version française

Current position

After my PhD, I had a post-doctoral position at PDBe (Protein Data Bank Europe) of EBI (European Bioinformatic Institute), Cambridge (UK). Now, I have a one-year lecturer contract at the University of Lille1.

Cursus

After obtained a DEUG Sciences et Vie, in University Jean Perrin of Lens, i integrate IUP Génie Biologique et Informatique of Evry. This IUP is a three-years formation, balanced between theoretical and practical teaching. It also allows to obtain a double competence in biology and bioinformatics [teaching program]. I then integrate the Master Informatique et Mathématiques pour la Biologie Intégrative of University of Evry Val d'essonne.

Curriculum Vitae [pdf]

Thesis

I defended my PhD the 8th of septembre of 2009 ( manuscript, slides ).

Jury:

• Thesis supervisor: Gregory Kucherov (LIFL, France)
• co-supervisor: Maude Pupin (LIFL, France)
• co-supervisor: Valérie Leclère (ProBioGEM, France)
• Reviewer: Marie-Dominique Devignes (LORIA, France)
• Reviewer: Pierre Cornelis (VIB, Belgique)
• Examiner: Bernard Wathelet (UCBI, Belgique)
• Examiner: Daslav Hranueli (PBF, Croatie)
• President: Philippe Jacques (ProBioGEM, France)

Abstract: Nonribosomal peptides are molecules produced by microorganisms and displaying a broad spectrum of biological activities and pharmaceutical applications. They can harbor anti-microbial, immuno-modulating or anti-tumor activities. These peptides are synthesized by huge multi-enzymatic complexes, called NonRibosomal Peptide Synthetases. Two main structural traits distinguish these peptides from the ribosomally synthesized ones : first, their primary structure is not always linear but is often cyclic (partially or totally), branched or poly-cyclic, and second, the diversity of monomers incorporated into nonribosomal peptides extends far beyond the 20 proteogenic amino acids residues. We have developed Norine, the first public resource entirely dedicated to nonribosomal peptides. Norine currently contains more than 1 000 peptides, modeled by non-oriented labeled graphs, and computational tools allowing their analysis, such as monomer composition comparison, structural pattern matching or similarity search. Statistical analysis of Norine data highlighted interesting biological properties such as a speci?c monomer composition depending on the biological activity, that led us to develop a tool for helping the prediction of peptide activity from its monomeric composition. In three years, Norine became the international resource for nonribosomal peptides.

I have done my PhD (INRIA/Région) in the BioInfo team (INRIA Sequoia) of LIFL and at the ProBioGEM laboratory.

Teaching

I gave 74 teaching hours in three years for different formations of Lille1 University:

• Bioinformatic: TD in M1 of Genomic and Proteomic, 24 hours in 2007--2008 and 20 hours in 2008--2009
• Bioinformatic Option: TD in L3 et M1 of computer sciences, 10 hours in 2006--2007 and 10 hours in 2007--2008
• Advanced Databases: TD in L3 et M1 of computer sciences, 10 hours in 2008--2009

International publications

• PDBe: Protein Data Bank in Europe
  Velankar S. et al.
  Nucleic Acids Research - Database issue, 2011, 39:D402-10 ( abstract )


• Diversity of monomers in nonribosomal peptides: towards the prediction of origin and biological activity
  Caboche S; Leclere V; Pupin M; Kucherov G; Jacques P
  Journal of Bacteriology 2010; Oct:192(19):5143-50 (abstract)


• Structural pattern matching of nonribosomal peptides
  Caboche S; Pupin M; Leclere 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)

National Publication

• 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

International communications with selection board

• 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


• Norine : a public resource for nonribosomal peptides
  Caboche S
  EuroDocInfo 2009, Mons (Belgium) 2009, communication

National communications with selection board

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

Communications without selection board

• Norine : une plate-forme dédiée aux peptides non ribosomiaux
  Caboche S
  Rencontres PPF, Lille, 2008, communication


• Norine : une base de données de peptides non-ribosomaux
  Caboche S
  Rencontres PPF, Lille, 2007, communication

Posters

• 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)

Contact

LIFL - Extension batiment M3
Cité Scientifique
Université des Sciences et Technologies de Lille
F-59655 Villeneuve d'Ascq Cedex
mail : segolene.caboche{AT}lifl.fr