Stephane Cruveiller

Stephane Cruveiller

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Stephane Cruveiller

Publications by authors named "Stephane Cruveiller"

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High-Throughput Sequencing (HTS) of newly synthetized RNAs enables one shot detection and identification of live mycoplasmas and differentiation from inert nucleic acids.

Biologicals 2020 May 26;65:18-24. Epub 2020 Mar 26.

PathoQuest, Paris, France; Ecole Nationale Vétérinaire d'Alfort, Université Paris-Est, Maisons-Alfort, 94704 Cedex, France; Pathogen Discovery Laboratory, Institut Pasteur, Paris, France. Electronic address:

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http://dx.doi.org/10.1016/j.biologicals.2020.03.002DOI Listing
May 2020

Repeated horizontal gene transfers triggered parallel evolution of magnetotaxis in two evolutionary divergent lineages of magnetotactic bacteria.

ISME J 2020 Apr 15. Epub 2020 Apr 15.

Aix-Marseille University, CEA, CNRS, Biosciences and Biotechnologies Institute of Aix-Marseille, Saint Paul lez Durance, France.

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http://dx.doi.org/10.1038/s41396-020-0647-xDOI Listing
April 2020

PPanGGOLiN: Depicting microbial diversity via a partitioned pangenome graph.

PLoS Comput Biol 2020 Mar 19;16(3):e1007732. Epub 2020 Mar 19.

LABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d'Évry, Université Paris-Saclay, CNRS, Evry, France.

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http://dx.doi.org/10.1371/journal.pcbi.1007732DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7108747PMC
March 2020

Genomic study of a novel magnetotactic Alphaproteobacteria uncovers the multiple ancestry of magnetotaxis.

Environ Microbiol 2018 12 16;20(12):4415-4430. Epub 2018 Oct 16.

Institute of Biosciences and Biotechnologies of Aix Marseille (BIAM), UMR7265 CEA - CNRS - Aix Marseille University, CEA Cadarache, 13108, Saint-Paul-lez-Durance, France.

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http://dx.doi.org/10.1111/1462-2920.14364DOI Listing
December 2018

The genomic and transcriptomic basis of the potential of Lactobacillus plantarum A6 to improve the nutritional quality of a cereal based fermented food.

Int J Food Microbiol 2018 Feb 6;266:346-354. Epub 2017 Oct 6.

IRD, UMR NUTRIPASS, IRD/Montpellier2/Montpellier1, F-34394 Montpellier, France. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S01681605173042
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http://dx.doi.org/10.1016/j.ijfoodmicro.2017.10.011DOI Listing
February 2018

Genomic and Transcriptomic Analysis of Growth-Supporting Dehalogenation of Chlorinated Methanes in .

Front Microbiol 2017 1;8:1600. Epub 2017 Sep 1.

Department of Molecular Genetics, Genomics, and Microbiology, UMR 7156 Université de Strasbourg (UNISTRA)-Centre National de la Recherche ScientifiqueStrasbourg, France.

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http://dx.doi.org/10.3389/fmicb.2017.01600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5585157PMC
September 2017

DNA Adenine Methyltransferase (Dam) Overexpression Impairs Motility and Virulence.

Front Microbiol 2017 1;8:1671. Epub 2017 Sep 1.

Diversité, Génomes Interactions Microorganismes Insectes (DGIMI), Institut National De La Recherche Agronomique, Université de MontpellierMontpellier, France.

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http://dx.doi.org/10.3389/fmicb.2017.01671DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5585154PMC
September 2017

Strand-specific transcriptomes of Enterohemorrhagic Escherichia coli in response to interactions with ground beef microbiota: interactions between microorganisms in raw meat.

BMC Genomics 2017 08 3;18(1):574. Epub 2017 Aug 3.

UMR 5557 Ecologie Microbienne, Research Group on Bacterial Opportunistic Pathogens and Environment, CNRS, VetAgro Sup and Université de Lyon, Lyon, France.

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http://dx.doi.org/10.1186/s12864-017-3957-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5543532PMC
August 2017

Complete Genome Sequence of sp. ORS285, a Photosynthetic Strain Able To Establish Nod Factor-Dependent or Nod Factor-Independent Symbiosis with Legumes.

Genome Announc 2017 Jul 27;5(30). Epub 2017 Jul 27.

IRD, Laboratoire des Symbioses Tropicales et Méditerranéennes, UMR IRD/SupAgro/INRA/UM/CIRAD, Campus International de Baillarguet, TA A-82/J, Montpellier, France

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http://dx.doi.org/10.1128/genomeA.00421-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5532818PMC
July 2017

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes.

Nucleic Acids Res 2017 01 29;45(D1):D517-D528. Epub 2016 Nov 29.

UMR 8030, CNRS, Université Évry-Val-d'Essonne, CEA, Institut de Génomique - Genoscope, Laboratoire d'Analyses Bioinformatiques pour la Génomique et le Métabolisme, F-91000 Évry, France

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http://dx.doi.org/10.1093/nar/gkw1101DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5210572PMC
January 2017

The revisited genome of Pseudomonas putida KT2440 enlightens its value as a robust metabolic chassis.

Environ Microbiol 2016 10 28;18(10):3403-3424. Epub 2016 Apr 28.

Alternative Energies and Atomic Energy Commission (CEA), Genomic Institute & CNRS-UMR8030 & Evry University, Laboratory of Bioinformatics Analysis in Genomics and Metabolism, 2 rue Gaston Crémieux, 91057, Evry, France.

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http://dx.doi.org/10.1111/1462-2920.13230DOI Listing
October 2016

Draft Genome Sequence of Campylobacter jejuni Bf, an Atypical Strain Able To Grow under Aerobiosis.

Genome Announc 2016 Apr 7;4(2). Epub 2016 Apr 7.

Institut National de Recherche Agronomique, UMR1014, Secalim, Nantes, France LUNAM Université, Oniris, Nantes, France

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http://dx.doi.org/10.1128/genomeA.00120-16DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4824246PMC
April 2016

Contrasting effects of historical contingency on phenotypic and genomic trajectories during a two-step evolution experiment with bacteria.

BMC Evol Biol 2016 Apr 23;16:86. Epub 2016 Apr 23.

Univ. Grenoble Alpes, Laboratoire Technologies de l'Ingénierie Médicale et de la Complexité - Informatique, Mathématiques et Applications (TIMC-IMAG), F-38000, Grenoble, France.

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http://dx.doi.org/10.1186/s12862-016-0662-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4841947PMC
April 2016

In planta comparative transcriptomics of host-adapted strains of Ralstonia solanacearum.

PeerJ 2016 5;4:e1549. Epub 2016 Jan 5.

UMR Peuplements Végétaux et Bioagresseurs en Milieu Tropical, Centre de coopération International en Recherche Agronomique pour le Développement, Saint-Pierre, France; Département de Santé des Plantes et Environnement, Institut National de la Recherche Agronomique, Sophia Antipolis, France.

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http://dx.doi.org/10.7717/peerj.1549DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4715432PMC
January 2016

Synonymous Genetic Variation in Natural Isolates of Escherichia coli Does Not Predict Where Synonymous Substitutions Occur in a Long-Term Experiment.

Mol Biol Evol 2015 Nov 20;32(11):2897-904. Epub 2015 Jul 20.

Ecology, Evolutionary Biology, and Behavior Program, Michigan State University BEACON Center for the Study of Evolution in Action, Michigan State University.

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http://dx.doi.org/10.1093/molbev/msv161DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4651231PMC
November 2015

Characterization of a P1-like bacteriophage carrying an SHV-2 extended-spectrum β-lactamase from an Escherichia coli strain.

Antimicrob Agents Chemother 2014 Nov 18;58(11):6550-7. Epub 2014 Aug 18.

INSERM, IAME, UMR 1137, Paris, France Université Paris Diderot, IAME, UMR 1137, Sorbonne Paris Cité, Paris, France APHP, Hôpital Louis Mourier, Service de Microbiologie, Colombes, France

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http://dx.doi.org/10.1128/AAC.03183-14DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4249366PMC
November 2014

Transient hypermutagenesis accelerates the evolution of legume endosymbionts following horizontal gene transfer.

PLoS Biol 2014 Sep 2;12(9):e1001942. Epub 2014 Sep 2.

INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France; CNRS, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR2594, Castanet-Tolosan, France.

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http://dx.doi.org/10.1371/journal.pbio.1001942DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4151985PMC
September 2014

Novel metabolic features in ADP1 revealed by a multiomics approach.

Metabolomics 2014 29;10(6):1223-1238. Epub 2014 Apr 29.

Direction des Sciences du Vivant, Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Institut de Génomique, Evry, France.

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http://dx.doi.org/10.1007/s11306-014-0662-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4213383PMC
April 2014

Epistasis and allele specificity in the emergence of a stable polymorphism in Escherichia coli.

Science 2014 Mar 6;343(6177):1366-9. Epub 2014 Mar 6.

Laboratoire Adaptation et Pathogénie des Microorganismes, Université Joseph Fourier, Institut Jean Roget, F-38041 Grenoble, France.

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http://dx.doi.org/10.1126/science.1248688DOI Listing
March 2014

Experimental evolution of nodule intracellular infection in legume symbionts.

ISME J 2013 Jul 21;7(7):1367-77. Epub 2013 Feb 21.

INRA, Laboratoire des Interactions Plantes-Microorganismes (LIPM), UMR441, Castanet-Tolosan, France.

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http://dx.doi.org/10.1038/ismej.2013.24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3695290PMC
July 2013

Mutation rate dynamics in a bacterial population reflect tension between adaptation and genetic load.

Proc Natl Acad Sci U S A 2013 Jan 17;110(1):222-7. Epub 2012 Dec 17.

Laboratoire Adaptation et Pathogénie des Micro-Organismes, Université Joseph Fourier Grenoble, F-38042 Grenoble Cedex 9, France.

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http://dx.doi.org/10.1073/pnas.1219574110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3538217PMC
January 2013

Chemical evolution of a bacterium's genome.

Angew Chem Int Ed Engl 2011 Jul 27;50(31):7109-14. Epub 2011 Jun 27.

Heurisko USA Inc., Delaware, USA.

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http://dx.doi.org/10.1002/anie.201100535DOI Listing
July 2011

Proteomic analysis of Marinobacter hydrocarbonoclasticus SP17 biofilm formation at the alkane-water interface reveals novel proteins and cellular processes involved in hexadecane assimilation.

Res Microbiol 2009 Dec 26;160(10):829-37. Epub 2009 Sep 26.

Institut Pluridisciplinaire de Recherche en Environnement et Matériaux, Equipe Environnement et Microbiologie UMR5254 CNRS, IBEAS, Université de Pau et des Pays de l'Adour, BP1155, 64013 Pau Cedex, France.

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http://linkinghub.elsevier.com/retrieve/pii/S092325080900158
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http://dx.doi.org/10.1016/j.resmic.2009.09.010DOI Listing
December 2009

From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later.

Microbiology 2009 Jun 21;155(Pt 6):1758-1775. Epub 2009 Apr 21.

Institut Pasteur, Génétique des Génomes Bactériens/CNRS URA2171, 28 rue du Docteur Roux, 75724 Paris Cedex 15, France.

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http://dx.doi.org/10.1099/mic.0.027839-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2885750PMC
June 2009

Simple proteomic checks for detecting noncoding RNA.

Proteomics 2007 Feb;7(3):361-3

Atelier de Génomique Comparative, Genoscope, Centre National de Séquençage, Evry, France.

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http://dx.doi.org/10.1002/pmic.200600813DOI Listing
February 2007

MaGe: a microbial genome annotation system supported by synteny results.

Nucleic Acids Res 2006 10;34(1):53-65. Epub 2006 Jan 10.

Atelier de Génomique Comparative, CNRS-UMR8030, 2 rue Gaston Crémieux, 91057 Evry, Cedex, France.

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http://dx.doi.org/10.1093/nar/gkj406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1326237PMC
January 2006

MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.

Nucleic Acids Res 2005 Jul;33(Web Server issue):W471-9

Genoscope/UMR-CNRS 8030, Atelier de Génomique Comparative, 2 rue Gaston Crémieux, F-91006 Evry, France.

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http://dx.doi.org/10.1093/nar/gki498DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160258PMC
July 2005

The new genes of rice: a closer look.

Trends Plant Sci 2004 Jun;9(6):281-5

Laboratoire di Evoluzione Molecolare, Stazione Zoologica Anton Dohrn, Villa Comunale, 80121 Naples, Italy.

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http://dx.doi.org/10.1016/j.tplants.2004.04.006DOI Listing
June 2004

Inaccurate reconstruction of ancestral GC levels creates a "vanishing isochores" effect.

Mol Phylogenet Evol 2004 May;31(2):788-93

Secciòn Biomatemàtica, Facultad de Ciencias, Montevideo 11400, Uruguay.

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http://dx.doi.org/10.1016/j.ympev.2004.01.016DOI Listing
May 2004

Compositional gene landscapes in vertebrates.

Genome Res 2004 May;14(5):886-92

Laboratorio di Evoluzione Molecolare, Stazione Zoologica Anton Dohrn, 80121 Napoli, Italy.

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http://dx.doi.org/10.1101/gr.2246704DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC479116PMC
May 2004

Incorrectly predicted genes in rice?

Gene 2004 May;333:187-8

Laboratorio di Evoluzione Molecolare, Stazione Zoologica Anton Dohrn, Villa comunale, 80121 Naples, Italy.

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http://dx.doi.org/10.1016/j.gene.2004.02.039DOI Listing
May 2004

The correlation between GC3 and hydropathy in human genes.

Gene 2003 Oct;317(1-2):137-40

Laboratoire de Génétique Moléculaire, Institut Jacques Monod, 2 Place Jussieu, 75005 Paris, France.

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http://dx.doi.org/10.1016/s0378-1119(03)00663-2DOI Listing
October 2003

AMIGene: Annotation of MIcrobial Genes.

Nucleic Acids Res 2003 Jul;31(13):3723-6

Génoscope/UMR-CNRS 8030, Atelier de Génomique Comparative, 2 rue Gaston Crémieux, F-91006 Evry, France.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC168996PMC
http://dx.doi.org/10.1093/nar/gkg590DOI Listing
July 2003

Compositional features of eukaryotic genomes for checking predicted genes.

Brief Bioinform 2003 Mar;4(1):43-52

Genoscope, French National Sequencing Center, Evry.

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http://dx.doi.org/10.1093/bib/4.1.43DOI Listing
March 2003