Julie Thompson

Documents

Publications

	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
	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
	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
	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
	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
	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
	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
	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
	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 J. Michel , Julie Thompson RNA Biology, 2020, 17 (4), pp.571-583. ⟨10.1080/15476286.2020.1719311⟩ Article dans une revue hal-03078903v1
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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
	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

	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

	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

	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

Julie Thompson

Publications

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

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

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

Spliceator: multi-species splice site prediction 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

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

Characterization of accessory genes in coronavirus genomes

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

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?

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

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

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

OrthoInspector 3.0: open portal for comparative genomics

Novel SPEG Mutations in Congenital Myopathy without Centralized Nuclei

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

Recessive MYPN mutations cause cap myopathy with occasional nemaline rods

HSPB8 haploinsufficiency causes dominant adult-onset axial and distal myopathy

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

Dihydropyridine receptor (DHPR, CACNA1S) congenital 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

The chordate proteome history database.

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

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

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

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

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.

Visualization of multiple alignments, phylogenies and gene family evolution.

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.

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

Initial implementation of a comparative data analysis ontology.

Strategies for reliable exploitation of evolutionary concepts in high throughput biology

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

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

MACSIMS: multiple alignment of complete sequences information management system.

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

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

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

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

PipeAlign: A new toolkit for protein family analysis

RASCAL: rapid scanning and correction of multiple sequence alignments

Towards a reliable objective function for multiple sequence alignments

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

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

A comprehensive comparison of multiple sequence alignment programs

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

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

EvoKEN: evolutionary knowledge extraction in networks