Quality Assessment of Peptide Tandem Mass Spectra. - Fang-Xiang Wu; Pierre Gagné; Arnaud Droit; Guy G. Poirier (IMSCCS (1), 2006)

PARPs database: A LIMS systems for protein-protein interaction data mining or laboratory information management system. - Arnaud Droit; Joanna M. Hunter; Michèle Rouleau; Chantal Ethier; Aude Picard-Cloutier; David Bourgais; Guy G. Poirier (BMC Bioinform., 2007)

rMAT - an R/Bioconductor package for analyzing ChIP-chip experiments. - Arnaud Droit; Charles Cheung; Raphael Gottardo (Bioinform., 2010)

NGS++: a library for rapid prototyping of epigenomics software tools. - Alexei Nordell-Markovits; Charles Joly Beauparlant; Dominique Toupin; Shengrui Wang; Arnaud Droit; Nicolas Gevry (Bioinform., 2013)

Bio2RDF Release 3: A larger, more connected network of Linked Data for the Life Sciences. - Michel Dumontier; Alison Callahan; Jose Cruz-Toledo; Peter Ansell; Vincent Emonet; François Belleau; Arnaud Droit (ISWC (Posters & Demos), 2014)

rTANDEM, an R/Bioconductor package for MS/MS protein identification. - Frédéric Fournier; Charles Joly Beauparlant; René Paradis; Arnaud Droit (Bioinform., 2014)

metagene Profiles Analyses Reveal Regulatory Element's Factor-Specific Recruitment Patterns. - Charles Joly Beauparlant; Fabien C. Lamaze; Astrid Deschênes; Rawane Samb; Audrey Lemaçon; Pascal Belleau; Steve Bilodeau; Arnaud Droit (PLoS Comput. Biol., 2016)

VEXOR: an integrative environment for prioritization of functional variants in fine-mapping analysis. - Audrey Lemaçon; Charles Joly Beauparlant; Penny Soucy; Jamie Allen; Douglas F. Easton; Peter Kraft; Jacques Simard; Arnaud Droit (Bioinform., 2017)

KibioR & Kibio: a new architecture for next-generation data querying and sharing in big biology. - Régis Ongaro-Carcy; Marie-Pier Scott-Boyer; Adrien Dessemond; François Belleau; Mickaël Leclercq; Olivier Périn; Arnaud Droit (Bioinform., 2021)

GWENA: gene co-expression networks analysis and extended modules characterization in a single Bioconductor package. - Gwenaëlle G. Lemoine; Marie-Pier Scott-Boyer; Bathilde Ambroise; Olivier Périn; Arnaud Droit (BMC Bioinform., 2021)

eTumorMetastasis: A Network-based Algorithm Predicts Clinical Outcomes Using Whole-exome Sequencing Data of Cancer Patients. - Jean-Sébastien Milanese; Chabane Tibiche; Naif Zaman; Jinfeng Zou; Pengyong Han; Zhigang Meng; André Nantel; Arnaud Droit; Edwin Wang (Genom. Proteom. Bioinform., 2021)

Generalised Mutual Information for Discriminative Clustering. - Louis Ohl; Pierre-Alexandre Mattei; Charles Bouveyron; Warith Harchaoui; Mickaël Leclercq; Arnaud Droit; Frédéric Precioso (NeurIPS, 2022)

timeOmics: an R package for longitudinal multi-omics data integration. - Antoine Bodein; Marie-Pier Scott-Boyer; Olivier Périn; Kim-Anh Lê Cao; Arnaud Droit (Bioinform., 2022)

Sparse GEMINI for Joint Discriminative Clustering and Feature Selection. - Louis Ohl; Pierre-Alexandre Mattei; Charles Bouveyron; Mickaël Leclercq; Arnaud Droit; Frédéric Precioso (CoRR, 2023)

Generalised Mutual Information: a Framework for Discriminative Clustering. - Louis Ohl; Pierre-Alexandre Mattei; Charles Bouveyron; Warith Harchaoui; Mickaël Leclercq; Arnaud Droit; Frédéric Precioso (CoRR, 2023)

Use of Elasticsearch-based business intelligence tools for integration and visualization of biological data. - Marie-Pier Scott-Boyer; Pascal Dufour; François Belleau; Régis Ongaro-Carcy; Clément Plessis; Olivier Périn; Arnaud Droit (Briefings Bioinform., 2023)

Kernel KMeans clustering splits for end-to-end unsupervised decision trees. - Louis Ohl; Pierre-Alexandre Mattei; Mickaël Leclercq; Arnaud Droit; Frédéric Precioso (CoRR, 2024)

Sparse and geometry-aware generalisation of the mutual information for joint discriminative clustering and feature selection. - Louis Ohl; Pierre-Alexandre Mattei; Charles Bouveyron; Mickaël Leclercq; Arnaud Droit; Frédéric Precioso (Stat. Comput., 2024)

Improving drug repositioning with negative data labeling using large language models. - Milan Picard; Mickaël Leclercq; Antoine Bodein; Marie-Pier Scott-Boyer; Olivier Périn; Arnaud Droit (J. Cheminformatics, 2025)