Publications internationales

• Chronic ingestion of deoxynivalenol at human dietary levels impairs intestinal homeostasis and gut microbiota in mice
  Vignal C, Djouina M, Pichavant M, Caboche S, Waxin C, Beury D, Hot D, Gower-Rousseau C and Body-Malapel M
  Archives of toxicology, 2018, 92(7) :2327-2338. (abstract)
  


• Primary transcriptome analysis reveals importance of IS elements for the transcriptome landscape of Bordetella pertussis
  Amman F, D’Halluin A, Huot L, Bibova I, Keidel K, Slupek S, Bouquet P, Coutte L, Antoine R, Caboche S, Locht C, Vecerek B, Hot D
  RNA biology, 2018, 15(7) :967-975.(abstract)
  


• Les perspectives d'applications en santé humaine du séquençage par nanopores
  Audebert C, Hot D and Caboche S
  Medecine/Sciences, 2018, 34(4) :319-325. (abstract)
  


• MICRA: an automatic pipeline for fast characterization of microbial genomes from high-throughput sequencing data
  Caboche S; Even G; Loywick A; Audebert C and Hot D
  Genome Biology, 2017 (abstract)
  


• Assessment of Common and Emerging Bioinformatics Pipelines for Targeted Metagenomics
  Siegwald L; Touzet H; Lemoine Y; Hot D; Audebert C and Caboche S
  PLoS One, 2017 (abstract)
  


• Targeted metagenomic sequencing data of human gut microbiota associated with Blastocystis colonization
  Siegwald L, Audebert C, Even G, Viscogliosi E, Caboche S and Chabé M
  Scientific Data,2017, (abstract)
  


• Le séquençage haut-débit: Vers un diagnostic basé sur la séquence complète du génome de l'agent infectieux
  Audebert C; Hot D; Lemoine Y; Caboche S
  Médecine/Sciences (Paris), 2014, 30(12):1144-51. doi: 10.1051/medsci/20143012018. ( abstract )
  


• Bioinformatics bolster a renaissance.
  Caboche S
  Nature Chemical biology, 2014, 10(10):798-800 ; doi:10.1038/nchembio.1634 ( abstract )
  


• Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data
  Caboche S; Audebert C; Lemoine Y; Hot D
  BMC Genomics, 2014, 15(1) :264 ( abstract )
  


• High-Throughput Sequencing, a VersatileWeapon to Support Genome-Based Diagnosis in Infectious Diseases: Applications to Clinical Bacteriology
  Caboche S; Audebert C; Hot D
  Pathogens, 2014, 3(2) :258-279 ( abstract )
  


• LeView: automatic and interactive generation of 2D diagrams for biomacromolecule/ligand interactions
  Caboche S;
  Journal of Cheminformatics 2013, 5:40; doi:10.1186/1758-2946-5-40 ( abstract )
  


• A new fingerprint to predict nonribosomal peptides activity
  Abdo A; Caboche S; Leclère V; Jacques P; Pupin M;
  Journal of Computer-Aided Molecular Design 2012; DOI: 10.1007/s10822-012-9608-4 ( abstract )


• PDBe: Protein Data Bank in Europe
  Velankar S. et al.
  Nucleic Acids Research - Database issue, 2012, 40:D445-52 ( abstract )


• PDBe: Protein Data Bank in Europe
  Velankar S. et al.
  Nucleic Acids Research - Database issue, 2011, 39:D402-10 ( abstract )
  article sélectionné parmi les 5% d'articles de qualité scientifique exceptionnelle


• Diversity of monomers in nonribosomal peptides: towards the prediction of origin and biological activity
  Caboche S; Leclère V; Pupin M; Kucherov G; Jacques P
  Journal of Bacteriology 2010; Oct:192(19):5143-50 (abstract)
  article sélectionné pour la section "Journal Highlights" de Microbe qui sélectionne les meilleurs articles du mois parus dans ASM.


• Structural pattern matching of nonribosomal peptides
  Caboche S; Pupin M; Leclère V; Jacques P; Kucherov G
  BMC Structural Biology 2009; 9(1):15. (abstact)


• NORINE: a database of nonribosomal peptides
  Caboche S; Pupin M; Leclere V; Fontaine A; Jacques P; Kucherov G
  Nucleic Acids Research - Database issue, 2008, 36:D326-31 (abstract,PDF)

Publications nationales

• La synthèse peptidique non-ribosomiale, source de biodiversité de composés actifs
  Jacques P; Gancel F; Chollet-Imbert M; Guez JS; Béchet M; Caboche S; Coucheney F; Coutte F; Tapi A; Leclère V
  SFM letter, 2007

Communications d'audience internationale avec comité de sélection

• How Can You Trust your Analysis Results from Targeted Metagenomics Studies ?
  Caboche S
  Pharmabiotics, Paris (France), 2018 Invited speaker


• Analytical biases in targeted metagenomics studies
  Siegwald L and Caboche S
  RCAM 2017, Institut Pasteur, Paris (France), 2017 Invited speaker


• A pipeline to quickly and automatically characterize microbial genomes from high-throughput sequencing data
  Caboche S
  6th Clinical Microbiology Conference, Rome (Italie), 2016


• Comparison of mapping algorithms used in high-throughput sequencing: application to Ion Torrent data
  Caboche S; Audebert C; Lemoine Y; Hot D
  European Conference on Computational Biology, Strasbourg (France), 2014


• Bioinformatics tools to decrypt NonRibosomal Peptide diversity in Bacilli
  Leclère V, Pupin M, Hussein W, Béchet M, Gancel F, Chollet M, Caboche S and Jacques P
  BACELL, Gottingen (Germany), 2010


• Novel approaches to isolate antimicrobial peptides using bioinformatics and molecular tools
  Jacques P; Froidevaux R; Chollet-Imbert M; Tapi A; Caboche S; Pupin M; Kucherov G; Dhulster P; Le Flem G; Vercaigne-Marko D; Leclère V
  Second International Symposium on Antimicrobial Peptides, Saint Malo (France) 2009, communication


• Relationships between producing organisms, activities and monomers incorporated into NRPS peptides
  Leclère V; Caboche S; Pupin M; Kucherov G; Jacques P
  FEMS, congress of european microbiologists, Gothenburg (Sweden), 2009, communication et poster

Communications d'audience nationale avec comité de sélection

• La synthèse non-ribosomiale chez les actinomycètes
  Leclère V, Tonon L, Caboche S, Pupin M and Jacques P
  Journées Actinomycètes, Paris (France), 2010


• Database and comparison of non ribosomal peptides
  Caboche S, Leclère V, Jacques P, Pupin M and Kucherov G
  JOBIM 2006, (Bordeaux, France)(PDF, présentation)

Posters

• A new protocol for sequencing and analysis of virus genomes in clinical context with amplicon-seq data
  Maurier F, Beury D, Goffard A, Hot D and Caboche S, JOBIM, Marseille (France), 2018.


• How can you trust your metagenomic analysis pipeline ?
  Siegwald L, Hot D, Lemoine Y, Touzet H and Caboche S, European Conference on Computational Biology, Strasbourg (France),2014.


• Pipeline for automatic analysis of Whole Genome Sequencing data : Application to bacterial genome characterisation
  Caboche S, Audebert C, Even G, Blervaque R, Lemoine Y and Hot D, EMBO Conference on Microbiology after the genomics revolution, Paris (France), 2014.


• Bacillus mojavensis A21 a new strain for non-ribosomal peptide production
  Ben Ayed H, Hmidet N, Haddar A, Jacques P, Leclère V, Caboche S, Hot D, Béchet M, Chollet M and Nasri M
  Third international symposium on antimicrobial peptides (AMP), Lille (France), 2012.


• Discovery and annotation strategies of nonribosomal peptide synthetases from bacterial genomes
  Saci Z, Pupin M, Deravel J, Krier F, Caboche S, Jacques P and Leclère
  European Congress on Computational Biology (ECCB), Gent (Belgium), 2010.


• Stratégie de recherche et d'annotations de nouvelles synthétases non-ribosomiales à partir génomes bactériens
  Saci Z, Pupin M, Deravel J, Krier F, Caboche S, Jacques P and Leclère V
  JOBIM, Montpellier (France), 2010.


• Statistical approach of monomer diversity in non ribosomal peptides
  Caboche S, Leclère, Pupin M, Kucherov G and Jacques P
  Systems Biology of Microorganisms Conference, Paris (France), 2010.


• Relationships between producing organisms, activities and monomers incorporated into NRPS peptides
  Leclère V, Caboche S, Pupin M, Kucherov G and Jacques P
  FEMS, congress of european microbiologists, Gothenburg (Sweden), 2009.


• Norine: database and efficient algorithms dedicated to nonribosomal peptides
  Caboche S; Pupin M; Leclere V; Jacques P; Kucherov G
  ECCB 2008, Cagliari (Ilatly) 2008, poster


• Norine: a public resource of nonribosomal peptides
  Caboche S; Pupin M; Leclere V; Jacques P; Kucherov G
  EMBnet Conference 2008, Martina Franca (Italy) 2008, poster


• Norine: a platform dedicated to nonribosomal peptides
  Caboche S; Pupin M; Leclere V; Jacques P; Kucherov G
  JOBIM 2008 (Lille, France), poster


• Norine: une nouvelle base de données qui met en exergue la biodiversité des structures et des activités des peptides synthétisés par la voie non-ribosomale (NRPS)
  Caboche S, Leclère V, Pupin M, Kucherov G and Jacques P
  Poster 7ième congrés de la Société Francaise de Microbiologie, Nantes, 2007
  Prix du meilleur Poster (sur plus de 300 posters)


• NORINE: a recent database highlighting a large biodiversity among NRPS peptide structures and activities
  Leclère V, Caboche S, Pupin M, Kucherov G and Jacques P.
  RSC conference, Chemical Biology: directing biosynthesis, 2006 (PDF)