Julie Thompson

Documents

Publications

	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-04075117v2
	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⟩ Article dans une revue hal-04253824v1
	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-04253859v1
	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⟩ Article dans une revue hal-03245652v1
	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⟩ Article dans une revue hal-03269307v1
	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⟩ Article dans une revue hal-03464474v1
	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-03464195v1
	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⟩ Article dans une revue hal-03243954v1
	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⟩ Article dans une revue hal-03464230v1
	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-03464220v1
	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⟩ Article dans une revue hal-03464210v1
	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-03464223v1
	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-03484275v1
	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⟩ Article dans une revue inserm-02916951v1
	Identification of a circular code periodicity in the bacterial ribosome: origin of codon periodicity in genes? Christian Michel , Julie Thompson RNA Biology, 2020, 17, ⟨10.1080/15476286.2020.1719311⟩ Article dans une revue hal-03078903v1
	Circular code motifs in the ribosome: a missing link in the evolution of translation? Gopal Dila , Raymond Ripp , Claudine Mayer , Olivier Poch , Christian Michel RNA, 2019, 25 (12), pp.1714-1730. ⟨10.1261/rna.072074.119⟩ Article dans une revue hal-02381481v1
	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⟩ Article dans une revue hal-02045054v1
	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⟩ Article dans une revue hal-01984857v1
	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-02381474v1
	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⟩ Article dans une revue 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⟩ Article dans une revue hal-02332968v1
	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⟩ Article dans une revue hal-01741730v1
	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⟩ Article dans une revue hal-03618033v1
	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⟩ Article dans une revue hal-03680439v1
	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⟩ Article dans une revue hal-03676425v1
	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⟩ Article dans une revue hal-03677795v1
	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⟩ Article dans une revue hal-01636893v1
	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-00988598v1
	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⟩ Article dans une revue hal-01636894v1
	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-01636866v1
	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-00682055v1
	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⟩ Article dans une revue hal-00831115v1
	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⟩ Article dans une revue inserm-00742840v1
	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⟩ Article dans une revue hal-01636871v1
	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-00663697v1
	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⟩ Article dans une revue inserm-00691543v1
	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-01636867v1
	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⟩ Article dans une revue hal-00530522v1
	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-04029377v1
	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-04010699v1
	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⟩ Article dans une revue inserm-00663877v1
	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-00663560v1
	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-00438663v1
	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⟩ Article dans une revue inserm-00370108v1
	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-00663932v1
	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-00368022v1
	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-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⟩ Article dans une revue hal-00283115v1
	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⟩ Article dans une revue 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 Article dans une revue 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⟩ Article dans une revue 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⟩ Article dans une revue hal-00187784v1
	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 hal-00187813v1
	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 hal-00187785v1
	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-04130440v1
	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-04151457v1
	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⟩ Article dans une revue hal-04156292v1
	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 hal-04107023v1
	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 hal-04128945v1
	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-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⟩ Article dans une revue hal-03991584v1

	INEX-MED: INtegration and EXploration of heterogeneous bio-MEDical data Alban Gaignard , Julie D. Thompson , Kirsley Chennen , Maxime Folschette , Jocelyn Laporte JOBIM 2019, Jul 2019, Nantes, France Poster de conférence hal-02330853v1

	EvoKEN: evolutionary knowledge extraction in networks Benjamin Linard , Ngoc Thanh Nguyen , Odile Lecompte , Olivier Poch , Julie D. Thompson 2017 Pré-publication, Document de travail hal-01636898v1

	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-04317586v3
	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 22ième Conférence Extraction et Gestion des Connaissances (EGC'22), 24-28 janvier 2022, Tours, Jan 2020, Tours, France Communication dans un congrès hal-03797657v1
	INEX-MED: a Knowledge Graph to explore and link heterogeneous bio-medical data Maxime Folschette , Kirsley Chennen , Alban Gaignard , Richard Redon , Hala Skaf-Molli JOBIM 2019, Jul 2019, Nantes, France Communication dans un congrès hal-02330809v1
	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-03204153v1

Julie Thompson

Publications

Real or fake? Measuring the impact of protein annotation errors on estimates of domain gain and loss events

CeGAL: Redefining a Widespread Fungal-Specific Transcription Factor Family Using an In Silico Error-Tracking Approach

De-MISTED: Image-based classification of erroneous multiple sequence alignments using convolutional neural networks

Multi-omics comparisons of different forms of centronuclear myopathies and the effects of several therapeutic strategies

Integrative approach to interpret DYRK1A variants, leading to a frequent neurodevelopmental disorder

Spliceator: multi-species splice site prediction using convolutional neural networks

A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms

Proteome-scale detection of differential conservation patterns at protein and sub-protein levels with BLUR

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

Characterization of accessory genes in coronavirus genomes

Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes

Optimality of circular codes versus the genetic code after frameshift errors

BNO An ontology for understanding the transittability of complex biomolecular networks

MISTIC: A prediction tool to reveal disease-relevant deleterious missense variants

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

Circular code motifs in the ribosome: a missing link in the evolution of translation?

BNO: An ontology for understanding the transittability of complex biomolecular networks

OrthoInspector 3.0: open portal for comparative genomics

Evolutionary conservation and functional implications of circular code motifs in eukaryotic genomes

Novel SPEG Mutations in Congenital Myopathy without Centralized Nuclei

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

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

Insights into ciliary genes and evolution from multi-level phylogenetic profiling

Recessive MYPN mutations cause cap myopathy with occasional nemaline rods

Dihydropyridine receptor (DHPR, CACNA1S) congenital myopathy

HSPB8 haploinsufficiency causes dominant adult-onset axial and distal myopathy

OrthoInspector 2.0: Software and database updates

A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i).

Functional insights into the core-TFIIH from a comparative survey

EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data

Controversies in modern evolutionary biology: the imperative for error detection and quality control.

The chordate proteome history database.

Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism.

KD4v: comprehensible knowledge discovery system for missense variant

OrthoInspector: comprehensive orthology analysis and visual exploration.

Identifying single copy orthologs in Metazoa.

A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives

Visualization of multiple alignments, phylogenies and gene family evolution.

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

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

Lessons from genome-wide studies: an integrated definition of the coactivator function of histone acetyl transferases.

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

Initial implementation of a comparative data analysis ontology.

Knowledge-based expert systems and a proof-of-concept case study for multiple sequence alignment construction and analysis.

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

Strategies for reliable exploitation of evolutionary concepts in high throughput biology.

Strategies for reliable exploitation of evolutionary concepts in high throughput biology

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

MACSIMS: multiple alignment of complete sequences information management system.

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

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

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

Identifying sigma factors in Mycobacterium smegmatis by comparative genomic analysis.

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

LEON: multiple aLignment Evaluation Of Neighbours

RASCAL: rapid scanning and correction of multiple sequence alignments

PipeAlign: A new toolkit for protein family analysis

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

Towards a reliable objective function for multiple sequence alignments

A comprehensive comparison of multiple sequence alignment programs

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

INEX-MED: INtegration and EXploration of heterogeneous bio-MEDical data

EvoKEN: evolutionary knowledge extraction in networks

MERLIN: Identifying inaccuracies in Multiple Sequence Alignments using Object Detection

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

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

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