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Items: 1 to 20 of 37


OrthoInspector 3.0: open portal for comparative genomics.

Nevers Y, Kress A, Defosset A, Ripp R, Linard B, Thompson JD, Poch O, Lecompte O.

Nucleic Acids Res. 2019 Jan 8;47(D1):D411-D418. doi: 10.1093/nar/gky1068.


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

Dila G, Michel CJ, Poch O, Ripp R, Thompson JD.

Biosystems. 2019 Jan;175:57-74. doi: 10.1016/j.biosystems.2018.10.014. Epub 2018 Oct 24.


PROBE: analysis and visualization of protein block-level evolution.

Kress A, Lecompte O, Poch O, Thompson JD.

Bioinformatics. 2018 Oct 1;34(19):3390-3392. doi: 10.1093/bioinformatics/bty367.


Enrichment of Circular Code Motifs in the Genes of the Yeast Saccharomyces cerevisiae.

Michel CJ, Ngoune VN, Poch O, Ripp R, Thompson JD.

Life (Basel). 2017 Dec 3;7(4). pii: E52. doi: 10.3390/life7040052.


Insights into Ciliary Genes and Evolution from Multi-Level Phylogenetic Profiling.

Nevers Y, Prasad MK, Poidevin L, Chennen K, Allot A, Kress A, Ripp R, Thompson JD, Dollfus H, Poch O, Lecompte O.

Mol Biol Evol. 2017 Aug 1;34(8):2016-2034. doi: 10.1093/molbev/msx146.


LEON-BIS: multiple alignment evaluation of sequence neighbours using a Bayesian inference system.

Vanhoutreve R, Kress A, Legrand B, Gass H, Poch O, Thompson JD.

BMC Bioinformatics. 2016 Jul 7;17(1):271. doi: 10.1186/s12859-016-1146-y.


Metazoan remaining genes for essential amino acid biosynthesis: sequence conservation and evolutionary analyses.

Costa IR, Thompson JD, Ortega JM, Prosdocimi F.

Nutrients. 2014 Dec 24;7(1):1-16. doi: 10.3390/nu7010001.


OrthoInspector 2.0: Software and database updates.

Linard B, Allot A, Schneider R, Morel C, Ripp R, Bigler M, Thompson JD, Poch O, Lecompte O.

Bioinformatics. 2015 Feb 1;31(3):447-8. doi: 10.1093/bioinformatics/btu642. Epub 2014 Oct 1.


SIBIS: a Bayesian model for inconsistent protein sequence estimation.

Khenoussi W, Vanhoutrève R, Poch O, Thompson JD.

Bioinformatics. 2014 Sep 1;30(17):2432-9. doi: 10.1093/bioinformatics/btu329. Epub 2014 May 13.


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

Bermejo-Das-Neves C, Nguyen HN, Poch O, Thompson JD.

BMC Bioinformatics. 2014 Apr 17;15:111. doi: 10.1186/1471-2105-15-111.


Knowledge discovery in variant databases using inductive logic programming.

Nguyen H, Luu TD, Poch O, Thompson JD.

Bioinform Biol Insights. 2013 Mar 18;7:119-31. doi: 10.4137/BBI.S11184. Print 2013.


Functional insights into the core-TFIIH from a comparative survey.

Bedez F, Linard B, Brochet X, Ripp R, Thompson JD, Moras D, Lecompte O, Poch O.

Genomics. 2013 Mar;101(3):178-86. doi: 10.1016/j.ygeno.2012.11.003. Epub 2012 Nov 10.


The chordate proteome history database.

Levasseur A, Paganini J, Dainat J, Thompson JD, Poch O, Pontarotti P, Gouret P.

Evol Bioinform Online. 2012;8:437-47. doi: 10.4137/EBO.S9186. Epub 2012 Aug 1.


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

De Craene JO, Ripp R, Lecompte O, Thompson JD, Poch O, Friant S.

BMC Genomics. 2012 Jul 2;13:297. doi: 10.1186/1471-2164-13-297.


KD4v: Comprehensible Knowledge Discovery System for Missense Variant.

Luu TD, Rusu A, Walter V, Linard B, Poidevin L, Ripp R, Moulinier L, Muller J, Raffelsberger W, Wicker N, Lecompte O, Thompson JD, Poch O, Nguyen H.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W71-5. doi: 10.1093/nar/gks474. Epub 2012 May 27.


MSV3d: database of human MisSense Variants mapped to 3D protein structure.

Luu TD, Rusu AM, Walter V, Ripp R, Moulinier L, Muller J, Toursel T, Thompson JD, Poch O, Nguyen H.

Database (Oxford). 2012 Apr 3;2012:bas018. doi: 10.1093/database/bas018. Print 2012.


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

Linard B, Nguyen NH, Prosdocimi F, Poch O, Thompson JD.

Evol Bioinform Online. 2012;8:61-77. doi: 10.4137/EBO.S8814. Epub 2011 Dec 21.


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

Prosdocimi F, Linard B, Pontarotti P, Poch O, Thompson JD.

BMC Genomics. 2012 Jan 4;13:5. doi: 10.1186/1471-2164-13-5.


Identifying single copy orthologs in Metazoa.

Creevey CJ, Muller J, Doerks T, Thompson JD, Arendt D, Bork P.

PLoS Comput Biol. 2011 Dec;7(12):e1002269. doi: 10.1371/journal.pcbi.1002269. Epub 2011 Dec 1.


Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega.

Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG.

Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75.

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