Sébastien Moretti

Skills

Bioinformatics & Computer Science
Annotation, gene prediction, SNP identification, multiple sequence alignment, phylogeny, structure analysis and visualization, EST clustering, mRNA/prot alignment vs. genomic sequences.
Databanks management and up-date, BASE & SRS installation and administration, installation of bioinformatic tool for application server, Apache and SVN management.

OS & Programming
Linux, Unix, Windows. Perl, Shell (bash), R, HTML, CSS, XML, CGI scripts and Javascript. Basics in PHP, JSP, Python, C/C++ and Java.

Databases
SQL, MySQL, Perl DBI.

Statistics
Parametric and non-parametric statistics.

Biology
Evolution biology, molecular biology, population genetics, eco-ethology.

Experiences

2006 to 2007
Engineer for the Swiss Institute of Bioinformatics (SIB) - EMBNet and the University of Lausanne (UNIL):
EMBNet: Java applet development and enhancement of the MyHits web site (Lausanne, Dr. L. Falquet).
UNIL: HomolEns database integration and adaptation (Lausanne, Pr. M. Robinson-Rechavi).
UNIL: PC cluster management and statistical programming (Lausanne, Pr. J. Goudet).

2003 to 2006
Engineer for Sanofi-Aventis in the Genomic and Structural Information lab. (CNRS): Structural and genomic research about kinase proteins (Marseilles, 34 months contract, Dr. C. Notredame CNRS, Dr. V. Saudek Aventis, Pr. J.-M. Claverie CNRS): Polymorphism, from SNPs to structures, multiple sequence alignments & phylogeny, management of a bioinformatic application server, web site management, technological survey.

2002 to 2003
Engineer for Genoplante-Biogemma, assigned to ENSAT: Biotechnology and Plant Innovation lab. (Toulouse, 16 months contract, Pr. L. GENTZBITTEL): Set up of an automated annotation system for Sunflower EST program, and EST annotation.

2001
INSERM, Psychiatry and Neurobiology unit (Créteil, 6 months, Pr. Bruno GIROS): SNP physical maps construction for target genes, phylogeny, two-hybrid analyses.

2000
INRA, Phytopharmacy and Semiochemicals unit (Versailles, 8 months, Dr. B. Frérot): Pheromonal polymorphism for the European Corn Borer (Ostrinia nubilalis Hbn.)

1997 - 1999
CNRS, Biometry and Evolution Biology lab. (Lyons, whole: 10 months).

Education

2001
Master Science: Functional Genomics Engineering - Paris VII & Evry (MCL).

2000
Master Y2: Population Biology, Genetics and Eco-ethology - Tours (CL).

1999
Master Y1: Population Biology and Ecosystems - Lyons I (CL).

1998
Licence: Organism and Population Biology - Lyons I (CL).

Languages:
English: read, written and spoken
French: mother language
German: elementary knowledge

Publications

Advanced search is available through Serval

Publications can be managed by accessing Serval via MyUnil

Publications

2022 | 2021 | 2019 | 2017 | 2016 | 2014 | 2013 | 2012 | 2011 | 2010 | ...

2022

Ni<sup>2+</sup>-Assisted Hydrolysis May Affect the Human Proteome; Filaggrin Degradation Ex Vivo as an Example of Possible Consequences.

Podobas E.I., Gutowska-Owsiak D., Moretti S., Poznański J., Kulińczak M., Grynberg M., Gruca A., Bonna A., Płonka D., Ogg G. et al., 2022. Frontiers in molecular biosciences, 9 p. 828674. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_EACE2D906304]

2021

The Bgee suite: integrated curated expression atlas and comparative transcriptomics in animals.

Bastian F.B., Roux J., Niknejad A., Comte A., Fonseca Costa S.S., de Farias T.M., Moretti S., Parmentier G., de Laval V.R., Rosikiewicz M. et al., 2021/01/08. Nucleic acids research, 49 (D1) pp. D831-D847. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_FD0CF4F734E7]

MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models

Moretti Sébastien, Tran Van Du T, Mehl Florence, Ibberson Mark, Pagni Marco, 2021/01/08. Nucleic Acids Research, 49 (D1) pp. D570-D574.

[DOI][WoS][Pmid][serval:BIB_F967CC226F37]

2019

Condition-specific series of metabolic sub-networks and its application for gene set enrichment analysis.

Tran VDT, Moretti S., Coste A.T., Amorim-Vaz S., Sanglard D., Pagni M., 2019/07/01. Bioinformatics, 35 (13) pp. 2258-2266. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_3E96F1A1B541]

2017

Taxon sampling unequally affects individual nodes in a phylogenetic tree: consequences for model gene tree construction in SwissTree

Boeckmann Brigitte, Dylus David, Moretti Sebastien, Altenhoff Adrian, Train Clement-Marie, Kriventseva Evgenia, Bougueleret Lydie, Xenarios Ioannis, Privman Eyal, Gabaldon Toni et al., 2017/09/05. biorxiv.

[DOI][serval:BIB_7579ACF1CAEA]

Updates in Rhea - an expert curated resource of biochemical reactions.

Morgat A., Lombardot T., Axelsen K.B., Aimo L., Niknejad A., Hyka-Nouspikel N., Coudert E., Pozzato M., Pagni M., Moretti S. et al., 2017/01/04. Nucleic acids research, 45 (D1) pp. D415-D418. Peer-reviewed.

[URN][DOI][Pmid][serval:BIB_D4F55C24D893]

Detection of Pathways Affected by Positive Selection in Primate Lineages Ancestral to Humans.

Daub J.T., Moretti S., Davydov I.I., Excoffier L., Robinson-Rechavi M., 2017. Molecular Biology and Evolution, 34 (6) pp. 1391-1402. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_E977192342AB]

2016

Tools and data services registry: a community effort to document bioinformatics resources.

Ison J., Rapacki K., Ménager H., Kalaš M., Rydza E., Chmura P., Anthon C., Beard N., Berka K., Bolser D. et al., 2016. Nucleic Acids Research, 44 (D1) pp. D38-D47.

[URN][DOI][WoS][Pmid][serval:BIB_B3F966DA99C6]

MetaNetX/MNXref - reconciliation of metabolites and biochemical reactions to bring together genome-scale metabolic networks.

Moretti S., Martin O., Van Du Tran T., Bridge A., Morgat A., Pagni M., 2016. Nucleic Acids Research, 44 (D1) pp. D523-D526.

[URN][DOI][WoS][Pmid][serval:BIB_58AEB83D57CC]

The SIB Swiss Institute of Bioinformatics' resources: focus on curated databases.

SIB Swiss Institute of Bioinformatics Members, Maillard A. M., 2016. Nucleic Acids Research, 44 (D1) pp. D27-D37.

[URN][DOI][WoS][Pmid][serval:BIB_71EF45D9A3D9]

2014

Reconciliation of metabolites and biochemical reactions for metabolic networks.

Bernard T., Bridge A., Morgat A., Moretti S., Xenarios I., Pagni M., 2014. Briefings in Bioinformatics, 15 (1) pp. 123-135.

[URN][DOI][WoS][Pmid][serval:BIB_6FC073DA2CF5]

Selectome update: quality control and computational improvements to a database of positive selection.

Moretti S., Laurenczy B., Gharib W.H., Castella B., Kuzniar A., Schabauer H., Studer R.A., Valle M., Salamin N., Stockinger H. et al., 2014. Nucleic Acids Research, 42 (1) pp. D917-D921. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_BD16E97A0D18]

Patterns of positive selection in seven ant genomes.

Roux J., Privman E., Moretti S., Daub J.T., Robinson-Rechavi M., Keller L., 2014. Molecular Biology and Evolution, 31 (7) pp. 1661-1685. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_95722591AAD3]

2013

Developmental and Environmental Regulation of Aquaporin Gene Expression across Populus Species: Divergence or Redundancy?

Cohen D., Bogeat-Triboulot M.B., Vialet-Chabrand S., Merret R., Courty P.E., Moretti S., Bizet F., Guilliot A., Hummel I., 2013. PLoS One, 8 (2) pp. e55506. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_87FBFC197FE8]

MetaNetX.org: a website and repository for accessing, analysing and manipulating metabolic networks.

Ganter M., Bernard T., Moretti S., Stelling J., Pagni M., 2013. Bioinformatics, 29 (6) pp. 815-816. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_364863E29541]

The hourglass and the early conservation models--co-existing patterns of developmental constraints in vertebrates.

Piasecka B., Lichocki P., Moretti S., Bergmann S., Robinson-Rechavi M., 2013. Plos Genetics, 9 (4) pp. e1003476. Peer-reviewed.

[URN][DOI][WoS][Pmid][serval:BIB_B03DCB0498A7]

2012

ExPASy: SIB bioinformatics resource portal.

Artimo P., Jonnalagedda M., Arnold K., Baratin D., Csardi G., de Castro E., Duvaud S., Flegel V., Fortier A., Gasteiger E. et al., 2012. Nucleic Acids Research, 40 pp. W597-W603.

[URN][DOI][WoS][Pmid][serval:BIB_60D126CF045C]

gcodeml: A Grid-enabled Tool for Detecting Positive Selection in Biological Evolution

Moretti S., Murri R., Maffioletti S., Kuzniar A., Castella B, Salamin N., Robinson-Rechavi M., Stockinger H., 2012. pp. 59-68 dans Glatard T, Silverstein J (eds.) HealthGrid Applications and Technologies Meet Science Gateways for Life Sciences, IOS Press Books online.

[URN][DOI][serval:BIB_542C5BE6E2B7]

2011

T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension.

Di Tommaso P., Moretti S., Xenarios I., Orobitg M., Montanyola A., Chang J.M., Taly J.F., Notredame C., 2011. Nucleic Acids Research, 39 (Web Server issue) pp. W13-W17.

[URN][DOI][Pmid][serval:BIB_EE8EDC0ACBE8]

2010

Phylogenetic Code in the Cloud - Can it Meet the Expectations?

Kraut A., Moretti S., Robinson-Rechavi M., Stockinger H., Flanders D., 2010. Studies in Health Technology and Informatics, 159 pp. 55-63. Peer-reviewed.

[DOI][Pmid][serval:BIB_1F5A96C03D27]

Training courses given

Installation of T-coffee web server
Course for CNRS and CRS4 T-coffee users (Sept 2006).
Multiple Sequences Alignment and T-Coffee tools.
Course for SwissProt team (June 2006).
Query biological databases and BLAST tool.
Course for a small group of Biogemma engineers (October 2002).

Sébastien Moretti

Skills

Experiences

Education

Publications

Publications

Training courses given

Software and plugins

Hobbies

Web sites