PAR: a PARallel and distributed job crusher. - Francois Berenger; Camille Coti; Kam Y. J. Zhang (Bioinform., 2010)

Entropy-accelerated exact clustering of protein decoys. - Francois Berenger; Yong Zhou; Rojan Shrestha; Kam Y. J. Zhang (Bioinform., 2011)

Durandal: Fast exact clustering of protein decoys. - Francois Berenger; Rojan Shrestha; Yong Zhou; David Simoncini; Kam Y. J. Zhang (J. Comput. Chem., 2012)

Combining in silico and in cerebro approaches for virtual screening and pose prediction in SAMPL4. - Arnout R. D. Voet; Ashutosh Kumar 001; Francois Berenger; Kam Y. J. Zhang (J. Comput. Aided Mol. Des., 2014)

A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening. - Francois Berenger; Arnout R. D. Voet; Xiao Yin Lee; Kam Y. J. Zhang (J. Cheminformatics, 2014)

Semantic-directed clumping of disjunctive abstract states. - Huisong Li; Francois Berenger; Bor-Yuh Evan Chang; Xavier Rival (POPL, 2017)

Fragger: a protein fragment picker for structural queries. - Francois Berenger; David Simoncini; Arnout R. D. Voet; Rojan Shrestha; Kam Y. J. Zhang (F1000Research, 2017)

Consensus queries in ligand-based virtual screening experiments. - Francois Berenger; Oanh Vu; Jens Meiler (J. Cheminformatics, 2017)

Predicting drug-induced transcriptome responses of a wide range of human cell lines by a novel tensor-train decomposition algorithm. - Michio Iwata; Longhao Yuan; Qibin Zhao; Yasuo Tabei; Francois Berenger; Ryusuke Sawada; Sayaka Akiyoshi; Momoko Hamano; Yoshihiro Yamanishi (Bioinform., 2019)

Chemoinformatics and structural bioinformatics in OCaml. - Francois Berenger; Kam Y. J. Zhang; Yoshihiro Yamanishi (J. Cheminformatics, 2019)

A Distance-Based Boolean Applicability Domain for Classification of High Throughput Screening Data. - Francois Berenger; Yoshihiro Yamanishi (J. Chem. Inf. Model., 2019)

Ranking Molecules with Vanishing Kernels and a Single Parameter: Active Applicability Domain Included. - Francois Berenger; Yoshihiro Yamanishi (J. Chem. Inf. Model., 2020)

Molecular generation by Fast Assembly of (Deep)SMILES fragments. - Francois Berenger; Koji Tsuda (J. Cheminformatics, 2021)

Lean-Docking: Exploiting Ligands' Predicted Docking Scores to Accelerate Molecular Docking. - Francois Berenger; Ashutosh Kumar 001; Kam Y. J. Zhang; Yoshihiro Yamanishi (J. Chem. Inf. Model., 2021)

3D-Sensitive Encoding of Pharmacophore Features. - Francois Berenger; Koji Tsuda (J. Chem. Inf. Model., 2023)

CACHE Challenge #1: Targeting the WDR Domain of LRRK2, A Parkinson's Disease Associated Protein. - Fengling Li; Suzanne Ackloo; Cheryl H. Arrowsmith; Fuqiang Ban; Christopher J. Barden; Hartmut Beck; Jan Beránek; Francois Berenger; Albina Bolotokova; Guillaume Bret; Marko Breznik; Emanuele Carosati; et al. (J. Chem. Inf. Model., 2024)

An ANI-2 enabled open-source protocol to estimate ligand strain after docking. - Francois Berenger; Koji Tsuda (J. Comput. Chem., 2025)