klötzl, David Koslicki, Marisa Lim, Ricky Lim, Bradley Nelson, Ivan Ogasawara, Taylor Reiter, Camille Scott, Andreas Sjödin, Daniel S. Standage, S. Joshua Swamidass, Connor Tiffany, Pranathi Vemuri, Erik Young, C. Titus Brown
2023 J jnl
Message Passing Neural Networks Improve Prediction of Metabolite Authenticity.
J. Chem. Inf. Model.
Noah R. Flynn, S. Joshua Swamidass
2022 — conf
Fair-Net: A Network Architecture for Reducing Performance Disparity between Identifiable Sub-populations.
ICAART (3)
Arghya Datta, S. Joshua Swamidass
2021 B conf
Cal-Net: Jointly Learning Classification and Calibration On Imbalanced Binary Classification Tasks.
IJCNN
Arghya Datta, Noah R. Flynn, S. Joshua Swamidass
2021 J jnl
Fair-Net: A Network Architecture For Reducing Performance Disparity Between Identifiable Sub-Populations.
CoRR
Arghya Datta, S. Joshua Swamidass
2021 J jnl
Machine learning liver-injuring drug interactions with non-steroidal anti-inflammatory drugs (NSAIDs) from a retrospective electronic health record (EHR) cohort.
PLoS Comput. Biol.
Arghya Datta, Noah R. Flynn, Dustyn A. Barnette, Keith F. Woeltje, Grover P. Miller, S. Joshua Swamidass
2020 J jnl
Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites.
J. Chem. Inf. Model.
Tyler B. Hughes, Na Le Dang, Ayush Kumar, Noah R. Flynn, S. Joshua Swamidass
2020 J jnl
The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five Colors.
J. Chem. Inf. Model.
Na Le Dang, Matthew K. Matlock, Tyler B. Hughes, S. Joshua Swamidass
2020 J jnl
XenoNet: Inference and Likelihood of Intermediate Metabolite Formation.
J. Chem. Inf. Model.
Noah R. Flynn, Na Le Dang, Michael D. Ward, S. Joshua Swamidass
2019 B conf
Deep learning long-range information in undirected graphs with wave networks.
IJCNN
Matthew K. Matlock, Arghya Datta, Na Le Dang, Kevin Jiang, S. Joshua Swamidass
2018 J jnl
Deep Learning Global Glomerulosclerosis in Transplant Kidney Frozen Sections.
IEEE Trans. Medical Imaging
Jon N. Marsh, Matthew K. Matlock, Satoru Kudose, Ta-Chiang Liu, Thaddeus S. Stappenbeck, Joseph P. Gaut, S. Joshua Swamidass
2018 J jnl
Deep learning long-range information in undirected graphs with wave networks.
CoRR
Matthew K. Matlock, Arghya Datta, Na Le Dang, Kevin Jiang, S. Joshua Swamidass
2018 J jnl
Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive Compounds.
J. Chem. Inf. Model.
Matthew K. Matlock, Tyler B. Hughes, Jayme L. Dahlin, S. Joshua Swamidass
2018 Misc conf
The diversity and disparity in biomedical informatics (DDBI) workshop.
PSB
William M. Southerland, S. Joshua Swamidass, Philip R. O. Payne, Laura K. Wiley, ClarLynda R. Williams-DeVane
2017 J jnl
BEESEM: estimation of binding energy models using HT-SELEX data.
Bioinform.
Shuxiang Ruan, S. Joshua Swamidass, Gary D. Stormo
2016 J jnl
A simple model predicts UGT-mediated metabolism.
Bioinform.
Na Le Dang, Tyler B. Hughes, Varun Krishnamurthy, S. Joshua Swamidass
2016 J jnl
A survey of current trends in computational drug repositioning.
Briefings Bioinform.
Jiao Li, Si Zheng, Bin Chen, Atul J. Butte, S. Joshua Swamidass, Zhiyong Lu
2015 J jnl
Accurate and efficient target prediction using a potency-sensitive influence-relevance voter.
J. Cheminformatics
Alessandro Lusci, Michael R. Browning, David Fooshee, S. Joshua Swamidass, Pierre Baldi
2015 J jnl
Extending P450 site-of-metabolism models with region-resolution data.
Bioinform.
Jed M. Zaretzki, Michael R. Browning, Tyler B. Hughes, S. Joshua Swamidass
2015 J jnl
Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data.
Bioinform.
Runjun D. Kumar, Adam C. Searleman, S. Joshua Swamidass, Obi L. Griffith, Ron Bose
2014 J jnl
Bigger data, collaborative tools and the future of predictive drug discovery.
J. Comput. Aided Mol. Des.
Sean Ekins, Alex M. Clark, S. Joshua Swamidass, Nadia K. Litterman, Antony J. Williams
2014 Misc conf
Session Introduction.
Pacific Symposium on Biocomputing
S. Joshua Swamidass, Zhiyong Lu, Pankaj Agarwal, Atul J. Butte
2014 J jnl
Sharing Chemical Relationships Does Not Reveal Structures.
J. Chem. Inf. Model.
Matthew K. Matlock, S. Joshua Swamidass
2013 J jnl
Accounting for noise when clustering biological data.
Briefings Bioinform.
Roman Sloutsky, Nicolas Jimenez, S. Joshua Swamidass, Kristen M. Naegle
2013 J jnl
RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules.
Bioinform.
Jed Zaretzki, Charles Bergeron, Tao-wei Huang, Patrik Rydberg, S. Joshua Swamidass, Curt M. Breneman
2013 J jnl
Scaffold network generator: a tool for mining molecular structures.
Bioinform.
Matthew K. Matlock, Jed Zaretzki, S. Joshua Swamidass
2013 J jnl
XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks.
J. Chem. Inf. Model.
Jed Zaretzki, Matthew K. Matlock, S. Joshua Swamidass
2012 J jnl
Utility-Aware Screening with Clique-Oriented Prioritization.
J. Chem. Inf. Model.
S. Joshua Swamidass, Bradley T. Calhoun, Joshua A. Bittker, Nicole E. Bodycombe, Paul A. Clemons
2009 J jnl
Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method.
J. Chem. Inf. Model.
S. Joshua Swamidass, Chloé-Agathe Azencott, Ting-Wan Lin, Hugo Gramajo, Shiou-Chuan Tsai, Pierre Baldi
2008 J jnl
Discovery of Power-Laws in Chemical Space.
J. Chem. Inf. Model.
Ryan W. Benz, S. Joshua Swamidass, Pierre Baldi
2007 J jnl
Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time.
J. Chem. Inf. Model.
S. Joshua Swamidass, Pierre Baldi
2007 J jnl
Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval.
J. Chem. Inf. Model.
Pierre Baldi, Ryan W. Benz, Daniel S. Hirschberg, S. Joshua Swamidass
2007 J jnl
Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval.
J. Chem. Inf. Model.
S. Joshua Swamidass, Pierre Baldi
2007 J jnl
One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties.
J. Chem. Inf. Model.
Chloé-Agathe Azencott, Alexandre Ksikes, S. Joshua Swamidass, Jonathan H. Chen, Liva Ralaivola, Pierre Baldi