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Julie Thompson

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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⟩
Journal articles hal-04075117v2
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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
Journal of Fungi, 2023, 9 (4), pp.424. ⟨10.3390/jof9040424⟩
Journal articles hal-04253824v1
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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⟩
Journal articles hal-04253859v1
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Spliceator: multi-species splice site prediction using convolutional neural networks

Nicolas Scalzitti , Arnaud Kress , Romain Orhand , Thomas Weber , Luc Moulinier
BMC Bioinformatics, 2021, 22, pp.561. ⟨10.1186/s12859-021-04471-3⟩
Journal articles hal-03464474v1
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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
Genetics in Medicine, 2021, 23 (11), pp.2150-2159. ⟨10.1038/s41436-021-01263-1⟩
Journal articles hal-03269307v1
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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
Molecular Therapy, 2021, ⟨10.1016/j.ymthe.2021.04.033⟩
Journal articles hal-03245652v1
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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
Genome Biology and Evolution, 2020, ⟨10.1093/gbe/evaa248⟩
Journal articles hal-03243954v1
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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⟩
Journal articles hal-03464195v1

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
BMC Bioinformatics, 2020, 21 (1), ⟨10.1186/s12859-020-03855-1⟩
Journal articles hal-03464210v1

Identification of a circular code periodicity in the bacterial ribosome: origin of codon periodicity in genes?

Julie D. Thompson , Christian Michel
RNA Biology, 2020, 17 (4), pp.571-583. ⟨10.1080/15476286.2020.1719311⟩
Journal articles hal-03464230v1
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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⟩
Journal articles hal-03464220v1

Identification of a circular code periodicity in the bacterial ribosome: origin of codon periodicity in genes?

Christian Michel , Julie Thompson
Journal articles hal-03078903v1

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⟩
Journal articles hal-03484275v1
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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⟩
Journal articles hal-03464223v1
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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
PLoS ONE, 2020, 15 (7), pp.e0236962. ⟨10.1371/journal.pone.0236962⟩
Journal articles inserm-02916951v1
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Evolutionary conservation and functional implications of circular code motifs in eukaryotic genomes

Gopal Dila , Christian C. Michel , Olivier Poch , Raymond Ripp , Julie D Thompson
BioSystems, 2019, 175, pp.57-74. ⟨10.1016/j.biosystems.2018.10.014⟩
Journal articles hal-02381474v1
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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
Journal of Web Semantics, 2019, 57, pp.100495. ⟨10.1016/j.websem.2019.01.002⟩
Journal articles hal-02045054v1
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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 C. Michel
RNA, 2019, 25 (12), pp.1714-1730. ⟨10.1261/rna.072074.119⟩
Journal articles hal-02381481v1
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OrthoInspector 3.0: open portal for comparative genomics

Yannis Nevers , Arnaud Kress , Audrey Defosset , Raymond Ripp , Benjamin Linard
Nucleic Acids Research, 2019, 47 (D1), pp.D411-D418. ⟨10.1093/nar/gky1068⟩
Journal articles hal-01984857v1

Novel SPEG Mutations in Congenital Myopathy without Centralized Nuclei

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

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
Journal of Neuropathology and Experimental Neurology, 2018, 77 (12), pp.1101-1114. ⟨10.1093/jnen/nly095⟩
Journal articles hal-02332968v1

HSPB8 haploinsufficiency causes dominant adult-onset axial and distal myopathy

Yon Andoni Echaniz-Laguna , Xavière Lornage , Beatrice Lannes , Raphael Schneider , Guillaume Bierry
Acta Neuropathologica, 2017, 134 (1), pp.163-165. ⟨10.1007/s00401-017-1724-8⟩
Journal articles hal-03677795v1

Recessive MYPN mutations cause cap myopathy with occasional nemaline rods

Xavière Lornage , Edoardo Malfatti , Raphael Schneider , Valerie Biancalana , Jean Cuisset
Ann Neurol, 2017, 81 (3), pp.467-473. ⟨10.1002/ana.24900⟩
Journal articles hal-03680439v1

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
Neuromuscular Disorders, 2017, 27 (11), pp.975-985. ⟨10.1016/j.nmd.2017.05.016⟩
Journal articles hal-01741730v1
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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
Molecular Biology and Evolution, 2017, 34 (8), pp.2016-2034. ⟨10.1093/molbev/msx146⟩
Journal articles hal-03618033v1

Dihydropyridine receptor (DHPR, CACNA1S) congenital myopathy

Vanessa Schartner , Norma Romero , Sandra Donkervoort , Susan Treves , Pinki Munot
Acta Neuropathologica, 2017, 133 (4), pp.517-533. ⟨10.1007/s00401-016-1656-8⟩
Journal articles hal-03676425v1
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OrthoInspector 2.0: Software and database updates

Benjamin Linard , Alexis Allot , Raphaël Schneider , Can Morel , Raymond Ripp
Bioinformatics, 2015, 31 (3), pp.447-448. ⟨10.1093/bioinformatics/btu642⟩
Journal articles hal-01636893v1
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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⟩
Journal articles inserm-00988598v1
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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
Genomics, 2013, 101 (3), pp.178-186. ⟨10.1016/j.ygeno.2012.11.003⟩
Journal articles hal-01636894v1
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The chordate proteome history database.

Anthony Levasseur , Julien Paganini , Jacques Dainat , Julie D Thompson , Olivier Poch
Evolutionary Bioinformatics, 2012, 8, pp.437-47. ⟨10.4137/EBO.S9186⟩
Journal articles hal-00831115v1
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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
BMC Genomics, 2012, 13 (1), pp.297. ⟨10.1186/1471-2164-13-297⟩
Journal articles inserm-00742840v1
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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⟩
Journal articles hal-01636866v1
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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⟩
Journal articles inserm-00682055v1
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KD4v: comprehensible knowledge discovery system for missense variant

Tien-Dao Luu , Alin Rusu , Vincent Walter , Benjamin Linard , Laetitia Poidevin
Nucleic Acids Research, 2012, 40 (W1), pp.W71-W75. ⟨10.1093/nar/gks474⟩
Journal articles hal-01636871v1
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Identifying single copy orthologs in Metazoa.

Christopher J. Creevey , Jean Muller , Tobias Doerks , Julie D. Thompson , Detlev Arendt
PLoS Computational Biology, 2011, 7 (12), pp.e1002269. ⟨10.1371/journal.pcbi.1002269⟩
Journal articles inserm-00691543v1
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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⟩
Journal articles inserm-00663697v1
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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⟩
Journal articles hal-01636867v1
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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
Epigenetics & Chromatin, 2010, 3 (1), pp.18. ⟨10.1186/1756-8935-3-18⟩
Journal articles inserm-00663877v1

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⟩
Journal articles hal-04010699v1

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⟩
Journal articles hal-04029377v1

Visualization of multiple alignments, phylogenies and gene family evolution.

James B Procter , Julie D. Thompson , Ivica Letunic , Chris Creevey , Fabrice Jossinet
Nature Methods, 2010, 7 (3 Suppl), pp.S16-25. ⟨10.1038/nmeth.1434⟩
Journal articles hal-00530522v1
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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⟩
Journal articles inserm-00663560v1

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
Briefings in Bioinformatics, 2009, 10 (1), pp.11-23. ⟨10.1093/bib/bbn045⟩
Journal articles inserm-00370108v1
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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⟩
Journal articles inserm-00663932v1
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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
Journal articles inserm-00438663v1
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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⟩
Journal articles hal-04127572v1

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⟩
Journal articles hal-00283115v1
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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
Journal articles inserm-00368022v1

MACSIMS: multiple alignment of complete sequences information management system.

Julie D Thompson , Arnaud H. Muller , Andrew Waterhouse , Jim Procter , Geoffrey J Barton
BMC Bioinformatics, 2006, 7, pp.318. ⟨10.1186/1471-2105-7-318⟩
Journal articles hal-00188166v1

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
Journal articles hal-00187446v1

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⟩
Journal articles hal-04143695v1

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

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

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⟩
Journal articles hal-00187785v1

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⟩
Journal articles hal-00187813v1

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⟩
Journal articles hal-04130440v1

PipeAlign: A new toolkit for protein family analysis

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

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⟩
Journal articles hal-04151457v1

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⟩
Journal articles hal-04128945v1

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⟩
Journal articles hal-04107023v1

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⟩
Journal articles hal-03989698v1

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⟩
Journal articles hal-03991584v1