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TPMS: a set of utilities for querying collections of gene trees.

Bigot T, Daubin V, Lassalle F, Perrière G.

BMC Bioinformatics. 2013 Mar 27;14:109. doi: 10.1186/1471-2105-14-109.


Databases of homologous gene families for comparative genomics.

Penel S, Arigon AM, Dufayard JF, Sertier AS, Daubin V, Duret L, Gouy M, Perrière G.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S3. doi: 10.1186/1471-2105-10-S6-S3.


Bioinformatics in the complete genome sequence era.

Perrière G.

Biochimie. 2008 Apr;90(4):553-4. doi: 10.1016/j.biochi.2008.02.008. Epub 2008 Feb 19. No abstract available.


Horizontal gene transfer regulation in bacteria as a "spandrel" of DNA repair mechanisms.

Fall S, Mercier A, Bertolla F, Calteau A, Gueguen L, Perrière G, Vogel TM, Simonet P.

PLoS One. 2007 Oct 24;2(10):e1055.


Automatic identification of large collections of protein-coding or rRNA sequences.

Arigon AM, Perrière G, Gouy M.

Biochimie. 2008 Apr;90(4):609-14. Epub 2007 Sep 2.


Integrating transcription factor binding site information with gene expression datasets.

Jeffery IB, Madden SF, McGettigan PA, Perrière G, Culhane AC, Higgins DG.

Bioinformatics. 2007 Feb 1;23(3):298-305. Epub 2006 Nov 24.


HoSeqI: automated homologous sequence identification in gene family databases.

Arigon AM, Perrière G, Gouy M.

Bioinformatics. 2006 Jul 15;22(14):1786-7. Epub 2006 May 8.


Physiological oxygenation status is required for fully differentiated phenotype in kidney cortex proximal tubules.

de Laplanche E, Gouget K, Cléris G, Dragounoff F, Demont J, Morales A, Bezin L, Godinot C, Perrière G, Mouchiroud D, Simonnet H.

Am J Physiol Renal Physiol. 2006 Oct;291(4):F750-60. Epub 2006 Apr 4.


Origin and molecular evolution of receptor tyrosine kinases with immunoglobulin-like domains.

Grassot J, Gouy M, Perrière G, Mouchiroud G.

Mol Biol Evol. 2006 Jun;23(6):1232-41. Epub 2006 Mar 21.


Optimized between-group classification: a new jackknife-based gene selection procedure for genome-wide expression data.

Baty F, Bihl MP, Perrière G, Culhane AC, Brutsche MH.

BMC Bioinformatics. 2005 Sep 28;6:239.


Horizontal transfer of two operons coding for hydrogenases between bacteria and archaea.

Calteau A, Gouy M, Perrière G.

J Mol Evol. 2005 May;60(5):557-65.


Type I polyketide synthases may have evolved through horizontal gene transfer.

Ginolhac A, Jarrin C, Robe P, Perrière G, Vogel TM, Simonet P, Nalin R.

J Mol Evol. 2005 Jun;60(6):716-25. Epub 2005 May 16.


MADE4: an R package for multivariate analysis of gene expression data.

Culhane AC, Thioulouse J, Perrière G, Higgins DG.

Bioinformatics. 2005 Jun 1;21(11):2789-90. Epub 2005 Mar 29.


Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases.

Dufayard JF, Duret L, Penel S, Gouy M, Rechenmann F, Perrière G.

Bioinformatics. 2005 Jun 1;21(11):2596-603. Epub 2005 Feb 15.


Online synonymous codon usage analyses with the ade4 and seqinR packages.

Charif D, Thioulouse J, Lobry JR, Perrière G.

Bioinformatics. 2005 Feb 15;21(4):545-7. Epub 2004 Sep 16.


Phylogenetic analysis of polyketide synthase I domains from soil metagenomic libraries allows selection of promising clones.

Ginolhac A, Jarrin C, Gillet B, Robe P, Pujic P, Tuphile K, Bertrand H, Vogel TM, Perrière G, Simonet P, Nalin R.

Appl Environ Microbiol. 2004 Sep;70(9):5522-7.


Update of NUREBASE: nuclear hormone receptor functional genomics.

Ruau D, Duarte J, Ourjdal T, Perrière G, Laudet V, Robinson-Rechavi M.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D165-7.


The European ribosomal RNA database.

Wuyts J, Perrière G, Van De Peer Y.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D101-3.


Cross-platform comparison and visualisation of gene expression data using co-inertia analysis.

Culhane AC, Perrière G, Higgins DG.

BMC Bioinformatics. 2003 Nov 21;4:59.


The source of laterally transferred genes in bacterial genomes.

Daubin V, Lerat E, Perrière G.

Genome Biol. 2003;4(9):R57. Epub 2003 Aug 21.

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