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Research

Comparative Bioinformatics

Group Leader:



1994-1997 PhD in Bioinformatics, under the supervision of Des Higgins at EMBL (Heidelberg) and EMBL-EBI (Cambridge).
1997-1999 Post Doctoral researcher at ISREC (Lausanne) and NIMR-MRC (London).
2000-2001 Assistant Professor, Marseilles University/CNRS-IBSM.
2001-2007 CNRS investigator, IBSM (Marseille).
2001-2005 Assistant Professor, Lausanne University. Group Leader at the Swiss Bioinformatics Institute (SIB) and member of the SIB executive board.
Since 2007 Senior Group Leader in the Bioinformatics and Genomics Programme, at the CRG (Barcelona)

Summary
The main focus of the group is the development of novel algorithms for the comparison of multiple biological sequences. Multiple comparisons have the advantage of precisely revealing evolutionary traces, thus allowing the identification of functional constraints imposed on the evolution of biological entities. Most comparisons are currently carried out on the basis of sequence similarity. Our goal is to extend this scope by allowing comparisons based on any relevant biological signal such as sequence homology, structural similarity, genomic structure, functional similarity and more generally any signal that may be identified within biological sequences. Using such heterogeneous signals serves two complementary purposes: (i) producing better models that take advantage of the signal evolutionary resilience, (ii) improving our understanding of the evolutionary processes that lead to the diversification of biological functions. All the applications related to our work are provided to the community through an international network of web servers that can be accessed from http://www.tcoffee.org

Ongoing projects include:

Analysis of Copy Number Variations in eukaryotic genomes
Improvement of RNA Multiple Sequence Alignments
Post Processing of Multiple Sequence Alignments
Benchmarking and Validation of Multiple Sequence Alignment Methods
Combination of sequence and structural information
Protein Structure comparisons
Incorporation of Genomic information within multiple sequence alignments
Analysis of the sequence/function relationship
Multiple Genome Comparisons
Evolution of Bacterial genomes
Research Lines
Extension of the scope of Multiple Sequence Alignment Methods
Maintenance and upgrade of www.tcoffee.org common server
Selected Publications

Orom UA, Derrien T, Beringer M, Gumireddy K, Gardini A, Bussotti G, Lai F, Zytnicki M, Notredame C, Huang Q, Guigo R, Shiekhattar R..
Long Noncoding RNAs with Enhancer-like Function in Human Cells.
Cell 143(1):46-58 (2010). PubMed ID: 20887892.
Coll O, Villalba A, Bussotti G, Notredame C, Gebauer F..
A novel, noncanonical mechanism of cytoplasmic polyadenylation operates in Drosophila embryogenesis.
Genes Dev. 24(2):129-34. (2010). PubMed ID: 20080951.abstract
Moretti S, Armougom F, Wallace IC, Higgins DG, Jongeneel CV and Notredame C.
"The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods"
Nucleic Acids Res 35(Web Server issue):W645-8 (2007).
Armougon F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V and Notredame C.
"Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee"
Nucleic Acids Res 34(Web Server issue):W604-8 (2006).
Claverie JM and Notredame C.
"Bioinformatics for dummies", 2nd
Wiley Publishing, Inc. (2006).

 
 
 

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