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Items: 29

1.

Routine Whole-Genome Sequencing for Outbreak Investigations of Staphylococcus aureus in a National Reference Center.

Durand G, Javerliat F, Bes M, Veyrieras JB, Guigon G, Mugnier N, Schicklin S, Kaneko G, Santiago-Allexant E, Bouchiat C, Martins-Simões P, Laurent F, Van Belkum A, Vandenesch F, Tristan A.

Front Microbiol. 2018 Mar 20;9:511. doi: 10.3389/fmicb.2018.00511. eCollection 2018.

2.

Correlation between phenotypic antibiotic susceptibility and the resistome in Pseudomonas aeruginosa.

Jaillard M, van Belkum A, Cady KC, Creely D, Shortridge D, Blanc B, Barbu EM, Dunne WM Jr, Zambardi G, Enright M, Mugnier N, Le Priol C, Schicklin S, Guigon G, Veyrieras JB.

Int J Antimicrob Agents. 2017 Aug;50(2):210-218. doi: 10.1016/j.ijantimicag.2017.02.026. Epub 2017 May 26.

PMID:
28554735
3.

A comprehensive hybridization model allows whole HERV transcriptome profiling using high density microarray.

Becker J, Pérot P, Cheynet V, Oriol G, Mugnier N, Mommert M, Tabone O, Textoris J, Veyrieras JB, Mallet F.

BMC Genomics. 2017 Apr 8;18(1):286. doi: 10.1186/s12864-017-3669-7.

4.

Optimization of alignment-based methods for taxonomic binning of metagenomics reads.

Jaillard M, Tournoud M, Meynier F, Veyrieras JB.

Bioinformatics. 2016 Jun 15;32(12):1779-87. doi: 10.1093/bioinformatics/btw040. Epub 2016 Feb 1.

PMID:
26833346
5.

Phylogenetic Distribution of CRISPR-Cas Systems in Antibiotic-Resistant Pseudomonas aeruginosa.

van Belkum A, Soriaga LB, LaFave MC, Akella S, Veyrieras JB, Barbu EM, Shortridge D, Blanc B, Hannum G, Zambardi G, Miller K, Enright MC, Mugnier N, Brami D, Schicklin S, Felderman M, Schwartz AS, Richardson TH, Peterson TC, Hubby B, Cady KC.

MBio. 2015 Nov 24;6(6):e01796-15. doi: 10.1128/mBio.01796-15.

6.

Large-scale machine learning for metagenomics sequence classification.

Vervier K, Mahé P, Tournoud M, Veyrieras JB, Vert JP.

Bioinformatics. 2016 Apr 1;32(7):1023-32. doi: 10.1093/bioinformatics/btv683. Epub 2015 Nov 20.

7.

A strategy to build and validate a prognostic biomarker model based on RT-qPCR gene expression and clinical covariates.

Tournoud M, Larue A, Cazalis MA, Venet F, Pachot A, Monneret G, Lepape A, Veyrieras JB.

BMC Bioinformatics. 2015 Mar 28;16:106. doi: 10.1186/s12859-015-0537-9.

8.

Three-dimensional characterization of bacterial microcolonies on solid agar-based culture media.

Drazek L, Tournoud M, Derepas F, Guicherd M, Mahé P, Pinston F, Veyrieras JB, Chatellier S.

J Microbiol Methods. 2015 Feb;109:149-56. doi: 10.1016/j.mimet.2014.12.011. Epub 2014 Dec 20.

PMID:
25533218
9.

Comparison of two approaches for the classification of 16S rRNA gene sequences.

Chatellier S, Mugnier N, Allard F, Bonnaud B, Collin V, van Belkum A, Veyrieras JB, Emler S.

J Med Microbiol. 2014 Oct;63(Pt 10):1311-5. doi: 10.1099/jmm.0.074377-0. Epub 2014 Jul 25.

PMID:
25062942
10.

Challenges in the culture-independent analysis of oral and respiratory samples from intubated patients.

Lazarevic V, Gaïa N, Emonet S, Girard M, Renzi G, Despres L, Wozniak H, Yugueros Marcos J, Veyrieras JB, Chatellier S, van Belkum A, Pugin J, Schrenzel J.

Front Cell Infect Microbiol. 2014 May 23;4:65. doi: 10.3389/fcimb.2014.00065. eCollection 2014.

11.

Automatic identification of mixed bacterial species fingerprints in a MALDI-TOF mass-spectrum.

Mahé P, Arsac M, Chatellier S, Monnin V, Perrot N, Mailler S, Girard V, Ramjeet M, Surre J, Lacroix B, van Belkum A, Veyrieras JB.

Bioinformatics. 2014 May 1;30(9):1280-6. doi: 10.1093/bioinformatics/btu022. Epub 2014 Jan 17.

PMID:
24443381
12.

De novo finished 2.8 Mbp Staphylococcus aureus genome assembly from 100 bp short and long range paired-end reads.

Hernandez D, Tewhey R, Veyrieras JB, Farinelli L, Østerås M, François P, Schrenzel J.

Bioinformatics. 2014 Jan 1;30(1):40-9. doi: 10.1093/bioinformatics/btt590. Epub 2013 Oct 15.

13.

The contribution of RNA decay quantitative trait loci to inter-individual variation in steady-state gene expression levels.

Pai AA, Cain CE, Mizrahi-Man O, De Leon S, Lewellen N, Veyrieras JB, Degner JF, Gaffney DJ, Pickrell JK, Stephens M, Pritchard JK, Gilad Y.

PLoS Genet. 2012;8(10):e1003000. doi: 10.1371/journal.pgen.1003000. Epub 2012 Oct 11.

14.

Genetic modifiers of chromatin acetylation antagonize the reprogramming of epi-polymorphisms.

Abraham AL, Nagarajan M, Veyrieras JB, Bottin H, Steinmetz LM, Yvert G.

PLoS Genet. 2012 Sep;8(9):e1002958. doi: 10.1371/journal.pgen.1002958. Epub 2012 Sep 20.

15.

Exon-specific QTLs skew the inferred distribution of expression QTLs detected using gene expression array data.

Veyrieras JB, Gaffney DJ, Pickrell JK, Gilad Y, Stephens M, Pritchard JK.

PLoS One. 2012;7(2):e30629. doi: 10.1371/journal.pone.0030629. Epub 2012 Feb 16.

16.

DNase I sensitivity QTLs are a major determinant of human expression variation.

Degner JF, Pai AA, Pique-Regi R, Veyrieras JB, Gaffney DJ, Pickrell JK, De Leon S, Michelini K, Lewellen N, Crawford GE, Stephens M, Gilad Y, Pritchard JK.

Nature. 2012 Feb 5;482(7385):390-4. doi: 10.1038/nature10808.

17.

Dissecting the regulatory architecture of gene expression QTLs.

Gaffney DJ, Veyrieras JB, Degner JF, Pique-Regi R, Pai AA, Crawford GE, Stephens M, Gilad Y, Pritchard JK.

Genome Biol. 2012 Jan 31;13(1):R7. doi: 10.1186/gb-2012-13-1-r7.

18.

Deciphering the genetics of flowering time by an association study on candidate genes in bread wheat (Triticum aestivum L.).

Rousset M, Bonnin I, Remoué C, Falque M, Rhoné B, Veyrieras JB, Madur D, Murigneux A, Balfourier F, Le Gouis J, Santoni S, Goldringer I.

Theor Appl Genet. 2011 Oct;123(6):907-26. doi: 10.1007/s00122-011-1636-2. Epub 2011 Jul 15.

PMID:
21761163
19.
20.

Natural single-nucleosome epi-polymorphisms in yeast.

Nagarajan M, Veyrieras JB, de Dieuleveult M, Bottin H, Fehrmann S, Abraham AL, Croze S, Steinmetz LM, Gidrol X, Yvert G.

PLoS Genet. 2010 Apr 22;6(4):e1000913. doi: 10.1371/journal.pgen.1000913.

21.

Understanding mechanisms underlying human gene expression variation with RNA sequencing.

Pickrell JK, Marioni JC, Pai AA, Degner JF, Engelhardt BE, Nkadori E, Veyrieras JB, Stephens M, Gilad Y, Pritchard JK.

Nature. 2010 Apr 1;464(7289):768-72. doi: 10.1038/nature08872. Epub 2010 Mar 10.

22.

Gene expression levels are a target of recent natural selection in the human genome.

Kudaravalli S, Veyrieras JB, Stranger BE, Dermitzakis ET, Pritchard JK.

Mol Biol Evol. 2009 Mar;26(3):649-58. doi: 10.1093/molbev/msn289. Epub 2008 Dec 17.

23.

High-resolution mapping of expression-QTLs yields insight into human gene regulation.

Veyrieras JB, Kudaravalli S, Kim SY, Dermitzakis ET, Gilad Y, Stephens M, Pritchard JK.

PLoS Genet. 2008 Oct;4(10):e1000214. doi: 10.1371/journal.pgen.1000214. Epub 2008 Oct 10.

24.

Association mapping reveals gene action and interactions in the determination of flowering time in barley.

Stracke S, Haseneyer G, Veyrieras JB, Geiger HH, Sauer S, Graner A, Piepho HP.

Theor Appl Genet. 2009 Jan;118(2):259-73. doi: 10.1007/s00122-008-0896-y. Epub 2008 Oct 2.

PMID:
18830577
25.

Genetic variation for N-remobilization and postsilking N-uptake in a set of maize recombinant inbred lines. 3. QTL detection and coincidences.

Coque M, Martin A, Veyrieras JB, Hirel B, Gallais A.

Theor Appl Genet. 2008 Sep;117(5):729-47. doi: 10.1007/s00122-008-0815-2. Epub 2008 Jun 20.

PMID:
18566796
26.

Key impact of Vgt1 on flowering time adaptation in maize: evidence from association mapping and ecogeographical information.

Ducrocq S, Madur D, Veyrieras JB, Camus-Kulandaivelu L, Kloiber-Maitz M, Presterl T, Ouzunova M, Manicacci D, Charcosset A.

Genetics. 2008 Apr;178(4):2433-7. doi: 10.1534/genetics.107.084830.

27.

MetaQTL: a package of new computational methods for the meta-analysis of QTL mapping experiments.

Veyrieras JB, Goffinet B, Charcosset A.

BMC Bioinformatics. 2007 Feb 8;8:49.

28.

Maize adaptation to temperate climate: relationship between population structure and polymorphism in the Dwarf8 gene.

Camus-Kulandaivelu L, Veyrieras JB, Madur D, Combes V, Fourmann M, Barraud S, Dubreuil P, Gouesnard B, Manicacci D, Charcosset A.

Genetics. 2006 Apr;172(4):2449-63. Epub 2006 Jan 16.

29.

GénoPlante-Info (GPI): a collection of databases and bioinformatics resources for plant genomics.

Samson D, Legeai F, Karsenty E, Reboux S, Veyrieras JB, Just J, Barillot E.

Nucleic Acids Res. 2003 Jan 1;31(1):179-82.

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