Publications

Info about publications here

2010

Lingner, T, Muhlhausen S, Gabaldón T, Notredame C, Meinicke P. 2010. Predicting phenotypic traits of prokaryotes from protein domain frequencies.. BMC bioinformatics. 11:481. Abstract

Pubmed

2009

Kemena, C, Notredame C. 2009. Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics. 25:2455-65. Abstract

Pubmed

Gauthier, JA, Widmer E, Bucher P, Notredame C. 2009. How much does it cost? Optimization of costs in sequence analysis of social science data Sociological Methods and Research. Volume 38:Pages197-231.

Varas, F, Stadtfeld M, de Andres-Aguayo L, Maherali N, di Tullio A, Pantano L, Notredame C, Hochedlinger K, Graf T. 2009. Fibroblast-derived induced pluripotent stem cells show no common retroviral vector insertions. Stem Cells. 27:300-6. Abstract

Pubmed

2008

Rausch, T, Emde AK, Weese D, Doring A, Notredame C, Reinert K. 2008. Segment-based multiple sequence alignment. Bioinformatics. 24:i187-92. Abstract

Moretti, S, Wilm A, Higgins DG, Xenarios I, Notredame C. 2008. R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Res. 36:W10-3. Abstract

Wilm, A, Higgins DG, Notredame C. 2008. R-Coffee: a method for multiple alignment of non-coding RNA. Nucleic Acids Res. 36:e52. Abstract

2007

Retelska, D, Beaudoing E, Notredame C, Jongeneel CV, Bucher P. 2007. Vertebrate conserved non coding DNA regions have a high persistence length and a short persistence time. BMC Genomics. 8:398. Abstract

Notredame, C. 2007. Recent evolutions of multiple sequence alignment algorithms. PLoS Comput Biol. 3:e123.

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

2006

Armougom, F, Moretti S, Keduas V, Notredame C. 2006. The iRMSD: a local measure of sequence alignment accuracy using structural information. Bioinformatics. 22:e35-9. Abstract

Armougom, F, Poirot O, Moretti S, Higgins DG, Bucher P, Keduas V, Notredame C. 2006. APDB: a web server to evaluate the accuracy of sequence alignments using structural information. Bioinformatics. 22:2439-40. Abstract

Moretti, S, Reinier F, Poirot O, Armougom F, Audic S, Keduas V, Notredame C. 2006. PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. Nucleic Acids Res. 34:W600-3. Abstract

Armougom, F, Moretti S, Poirot O, Audic S, Dumas P, Schaeli B, Keduas V, Notredame C. 2006. Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res. 34:W604-8. Abstract

Wallace, IM, O'Sullivan O, Higgins DG, Notredame C. 2006. M-Coffee: combining multiple sequence alignment methods with T-Coffee. Nucleic Acids Res. 34:1692-9. Abstract

2004

Notredame, C, Suhre K. 2004. Computing multiple sequence/structure alignments with the T-coffee package. Curr Protoc Bioinformatics. Chapter 3:Unit38. Abstract

Poirot, O, Suhre K, Abergel C, O'Toole E, Notredame C. 2004. 3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Res. 32:W37-40. Abstract

Claude, JB, Suhre K, Notredame C, Claverie JM, Abergel C. 2004. CaspR: a web server for automated molecular replacement using homology modelling. Nucleic Acids Res. 32:W606-9. Abstract

O'Sullivan, O, Suhre K, Abergel C, Higgins DG, Notredame C. 2004. 3DCoffee: combining protein sequences and structures within multiple sequence alignments. J Mol Biol. 340:385-95. Abstract

2003

Abergel, C, Coutard B, Byrne D, Chenivesse S, Claude JB, Deregnaucourt C, Fricaux T, Gianesini-Boutreux C, Jeudy S, Lebrun R et al.. 2003. Structural genomics of highly conserved microbial genes of unknown function in search of new antibacterial targets. J Struct Funct Genomics. 4:141-57. Abstract

O'Sullivan, O, Zehnder M, Higgins D, Bucher P, Grosdidier A, Notredame C. 2003. APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. Bioinformatics. 19 Suppl 1:i215-21. Abstract

Poirot, O, O'Toole E, Notredame C. 2003. Tcoffee@igs: A web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res. 31:3503-6. Abstract

2002

Notredame, C. 2002. Recent progress in multiple sequence alignment: a survey. Pharmacogenomics. 3:131-44. Abstract

2001

Notredame, C. 2001. Mocca: semi-automatic method for domain hunting. Bioinformatics. 17:373-4. Abstract

Dietmann, S, Park J, Notredame C, Heger A, Lappe M, Holm L. 2001. A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res. 29:55-7. Abstract

2000

Notredame, C, Higgins DG, Heringa J. 2000. T-Coffee: A novel method for fast and accurate multiple sequence alignment. J Mol Biol. 302:205-17. Abstract

1998

O'Brien, EA, Notredame C, Higgins DG. 1998. Optimization of ribosomal RNA profile alignments. Bioinformatics. 14:332-41. Abstract

Notredame, C, Holm L, Higgins DG. 1998. COFFEE: an objective function for multiple sequence alignments. Bioinformatics. 14:407-22. Abstract

1997

Notredame, C, O'Brien EA, Higgins DG. 1997. RAGA: RNA sequence alignment by genetic algorithm. Nucleic Acids Res. 25:4570-80. Abstract

1996

Notredame, C, Higgins DG. 1996. SAGA: sequence alignment by genetic algorithm. Nucleic Acids Res. 24:1515-24. Abstract