Illuminating the landscape of host-pathogen interactions with the bacterium Listeria monocytogenes, Proceedings of the National Academy of Sciences, vol.22, issue.3, pp.19484-19491, 2011. ,
DOI : 10.1016/j.smim.2010.02.002
Listeria monocytogenes: a multifaceted model, Nature Reviews Microbiology, vol.73, issue.6, pp.423-434, 2006. ,
DOI : 10.2741/A808
Human listeriosis and animal models, Microbes and Infection, vol.9, issue.10, pp.1216-1225, 2007. ,
DOI : 10.1016/j.micinf.2007.05.009
Sensu Lato: Genus-Wide Differences in Evolutionary Dynamics and the Progressive Gain of Complex, Potentially Pathogenicity-Related Traits through Lateral Gene Transfer, Genome Biology and Evolution, vol.7, issue.8, pp.2154-2172, 2015. ,
DOI : 10.1093/gbe/evv131
Listeria marthii sp. nov., isolated from the natural environment, Finger Lakes National Forest, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.60, issue.6, pp.1280-1288, 2010. ,
DOI : 10.1099/ijs.0.014118-0
Listeria rocourtiae sp. nov., INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.60, issue.9, pp.2210-2214, 2010. ,
DOI : 10.1099/ijs.0.017376-0
Listeria weihenstephanensis sp. nov., isolated from the water plant Lemna trisulca taken from a freshwater pond, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.63, issue.Pt 2, pp.641-647, 2013. ,
DOI : 10.1099/ijs.0.036830-0
Listeria fleischmannii sp. nov., isolated from cheese, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.63, issue.Pt 2, pp.526-532, 2013. ,
DOI : 10.1099/ijs.0.036947-0
Listeria floridensis sp. nov., Listeria aquatica sp. nov., Listeria cornellensis sp. nov., Listeria riparia sp. nov. and Listeria grandensis sp. nov., from agricultural and natural environments, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.64, issue.Pt 6, pp.1882-1889, 2014. ,
DOI : 10.1099/ijs.0.052720-0
Listeria booriae sp. nov. and Listeria newyorkensis sp. nov., from food processing environments in the USA, INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY, vol.65, issue.Pt 1, pp.286-292, 2015. ,
DOI : 10.1099/ijs.0.070839-0
Comparative genomics of Listeria species, Science, vol.294, pp.849-852, 2001. ,
Whole genome comparisons of serotype 4b and 1/2a strains of the food-borne pathogen Listeria monocytogenes reveal new insights into the core genome components of this species, Nucleic Acids Research, vol.32, issue.8, pp.2386-2395, 2004. ,
DOI : 10.1093/nar/gkh562
New Aspects Regarding Evolution and Virulence of Listeria monocytogenes Revealed by Comparative Genomics and DNA Arrays, Infection and Immunity, vol.72, issue.2, pp.1072-1083, 2004. ,
DOI : 10.1128/IAI.72.2.1072-1083.2004
High-throughput genome sequencing of two Listeria monocytogenes clinical isolates during a large foodborne outbreak, BMC Genomics, vol.11, issue.1, 2010. ,
DOI : 10.1093/bioinformatics/btn578
Listeria monocytogenes lineages: Genomics, evolution, ecology, and phenotypic characteristics, International Journal of Medical Microbiology, vol.301, issue.2, 2011. ,
DOI : 10.1016/j.ijmm.2010.05.002
Reassessment of the Listeria monocytogenes pan-genome reveals dynamic integration hotspots and mobile genetic elements as major components of the accessory genome, BMC Genomics, vol.14, issue.1, pp.471471-2164, 2013. ,
DOI : 10.1186/1471-2164-13-384.:384-13
Comparison of Widely Used Listeria monocytogenes Strains EGD, 10403S, and EGD-e Highlights Genomic Differences Underlying Variations in Pathogenicity, mBio, vol.5, issue.2, pp.969-1400969, 2014. ,
DOI : 10.1128/mBio.00969-14
GenoList: an integrated environment for comparative analysis of microbial genomes, Nucleic Acids Research, vol.36, issue.Database, pp.469-474, 2008. ,
DOI : 10.1093/nar/gkm1042
Development of ListeriaBase and comparative analysis of Listeria monocytogenes, BMC Genomics, vol.51, issue.6, pp.755-12864, 2015. ,
DOI : 10.1093/nar/16.22.10881
Characterization of relA and codY mutants of Listeria monocytogenes: identification of the CodY regulon and its role in virulence, Molecular Microbiology, vol.21, issue.5, pp.1453-1467, 2007. ,
DOI : 10.1128/JB.187.21.7243-7253.2005
ArrayExpress update--trends in database growth and links to data analysis tools, Nucleic Acids Research, vol.41, issue.D1, pp.987-990, 2013. ,
DOI : 10.1093/nar/gks1174
Comparative transcriptomics of pathogenic and non-pathogenic Listeria species, Molecular Systems Biology, vol.270, p.583, 2012. ,
DOI : 10.1093/nar/gkm951
sRNAdb: A small non-coding RNA database for gram-positive bacteria, BMC Genomics, vol.13, issue.1, p.384, 2012. ,
DOI : 10.1186/1471-2164-13-384
URL : http://doi.org/10.1186/1471-2164-13-384
House-keeping Protein Secretion Systems, Molecular & Cellular Proteomics, vol.174, issue.11, pp.3063-3081, 2014. ,
DOI : 10.1073/pnas.0401742101
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4223492
EGD-e by Secretomics, Journal of Proteome Research, vol.9, issue.10, pp.5076-5092, 2010. ,
DOI : 10.1021/pr1003642
URL : https://hal.archives-ouvertes.fr/hal-00964252
Exoproteomic analysis of the SecA2-dependent secretion in Listeria monocytogenes EGD-e, Journal of Proteomics, vol.80, pp.183-195, 2013. ,
DOI : 10.1016/j.jprot.2012.11.027
Subcellular Localization of Extracytoplasmic Proteins in Monoderm Bacteria: Rational Secretomics-Based Strategy for Genomic and Proteomic Analyses, PLoS ONE, vol.7, issue.8, 2012. ,
DOI : 10.1371/journal.pone.0042982.s008
species, PROTEOMICS, vol.24, issue.6, pp.1544-1557, 2005. ,
DOI : 10.1016/S0968-0004(98)01335-8
cell wall proteome by two-dimensional nanoliquid chromatography coupled to mass spectrometry, PROTEOMICS, vol.69, issue.2, pp.433-443, 2005. ,
DOI : 10.1128/AEM.69.6.3368-3376.2003
Occurrence of mutations impairing sigma factor B (SigB) function upon inactivation of Listeria monocytogenes genes encoding surface proteins, Microbiology, vol.159, issue.Pt_7, pp.1328-1339, 2013. ,
DOI : 10.1099/mic.0.067744-0
???LANESPECTOR???, a tool for membrane proteome profiling based on sodium dodecyl sulfate-polyacrylamide gel electrophoresis/liquid chromatography - tandem mass spectrometry analysis: Application toListeria monocytogenes membrane proteins, ELECTROPHORESIS, vol.4, issue.12, pp.2450-2460, 2005. ,
DOI : 10.1002/elps.200410348
LEGER: knowledge database and visualization tool for comparative genomics of pathogenic and non-pathogenic Listeria species, Nucleic Acids Research, vol.34, issue.90001, pp.402-406, 2006. ,
DOI : 10.1093/nar/gkj071
Proteomic identification of Listeria monocytogenes surfaceassociated proteins, Proteomics, vol.13, pp.3040-3045, 2013. ,
Transcription factor B plays an important role in the production of extracellular membranederived vesicles in Listeria monocytogenes, PLoS One, vol.8, 2013. ,
Comparison of five methods for direct extraction of surface proteins from Listeria monocytogenes for proteomic analysis by orbitrap mass spectrometry, Journal of Microbiological Methods, vol.110, pp.54-60, 2015. ,
DOI : 10.1016/j.mimet.2015.01.004
Comparative Proteomic Analysis of Listeria monocytogenes Strains F2365 and EGD, Applied and Environmental Microbiology, vol.75, issue.2, pp.366-373, 2009. ,
DOI : 10.1128/AEM.01847-08
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2620715
Proteomic expression profiles of virulent and avirulent strains of Listeria monocytogenes isolated from macrophages, Journal of Proteomics, vol.74, issue.10, pp.1906-1917, 2011. ,
DOI : 10.1016/j.jprot.2011.05.008
Under Thermotolerance-Inducing, Heat Shock, and Prolonged Heat Shock Conditions, Foodborne Pathogens and Disease, vol.6, issue.9, pp.1133-1140, 2009. ,
DOI : 10.1089/fpd.2009.0286
Proteomics for the elucidation of cold adaptation mechanisms in Listeria monocytogenes, Journal of Proteomics, vol.73, issue.10, pp.2021-2030, 2010. ,
DOI : 10.1016/j.jprot.2010.06.011
Isolation and 2-D-DIGE proteomic analysis of intracellular and extracellular forms of Listeria monocytogenes, PROTEOMICS, vol.17, issue.24, pp.5484-5496, 2009. ,
DOI : 10.1128/AAC.34.4.539
Carbon Catabolite Control is Important for Listeria monocytogenes Biofilm Formation in Response to Nutrient Availability, Current Microbiology, vol.77, issue.5, pp.35-43, 2012. ,
DOI : 10.1128/IAI.00195-09
Two-dimensional electrophoresis database of Listeria monocytogenes EGDe proteome and proteomic analysis of mid-log and stationary Listeriomics: Web Platform for Listeria Systems Biology, pp.186-202, 2004. ,
Proteomic Analyses of a Listeria monocytogenes Mutant Lacking ??B Identify New Components of the ??B Regulon and Highlight a Role for ??B in the Utilization of Glycerol, Applied and Environmental Microbiology, vol.74, issue.3, pp.594-60401921, 2008. ,
DOI : 10.1128/AEM.01921-07
ENCODE Data in the UCSC Genome Browser: year 5 update, Nucleic Acids Research, vol.41, issue.D1, pp.56-63, 2013. ,
DOI : 10.1093/nar/gks1172
The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases, Nucleic Acids Research, vol.42, issue.D1, pp.459-471, 2014. ,
DOI : 10.1093/nar/gkt1103
The Listeria monocytogenes strain 10403S BioCyc database. Database (Oxford) 2015. https, 2015. ,
DOI : 10.1093/database/bav027
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4377088
PATRIC, the bacterial bioinformatics database and analysis resource, Nucleic Acids Research, vol.42, issue.D1, pp.581-591, 2014. ,
DOI : 10.1093/nar/gkt1099
URL : http://doi.org/10.1093/nar/gkt1099
Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria, Current Opinion in Microbiology, vol.14, issue.5, pp.599-607, 2011. ,
DOI : 10.1016/j.mib.2011.09.003
RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more, Nucleic Acids Research, vol.41, issue.D1, pp.203-213, 2013. ,
DOI : 10.1093/nar/gks1201
PortEco: a resource for exploring bacterial biology through high-throughput data and analysis tools, Nucleic Acids Research, vol.42, issue.D1, pp.677-684, 2014. ,
DOI : 10.1093/nar/gkt1203
URL : http://doi.org/10.1093/nar/gku902
SubtiWiki--a comprehensive community resource for the model organism Bacillus subtilis, Nucleic Acids Research, vol.40, issue.D1, pp.1278-1287, 2012. ,
DOI : 10.1093/nar/gkr923
BLAST+: architecture and applications, BMC Bioinformatics, vol.10, issue.1, p.421, 2009. ,
DOI : 10.1186/1471-2105-10-421
URL : http://doi.org/10.1186/1471-2105-10-421
SynTView ??? an interactive multi-view genome browser for next-generation comparative microorganism genomics, BMC Bioinformatics, vol.14, issue.1, pp.2771471-2105, 2013. ,
DOI : 10.1126/science.1182395
URL : https://hal.archives-ouvertes.fr/pasteur-00870285
Identification of new noncoding RNAs in Listeria monocytogenes and prediction of mRNA targets, Nucleic Acids Research, vol.35, issue.3, pp.962-974, 2007. ,
DOI : 10.1093/nar/gkl1096
URL : https://hal.archives-ouvertes.fr/hal-00129258
The Listeria transcriptional landscape from saprophytism to virulence, Nature, vol.99, issue.7249, pp.950-956, 2009. ,
DOI : 10.1016/S1438-4221(00)80086-7
Deep RNA sequencing of L. monocytogenes reveals overlapping and extensive stationary phase and sigma B-dependent transcriptomes, including multiple highly transcribed noncoding RNAs, BMC Genomics, vol.10, issue.1, p.641, 2009. ,
DOI : 10.1186/1471-2164-10-641
The intracellular sRNA transcriptome of Listeria monocytogenes during growth in macrophages, Nucleic Acids Research, vol.39, issue.10, pp.4235-4248, 2011. ,
DOI : 10.1093/nar/gkr033
Listeria monocytogenes Surface Proteins: from Genome Predictions to Function, Microbiology and Molecular Biology Reviews, vol.71, issue.2, pp.377-39700039, 2007. ,
DOI : 10.1128/MMBR.00039-06
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1899877
Guilt by Association: Contextual Information in Genome Analysis, Genome Research, vol.10, issue.8, pp.1074-1077, 2000. ,
DOI : 10.1101/gr.10.8.1074
URL : http://genome.cshlp.org/content/10/8/1074.full.pdf
The Sequence Read Archive, Nucleic Acids Research, vol.39, issue.Database, pp.19-21, 2011. ,
DOI : 10.1093/nar/gkq1019
URL : http://doi.org/10.1093/nar/gkq1019
Detection of Very Long Antisense Transcripts by Whole Transcriptome RNA-Seq Analysis of Listeria monocytogenes by Semiconductor Sequencing Technology, PLoS ONE, vol.185, issue.10, 2014. ,
DOI : 10.1371/journal.pone.0108639.t003
Term-seq reveals abundant ribo-regulation of antibiotics [sic] resistance in bacteria, Science, vol.352, 2016. ,
ActA Is Required for Crossing of the Fetoplacental Barrier by Listeria monocytogenes, Infection and Immunity, vol.75, issue.2, pp.950-957, 2007. ,
DOI : 10.1128/IAI.01570-06
Listeria monocytogenes ActA-mediated escape from autophagic recognition, Nature Cell Biology, vol.113, issue.10, pp.1233-1240, 2009. ,
DOI : 10.1038/ni.1634
ActA Promotes Listeria monocytogenes Aggregation, Intestinal Colonization and Carriage, PLoS Pathogens, vol.56, issue.1, 2013. ,
DOI : 10.1371/journal.ppat.1003131.s005
URL : http://doi.org/10.1371/journal.ppat.1003131
Enrichment analysis in high-throughput genomics???accounting for dependency in the NULL, Briefings in Bioinformatics, vol.8, issue.2, pp.71-77, 2007. ,
DOI : 10.1093/bib/bbl019
The PrfA virulence regulon, Microbes and Infection, vol.9, issue.10, pp.1196-1207, 2007. ,
DOI : 10.1016/j.micinf.2007.05.007
Contribution of Three Bile-Associated Loci, bsh, pva, and btlB, to Gastrointestinal Persistence and Bile Tolerance of Listeria monocytogenes, Infection and Immunity, vol.73, issue.2, pp.894-904, 2005. ,
DOI : 10.1128/IAI.73.2.894-904.2005
A riboswitch-regulated antisense RNA in Listeria monocytogenes, Proceedings of the National Academy of Sciences, vol.109, issue.41, pp.13132-13137, 2013. ,
DOI : 10.1073/pnas.1212809109
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3740843
Annotation, comparison and databases for hundreds of bacterial genomes, Research in Microbiology, vol.158, issue.10, pp.724-736, 2007. ,
DOI : 10.1016/j.resmic.2007.09.009
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki, Database, vol.2009, issue.0, p.12, 2009. ,
DOI : 10.1093/database/bap012
A New Perspective on Listeria monocytogenes Evolution, PLoS Pathogens, vol.35, issue.9, 2008. ,
DOI : 10.1371/journal.ppat.1000146.s003
URL : http://doi.org/10.1371/journal.ppat.1000146
UNAFold, Methods Mol Biol, vol.453, pp.3-31, 2008. ,
DOI : 10.1007/978-1-60327-429-6_1
PanOCT: automated clustering of orthologs using conserved gene neighborhood for pan-genomic analysis of bacterial strains and closely related species, Nucleic Acids Research, vol.40, issue.22, 2012. ,
DOI : 10.1093/nar/gks757
ProbCons: Probabilistic consistency-based multiple sequence alignment, Genome Research, vol.15, issue.2, pp.330-340, 2005. ,
DOI : 10.1101/gr.2821705
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC546535
Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein, 2007. ,
FastTree 2?approximately maximum-likelihood trees for large alignments. PLoS One 5:e9490. https, 2010. ,
DOI : 10.1371/journal.pone.0009490
URL : http://doi.org/10.1371/journal.pone.0009490
A simple spreadsheet-based, MIAME-supportive format for microarray data: MAGE-TAB, BMC Bioinformatics, vol.7, issue.1, p.489, 1471. ,
DOI : 10.1186/1471-2105-7-489
URL : https://academic.oup.com/bioinformatics/article-pdf/25/2/279/589233/btn617.pdf
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biology, vol.10, issue.3, 2009. ,
DOI : 10.1186/gb-2009-10-3-r25
Fast Mapping of Short Sequences with Mismatches, Insertions and Deletions Using Index Structures, PLoS Computational Biology, vol.12, issue.9, 2009. ,
DOI : 10.1371/journal.pcbi.1000502.t001
Differential expression analysis for sequence count data, Genome Biol, vol.11, 2010. ,
DOI : 10.1038/npre.2010.4282.1
URL : https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3218662/pdf