The ERPIN server: an interface to profile-based RNA motif identification. - André Lambert; Jean-Fred Fontaine; Matthieu Legendre; Fabrice Leclerc; Emmanuelle Permal; François Major; Harald Putzer; Olivier Delfour; Bernard Michot; Daniel Gautheret (Nucleic Acids Res., 2004)

Computing expectation values for RNA motifs using discrete convolutions. - André Lambert; Matthieu Legendre; Jean-Fred Fontaine; Daniel Gautheret (BMC Bioinform., 2005)

MedlineRanker: flexible ranking of biomedical literature. - Jean-Fred Fontaine; Adriano Barbosa-Silva; Martin H. Schaefer 001; Matthew R. Huska; Enrique M. Muro; Miguel A. Andrade-Navarro (Nucleic Acids Res., 2009)

LAITOR - Literature Assistant for Identification of Terms co-Occurrences and Relationships. - Adriano Barbosa-Silva; Theodoros G. Soldatos; Ivan L. F. Magalhães; Georgios A. Pavlopoulos; Jean-Fred Fontaine; Miguel A. Andrade-Navarro; Reinhard Schneider 002; José Miguel Ortega (BMC Bioinform., 2010)

Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases. - Tiago J. S. Lopes; Martin H. Schaefer 001; Jason E. Shoemaker; Yukiko Matsuoka; Jean-Fred Fontaine; Gabriele Neumann; Miguel A. Andrade-Navarro; Yoshihiro Kawaoka; Hiroaki Kitano (Bioinform., 2011)

PESCADOR, a web-based tool to assist text-mining of biointeractions extracted from PubMed queries. - Adriano Barbosa-Silva; Jean-Fred Fontaine; Elisa R. Donnard; Fernanda Stussi; José Miguel Ortega; Miguel A. Andrade-Navarro (BMC Bioinform., 2011)

Génie: literature-based gene prioritization at multi genomic scale. - Jean-Fred Fontaine; Florian Priller; Adriano Barbosa-Silva; Miguel A. Andrade-Navarro (Nucleic Acids Res., 2011)

Preliminary evaluation of the CellFinder literature curation pipeline for gene expression in kidney cells and anatomical parts. - Mariana L. Neves; Alexander Damaschun; Nancy Mah; Fritz Lekschas; Stefanie Seltmann; Harald Stachelscheid; Jean-Fred Fontaine; Andreas Kurtz 003; Ulf Leser (Database J. Biol. Databases Curation, 2013)

Using cited references to improve the retrieval of related biomedical documents. - Francisco M. Ortuño Guzman; Ignacio Rojas; Miguel A. Andrade-Navarro; Jean-Fred Fontaine (BMC Bioinform., 2013)

CELDA - an ontology for the comprehensive representation of cells in complex systems. - Stefanie Seltmann; Harald Stachelscheid; Alexander Damaschun; Ludger Jansen; Fritz Lekschas; Jean-Fred Fontaine; Throng-Nghia Nguyen-Dobinsky; Ulf Leser; Andreas Kurtz 003 (BMC Bioinform., 2013)

Adding Protein Context to the Human Protein-Protein Interaction Network to Reveal Meaningful Interactions. - Martin H. Schaefer 001; Tiago J. S. Lopes; Nancy Mah; Jason E. Shoemaker; Yukiko Matsuoka; Jean-Fred Fontaine; Caroline Louis-Jeune; Amie J. Eisfeld; Gabriele Neumann; Carol Perez-Iratxeta; Yoshihiro Kawaoka; Hiroaki Kitano; et al. (PLoS Comput. Biol., 2013)

Alkemio: association of chemicals with biomedical topics by text and data mining. - José A. Gijón-Correas; Miguel A. Andrade-Navarro; Jean-Fred Fontaine (Nucleic Acids Res., 2014)

CellFinder: a cell data repository. - Harald Stachelscheid; Stefanie Seltmann; Fritz Lekschas; Jean-Fred Fontaine; Nancy Mah; Mariana L. Neves; Miguel A. Andrade-Navarro; Ulf Leser; Andreas Kurtz 003 (Nucleic Acids Res., 2014)

Disease-Genes Must Guide Data Source Integration in the Gene Prioritization Process. - Marco Frasca 001; Jean-Fred Fontaine; Giorgio Valentini; Marco Mesiti; Marco Notaro; Dario Malchiodi; Miguel A. Andrade-Navarro (CIBB, 2017)

Lost Strings in Genomes: What Sense Do They Make? - Michael G. Sadovsky; Jean-Fred Fontaine; Miguel A. Andrade-Navarro; Yury Yakubailik; Natalia Rudenko (IWBBIO (2), 2017)

LipiDisease: associate lipids to diseases using literature mining. - Piyush More; Laura Bindila; Philipp Wild; Miguel A. Andrade-Navarro; Jean-Fred Fontaine (Bioinform., 2021)

Batch effect detection and correction in RNA-seq data using machine-learning-based automated assessment of quality. - Maximilian Sprang; Miguel A. Andrade-Navarro; Jean-Fred Fontaine (BMC Bioinform., 2022)