Sanjay Joshua Swamidass

Orcid: 0000-0003-2191-0778

Affiliations:
  • Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA


According to our database1, Sanjay Joshua Swamidass authored at least 48 papers between 2005 and 2024.

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Bibliography

2024
GAiN: An integrative tool utilizing generative adversarial neural networks for augmented gene expression analysis.
Patterns, 2024

sourmash v4: A multitool to quickly search, compare, and analyze genomic and metagenomic data sets.
J. Open Source Softw., 2024

2023
Message Passing Neural Networks Improve Prediction of Metabolite Authenticity.
J. Chem. Inf. Model., March, 2023

2022
Fair-Net: A Network Architecture for Reducing Performance Disparity between Identifiable Sub-populations.
Proceedings of the 14th International Conference on Agents and Artificial Intelligence, 2022

2021
'Black Box' to 'Conversational' Machine Learning: Ondansetron Reduces Risk of Hospital-Acquired Venous Thromboembolism.
IEEE J. Biomed. Health Informatics, 2021

Machine learning liver-injuring drug interactions with non-steroidal anti-inflammatory drugs (NSAIDs) from a retrospective electronic health record (EHR) cohort.
PLoS Comput. Biol., 2021

Cal-Net: Jointly Learning Classification and Calibration On Imbalanced Binary Classification Tasks.
Proceedings of the International Joint Conference on Neural Networks, 2021

2020
Metabolic Forest: Predicting the Diverse Structures of Drug Metabolites.
J. Chem. Inf. Model., 2020

XenoNet: Inference and Likelihood of Intermediate Metabolite Formation.
J. Chem. Inf. Model., 2020

The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five Colors.
J. Chem. Inf. Model., 2020

2019
Deep learning long-range information in undirected graphs with wave networks.
Proceedings of the International Joint Conference on Neural Networks, 2019

2018
Deep Learning Global Glomerulosclerosis in Transplant Kidney Frozen Sections.
IEEE Trans. Medical Imaging, 2018

Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive Compounds.
J. Chem. Inf. Model., 2018

The diversity and disparity in biomedical informatics (DDBI) workshop.
Proceedings of the Biocomputing 2018: Proceedings of the Pacific Symposium, 2018

2017
BEESEM: estimation of binding energy models using HT-SELEX data.
Bioinform., 2017

2016
A simple model predicts UGT-mediated metabolism.
Bioinform., 2016

A survey of current trends in computational drug repositioning.
Briefings Bioinform., 2016

2015
Improved Prediction of CYP-Mediated Metabolism with Chemical Fingerprints.
J. Chem. Inf. Model., 2015

Accurate and efficient target prediction using a potency-sensitive influence-relevance voter.
J. Cheminformatics, 2015

Extending P450 site-of-metabolism models with region-resolution data.
Bioinform., 2015

XenoSite server: a web-available site of metabolism prediction tool.
Bioinform., 2015

Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data.
Bioinform., 2015

2014
Sharing Chemical Relationships Does Not Reveal Structures.
J. Chem. Inf. Model., 2014

Bigger data, collaborative tools and the future of predictive drug discovery.
J. Comput. Aided Mol. Des., 2014

Session Introduction.
Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

2013
XenoSite: Accurately Predicting CYP-Mediated Sites of Metabolism with Neural Networks.
J. Chem. Inf. Model., 2013

Managing missing measurements in small-molecule screens.
J. Comput. Aided Mol. Des., 2013

RS-WebPredictor: a server for predicting CYP-mediated sites of metabolism on drug-like molecules.
Bioinform., 2013

Scaffold network generator: a tool for mining molecular structures.
Bioinform., 2013

Accounting for noise when clustering biological data.
Briefings Bioinform., 2013

2012
Utility-Aware Screening with Clique-Oriented Prioritization.
J. Chem. Inf. Model., 2012

2011
Enhancing the rate of scaffold discovery with diversity-oriented prioritization.
Bioinform., 2011

Mining small-molecule screens to repurpose drugs.
Briefings Bioinform., 2011

2010
A CROC stronger than ROC: measuring, visualizing and optimizing early retrieval.
Bioinform., 2010

Bridging the Gap Between Neural Network and Kernel Methods: Applications to Drug Discovery.
Proceedings of the Neural Nets WIRN10, 2010

2009
Influence Relevance Voting: An Accurate And Interpretable Virtual High Throughput Screening Method.
J. Chem. Inf. Model., 2009

Large scale study of multiple-molecule queries.
J. Cheminformatics, 2009

2008
Discovery of Power-Laws in Chemical Space.
J. Chem. Inf. Model., 2008

2007
Mathematical Correction for Fingerprint Similarity Measures to Improve Chemical Retrieval.
J. Chem. Inf. Model., 2007

Bounds and Algorithms for Fast Exact Searches of Chemical Fingerprints in Linear and Sublinear Time.
J. Chem. Inf. Model., 2007

Lossless Compression of Chemical Fingerprints Using Integer Entropy Codes Improves Storage and Retrieval.
J. Chem. Inf. Model., 2007

One- to Four-Dimensional Kernels for Virtual Screening and the Prediction of Physical, Chemical, and Biological Properties.
J. Chem. Inf. Model., 2007

ChemDB update - full-text search and virtual chemical space.
Bioinform., 2007

2006
Functional Census of Mutation Sequence Spaces: The Example of p53 Cancer Rescue Mutants.
IEEE ACM Trans. Comput. Biol. Bioinform., 2006

2005
Graph kernels for chemical informatics.
Neural Networks, 2005

ChemDB: a public database of small molecules and related chemoinformatics resources.
Bioinform., 2005

Statistical Distribution of Chemical Fingerprints.
Proceedings of the Fuzzy Logic and Applications, 6th International Workshop, 2005

Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity.
Proceedings of the Proceedings Thirteenth International Conference on Intelligent Systems for Molecular Biology 2005, 2005


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