Julie Dawn Thompson

According to our database, Julie Dawn Thompson authored at least 46 papers between 1994 and 2024.

Collaborative distances:

• Dijkstra number of three.
• Erdős number of three.

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., December, 2024

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, January, 2024

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., August, 2023

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., May, 2023

2022

MERLIN: Identifying Inaccuracies in Multiple Sequence Alignments Using Object Detection.

Hiba Khodji, Lucille Herbay, Pierre Collet, Julie Dawn Thompson, Anne Jeannin-Girardon

Proceedings of the Artificial Intelligence Applications and Innovations, 2022

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

Proceedings of the Extraction et Gestion des Connaissances, 2022

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

Potential role of the <i>X</i> circular code in the regulation of gene expression.

Julie Dawn Thompson, Raymond Ripp, Claudine Mayer, Olivier Poch, Christian J. Michel

Biosyst., 2021

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

Optimality of circular codes versus the genetic code after frameshift errors.

Gopal Dila, Christian J. Michel, Julie Dawn Thompson

Biosyst., 2020

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

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

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

2018

PROBE: analysis and visualization of protein block-level evolution.

Arnaud Kress, Odile Lecompte, Olivier Poch, Julie Dawn Thompson

Bioinform., 2018

2017

MEMSA: A Robust Parisian EA for Multidimensional Multiple Sequence Alignment.

Julie Dawn Thompson, Renaud Vanhoutrève, Pierre Collet

Proceedings of the Artificial Evolution, 2017

2016

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

2015

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

2014

Intelligent Integrative Knowledge Bases: Bridging Genomics, Integrative Biology and Translational Medicine.

Hoan Nguyen, Julie Dawn Thompson, Patrick Schutz, Olivier Poch

Proceedings of the Interactive Knowledge Discovery and Data Mining in Biomedical Informatics, 2014

Heterogeneous biological data integration with declarative query language.

Hoan Nguyen, Laurent Michel, Julie Dawn Thompson, Olivier Poch

IBM J. Res. Dev., 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

SIBIS: a Bayesian model for inconsistent protein sequence estimation.

Walyd Khenoussi, Renaud Vanhoutrève, Olivier Poch, Julie Dawn Thompson

Bioinform., 2014

2013

Classification multi-étiquettes pour l'alignement multiple de séquences protéiques.

Lina Fahed, Gabriel Frey, Julie Dawn Thompson, Nicolas Lachiche

Proceedings of the Extraction et gestion des connaissances (EGC'2013), Actes, 29 janvier, 2013

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, Olivier Poch, Hoan Nguyen

Nucleic Acids Res., 2012

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

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

OrthoInspector: comprehensive orthology analysis and visual exploration.

Benjamin Linard, Julie Dawn Thompson, Olivier Poch, Odile Lecompte

BMC Bioinform., 2011

2010

AQUA: automated quality improvement for multiple sequence alignments.

Jean Muller, Christopher J. Creevey, Julie Dawn Thompson, Detlev Arendt, Peer Bork

Bioinform., 2010

2009

Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods.

Valentín Ruano-Rubio, Olivier Poch, Julie Dawn Thompson

BMC Bioinform., 2009

PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees.

Philippe Gouret, Julie Dawn Thompson, Pierre Pontarotti

BMC Bioinform., 2009

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

2008

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

2007

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, Desmond G. Higgins

Bioinform., 2007

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

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

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

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

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, Jean-Claude Thierry, Julie Dawn Thompson, Nicolas Wicker, Olivier Poch

Nucleic Acids Res., 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

RASCAL: Rapid Scanning and Correction of Multiple Sequence Alignments.

Julie Dawn Thompson, Jean-Claude Thierry, Olivier Poch

Bioinform., 2003

2001

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

2000

Ballast: Blast post-processing based on locally conserved segments.

Frédéric Plewniak, Julie Dawn Thompson, Olivier Poch

Bioinform., 2000

1999

A comprehensive comparison of multiple sequence alignment programs.

Julie Dawn Thompson, Frédéric Plewniak, Olivier Poch

Nucleic Acids Res., 1999

BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs.

Julie Dawn Thompson, Frédéric Plewniak, Olivier Poch

Bioinform., 1999

1995

Introducing variable gap penalties to sequence alignment in linear space.

Julie Dawn Thompson

Comput. Appl. Biosci., 1995

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

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