2D Structure Depiction. - Alex M. Clark; Paul Labute; Martin Santavy (J. Chem. Inf. Model., 2006)

2D Depiction of Protein-Ligand Complexes. - Alex M. Clark; Paul Labute (J. Chem. Inf. Model., 2007)

Basic primitives for molecular diagram sketching. - Alex M. Clark (J. Cheminformatics, 2010)

2D Depiction of Fragment Hierarchies. - Alex M. Clark (J. Chem. Inf. Model., 2010)

Accurate Specification of Molecular Structures: The Case for Zero-Order Bonds and Explicit Hydrogen Counting. - Alex M. Clark (J. Chem. Inf. Model., 2011)

TB mobile: a mobile app for anti-tuberculosis molecules with known targets. - Sean Ekins; Alex M. Clark; Malabika Sarker (J. Cheminformatics, 2013)

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)

New target prediction and visualization tools incorporating open source molecular fingerprints for TB Mobile 2.0. - Alex M. Clark; Malabika Sarker; Sean Ekins (J. Cheminformatics, 2014)

Looking Back to the Future: Predicting in Vivo Efficacy of Small Molecules versus Mycobacterium tuberculosis. - Sean Ekins; Richard Pottorf; Robert C. Reynolds; Antony J. Williams; Alex M. Clark; Joel S. Freundlich (J. Chem. Inf. Model., 2014)

Machine learning models identify molecules active against the Ebola virus in vitro. - Sean Ekins; Joel S. Freundlich; Alex M. Clark; Manu Anantpadma; Robert A. Davey; Peter B. Madrid (F1000Research, 2015)

Machines first, humans second: on the importance of algorithmic interpretation of open chemistry data. - Alex M. Clark; Antony J. Williams; Sean Ekins (J. Cheminformatics, 2015)

Open Source Bayesian Models. 1. Application to ADME/Tox and Drug Discovery Datasets. - Alex M. Clark; Krishna Dole; Anna Coulon-Spektor; Andrew M. McNutt; George Grass; Joel S. Freundlich; Robert C. Reynolds; Sean Ekins (J. Chem. Inf. Model., 2015)

Open Source Bayesian Models. 2. Mining a "Big Dataset" To Create and Validate Models with ChEMBL. - Alex M. Clark; Sean Ekins (J. Chem. Inf. Model., 2015)

Open Source Bayesian Models. 3. Composite Models for Prediction of Binned Responses. - Alex M. Clark; Krishna Dole; Sean Ekins (J. Chem. Inf. Model., 2016)

Machine Learning Model Analysis and Data Visualization with Small Molecules Tested in a Mouse Model of Mycobacterium tuberculosis Infection (2014-2015). - Sean Ekins; Alexander L. Perryman; Alex M. Clark; Robert C. Reynolds; Joel S. Freundlich (J. Chem. Inf. Model., 2016)

BioAssay templates for the semantic web. - Alex M. Clark; Nadia K. Litterman; Janice E. Kranz; Peter Gund; Kellan Gregory; Barry A. Bunin (PeerJ Prepr., 2016)

Capturing mixture composition: an open machine-readable format for representing mixed substances. - Alex M. Clark; Leah McEwen; Peter Gedeck; Barry A. Bunin (J. Cheminformatics, 2019)