Cédric Notredame

Carsten Kemena, Giovanni Bussotti, Emidio Capriotti, Marc A. Martí-Renom, Cédric Notredame: Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package. Bioinformatics 29(9): 1112-1119 (2013)

Alberto Montañola, Concepció Roig, Fernando Guirado, Porfidio Hernández, Cédric Notredame: Performance analysis of computational approaches to solve Multiple Sequence Alignment. The Journal of Supercomputing 64(1): 69-78 (2013)

Marc Torrent, Paolo Di Tommaso, David Pulido, Victòria M. Nogués, Cédric Notredame, Ester Boix, David Andreu: AMPA: an automated web server for prediction of protein antimicrobial regions. Bioinformatics 28(1): 130-131 (2012)

Jia-Ming Chang, Paolo Di Tommaso, Jean-François Taly, Cédric Notredame: Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. BMC Bioinformatics 13(S-4): S1 (2012)

Miquel Orobitg, Fernando Cores, Fernando Guirado, Carsten Kemena, Cédric Notredame, Ana Ripoll: Enhancing the Scalability of Consistency-based Progressive Multiple Sequences Alignment Applications. IPDPS 2012: 71-82

Carsten Kemena, Jean-François Taly, Jens Kleinjung, Cédric Notredame: STRIKE: evaluation of protein MSAs using a single 3D structure. Bioinformatics 27(24): 3385-3391 (2011)

Josep Rius Torrento, Fernando Cores, Francesc Solsona, Jano I. van Hemert, Jos Koetsier, Cédric Notredame: A user-friendly web portal for T-Coffee on supercomputers. BMC Bioinformatics 12: 150 (2011)

Paolo Di Tommaso, Sébastien Moretti, Ioannis Xenarios, Miquel Orobitg, Alberto Montanyola, Jia-Ming Chang, Jean-François Taly, Cédric Notredame: T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Research 39(Web-Server-Issue): 13-17 (2011)

Miquel Orobitg, Fernando Guirado, Cédric Notredame, Fernando Cores: Exploiting parallelism on progressive alignment methods. The Journal of Supercomputing 58(2): 186-194 (2011)

Paolo Di Tommaso, Miquel Orobitg, Fernando Guirado, Fernando Cores, Toni Espinosa, Cédric Notredame: Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud. Bioinformatics 26(15): 1903-1904 (2010)

Thomas Lingner, Stefanie Mühlhausen, Toni Gabaldón, Cédric Notredame, Peter Meinicke: Predicting phenotypic traits of prokaryotes from protein domain frequencies. BMC Bioinformatics 11: 481 (2010)

Carsten Kemena, Cédric Notredame: Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinformatics 25(19): 2455-2465 (2009)

Sébastien Moretti, Andreas Wilm, Desmond G. Higgins, Ioannis Xenarios, Cédric Notredame: R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Research 36(Web-Server-Issue): 10-13 (2008)

Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Döring, Cédric Notredame, Knut Reinert: Segment-based multiple sequence alignment. ECCB 2008: 187-192

Sébastien Moretti, Fabrice Armougom, Iain M. Wallace, Desmond G. Higgins, C. Victor Jongeneel, Cédric Notredame: The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Research 35(Web-Server-Issue): 645-648 (2007)

Cédric Notredame: Recent Evolutions of Multiple Sequence Alignment Algorithms. PLoS Computational Biology 3(8) (2007)

Fabrice Armougom, Olivier Poirot, Sébastien Moretti, Desmond G. Higgins, Phillip Bucher, Vladimir Keduas, Cédric Notredame: APDB: a web server to evaluate the accuracy of sequence alignments using structural information. Bioinformatics 22(19): 2439-2440 (2006)

Sébastien Moretti, Frédéric Reinier, Olivier Poirot, Fabrice Armougom, Stéphane Audic, Vladimir Keduas, Cédric Notredame: PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. Nucleic Acids Research 34(Web-Server-Issue): 600-603 (2006)

Fabrice Armougom, Sébastien Moretti, Olivier Poirot, Stéphane Audic, Pierre Dumas, Basile Schaeli, Vladimir Keduas, Cédric Notredame: Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Research 34(Web-Server-Issue): 604-608 (2006)

Cédric Notredame: Invited Talk: Combining Sequence Information with T-Coffee. German Conference on Bioinformatics 2006: 103

Fabrice Armougom, Sébastien Moretti, Vladimir Keduas, Cédric Notredame: The iRMSD: a local measure of sequence alignment accuracy using structural information. ISMB (Supplement of Bioinformatics) 2006: 35-39

Olivier Poirot, Karsten Suhre, Chantal Abergel, Eamonn O'Toole, Cédric Notredame: 3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Research 32(Web-Server-Issue): 37-40 (2004)

Jean-Baptiste Claude, Karsten Suhre, Cédric Notredame, Jean-Michel Claverie, Chantal Abergel: CaspR: a web server for automated molecular replacement using homology modelling. Nucleic Acids Research 32(Web-Server-Issue): 606-609 (2004)

Olivier Poirot, Eamonn O'Toole, Cédric Notredame: Tcoffee add igs: a web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Research 31(13): 3503-3506 (2003)

Orla O'Sullivan, Mark Zehnder, Desmond G. Higgins, Philipp Bucher, Aurélien Grosdidier, Cédric Notredame: APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. ISMB (Supplement of Bioinformatics) 2003: 215-221

Cédric Notredame: Mocca: semi-automatic method for domain hunting. Bioinformatics 17(4): 373-374 (2001)

Sabine Dietmann, Jong Park, Cédric Notredame, Andreas Heger, Michael Lappe, Liisa Holm: A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Research 29(1): 55-57 (2001)

Emmet A. O'Brien, Cédric Notredame, Desmond G. Higgins: Optimization of ribosomal RNA profile alignments. Bioinformatics 14(4): 332-341 (1998)

Cédric Notredame, Liisa Holm, Desmond G. Higgins: COFFEE: an objective function for multiple sequence alignments. Bioinformatics 14(5): 407-422 (1998)