Sébastien MORETTI's CV

Sébastien MORETTI
Curriculum Vitae

Personal address:	14 rue de l'eau vive, FR-25300 Doubs	Personal phone:	+33 (0)6 1862 6300
Date of birth:	07 June 1977	Office phone:	+41 (21) 692 4221/4056
Nationality:	French	E-mail:
CV in PDF format

CURRENT POSITION

Bioinformatician Engineer - Computer Scientist
Swiss Institute of Bioinformatics, Vital-IT group
Department of Ecology & Evolution, Lausanne University
Switzerland

EDUCATION & EXPERIENCES

2006-now

Contract engineer, Swiss Institute of Bioinformatics, Vital-IT group and Department of Ecology & Evolution (DEE), University of Lausanne, Switzerland

	Projects:	Genome-wide metabolic network reconstruction (MetaNetX).
		Java applet development and enhancement of the MyHits web site.
		Web services implementation via Soaplab and Taverna.
	Advisor:	Dr. M. Pagni (Vital-IT)
	Projects:	Bgee (gene expression evolution db) database, tool and web site development.
		Selectome (positive selection db) database, tools and web site development.
	Advisor:	Pr. M. Robinson-Rechavi (SIB/Evol Bioinfo Group & DEE, University of Lausanne)

2003-2006

Contract engineer, Sanofi-Aventis in the Genomic and Structural Information lab. (CNRS), University of Luminy, Marseilles, France

	Projects:	Structural and genomic research about kinase proteins.
		Multiple Sequence Alignments tools development.
	Advisors:	Dr. C. Notredame (CNRS), Dr. V. Saudek (Aventis), Pr. J.-M. Claverie (CNRS)

2001-2003

Contract engineer, Génoplante-Biogemma, Biotechnology and Plant Innovation lab. (ENSAT), Toulouse, France

	Projects:	Set up of an automated annotation system for Sunflower EST program, and EST annotation.
	Advisor:	Pr. L. Gentzbittel (ENSAT)

2000-2001

Master Science in Functional Genomics Engineering, Universities Paris VII & Evry, France

	Projects:	SNP physical maps construction for target genes, phylogeny, two-hybrid analyses.
	Advisor:	Pr. B. Giros (INSERM, Psychiatry and Neurobiology unit, Créteil, France)

1999-2000

Master Y2 in Population Biology, Genetics and Eco-ethology, University of Tours, France

	Thesis:	Pheromonal polymorphism for the European Corn Borer (Ostrinia nubilalis Hbn.).
	Advisor:	Dr. B. Frérot (INRA, Phytopharmacy and Semiochemicals unit, Versailles, France)

1998-1999

Master Y1 in Population Biology and Ecosystems, University of Lyons I, France

	Thesis:	Round of duplication in Vertebrate gene families.
		Parasitoid pheromonal interference in egg laying site.
	Advisors:	Dr. M. Gouy & Pr. M. Boulétreau (CNRS, Biometry and Evolution Biology lab., Lyons, France)

SKILLS

Bioinformatics & Computer Science
- Annotation, gene prediction, SNP identification, structure analysis and visualization, EST clustering, multiple sequence alignment, phylogeny.
- Databanks management and up-date, BASE & SRS installation and administration, installation of bioinformatic tool for application server.
OS, Servers & Programming
- OS: Linux (administration), Unix, Mac OS X, Windows.
- Servers: Apache, Tomcat and SVN management.
- IT: Server administration, RPM building.
- Programming: Perl, Java, Shell (bash), R, HTML, CSS, XML, CGI scripts and Javascript.
- Notions: C, C++, JSP, Python and PHP.
Databases
- SQL, MySQL (administration), Perl DBI.
Statistics
- Parametric and non-parametric statistics.
Biology
- Evolution biology, molecular biology, population genetics, eco-ethology.
Languages
- English: read, written and spoken
- French: mother language
- German: elementary knowledge

WEB SITES & SOFTWARE

Web sites
Software & Plugins
- ProtoGene: Turning amino acid alignments into bona-fide CDS nucleotide alignments.
- SoS: Mapping of SNPs onto Structures (http://bioanalyse.free.fr/Software/).
- Plugins for the molecular viewer PyMOL (http://bioanalyse.free.fr/Software/).

TEACHING

Master training bioinformatics course (Oct 2007).
Phylogeny and Evolution using bioinformatics - EMBnet course for doctorals and post-doctorals (Sept 2007).
Installation of T-coffee web server - Course for CNRS and CRS4 T-coffee users (Sept 2006).
Multiple Sequence Alignments and T-Coffee tools - Course for SwissProt team (June 2006).
Query biological databases and BLAST - Course for a small group of Biogemma engineers (October 2002).

PUBLICATIONS

Journal Publications

Morgat A, Lombardot T, Axelsen KB, Aimo L, Niknejad A, Hyka-Nouspikel N, Coudert E, Pozzato M, Pagni M, Moretti S, Rosanoff S, Onwubiko J, Bougueleret L, Xenarios I, Redaschi N, Bridge A.
Updates in Rhea - an expert curated resource of biochemical reactions
Nucleic Acids Res., 2017; 45(Database issue), D415-D418. [url]

Moretti S, Martin O, Van Du Tran T, Bridge A, Morgat A, Pagni M.
MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks
Nucleic Acids Res., 2016; 44(Database issue), D523-526. [url]

Ison J, Rapacki K, Ménager H, Kalaš M, Rydza E, Chmura P, Anthon C, Beard N, Berka K, Bolser D, Booth T, Bretaudeau A, Brezovsky J, Casadio R, Cesareni G, Coppens F, Cornell M, Cuccuru G, Davidsen K, Vedova GD, Dogan T, Doppelt-Azeroual O, Emery L, Gasteiger E, Gatter T, Goldberg T, Grosjean M, Grüning B, Helmer-Citterich M, Ienasescu H, Ioannidis V, Jespersen MC, Jimenez R, Juty N, Juvan P, Koch M, Laibe C, Li JW, Licata L, Mareuil F, Mičetić I, Friborg RM, Moretti S, Morris C, Möller S, Nenadic A, Peterson H, Profiti G, Rice P, Romano P, Roncaglia P, Saidi R, Schafferhans A, Schwämmle V, Smith C, Sperotto MM, Stockinger H, Vařeková RS, Tosatto SC, de la Torre V, Uva P, Via A, Yachdav G, Zambelli F, Vriend G, Rost B, Parkinson H, Løngreen P, Brunak S.
Tools and data services registry: a community effort to document bioinformatics resources
Nucleic Acids Res., 2016; 44(Database issue), D38-D47. [url]

SIB Swiss Institute of Bioinformatics Members
The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases
Nucleic Acids Res., 2016; 44(Database issue), D27-D37. [url]

Moretti S, Laurenczy B, Gharib WH, Castella B, Kuzniar A, Schabauer H, Studer RA, Valle M, Salamin N, Stockinger H, Robinson-Rechavi M.
Selectome update: quality control and computational improvements to a database of positive selection
Nucleic Acids Res., 2014; 42(Database issue), D917-D921. [url]

Bernard T, Bridge A, Morgat A, Moretti S, Xenarios I, Pagni M.
Reconciliation of metabolites and biochemical reactions for metabolic networks
Brief. Bioinformatics, 2014; 15(1), 123-135. [url]

Roux J, Privman E, Moretti S, Daub JT, Robinson-Rechavi M, Keller L.
Patterns of positive selection in seven ant genomes
Molecular Biology and Evolution, 2014; 31(7), 1661-1685. [url]

Piasecka B, Lichocki P, Moretti S, Bergmann S, Robinson-Rechavi M.
The hourglass and the early conservation models - co-existing evolutionary patterns in vertebrate development.
Plos Genetics, 2013; 9(4), e1003476. [url]

Ganter M, Bernard T, Moretti S, Stelling J, Pagni M.
MetaNetX.org: a website and repository for accessing, analyzing, and manipulating metabolic networks
Bioinformatics, 2013; 29(6), 815-816. [url]

Cohen D, Bogeat-Triboulot MB, Vialet-Chabrand S, Merret R, Courty PE, Moretti S, Bizet F, Guilliot A, Hummel I.
Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?
PLoS One, 2013; 8(2), e55506. [url]

Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, Duvaud S, Flegel V, Fortier A, Gasteiger E, Grosdidier A, Hernandez C, Ioannidis V, Kuznetsov D, Liechti R, Moretti S, Mostaguir K, Redaschi N, Rossier G, Xenarios I, Stockinger H.
ExPASy: SIB bioinformatics resource portal.
Nucleic Acids Res., 2012; 40(Web Server issue), W597-W603. [url]

Moretti S, Murri R, Maffioletti S, Kuzniar A, Castella B, Salamin N, Robinson-Rechavi M, Stockinger H.
gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution.
Studies in Health Technology and Informatics, 2012; 175, 59-68. [url]

Di Tommaso P, Moretti S, Xenarios I, Orobitg M, Montanyola A, Chang JM, Taly JF, Notredame C.
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.
Nucleic Acids Res., 2011; 39(Web Server issue), W13-W17. [url]

Kraut A, Moretti S, Robinson-Rechavi M, Stockinger H, Flanders D.
Phylogenetic Code in the Cloud - Can it Meet the Expectations?
Studies in Health Technology and Informatics, 2010; 159, 55-63. [url]

Proux E, Studer RA, Moretti S and Robinson-Rechavi M.
Selectome: a database of positive selection.
Nucleic Acids Res., 2009; 37(Database issue), D404-D407. [url]

Moretti S, Wilm A, Higgins DG, Xenarios I, Notredame C.
R-Coffee: a web server for accurately aligning noncoding RNA sequences.
Nucleic Acids Res., 2008; 36(Web Server issue), W10-W13. [url]

Bastian F, Parmentier G, Roux J, Moretti S, Laudet V, Robinson-Rechavi M.
Bgee: Integrating and Comparing Heterogeneous Transcriptome Data Among Species.
in DILS: Data Integration in Life Sciences. Lecture Notes in Computer Science, 2008; 5109:124-131. [url]

Moretti S, Armougom F, Wallace IM, Higgins DG, Jongeneel CV, Notredame C.
The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods.
Nucleic Acids Res., 2007; 35(Web Server issue):W645-8. [url]

Armougom F, Poirot O, Moretti S, Higgins DB, Bucher P, Keduas V, Notredame C.
APDB: a web server to evaluate the accuracy of Multiple Sequence Alignment using Structural Information.
Bioinformatics, 2006; 22(19):2439-40. [url]

Armougom F, Moretti S, Keduas V, Notredame C.
iRMSD, a local measure of sequence alignment accuracy using structural information.
ISMB 2006 - Bioinformatics, 2006; 22(14):e35-9. [url]

Moretti S, Reinier F, Poirot O, Armougom F, Audic S, Keduas V, Notredame C.
Protogene: Turning amino acid alignments into bona-fide CDS nucleotide alignments.
Nucleic Acids Res., 2006; 34(Web Server issue):W600-3. [url]

Armougom F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V, Notredame C.
Expresso: Automatic incorporation of Structural Information in Multiple Sequence Alignments using 3D-Coffee.
Nucleic Acids Res., 2006; 34(Web Server issue):W604-8. [url]

Ben C, Hewezi T, Jardinaud M-F, Bena F, Ladouce N, Moretti S, Tamborindeguy C, Liboz T, Petitprez M and Gentzbittel L.
Comparative analysis of early embryonic sunflower cDNA libraries.
Plant Mol. Biol., 2005 ;57(2):255-70. [url]

Posters

Moretti S, Armougom F, Saudek V, Notredame C.
Protogene: Turning amino acid alignments into bona-fide CDS nucleotide alignments.
10th Evolutionary Biology Meeting, Marseilles, 2006.

REFEREES

Dr. Cédric NOTREDAME (CRG/CNRS)
Dr. Vladimir Saudek (Sanofi-Aventis)
Pr. Laurent GENTZBITTEL (ENSAT)
Dr. Bruno GIROS (INSERM)