List of works - S. Joshua Swamidass

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

scientific article

A Time-Embedding Network Models the Ontogeny of 23 Hepatic Drug Metabolizing Enzymes

scientific article published on 29 July 2019

A simple model predicts UGT-mediated metabolism.

scientific article published on 20 June 2016

An economic framework to prioritize confirmatory tests after a high-throughput screen.

scientific article published on 14 June 2010

Automatically detecting workflows in PubChem.

scientific article

Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear time.

scientific article published on 28 February 2007

CYP2C19 and 3A4 Dominate Metabolic Clearance and Bioactivation of Terbinafine Based on Computational and Experimental Approaches

scientific article published on 10 April 2019

ChemDB update--full-text search and virtual chemical space.

scientific article

Combined Analysis of Phenotypic and Target-Based Screening in Assay Networks.

scientific article

Computational Approach to Structural Alerts: Furans, Phenols, Nitroaromatics, and Thiophenes.

scientific article published on 3 March 2017

Computationally Assessing the Bioactivation of Drugs by N-Dealkylation.

scientific article

Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets

scientific article published on 21 May 2021

Discovery of power-laws in chemical space.

scientific article

Drug repositioning from the combined evaluation of phenotypic and target-based screening.

scientific article

Education: Initiatives to bridge faith and science.

scientific article published in July 2015

Enhancing the rate of scaffold discovery with diversity-oriented prioritization ⬇️

scientific article published on June 17, 2011

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

scientific article

Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants.

scientific article published on April 2006

Improved Prediction of CYP-Mediated Metabolism with Chemical Fingerprints.

scientific article

Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity

scientific article published on 12 August 2016

Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity.

scientific article

Large scale study of multiple-molecule queries

scientific article (publication date: 4 June 2009)

Managing missing measurements in small-molecule screens.

scientific article

Mining small-molecule screens to repurpose drugs.

scientific article published on 29 June 2011

Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network.

scientific article published on 9 June 2015

Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive Compounds

scientific article published on 23 July 2018

One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties.

scientific article

Opportunities and obstacles for deep learning in biology and medicine.

scientific article published in April 2018

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

scientific article published on 14 December 2012

Scaffold network generator: a tool for mining molecular structures.

scientific article

Securely measuring the overlap between private datasets with cryptosets

scientific article

Sharing chemical relationships does not reveal structures

scientific article

Site of reactivity models predict molecular reactivity of diverse chemicals with glutathione.

scientific article

Site-Level Bioactivity of Small-Molecules from Deep-Learned Representations of Quantum Chemistry

scientific article published on 21 October 2020

Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data

scientific article

Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis

scholarly article

The Genealogical Adam and Eve

2019 book by S. Joshua Swamidass

The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five Colors

scientific article published on 24 February 2020

Utility-aware screening with clique-oriented prioritization.

scientific article

XenoSite server: a web-available site of metabolism prediction tool

scientific article

XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networks.

scientific article

List of works by S. Joshua Swamidass

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

A Time-Embedding Network Models the Ontogeny of 23 Hepatic Drug Metabolizing Enzymes

A simple model predicts UGT-mediated metabolism.

An economic framework to prioritize confirmatory tests after a high-throughput screen.

Automatically detecting workflows in PubChem.

Bounds and algorithms for fast exact searches of chemical fingerprints in linear and sublinear time.

CYP2C19 and 3A4 Dominate Metabolic Clearance and Bioactivation of Terbinafine Based on Computational and Experimental Approaches

ChemDB update--full-text search and virtual chemical space.

Combined Analysis of Phenotypic and Target-Based Screening in Assay Networks.

Computational Approach to Structural Alerts: Furans, Phenols, Nitroaromatics, and Thiophenes.

Computationally Assessing the Bioactivation of Drugs by N-Dealkylation.

Deep learning the structural determinants of protein biochemical properties by comparing structural ensembles with DiffNets

Discovery of power-laws in chemical space.

Drug repositioning from the combined evaluation of phenotypic and target-based screening.

Education: Initiatives to bridge faith and science.

Enhancing the rate of scaffold discovery with diversity-oriented prioritization ⬇️

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

Functional census of mutation sequence spaces: the example of p53 cancer rescue mutants.

Improved Prediction of CYP-Mediated Metabolism with Chemical Fingerprints.

Inhibition of DNA Methyltransferases Blocks Mutant Huntingtin-Induced Neurotoxicity

Kernels for small molecules and the prediction of mutagenicity, toxicity and anti-cancer activity.

Large scale study of multiple-molecule queries

Managing missing measurements in small-molecule screens.

Mining small-molecule screens to repurpose drugs.

Modeling Epoxidation of Drug-like Molecules with a Deep Machine Learning Network.

Modeling Small-Molecule Reactivity Identifies Promiscuous Bioactive Compounds

One- to four-dimensional kernels for virtual screening and the prediction of physical, chemical, and biological properties.

Opportunities and obstacles for deep learning in biology and medicine.

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

Scaffold network generator: a tool for mining molecular structures.

Securely measuring the overlap between private datasets with cryptosets

Sharing chemical relationships does not reveal structures

Site of reactivity models predict molecular reactivity of diverse chemicals with glutathione.

Site-Level Bioactivity of Small-Molecules from Deep-Learned Representations of Quantum Chemistry

Statistically identifying tumor suppressors and oncogenes from pan-cancer genome-sequencing data

Structure-based inhibitor design of AccD5, an essential acyl-CoA carboxylase carboxyltransferase domain of Mycobacterium tuberculosis

The Genealogical Adam and Eve

The Metabolic Rainbow: Deep Learning Phase I Metabolism in Five Colors

Utility-aware screening with clique-oriented prioritization.

XenoSite server: a web-available site of metabolism prediction tool

XenoSite: accurately predicting CYP-mediated sites of metabolism with neural networks.