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ORCIDSanjay Joshua Swamidass
Person information
- affiliation: Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
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2020 – today
- 2024
[j40]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:
sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets. J. Open Source Softw. 9(98): 6830 (2024)- [j39]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:
GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysis. Patterns 5(2): 100910 (2024) - 2023
- [j38]Noah R. Flynn, S. Joshua Swamidass:
Message Passing Neural Networks Improve Prediction of Metabolite Authenticity. J. Chem. Inf. Model. 63(6): 1675-1694 (2023) - 2022
- [c8]Arghya Datta, S. Joshua Swamidass:
Fair-Net: A Network Architecture for Reducing Performance Disparity between Identifiable Sub-populations. ICAART (3) 2022: 645-654 - 2021
- [j37]Arghya Datta, Noah R. Flynn, Dustyn A. Barnette, Keith F. Woeltje, Grover P. Miller, S. Joshua Swamidass:
Machine learning liver-injuring drug interactions with non-steroidal anti-inflammatory drugs (NSAIDs) from a retrospective electronic health record (EHR) cohort. PLoS Comput. Biol. 17(7) (2021) - [j36]Arghya Datta, Matthew K. Matlock, Na Le Dang, Thiago C. Moulin, Keith F. Woeltje, Elizabeth L. Yanik, Sanjay Joshua Swamidass:
'Black Box' to 'Conversational' Machine Learning: Ondansetron Reduces Risk of Hospital-Acquired Venous Thromboembolism. IEEE J. Biomed. Health Informatics 25(6): 2204-2214 (2021) - [c7]Arghya Datta, Noah R. Flynn, S. Joshua Swamidass:
Cal-Net: Jointly Learning Classification and Calibration On Imbalanced Binary Classification Tasks. IJCNN 2021: 1-8 - [i2]Arghya Datta, S. Joshua Swamidass:
Fair-Net: A Network Architecture For Reducing Performance Disparity Between Identifiable Sub-Populations. CoRR abs/2106.00720 (2021) - 2020
- [j35]Na Le Dang, Matthew K. Matlock, Tyler B. Hughes, S. Joshua Swamidass:
The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five Colors. J. Chem. Inf. Model. 60(3): 1146-1164 (2020) - [j34]Noah R. Flynn, Na Le Dang, Michael D. Ward, S. Joshua Swamidass:
XenoNet: Inference and Likelihood of Intermediate Metabolite Formation. J. Chem. Inf. Model. 60(7): 3431-3449 (2020) - [j33]Tyler B. Hughes, Na Le Dang, Ayush Kumar, Noah R. Flynn, S. Joshua Swamidass:
Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites. J. Chem. Inf. Model. 60(10): 4702-4716 (2020)
2010 – 2019
- 2019
- [c6]Matthew K. Matlock, Arghya Datta, Na Le Dang, Kevin Jiang, S. Joshua Swamidass:
Deep learning long-range information in undirected graphs with wave networks. IJCNN 2019: 1-8 - 2018
- [j32]Matthew K. Matlock, Tyler B. Hughes, Jayme L. Dahlin, S. Joshua Swamidass:
Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive Compounds. J. Chem. Inf. Model. 58(8): 1483-1500 (2018) - [j31]Jon N. Marsh, Matthew K. Matlock, Satoru Kudose, Ta-Chiang Liu, Thaddeus S. Stappenbeck, Joseph P. Gaut, S. Joshua Swamidass:
Deep Learning Global Glomerulosclerosis in Transplant Kidney Frozen Sections. IEEE Trans. Medical Imaging 37(12): 2718-2728 (2018) - [c5]William M. Southerland, S. Joshua Swamidass, Philip R. O. Payne, Laura K. Wiley, ClarLynda R. Williams-DeVane:
The diversity and disparity in biomedical informatics (DDBI) workshop. PSB 2018: 614-617 - [i1]Matthew K. Matlock, Arghya Datta, Na Le Dang, Kevin Jiang, S. Joshua Swamidass:
Deep learning long-range information in undirected graphs with wave networks. CoRR abs/1810.12153 (2018) - 2017
- [j30]Shuxiang Ruan, S. Joshua Swamidass, Gary D. Stormo:
BEESEM: estimation of binding energy models using HT-SELEX data. Bioinform. 33(15): 2288-2295 (2017) - 2016
- [j29]Jiao Li, Si Zheng, Bin Chen, Atul J. Butte, S. Joshua Swamidass, Zhiyong Lu:
A survey of current trends in computational drug repositioning. Briefings Bioinform. 17(1): 2-12 (2016) - [j28]Na Le Dang, Tyler B. Hughes, Varun Krishnamurthy, S. Joshua Swamidass:
A simple model predicts UGT-mediated metabolism. Bioinform. 32(20): 3183-3189 (2016) - 2015
- [j27]Matthew K. Matlock, Tyler B. Hughes, Sanjay Joshua Swamidass:
XenoSite server: a web-available site of metabolism prediction tool. Bioinform. 31(7): 1136-1137 (2015) - [j26]Jed M. Zaretzki, Michael R. Browning, Tyler B. Hughes, S. Joshua Swamidass:
Extending P450 site-of-metabolism models with region-resolution data. Bioinform. 31(12): 1966-1973 (2015) - [j25]Runjun D. Kumar, Adam C. Searleman, S. Joshua Swamidass, Obi L. Griffith, Ron Bose:
Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data. Bioinform. 31(22): 3561-3568 (2015) - [j24]Alessandro Lusci, Michael R. Browning, David Fooshee, S. Joshua Swamidass, Pierre Baldi:
Accurate and efficient target prediction using a potency-sensitive influence-relevance voter. J. Cheminformatics 7: 63:1-63:13 (2015) - [j23]Jed Zaretzki, Kevin Michael Boehm, Sanjay Joshua Swamidass:
Improved Prediction of CYP-Mediated Metabolism with Chemical Fingerprints. J. Chem. Inf. Model. 55(5): 972-982 (2015) - 2014
- [j22]Sean Ekins, Alex M. Clark, S. Joshua Swamidass, Nadia K. Litterman, Antony J. Williams:
Bigger data, collaborative tools and the future of predictive drug discovery. J. Comput. Aided Mol. Des. 28(10): 997-1008 (2014) - [j21]Matthew K. Matlock, S. Joshua Swamidass:
Sharing Chemical Relationships Does Not Reveal Structures. J. Chem. Inf. Model. 54(1): 37-48 (2014) - [c4]S. Joshua Swamidass, Zhiyong Lu, Pankaj Agarwal, Atul J. Butte:
Session Introduction. Pacific Symposium on Biocomputing 2014: 110-113 - 2013
- [j20]Roman Sloutsky, Nicolas Jimenez, S. Joshua Swamidass, Kristen M. Naegle:
Accounting for noise when clustering biological data. Briefings Bioinform. 14(4): 423-436 (2013) - [j19]Jed Zaretzki, Charles Bergeron, Tao-wei Huang, Patrik Rydberg, S. Joshua Swamidass, Curt M. Breneman:
RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules. Bioinform. 29(4): 497-498 (2013) - [j18]Matthew K. Matlock, Jed Zaretzki, S. Joshua Swamidass:
Scaffold network generator: a tool for mining molecular structures. Bioinform. 29(20): 2655-2656 (2013) - [j17]Michael R. Browning, Bradley T. Calhoun, Sanjay Joshua Swamidass:
Managing missing measurements in small-molecule screens. J. Comput. Aided Mol. Des. 27(5): 469-478 (2013) - [j16]Jed Zaretzki, Matthew K. Matlock, S. Joshua Swamidass:
XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks. J. Chem. Inf. Model. 53(12): 3373-3383 (2013) - 2012
- [j15]S. Joshua Swamidass, Bradley T. Calhoun, Joshua A. Bittker, Nicole E. Bodycombe, Paul A. Clemons:
Utility-Aware Screening with Clique-Oriented Prioritization. J. Chem. Inf. Model. 52(1): 29-37 (2012) - 2011
- [j14]Sanjay Joshua Swamidass:
Mining small-molecule screens to repurpose drugs. Briefings Bioinform. 12(4): 327-335 (2011) - [j13]Sanjay Joshua Swamidass, Bradley T. Calhoun, Joshua A. Bittker, Nicole E. Bodycombe, Paul A. Clemons:
Enhancing the rate of scaffold discovery with diversity-oriented prioritization. Bioinform. 27(16): 2271-2278 (2011) - 2010
- [j12]Sanjay Joshua Swamidass, Chloé-Agathe Azencott, Kenny Daily, Pierre Baldi:
A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval. Bioinform. 26(10): 1348-1356 (2010) - [c3]Pierre Baldi, Chloé-Agathe Azencott, Sanjay Joshua Swamidass:
Bridging the Gap Between Neural Network and Kernel Methods: Applications to Drug Discovery. WIRN 2010: 3-13
2000 – 2009
- 2009
- [j11]Ramzi Nasr, Sanjay Joshua Swamidass, Pierre Baldi:
Large scale study of multiple-molecule queries. J. Cheminformatics 1: 7 (2009) - [j10]S. Joshua Swamidass, Chloé-Agathe Azencott, Ting-Wan Lin, Hugo Gramajo, Shiou-Chuan Tsai, Pierre Baldi:
Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method. J. Chem. Inf. Model. 49(4): 756-766 (2009) - 2008
- [j9]Ryan W. Benz, S. Joshua Swamidass, Pierre Baldi:
Discovery of Power-Laws in Chemical Space. J. Chem. Inf. Model. 48(6): 1138-1151 (2008) - 2007
- [j8]Jonathan H. Chen, Erik Linstead, Sanjay Joshua Swamidass, Dennis Wang, Pierre Baldi:
ChemDB update - full-text search and virtual chemical space. Bioinform. 23(17): 2348-2351 (2007) - [j7]S. Joshua Swamidass, Pierre Baldi:
Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time. J. Chem. Inf. Model. 47(2): 302-317 (2007) - [j6]S. Joshua Swamidass, Pierre Baldi:
Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval. J. Chem. Inf. Model. 47(3): 952-964 (2007) - [j5]Chloé-Agathe Azencott, Alexandre Ksikes, S. Joshua Swamidass, Jonathan H. Chen, Liva Ralaivola, Pierre Baldi:
One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties. J. Chem. Inf. Model. 47(3): 965-974 (2007) - [j4]Pierre Baldi, Ryan W. Benz, Daniel S. Hirschberg, S. Joshua Swamidass:
Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval. J. Chem. Inf. Model. 47(6): 2098-2109 (2007) - 2006
- [j3]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, Pierre Baldi, Rainer K. Brachmann, Richard H. Lathrop:
Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants. IEEE ACM Trans. Comput. Biol. Bioinform. 3(2): 114-125 (2006) - 2005
- [j2]Jonathan H. Chen, Sanjay Joshua Swamidass, Yimeng Dou, Jocelyne Bruand, Pierre Baldi:
ChemDB: a public database of small molecules and related chemoinformatics resources. Bioinform. 21(22): 4133-4139 (2005) - [j1]Liva Ralaivola, Sanjay Joshua Swamidass, Hiroto Saigo, Pierre Baldi:
Graph kernels for chemical informatics. Neural Networks 18(8): 1093-1110 (2005) - [c2]Sanjay Joshua Swamidass, Jonathan H. Chen, Jocelyne Bruand, Peter Phung, Liva Ralaivola, Pierre Baldi:
Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity. ISMB (Supplement of Bioinformatics) 2005: 359-368 - [c1]Sanjay Joshua Swamidass, Pierre Baldi:
Statistical Distribution of Chemical Fingerprints. WILF 2005: 11-18
Coauthor Index
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