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Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae.
Published in:
Life (2075-1729), 2017, v. 7, n. 4, p. 52, doi. 10.3390/life7040052
By:
- Michel, Christian J.;
- Ngoune, Viviane Nguefack;
- Poch, Olivier;
- Ripp, Raymond;
- Thompson, Julie D.
Publication type:
Article
A benchmark study of ab initio gene prediction methods in diverse eukaryotic organisms.
Published in:
BMC Genomics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12864-020-6707-9
By:
- Scalzitti, Nicolas;
- Jeannin-Girardon, Anne;
- Collet, Pierre;
- Poch, Olivier;
- Thompson, Julie D.
Publication type:
Article
LEON-BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system.
Published in:
BMC Bioinformatics, 2016, v. 17, p. 1, doi. 10.1186/s12859-016-1146-y
By:
- Vanhoutreve, Renaud;
- Kress, Arnaud;
- Legrand, Baptiste;
- Gass, Hélène;
- Poch, Olivier;
- Thompson, Julie D.
Publication type:
Article
OrthoInspector 3.0: open portal for comparative genomics.
Published in:
Nucleic Acids Research, 2019, v. 47, n. D1, p. D411, doi. 10.1093/nar/gky1068
By:
- Nevers, Yannis;
- Kress, Arnaud;
- Defosset, Audrey;
- Ripp, Raymond;
- Linard, Benjamin;
- Thompson, Julie D;
- Poch, Olivier;
- Lecompte, Odile
Publication type:
Article
KD4v: comprehensible knowledge discovery system for missense variant.
Published in:
Nucleic Acids Research, 2012, v. 40, p. W71, doi. 10.1093/nar/gks474
By:
- Luu, Tien-Dao;
- Rusu, Alin;
- Walter, Vincent;
- Linard, Benjamin;
- Poidevin, Laetitia;
- Ripp, Raymond;
- Moulinier, Luc;
- Muller, Jean;
- Raffelsberger, Wolfgang;
- Wicker, Nicolas;
- Lecompte, Odile;
- Thompson, Julie D.;
- Poch, Olivier;
- Nguyen, Hoan
Publication type:
Article
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment.
Published in:
Nucleic Acids Research, 2010, v. 38, n. 21, p. 7353, doi. 10.1093/nar/gkq625
By:
- Aniba, Mohamed Radhouene;
- Poch, Olivier;
- Thompson, Julie D.
Publication type:
Article
The Chordate Proteome History Database.
Published in:
Evolutionary Bioinformatics, 2012, n. 8, p. 437, doi. 10.4137/EBO.S9186
By:
- Levasseur, Anthony;
- Paganini, Julien;
- Dainat, Jacques;
- Thompson, Julie D.;
- Poch, Olivier;
- Pontarotti, Pierre;
- Gouret, Philippe
Publication type:
Article
EvoluCode: Evolutionary Barcodes as a Unifying Framework for Multilevel Evolutionary Data.
Published in:
Evolutionary Bioinformatics, 2012, n. 8, p. 61, doi. 10.4137/EBO.S8814
By:
- Linard, Benjamin;
- Ngoc Hoan Nguyen;
- Prosdocimi, Francisco;
- Poch, Olivier;
- Thompson, Julie D.
Publication type:
Article
Strategies for Reliable Exploitation of Evolutionary Concepts in High Throughput Biology.
Published in:
Evolutionary Bioinformatics, 2008, n. 4, p. 121, doi. 10.4137/EBO.S597
By:
- Levasseur, Anthony;
- Pontarotti, Pierre;
- Poch, Olivier;
- Thompson, Julie D.
Publication type:
Article
A Comprehensive Benchmark Study of Multiple Sequence Alignment Methods: Current Challenges and Future Perspectives.
Published in:
PLoS ONE, 2011, v. 6, n. 3, p. 1, doi. 10.1371/journal.pone.0018093
By:
- Thompson, Julie D.;
- Linard, Benjamin;
- Lecompte, Odile;
- Poch, Olivier
Publication type:
Article
BAliBASE 3.0: Latest developments of the multiple sequence alignment benchmark.
Published in:
Proteins, 2005, v. 61, n. 1, p. 127, doi. 10.1002/prot.20527
By:
- Thompson, Julie D.;
- Koehl, Patrice;
- Ripp, Raymond;
- Poch, Olivier
Publication type:
Article
Knowledge Discovery in Variant Databases Using Inductive Logic programming.
Published in:
Bioinformatics & Biology Insights, 2013, n. 7, p. 119, doi. 10.4137/BBI.S11184
By:
- Hoan Nguyen;
- Tien-Dao Luu;
- Poch, Olivier;
- Thompson, Julie D.
Publication type:
Article
MSV3d: database of human MisSense variants mapped to 3D protein structure.
Published in:
Database: The Journal of Biological Databases & Curation, 2012, v. 2012, p. 1
By:
- Luu, Tien-Dao;
- Rusu, Alin-Mihai;
- Walter, Vincent;
- Ripp, Raymond;
- Moulinier, Luc;
- Muller, Jean;
- Toursel, Thierry;
- Thompson, Julie D.;
- Poch, Olivier;
- Nguyen, Hoan
Publication type:
Article
A comprehensive study of small non-frameshift insertions/deletions in proteins and prediction of their phenotypic effects by a machine learning method (KD4i).
Published in:
BMC Bioinformatics, 2014, v. 15, n. 1, p. 1, doi. 10.1186/1471-2105-15-111
By:
- Bermejo-Das-Neves, Carlos;
- Nguyen, Hoan-Ngoc;
- Poch, Olivier;
- Thompson, Julie D.
Publication type:
Article
OrthoInspector: comprehensive orthology analysis and visual exploration.
Published in:
BMC Bioinformatics, 2011, v. 12, n. 1, p. 1, doi. 10.1186/1471-2105-12-11
By:
- Linard, Benjamin;
- Thompson, Julie D.;
- Poch, Olivier;
- Lecompte, Odile
Publication type:
Article
A new protein linear motif benchmark for multiple sequence alignment software.
Published in:
BMC Bioinformatics, 2008, v. 9, p. 1, doi. 10.1186/1471-2105-9-213
By:
- Perrodou, Emmanuel;
- Chica, Claudia;
- Poch, Olivier;
- Gibson, Toby J.;
- Thompson, Julie D.
Publication type:
Article
Insights into Ciliary Genes and Evolution from Multi-Level Phylogenetic Profiling.
Published in:
Molecular Biology & Evolution, 2017, v. 34, n. 8, p. 2016, doi. 10.1093/molbev/msx146
By:
- Nevers, Yannis;
- Prasad, Megana K.;
- Poidevin, Laetitia;
- Chennen, Kirsley;
- Allot, Alexis;
- Kress, Arnaud;
- Ripp, Raymond;
- Thompson, Julie D.;
- Dollfus, Hélène;
- Poch, Olivier;
- Lecompte, Odile
Publication type:
Article
MAO: a Multiple Alignment Ontology for nucleic acid and protein sequences.
Published in:
Nucleic Acids Research, 2005, v. 33, n. 13, p. 4164, doi. 10.1093/nar/gki735
By:
- Thompson, Julie D.;
- Holbrook, Stephen R.;
- Katoh, Kazutaka;
- Koehl, Patrice;
- Moras, Dino;
- Westhof, Eric;
- Poch, Olivier
Publication type:
Article
LEON: multiple aLignment Evaluation Of Neighbours.
Published in:
Nucleic Acids Research, 2004, v. 32, n. 4, p. 1298, doi. 10.1093/nar/gkh294
By:
- Thompson, Julie D.;
- Prigent, Véronique;
- Poch, Olivier
Publication type:
Article
Multiple sequence alignment with the Clustal series of programs.
Published in:
Nucleic Acids Research, 2003, v. 31, n. 13, p. 3497, doi. 10.1093/nar/gkg500
By:
- Chenna, Ramu;
- Sugawara, Hideaki;
- Koike, Tadashi;
- Lopez, Rodrigo;
- Gibson, Toby J.;
- Higgins, Desmond G.;
- Thompson, Julie D.
Publication type:
Article
PipeAlign: a new toolkit for protein family analysis.
Published in:
Nucleic Acids Research, 2003, v. 31, n. 13, p. 3829, doi. 10.1093/nar/gkg518
By:
- Plewniak, Frédéric;
- Bianchetti, Laurent;
- Brelivet, Yann;
- Carles, Annaick;
- Chalmel, Frédéric;
- Lecompte, Odile;
- Mochel, Thiebaut;
- Moulinier, Luc;
- Muller, Arnaud;
- Muller, Jean;
- Prigent, Veronique;
- Ripp, Raymond;
- Thierry, Jean-Claude;
- Thompson, Julie D.;
- Wicker, Nicolas;
- Poch, Olivier
Publication type:
Article
BAliBASE (Benchmark Alignment dataBASE): enhancements for repeats, transmembrane sequences and circular permutations.
Published in:
Nucleic Acids Research, 2001, v. 29, n. 1, p. 323, doi. 10.1093/nar/29.1.323
By:
- Bahr, Anne;
- Thompson, Julie D.;
- Thierry, J.-C.;
- Poch, Olivier
Publication type:
Article
A comprehensive comparison of multiple sequence alignment programs.
Published in:
Nucleic Acids Research, 1999, v. 27, n. 13, p. 2682, doi. 10.1093/nar/27.13.2682
By:
- Thompson, Julie D.;
- Plewniak, Frédéric;
- Poch, Olivier;
- Pearson, W.R.;
- Altschul, S.F.;
- Sonnhammer, E.L.;
- Gracy, J.;
- Jiang, J.;
- Taylor, W.R.;
- Gupta, S.K.;
- Feng, D.F.;
- Barton, G.J.;
- Thompson, J.D.;
- Needleman, S.B.;
- Sneath, P.H.;
- Saitou, N.;
- Smith, R.F;
- Smith, R.F.;
- Morgenstein, B.;
- Gotoh, O.
Publication type:
Article
The CLUSTAL_X Windows Interface: Flexible Strategies for Multiple Sequence Alignment Aided by Quality Analysis Tools.
Published in:
Nucleic Acids Research, 1997, v. 25, n. 24, p. 4876
By:
- Thompson, Julie D.;
- Gibson, Toby J.;
- Plewniak, Frédéric;
- Jeanmougin, François;
- Higgins, Desmond G.
Publication type:
Article
PairWise and SearchWise: Finding the Optimal Alignment in a Simultaneous Comparison of a Protein Profile against All DNA Translation Frames.
Published in:
Nucleic Acids Research, 1996, v. 24, n. 14, p. 2730, doi. 10.1093/nar/24.14.2730
By:
- Birney, Ewan;
- Thompson, Julie D.;
- Gibson, Toby J.
Publication type:
Article
Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.
Published in:
Molecular Systems Biology, 2011, v. 7, n. 1, p. 1, doi. 10.1038/msb.2011.75
By:
- Sievers, Fabian;
- Wilm, Andreas;
- Dineen, David;
- Gibson, Toby J;
- Karplus, Kevin;
- Li, Weizhong;
- Lopez, Rodrigo;
- McWilliam, Hamish;
- Remmert, Michael;
- Söding, Johannes;
- Thompson, Julie D;
- Higgins, Desmond G
Publication type:
Article
Identifying Single Copy Orthologs in Metazoa.
Published in:
PLoS Computational Biology, 2011, v. 7, n. 12, p. 1, doi. 10.1371/journal.pcbi.1002269
By:
- Creevey, Christopher J.;
- Muller, Jean;
- Doerks, Tobias;
- Thompson, Julie D.;
- Arendt, Detlev;
- Bork, Peer
Publication type:
Article
Proteome-Scale Detection of Differential Conservation Patterns at Protein and Subprotein Levels with BLUR.
Published in:
Genome Biology & Evolution, 2021, v. 13, n. 1, p. 1, doi. 10.1093/gbe/evaa248
By:
- Defosset, Audrey;
- Kress, Arnaud;
- Nevers, Yannis;
- Ripp, Raymond;
- Thompson, Julie D;
- Poch, Olivier;
- Lecompte, Odile
Publication type:
Article
BAliBASE: a benchmark alignment database for the evaluation of multiple alignment programs.
Published in:
Bioinformatics, 1999, v. 15, n. 1, p. 87, doi. 10.1093/bioinformatics/15.1.87
By:
- Thompson, Julie D.;
- Plewniak, Frèdèric;
- Poch, Olivier
Publication type:
Article
Metazoan Remaining Genes for Essential Amino Acid Biosynthesis: Sequence Conservation and Evolutionary Analyses.
Published in:
2015
By:
- Costa, Igor R.;
- Thompson, Julie D.;
- Ortega, José Miguel;
- Prosdocimi, Francisco
Publication type:
Journal Article
CeGAL: Redefining a Widespread Fungal-Specific Transcription Factor Family Using an In Silico Error-Tracking Approach.
Published in:
Journal of Fungi, 2023, v. 9, n. 4, p. 424, doi. 10.3390/jof9040424
By:
- Mayer, Claudine;
- Vogt, Arthur;
- Uslu, Tuba;
- Scalzitti, Nicolas;
- Chennen, Kirsley;
- Poch, Olivier;
- Thompson, Julie D.
Publication type:
Article
Evolutionary analysis of the ENTH/ANTH/VHS protein superfamily reveals a coevolution between membrane trafficking and metabolism.
Published in:
BMC Genomics, 2012, v. 13, n. 1, p. 297, doi. 10.1186/1471-2164-13-297
By:
- De Craene, Johan-Owen;
- Ripp, Raymond;
- Lecompte, Odile;
- Thompson, Julie D.;
- Poch, Olivier;
- Friant, Sylvie
Publication type:
Article
PROBE: analysis and visualization of protein block-level evolution.
Published in:
Bioinformatics, 2018, v. 34, n. 19, p. 3390, doi. 10.1093/bioinformatics/bty367
By:
- Kress, Arnaud;
- Lecompte, Odile;
- Poch, Olivier;
- Thompson, Julie D
Publication type:
Article
OrthoInspector 2.0: Software and database updates.
Published in:
Bioinformatics, 2015, v. 31, n. 3, p. 447, doi. 10.1093/bioinformatics/btu642
By:
- Linard, Benjamin;
- Allot, Alexis;
- Schneider, Raphaël;
- Morel, Can;
- Ripp, Raymond;
- Bigler, Marc;
- Thompson, Julie D.;
- Poch, Olivier;
- Lecompte, Odile
Publication type:
Article
SIBIS: a Bayesian model for inconsistent protein sequence estimation.
Published in:
2014
By:
- Khenoussi, Walyd;
- Vanhoutrève, Renaud;
- Poch, Olivier;
- Thompson, Julie D.
Publication type:
Product Review
AQUA: automated quality improvement for multiple sequence alignments.
Published in:
Bioinformatics, 2010, v. 26, n. 2, p. 263, doi. 10.1093/bioinformatics/btp651
By:
- Muller, Jean;
- Creevey, Christopher J.;
- Thompson, Julie D.;
- Arendt, Detlev;
- Bork, Peer
Publication type:
Article
Spliceator: multi-species splice site prediction using convolutional neural networks.
Published in:
BMC Bioinformatics, 2021, v. 22, n. 1, p. 1, doi. 10.1186/s12859-021-04471-3
By:
- Scalzitti, Nicolas;
- Kress, Arnaud;
- Orhand, Romain;
- Weber, Thomas;
- Moulinier, Luc;
- Jeannin-Girardon, Anne;
- Collet, Pierre;
- Poch, Olivier;
- Thompson, Julie D.
Publication type:
Article
Understanding the causes of errors in eukaryotic protein-coding gene prediction: a case study of primate proteomes.
Published in:
BMC Bioinformatics, 2020, v. 21, n. 1, p. 1, doi. 10.1186/s12859-020-03855-1
By:
- Meyer, Corentin;
- Scalzitti, Nicolas;
- Jeannin-Girardon, Anne;
- Collet, Pierre;
- Poch, Olivier;
- Thompson, Julie D.
Publication type:
Article

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