CYCLONET - an integrated database on cell cycle regulation and carcinogenesis. - Fedor A. Kolpakov; Vladimir Poroikov; Ruslan N. Sharipov; Yury V. Kondrakhin; Alexey V. Zakharov; Alexey Lagunin; Luciano Milanesi; Alexander E. Kel (Nucleic Acids Res., 2007)

Functional classification of proteins based on projection of amino acid sequences: application for prediction of protein kinase substrates. - Boris Sobolev; Dmitry Filimonov; Alexey Lagunin; Alexey V. Zakharov; Olga Koborova; Alexander E. Kel; Vladimir Poroikov (BMC Bioinform., 2010)

Collaborative development of predictive toxicology applications. - Barry J. Hardy; Nicki Douglas; Christoph Helma; Micha Rautenberg; Nina Jeliazkova; Vedrin Jeliazkov; Ivelina Nikolova; Romualdo Benigni; Olga Tcheremenskaia; Stefan Kramer 001; Tobias Girschick; Fabian Buchwald; et al. (J. Cheminformatics, 2010)

Static analysis method for deadlock detection in SystemC designs. - Mikhail J. Moiseev; Alexey V. Zakharov; Ilya Klotchkov; Sergey I. Salishev (SoC, 2011)

Automatic data race detection in SystemC models. - Alexey V. Zakharov; Mikhail J. Moiseev (Autom. Control. Comput. Sci., 2012)

A static analysis approach to data race detection in SystemC designs. - Mikhail J. Moiseev; Mikhail Glukhikh; Alexey V. Zakharov; Harald Richter 001 (DDECS, 2013)

QSAR Modeling of Imbalanced High-Throughput Screening Data in PubChem. - Alexey V. Zakharov; Megan L. Peach; Markus Sitzmann; Marc C. Nicklaus (J. Chem. Inf. Model., 2014)

A New Approach to Radial Basis Function Approximation and Its Application to QSAR. - Alexey V. Zakharov; Megan L. Peach; Markus Sitzmann; Marc C. Nicklaus (J. Chem. Inf. Model., 2014)

QSAR Modeling Using Large-Scale Databases: Case Study for HIV-1 Reverse Transcriptase Inhibitors. - Olga A. Tarasova; Aleksandra F. Urusova; Dmitry Filimonov; Marc C. Nicklaus; Alexey V. Zakharov; Vladimir Poroikov (J. Chem. Inf. Model., 2015)

Rational Use of Heterogeneous Data in Quantitative Structure-Activity Relationship (QSAR) Modeling of Cyclooxygenase/Lipoxygenase Inhibitors. - Alexey Lagunin; Athina Geronikaki; Phaedra Eleftheriou; Pavel V. Pogodin; Alexey V. Zakharov (J. Chem. Inf. Model., 2019)

Novel Consensus Architecture To Improve Performance of Large-Scale Multitask Deep Learning QSAR Models. - Alexey V. Zakharov; Tongan Zhao; Dac-Trung Nguyen; Tyler Peryea; Timothy Sheils; Adam Yasgar; Ruili Huang; Noel Southall; Anton Simeonov (J. Chem. Inf. Model., 2019)

Predicting liver cytosol stability of small molecules. - Pranav Shah; Vishal B. Siramshetty; Alexey V. Zakharov; Noel Southall; Xin Xu; Dac-Trung Nguyen (J. Cheminformatics, 2020)

SCAM Detective: Accurate Predictor of Small, Colloidally Aggregating Molecules. - Vinicius M. Alves; Stephen J. Capuzzi; Rodolpho C. Braga; Daniel Robert Korn; Joshua E. Hochuli; Kyle H. Bowler; Adam Yasgar; Ganesha Rai; Anton Simeonov; Eugene N. Muratov; Alexey V. Zakharov; Alexander Tropsha (J. Chem. Inf. Model., 2020)

Critical Assessment of Artificial Intelligence Methods for Prediction of hERG Channel Inhibition in the "Big Data" Era. - Vishal B. Siramshetty; Dac-Trung Nguyen; Natalia J. Martinez; Noel Southall; Anton Simeonov; Alexey V. Zakharov (J. Chem. Inf. Model., 2020)

Large-Scale Modeling of Multispecies Acute Toxicity End Points Using Consensus of Multitask Deep Learning Methods. - Sankalp Jain; Vishal B. Siramshetty; Vinicius M. Alves; Eugene N. Muratov; Nicole C. Kleinstreuer; Alexander Tropsha; Marc C. Nicklaus; Anton Simeonov; Alexey V. Zakharov (J. Chem. Inf. Model., 2021)

Deep learning identifies synergistic drug combinations for treating COVID-19. - Wengong Jin; Jonathan M. Stokes; Richard T. Eastman; Zina Itkin; Alexey V. Zakharov; James J. Collins; Tommi S. Jaakkola; Regina Barzilay (Proc. Natl. Acad. Sci. USA, 2021)

Applications of Machine Learning Approaches for the Discovery of SARS-CoV-2 PLpro Inhibitors. - Sourav Pal; Kellie D. Nance; Dirgha Raj Joshi; Stephen C. Kales; Lin Ye; Xin Hu; Khalida Shamim; Alexey V. Zakharov (J. Chem. Inf. Model., 2025)

One size does not fit all: revising traditional paradigms for assessing accuracy of QSAR models used for virtual screening. - James Wellnitz; Sankalp Jain; Joshua E. Hochuli; Travis Maxfield; Eugene N. Muratov; Alexander Tropsha; Alexey V. Zakharov (J. Cheminformatics, 2025)