Cédric Notredame

Publication Activity (10 Years)

Years Active: 1998-2022
Publications (10 Years): 8

Top Topics

High Performance Computing

Protein Structural

Computational Approaches

Top Venues

Nucleic Acids Res.

J. Supercomput.

Publications

Athanasios Baltzis, Leila Mansouri, Suzanne Jin, Björn E. Langer, Ionas Erb, Cédric Notredame
Highly significant improvement of protein sequence alignments with AlphaFold2. Bioinform. 38 (22) (2022)
Jia-Ming Chang, Evan W. Floden, Javier Herrero, Olivier Gascuel, Paolo Di Tommaso, Cédric Notredame
Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability. Bioinform. 37 (11) (2021)
Ola Spjuth, Marco Capuccini, Matteo Carone, Anders Larsson, Wesley Schaal, Jon Ander Novella, Oliver Stein, Morgan Ekmefjord, Paolo Di Tommaso, Evan W. Floden, Cédric Notredame, Pablo Moreno, Andreas Hellander, Payam Emami Khoonsari, Stephanie Herman, Kim Kultima, Samuel Lampa
Approaches for containerized scientific workflows in cloud environments with applications in life science. F1000Research 10 (2021)
Jose Espinosa-Carrasco, Antonio Hermoso Pulido, Ionas Erb, Mara Dierssen, Julia V. Ponomarenko, Cédric Notredame
Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards. Nucleic Acids Res. 47 (Webserver-Issue) (2019)
Edgar Garriga Nogales, Paolo Di Tommaso, Cédric Notredame
Nextflow integration for the Research Object Specification. RO (2018)
Evan W. Floden, Paolo Di Tommaso, Maria Chatzou, Cedrik Magis, Cédric Notredame, Jia-Ming Chang
PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases. Nucleic Acids Res. 44 (Webserver-Issue) (2016)
Maria Chatzou, Cedrik Magis, Jia-Ming Chang, Carsten Kemena, Giovanni Bussotti, Ionas Erb, Cédric Notredame
Multiple sequence alignment modeling: methods and applications. Briefings Bioinform. 17 (6) (2016)
Ionas Erb, Cédric Notredame
How should we measure proportionality on relative gene expression data? Theory Biosci. 135 (1-2) (2016)
Miquel Orobitg, Fernando Guirado, Fernando Cores, Jordi Lladós, Cédric Notredame
High Performance computing improvements on bioinformatics consistency-based multiple sequence alignment tools. Parallel Comput. 42 (2015)
Jia-Ming Chang, Paolo Di Tommaso, Vincent Lefort, Olivier Gascuel, Cédric Notredame
TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction. Nucleic Acids Res. 43 (Webserver-Issue) (2015)
Jordi Lladós, Fernando Guirado, Fernando Cores, Josep Lluís Lérida, Cédric Notredame
Recovering accuracy methods for scalable consistency library. J. Supercomput. 71 (5) (2015)
Paolo Di Tommaso, Giovanni Bussotti, Carsten Kemena, Emidio Capriotti, Maria Chatzou, Pablo Prieto, Cédric Notredame
SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments. Nucleic Acids Res. 42 (Webserver-Issue) (2014)
Alberto Montañola, Concepció Roig, Fernando Guirado, Porfidio Hernández, Cédric Notredame
Performance analysis of computational approaches to solve Multiple Sequence Alignment. J. Supercomput. 64 (1) (2013)
Miquel Orobitg, Fernando Cores, Fernando Guirado, Concepció Roig, Cédric Notredame
Improving multiple sequence alignment biological accuracy through genetic algorithms. J. Supercomput. 65 (3) (2013)
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. Bioinform. 29 (9) (2013)
Cedrik Magis, Paolo Di Tommaso, Cédric Notredame
T-RMSD: a web server for automated fine-grained protein structural classification. Nucleic Acids Res. 41 (Webserver-Issue) (2013)
Miquel Orobitg, Jordi Lladós, Fernando Guirado, Fernando Cores, Cédric Notredame
Scalability and accuracy improvements of consistency-based multiple sequence alignment tools. EuroMPI (2013)
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)
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. Bioinform. 28 (1) (2012)
Jia-Ming Chang, Paolo Di Tommaso, Jean-François Taly, Cédric Notredame
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. BMC Bioinform. 13 (S-4) (2012)
Michael S. Breen, Carsten Kemena, Peter K. Vlasov, Cédric Notredame, Fyodor A. Kondrashov
Epistasis as the primary factor in molecular evolution. Nat. 490 (7421) (2012)
Josep Rius, Fernando Cores, Francesc Solsona, Jano I. van Hemert, Jos Koetsier, Cédric Notredame
A user-friendly web portal for T-Coffee on supercomputers. BMC Bioinform. 12 (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 Res. 39 (Web-Server-Issue) (2011)
Miquel Orobitg, Fernando Guirado, Cédric Notredame, Fernando Cores
Exploiting parallelism on progressive alignment methods. J. Supercomput. 58 (2) (2011)
Carsten Kemena, Jean-François Taly, Jens Kleinjung, Cédric Notredame
STRIKE: evaluation of protein MSAs using a single 3D structure. Bioinform. 27 (24) (2011)
Thomas Lingner, Stefanie Mühlhausen, Toni Gabaldón, Cédric Notredame, Peter Meinicke
Predicting phenotypic traits of prokaryotes from protein domain frequencies. BMC Bioinform. 11 (2010)
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. Bioinform. 26 (15) (2010)
Carsten Kemena, Cédric Notredame
Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinform. 25 (19) (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 Res. 36 (Web-Server-Issue) (2008)
Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Döring, Cédric Notredame, Knut Reinert
Segment-based multiple sequence alignment. ECCB (2008)
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 Res. 35 (Web-Server-Issue) (2007)
Cédric Notredame
Recent Evolutions of Multiple Sequence Alignment Algorithms. PLoS Comput. Biol. 3 (8) (2007)
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 Res. 34 (Web-Server-Issue) (2006)
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)
Cédric Notredame
Invited Talk: Combining Sequence Information with T-Coffee. German Conference on Bioinformatics (2006)
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. Bioinform. 22 (19) (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 Res. 34 (Web-Server-Issue) (2006)
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 Res. 32 (Web-Server-Issue) (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 Res. 32 (Web-Server-Issue) (2004)
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)
Olivier Poirot, Eamonn O'Toole, Cédric Notredame
Tcoffee add igs: a web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res. 31 (13) (2003)
Cédric Notredame
Mocca: semi-automatic method for domain hunting. Bioinform. 17 (4) (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 Res. 29 (1) (2001)
Emmet A. O'Brien, Cédric Notredame, Desmond G. Higgins
Optimization of ribosomal RNA profile alignments. Bioinform. 14 (4) (1998)
Cédric Notredame, Liisa Holm, Desmond G. Higgins
COFFEE: an objective function for multiple sequence alignments. Bioinform. 14 (5) (1998)