Improved sensitivity of profile searches through the use of sequence weights and gap excision. - Julie Dawn Thompson; Desmond G. Higgins; Toby J. Gibson (Comput. Appl. Biosci., 1994)

Detection of dsRNA-binding domains in RNA helicase A and Drosophila maleless: implications for monomeric RNA helicases. - Toby J. Gibson; Julie Dawn Thompson (Nucleic Acids Res., 1994)

Introducing variable gap penalties to sequence alignment in linear space. - Julie Dawn Thompson (Comput. Appl. Biosci., 1995)

BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs. - Julie Dawn Thompson; Frédéric Plewniak; Olivier Poch (Bioinform., 1999)

A comprehensive comparison of multiple sequence alignment programs. - Julie Dawn Thompson; Frédéric Plewniak; Olivier Poch (Nucleic Acids Res., 1999)

Ballast: Blast post-processing based on locally conserved segments. - Frédéric Plewniak; Julie Dawn Thompson; Olivier Poch (Bioinform., 2000)

BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations. - Anne Bahr; Julie Dawn Thompson; Jean-Claude Thierry; Olivier Poch (Nucleic Acids Res., 2001)

RASCAL: Rapid Scanning and Correction of Multiple Sequence Alignments. - Julie Dawn Thompson; Jean-Claude Thierry; Olivier Poch (Bioinform., 2003)

Multiple sequence alignment with the Clustal series of programs. - Chenna Ramu; Hideaki Sugawara; Tadashi Koike; Rodrigo Lopez; Toby J. Gibson; Desmond G. Higgins; Julie Dawn Thompson (Nucleic Acids Res., 2003)

PipeAlign: a new toolkit for protein family analysis. - Frédéric Plewniak; Laurent Bianchetti; Yann Brelivet; Annaick Carles; Frédéric Chalmel; Odile Lecompte; Thiebaut Mochel; Luc Moulinier; Arnaud Muller; Jean Muller; Veronique Prigent; Raymond Ripp; et al. (Nucleic Acids Res., 2003)

GOAnno: GO annotation based on multiple alignment. - Frédéric Chalmel; Aurélie Lardenois; Julie Dawn Thompson; Jean Muller; José-Alain Sahel; Thierry Léveillard; Olivier Poch (Bioinform., 2005)

Valid: Validation of Protein Sequence Quality Based on Multiple Alignment Data. - Laurent Bianchetti; Julie Dawn Thompson; Odile Lecompte; Frédéric Plewniak; Olivier Poch (J. Bioinform. Comput. Biol., 2005)

MAGOS: multiple alignment and modelling server. - Nicolas B. Garnier; Anne Friedrich; Raphael Bolze; Emmanuel Bettler; Luc Moulinier; Christophe Geourjon; Julie Dawn Thompson; Gilbert Deléage; Olivier Poch (Bioinform., 2006)

MACSIMS : multiple alignment of complete sequences information management system. - Julie Dawn Thompson; Arnaud Muller; Andrew M. Waterhouse; James B. Procter; Geoffrey J. Barton; Frédéric Plewniak; Olivier Poch (BMC Bioinform., 2006)

Clustal W and Clustal X version 2.0. - Mark A. Larkin; Gordon Blackshields; Nigel P. Brown; R. Chenna; Paul A. McGettigan; Hamish McWilliam; Franck Valentin; Iain M. Wallace; Andreas Wilm; Rodrigo Lopez; Julie Dawn Thompson; Toby J. Gibson; et al. (Bioinform., 2007)

A new protein linear motif benchmark for multiple sequence alignment software. - Emmanuel Perrodou; Claudia Chica; Olivier Poch; Toby J. Gibson; Julie Dawn Thompson (BMC Bioinform., 2008)

Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis. - Mohamed Radhouene Aniba; Sophie Siguenza; Anne Friedrich; Frédéric Plewniak; Olivier Poch; Aron Marchler-Bauer; Julie Dawn Thompson (Briefings Bioinform., 2009)

PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees. - Philippe Gouret; Julie Dawn Thompson; Pierre Pontarotti (BMC Bioinform., 2009)

Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods. - Valentín Ruano-Rubio; Olivier Poch; Julie Dawn Thompson (BMC Bioinform., 2009)

AQUA: automated quality improvement for multiple sequence alignments. - Jean Muller; Christopher J. Creevey; Julie Dawn Thompson; Detlev Arendt; Peer Bork (Bioinform., 2010)

OrthoInspector: comprehensive orthology analysis and visual exploration. - Benjamin Linard; Julie Dawn Thompson; Olivier Poch; Odile Lecompte (BMC Bioinform., 2011)

Identifying Single Copy Orthologs in Metazoa. - Christopher J. Creevey; Jean Muller; Tobias Doerks; Julie Dawn Thompson; Detlev Arendt; Peer Bork (PLoS Comput. Biol., 2011)

MSV3d: database of human MisSense variants mapped to 3D protein structure. - Tien-Dao Luu; Alin-Mihai Rusu; Vincent Walter; Raymond Ripp; Luc Moulinier; Jean Muller; Thierry Toursel; Julie Dawn Thompson; Olivier Poch; Hoan Nguyen (Database J. Biol. Databases Curation, 2012)

KD4v: comprehensible knowledge discovery system for missense variant. - Tien-Dao Luu; Alin Rusu; Vincent Walter; Benjamin Linard; Laetitia Poidevin; Raymond Ripp; Luc Moulinier; Jean Muller; Wolfgang Raffelsberger; Nicolas Wicker; Odile Lecompte; Julie Dawn Thompson; et al. (Nucleic Acids Res., 2012)

Classification multi-étiquettes pour l'alignement multiple de séquences protéiques. - Lina Fahed; Gabriel Frey; Julie Dawn Thompson; Nicolas Lachiche (EGC, 2013)

SIBIS: a Bayesian model for inconsistent protein sequence estimation. - Walyd Khenoussi; Renaud Vanhoutrève; Olivier Poch; Julie Dawn Thompson (Bioinform., 2014)

A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i). - Carlos Bermejo-Das-Neves; Hoan-Ngoc Nguyen; Olivier Poch; Julie Dawn Thompson (BMC Bioinform., 2014)

Heterogeneous biological data integration with declarative query language. - Hoan Nguyen; Laurent Michel; Julie Dawn Thompson; Olivier Poch (IBM J. Res. Dev., 2014)

Intelligent Integrative Knowledge Bases: Bridging Genomics, Integrative Biology and Translational Medicine. - Hoan Nguyen; Julie Dawn Thompson; Patrick Schutz; Olivier Poch (Interactive Knowledge Discovery and Data Mining in Biomedical Informatics, 2014)

OrthoInspector 2.0: Software and database updates. - Benjamin Linard; Alexis Allot; Raphael Schneider; Can Morel; Raymond Ripp; Marc Bigler; Julie Dawn Thompson; Olivier Poch; Odile Lecompte (Bioinform., 2015)

LEON-BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system. - Renaud Vanhoutrève; Arnaud Kress; Baptiste Legrand; Hélène Gass; Olivier Poch; Julie Dawn Thompson (BMC Bioinform., 2016)

MEMSA: A Robust Parisian EA for Multidimensional Multiple Sequence Alignment. - Julie Dawn Thompson; Renaud Vanhoutrève; Pierre Collet (Artificial Evolution, 2017)

PROBE: analysis and visualization of protein block-level evolution. - Arnaud Kress; Odile Lecompte; Olivier Poch; Julie Dawn Thompson (Bioinform., 2018)

Evolutionary conservation and functional implications of circular code motifs in eukaryotic genomes. - Gopal Dila; Christian J. Michel; Olivier Poch; Raymond Ripp; Julie Dawn Thompson (Biosyst., 2019)

OrthoInspector 3.0: open portal for comparative genomics. - Yannis Nevers; Arnaud Kress; Audrey Defosset; Raymond Ripp; Benjamin Linard; Julie Dawn Thompson; Olivier Poch; Odile Lecompte (Nucleic Acids Res., 2019)

BNO - An ontology for understanding the transittability of complex biomolecular networks. - Ali Ayadi; Cecilia Zanni-Merk; François de Bertrand de Beuvron; Julie Dawn Thompson; Saoussen Krichen (J. Web Semant., 2019)

Optimality of circular codes versus the genetic code after frameshift errors. - Gopal Dila; Christian J. Michel; Julie Dawn Thompson (Biosyst., 2020)

Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes. - Corentin Meyer; Nicolas Scalzitti; Anne Jeannin-Girardon; Pierre Collet; Olivier Poch; Julie Dawn Thompson (BMC Bioinform., 2020)

Potential role of the X circular code in the regulation of gene expression. - Julie Dawn Thompson; Raymond Ripp; Claudine Mayer; Olivier Poch; Christian J. Michel (Biosyst., 2021)

Spliceator: multi-species splice site prediction using convolutional neural networks. - Nicolas Scalzitti; Arnaud Kress; Romain Orhand; Thomas Weber; Luc Moulinier; Anne Jeannin-Girardon; Pierre Collet; Olivier Poch; Julie Dawn Thompson (BMC Bioinform., 2021)

Apprentissage automatique basé sur l'agrégation pour la prédiction de liens dans les réseaux d'interactions protéine-protéine. - Hajer Akid; Kirsley Chennen; Gabriel Frey; Julie Dawn Thompson; Mounir Ben Ayed; Nicolas Lachiche (EGC, 2022)

MERLIN: Identifying Inaccuracies in Multiple Sequence Alignments Using Object Detection. - Hiba Khodji; Lucille Herbay; Pierre Collet; Julie Dawn Thompson; Anne Jeannin-Girardon (AIAI (1), 2022)

Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events. - Arnaud Kress; Olivier Poch; Odile Lecompte; Julie Dawn Thompson (Frontiers Bioinform., 2023)

De-MISTED: Image-based classification of erroneous multiple sequence alignments using convolutional neural networks. - Hiba Khodji; Pierre Collet; Julie Dawn Thompson; Anne Jeannin-Girardon (Appl. Intell., 2023)

StopKB: a comprehensive knowledgebase for nonsense suppression therapies. - Nicolas Haas; Julie Dawn Thompson; Jean-Paul Renaud; Kirsley Chennen; Olivier Poch (Database J. Biol. Databases Curation, 2024)

Graph-based machine learning model for weight prediction in protein-protein networks. - Hajer Akid; Kirsley Chennen; Gabriel Frey; Julie Dawn Thompson; Mounir Ben Ayed; Nicolas Lachiche (BMC Bioinform., 2024)