Julie Thompson

71
Documents

Publications

Publications

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Transcriptomic characterization of postnatal muscle maturation in mice, with a focus on myopathy-associated genes

Alix Simon , Sarah Djeddi , Pauline Bournon , David Reiss , Julie Thompson et al.
Disease Models & Mechanisms, In press, ⟨10.1242/dmm.052098⟩
Article dans une revue hal-04939413 v1
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Graph-based machine learning model for weight prediction in protein–protein networks

Hajer Akid , Kirsley Chennen , Gabriel Frey , Julie D. Thompson , Mounir Ben Ayed et al.
BMC Bioinformatics, 2024, 25 (1), pp.349. ⟨10.1186/s12859-024-05973-6⟩
Article dans une revue hal-04941825 v1
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StopKB: a comprehensive knowledgebase for nonsense suppression therapies

Nicolas Haas , Julie Thompson , Jean-Paul Renaud , Kirsley Chennen , Olivier Poch
Database - The journal of Biological Databases and Curation, 2024, 2024, ⟨10.1093/database/baae108⟩
Article dans une revue hal-04752787 v1
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De-MISTED: Image-based classification of erroneous multiple sequence alignments using convolutional neural networks

Hiba Khodji , Pierre Collet , Julie D. Thompson , Anne Jeannin-Girardon
Applied Intelligence, 2023, 53 (15), pp.18806-18820. ⟨10.1007/s10489-022-04390-7⟩
Article dans une revue hal-04253859 v1
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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 Thompson
Frontiers in Bioinformatics, 2023, 3, ⟨10.3389/fbinf.2023.1178926⟩
Article dans une revue hal-04075117 v2
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CeGAL: Redefining a Widespread Fungal-Specific Transcription Factor Family Using an In Silico Error-Tracking Approach

Claudine Mayer , Arthur Vogt , Tuba Uslu , Nicolas Scalzitti , Kirsley Chennen et al.
Journal of Fungi, 2023, 9 (4), pp.424. ⟨10.3390/jof9040424⟩
Article dans une revue hal-04253824 v1
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Multi-omics comparisons of different forms of centronuclear myopathies and the effects of several therapeutic strategies

Sarah Djeddi , David Reiss , Alexia Menuet , Sébastien Freismuth , Juliana de Carvalho Neves et al.
Molecular Therapy, 2021, ⟨10.1016/j.ymthe.2021.04.033⟩
Article dans une revue hal-03245652 v1
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Integrative approach to interpret DYRK1A variants, leading to a frequent neurodevelopmental disorder

Jeremie Courraud , Eric Chater-Diehl , Benjamin Durand , Marie Vincent , Maria del Mar Muniz Moreno et al.
Genetics in Medicine, 2021, 23 (11), pp.2150-2159. ⟨10.1038/s41436-021-01263-1⟩
Article dans une revue hal-03269307 v1
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Spliceator: multi-species splice site prediction using convolutional neural networks

Nicolas Scalzitti , Arnaud Kress , Romain Orhand , Thomas Weber , Luc Moulinier et al.
BMC Bioinformatics, 2021, 22, pp.561. ⟨10.1186/s12859-021-04471-3⟩
Article dans une revue hal-03464474 v1
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Optimality of circular codes versus the genetic code after frameshift errors

Julie D. Thompson , Gopal Dila , Christian Michel
BioSystems, 2020, 195, pp.104134. ⟨10.1016/j.biosystems.2020.104134⟩
Article dans une revue hal-03464223 v1

BNO An ontology for understanding the transittability of complex biomolecular networks

Ali Ayadi , Cecilia Zanni-Merk , François de Bertrand de Beuvron , Julie D. Thompson , Saoussen Krichen
Journal of Web Semantics, 2020, 24 p. ⟨10.2139/ssrn.3320403⟩
Article dans une revue hal-03484275 v1
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Identification of a circular code periodicity in the bacterial ribosome: origin of codon periodicity in genes?

Christian J. Michel , Julie Thompson
RNA Biology, 2020, 17 (4), pp.571-583. ⟨10.1080/15476286.2020.1719311⟩
Article dans une revue hal-03078903 v1
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MISTIC: A prediction tool to reveal disease-relevant deleterious missense variants

Kirsley Chennen , Thomas Weber , Xavière Lornage , Arnaud Kress , Johann Böhm et al.
PLoS ONE, 2020, 15 (7), pp.e0236962. ⟨10.1371/journal.pone.0236962⟩
Article dans une revue inserm-02916951 v1
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Characterization of accessory genes in coronavirus genomes

Christian Jean Michel , Claudine Mayer , Olivier Poch , Julie D. Thompson
Virology Journal, 2020, 17 (1), pp.131. ⟨10.1186/s12985-020-01402-1⟩
Article dans une revue hal-03464220 v1

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 et al.
BMC Bioinformatics, 2020, 21 (1), ⟨10.1186/s12859-020-03855-1⟩
Article dans une revue hal-03464210 v1
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Proteome-scale detection of differential conservation patterns at protein and sub-protein levels with BLUR

Audrey Defosset , Arnaud Kress , Yannis Nevers , Raymond Ripp , Julie Thompson et al.
Genome Biology and Evolution, 2020, ⟨10.1093/gbe/evaa248⟩
Article dans une revue hal-03243954 v1
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A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms

Nicolas Scalzitti , Anne Jeannin-Girardon , Pierre Collet , Olivier Poch , Julie D. Thompson
BMC Genomics, 2020, 21 (1), ⟨10.1186/s12864-020-6707-9⟩
Article dans une revue hal-03464195 v1
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OrthoInspector 3.0: open portal for comparative genomics

Yannis Nevers , Arnaud Kress , Audrey Defosset , Raymond Ripp , Benjamin Linard et al.
Nucleic Acids Research, 2019, 47 (D1), pp.D411-D418. ⟨10.1093/nar/gky1068⟩
Article dans une revue hal-01984857 v1
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Evolutionary conservation and functional implications of circular code motifs in eukaryotic genomes

Gopal Dila , Christian Michel , Olivier Poch , Raymond Ripp , Julie D Thompson
BioSystems, 2019, 175, pp.57-74. ⟨10.1016/j.biosystems.2018.10.014⟩
Article dans une revue hal-02381474 v1
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Circular code motifs in the ribosome: a missing link in the evolution of translation?

Gopal Dila , Raymond Ripp , Claudine Mayer , Olivier Poch , Christian Michel et al.
RNA, 2019, 25 (12), pp.1714-1730. ⟨10.1261/rna.072074.119⟩
Article dans une revue hal-02381481 v1
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BNO: An ontology for understanding the transittability of complex biomolecular networks

François de Bertrand de Beuvron , Ali Ayadi , Cecilia Zanni-Merk , François de Bertrand de Beuvron , Julie Thompson et al.
Journal of Web Semantics, 2019, 57, pp.100495. ⟨10.1016/j.websem.2019.01.002⟩
Article dans une revue hal-02045054 v1

Loss of Sarcomeric Scaffolding as a Common Baseline Histopathologic Lesion in Titin-Related Myopathies

Rainiero Ávila-Polo , Edoardo Malfatti , Xavière Lornage , Chrystel Cheraud , Isabelle Nelson et al.
Journal of Neuropathology and Experimental Neurology, 2018, 77 (12), pp.1101-1114. ⟨10.1093/jnen/nly095⟩
Article dans une revue hal-02332968 v1

Novel SPEG Mutations in Congenital Myopathy without Centralized Nuclei

Xavière Lornage , Pascal Sabouraud , Béatrice Lannes , Dominique Gaillard , Raphael Schneider et al.
Journal of Neuromuscular Diseases, 2018, 5 (2), pp.257-260. ⟨10.3233/jnd-170265⟩
Article dans une revue hal-03664348 v1

Dihydropyridine receptor (DHPR, CACNA1S) congenital myopathy

Vanessa Schartner , Norma Romero , Sandra Donkervoort , Susan Treves , Pinki Munot et al.
Acta Neuropathologica, 2017, 133 (4), pp.517-533. ⟨10.1007/s00401-016-1656-8⟩
Article dans une revue hal-03676425 v1

HSPB8 haploinsufficiency causes dominant adult-onset axial and distal myopathy

Yon Andoni Echaniz-Laguna , Xavière Lornage , Beatrice Lannes , Raphael Schneider , Guillaume Bierry et al.
Acta Neuropathologica, 2017, 134 (1), pp.163-165. ⟨10.1007/s00401-017-1724-8⟩
Article dans une revue hal-03677795 v1
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Insights into ciliary genes and evolution from multi-level phylogenetic profiling

Yannis Nevers , Megana Prasad , Laetitia Poidevin , Kirsley Chennen , Alexis Allot et al.
Molecular Biology and Evolution, 2017, 34 (8), pp.2016-2034. ⟨10.1093/molbev/msx146⟩
Article dans une revue hal-03618033 v1

Common and variable clinical, histological, and imaging findings of recessive RYR1-related centronuclear myopathy patients

Osorio Abath Neto , Cristiane de Araujo Martins Moreno , Edoardo Malfatti , Sandra Donkervoort , Johann Bohm et al.
Neuromuscular Disorders, 2017, 27 (11), pp.975-985. ⟨10.1016/j.nmd.2017.05.016⟩
Article dans une revue hal-01741730 v1

Recessive MYPN mutations cause cap myopathy with occasional nemaline rods

Xavière Lornage , Edoardo Malfatti , Raphael Schneider , Valerie Biancalana , Jean Cuisset et al.
Ann Neurol, 2017, 81 (3), pp.467-473. ⟨10.1002/ana.24900⟩
Article dans une revue hal-03680439 v1
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OrthoInspector 2.0: Software and database updates

Benjamin Linard , Alexis Allot , Raphaël Schneider , Can Morel , Raymond Ripp et al.
Bioinformatics, 2015, 31 (3), pp.447-448. ⟨10.1093/bioinformatics/btu642⟩
Article dans une revue hal-01636893 v1
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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 Thompson
BMC Bioinformatics, 2014, 15 (1), pp.111. ⟨10.1186/1471-2105-15-111⟩
Article dans une revue inserm-00988598 v1
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Functional insights into the core-TFIIH from a comparative survey

Florence Bedez , Benjamin Linard , Xavier Brochet , Raymond Ripp , Julie D. Thompson et al.
Genomics, 2013, 101 (3), pp.178-186. ⟨10.1016/j.ygeno.2012.11.003⟩
Article dans une revue hal-01636894 v1
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KD4v: comprehensible knowledge discovery system for missense variant

Tien-Dao Luu , Alin Rusu , Vincent Walter , Benjamin Linard , Laetitia Poidevin et al.
Nucleic Acids Research, 2012, 40 (W1), pp.W71-W75. ⟨10.1093/nar/gks474⟩
Article dans une revue hal-01636871 v1
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MSV3d: database of human MisSense variants mapped to 3D protein structure

Tien-Dao Luu , Alin-Mihai Rusu , Vincent Walter , Raymond Ripp , Luc Moulinier et al.
Database - The journal of Biological Databases and Curation, 2012, 2012, pp.bas018-bas018. ⟨10.1093/database/bas018⟩
Article dans une revue hal-04975986 v1
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Controversies in modern evolutionary biology: the imperative for error detection and quality control.

Francisco Prosdocimi , Benjamin Linard , Pierre Pontarotti , Olivier Poch , Julie Thompson
BMC Genomics, 2012, 13 (1), pp.5. ⟨10.1186/1471-2164-13-5⟩
Article dans une revue inserm-00682055 v1
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The chordate proteome history database.

Anthony Levasseur , Julien Paganini , Jacques Dainat , Julie D Thompson , Olivier Poch et al.
Evolutionary Bioinformatics, 2012, 8, pp.437-47. ⟨10.4137/EBO.S9186⟩
Article dans une revue hal-00831115 v1
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Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism.

Johan-Owen de Craene , Raymond Ripp , Odile Lecompte , Julie D. Thompson , Olivier Poch et al.
BMC Genomics, 2012, 13 (1), pp.297. ⟨10.1186/1471-2164-13-297⟩
Article dans une revue inserm-00742840 v1
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EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data

Benjamin Linard , Ngoc Hoan Nguyen , Francisco Prosdocimi , Olivier Poch , Julie D. Thompson
Evolutionary Bioinformatics, 2012, 8, pp.61-77. ⟨10.4137/EBO.S8814⟩
Article dans une revue hal-01636866 v1
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A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

Julie D. Thompson , Benjamin Linard , Odile Lecompte , Olivier Poch
PLoS ONE, 2011, 6 (3), pp.18093 - 18093. ⟨10.1371/journal.pone.0018093⟩
Article dans une revue hal-01636867 v1
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Identifying single copy orthologs in Metazoa.

Christopher J. Creevey , Jean Muller , Tobias Doerks , Julie D. Thompson , Detlev Arendt et al.
PLoS Computational Biology, 2011, 7 (12), pp.e1002269. ⟨10.1371/journal.pcbi.1002269⟩
Article dans une revue inserm-00691543 v1
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OrthoInspector: comprehensive orthology analysis and visual exploration.

Benjamin Linard , Julie Thompson , Olivier Poch , Odile Lecompte
BMC Bioinformatics, 2011, 12 (1), pp.11. ⟨10.1186/1471-2105-12-11⟩
Article dans une revue inserm-00663697 v1

AlexSys: a knowledge-based expert system for multiple sequence alignment construction and analysis

Mohamed Radhouene Aniba , Olivier Poch , Aron Marchler-Bauer , Julie Thompson
Nucleic Acids Research, 2010, 38 (19), pp.6338-6349. ⟨10.1093/nar/gkq526⟩
Article dans une revue hal-04010699 v1
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Lessons from genome-wide studies: an integrated definition of the coactivator function of histone acetyl transferases.

Krishanpal Anamika , Arnaud R Krebs , Julie Thompson , Olivier Poch , Didier Devys et al.
Epigenetics & Chromatin, 2010, 3 (1), pp.18. ⟨10.1186/1756-8935-3-18⟩
Article dans une revue inserm-00663877 v1

Issues in bioinformatics benchmarking: the case study of multiple sequence alignment

Mohamed Radhouene Aniba , Olivier Poch , Julie Thompson
Nucleic Acids Research, 2010, 38 (21), pp.7353-7363. ⟨10.1093/nar/gkq625⟩
Article dans une revue hal-04029377 v1

Visualization of multiple alignments, phylogenies and gene family evolution.

James B Procter , Julie D. Thompson , Ivica Letunic , Chris Creevey , Fabrice Jossinet et al.
Nature Methods, 2010, 7 (3 Suppl), pp.S16-25. ⟨10.1038/nmeth.1434⟩
Article dans une revue hal-00530522 v1
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Initial implementation of a comparative data analysis ontology.

Francisco Prosdocimi , Brandon Chisham , Enrico Pontelli , Julie D. Thompson , Arlin Stoltzfus
Evolutionary Bioinformatics, 2009, 5, pp.47-66
Article dans une revue inserm-00438663 v1
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PhyloPattern: regular expressions to identify complex patterns in phylogenetic trees.

Philippe Gouret , Julie Thompson , Pierre Pontarotti
BMC Bioinformatics, 2009, 10 (1), pp.298. ⟨10.1186/1471-2105-10-298⟩
Article dans une revue inserm-00663932 v1

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 et al.
Briefings in Bioinformatics, 2009, 10 (1), pp.11-23. ⟨10.1093/bib/bbn045⟩
Article dans une revue inserm-00370108 v1
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Comparison of eukaryotic phylogenetic profiling approaches using species tree aware methods.

Valentín Ruano-Rubio , Olivier Poch , Julie Thompson
BMC Bioinformatics, 2009, 10 (1), pp.383. ⟨10.1186/1471-2105-10-383⟩
Article dans une revue inserm-00663560 v1
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Strategies for reliable exploitation of evolutionary concepts in high throughput biology.

Anthony Levasseur , Pierre Pontarotti , Olivier Poch , Julie D. Thompson
Evolutionary Bioinformatics, 2008, 4, pp.121-37
Article dans une revue inserm-00368022 v1

A new protein linear motif benchmark for multiple sequence alignment software.

Emmanuel Perrodou , Claudia Chica , Olivier Poch , Toby J Gibson , Julie D Thompson
BMC Bioinformatics, 2008, 9, pp.213. ⟨10.1186/1471-2105-9-213⟩
Article dans une revue hal-00283115 v1
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Strategies for reliable exploitation of evolutionary concepts in high throughput biology

Anthony Levasseur , Pierre Pontarotti , Olivier Poch , Julie D. Thompson
Evolutionary Bioinformatics, 2008, 4, pp.121-137. ⟨10.4137/ebo.s597⟩
Article dans une revue hal-04127572 v1

MACSIMS: multiple alignment of complete sequences information management system.

Julie D Thompson , Arnaud H. Muller , Andrew Waterhouse , Jim Procter , Geoffrey J Barton et al.
BMC Bioinformatics, 2006, 7, pp.318. ⟨10.1186/1471-2105-7-318⟩
Article dans une revue hal-00188166 v1

Identifying sigma factors in Mycobacterium smegmatis by comparative genomic analysis.

Andra Waagmeester , Julie D. Thompson , Jean-Marc Reyrat
Trends in Microbiology, 2005, 13 (11), pp.505-9. ⟨10.1016/j.tim.2005.08.009⟩
Article dans une revue istex hal-00187813 v1

BAliBASE 3.0: latest developments of the multiple sequence alignment benchmark.

Julie D Thompson , Patrice Koehl , Raymond Ripp , Olivier Poch
Proteins - Structure, Function and Bioinformatics, 2005, 61 (1), pp.127-36. ⟨10.1002/prot.20527⟩
Article dans une revue istex hal-00187785 v1

MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences.

Julie D Thompson , Stephen R Holbrook , Kazutaka Katoh , Patrice Koehl , Dino Moras et al.
Nucleic Acids Research, 2005, 33 (13), pp.4164-71. ⟨10.1093/nar/gki735⟩
Article dans une revue hal-00187784 v1

vALId: validation of protein sequence quality based on multiple alignment data

Laurent Bianchetti , Julie Thompson , Odile Lecompte , Frederic Plewniak , Olivier Poch
Journal of Bioinformatics and Computational Biology, 2005, 3 (4), pp.929-947. ⟨10.1142/s0219720005001326⟩
Article dans une revue hal-04143695 v1

vALId: validation of protein sequence quality based on multiple alignment data.

Laurent Bianchetti , Julie Dawn Thompson , Odile Lecompte , Frederic Plewniak , Olivier Poch
Journal of Bioinformatics and Computational Biology, 2005, 3 (4), pp.929-47
Article dans une revue hal-00187446 v1

LEON: multiple aLignment Evaluation Of Neighbours

Julie Thompson , Véronique Prigent , Olivier Poch
Nucleic Acids Research, 2004, 32 (4), pp.1298-1307. ⟨10.1093/nar/gkh294⟩
Article dans une revue hal-04130440 v1

RASCAL: rapid scanning and correction of multiple sequence alignments

Julie Thompson , J. C. Thierry , Olivier Poch
Bioinformatics, 2003, 19 (9), pp.1155-1161. ⟨10.1093/bioinformatics/btg133⟩
Article dans une revue hal-04151457 v1

PipeAlign: A new toolkit for protein family analysis

Frederic Plewniak , Laurent Bianchetti , Yann Brelivet , Annaick Carles , Frédéric Chalmel et al.
Nucleic Acids Research, 2003, 31 (13), pp.3829-3832. ⟨10.1093/nar/gkg518⟩
Article dans une revue hal-04156292 v1

Towards a reliable objective function for multiple sequence alignments

Julie Thompson , Frédéric Plewniak , Raymond Ripp , Jean-Claude Thierry , Olivier Poch
Journal of Molecular Biology, 2001, 314 (4), pp.937-951. ⟨10.1006/jmbi.2001.5187⟩
Article dans une revue istex hal-04128945 v1

Multiple alignment of complete sequences (MACS) in the post-genomic era

Odile Lecompte , Julie Thompson , Frederic Plewniak , Jean-Claude Thierry , Olivier Poch
Gene, 2001, 270 (1-2), pp.17-30. ⟨10.1016/s0378-1119(01)00461-9⟩
Article dans une revue istex hal-04107023 v1

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

Julie Thompson , Frederic Plewniak , Olivier Poch
Bioinformatics, 1999, 15 (1), pp.87-88. ⟨10.1093/bioinformatics/15.1.87⟩
Article dans une revue hal-03991584 v1

A comprehensive comparison of multiple sequence alignment programs

Julie D Thompson , Frederic Plewniak , Olivier Poch
Nucleic Acids Research, 1999, 27 (13), pp.2682-2690. ⟨10.1093/nar/27.13.2682⟩
Article dans une revue hal-03989698 v1
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MERLIN: Identifying inaccuracies in Multiple Sequence Alignments using Object Detection

Hiba Khodji , Lucille Herbay , Pierre Collet , Julie D. Thompson , Anne Jeannin-Girardon
18th IFIP International Conference on Artificial Intelligence Applications and Innovations (AIAI), Jun 2022, Hersonissos, Greece. pp.192-203, ⟨10.1007/978-3-031-08333-4_16⟩
Communication dans un congrès hal-04317586 v3

Apprentissage automatique basé sur l’agrégation pour la prédiction de liens dans les réseaux d’interactions protéine-protéine

Ajer Akid , Kirsley Chennen , Gabriel Frey , Julie Thompson , Mounir Ben Ayed et al.
22ième Conférence Extraction et Gestion des Connaissances (EGC'22), 24-28 janvier 2022, Tours, Jan 2020, Tours, France
Communication dans un congrès hal-03797657 v1

INEX-MED: a Knowledge Graph to explore and link heterogeneous bio-medical data

Maxime Folschette , Kirsley Chennen , Alban Gaignard , Richard Redon , Hala Skaf-Molli et al.
JOBIM 2019, Jul 2019, Nantes, France
Communication dans un congrès hal-02330809 v1

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

Lina Fahed , Gabriel Frey , Julie Dawn Thompson , Nicolas Lachiche
Extraction et gestion des connaissances (EGC'2013), Jan 2013, Toulouse, France. pp.431--436
Communication dans un congrès hal-03204153 v1