Cédric Notredame

45 papers A 1C 2Journal 38Unranked 4

Year	Rank	Type	Title / Venue / Authors
2022	J	`jnl`	Highly significant improvement of protein sequence alignments with AlphaFold2. Bioinform. Athanasios Baltzis, Leila Mansouri, Suzanne Jin, Björn E. Langer, Ionas Erb, Cédric Notredame
2021	J	`jnl`	Approaches for containerized scientific workflows in cloud environments with applications in life science. F1000Research 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 A. Moreno, Andreas Hellander, Payam Emami Khoonsari, Stephanie Herman, Kim Kultima, Samuel Lampa
2021	J	`jnl`	Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability. Bioinform. Jia-Ming Chang, Evan W. Floden, Javier Herrero, Olivier Gascuel, Paolo Di Tommaso, Cédric Notredame
2019	J	`jnl`	Pergola-web: a web server for the visualization and analysis of longitudinal behavioral data using repurposed genomics tools and standards. Nucleic Acids Res. Jose Espinosa-Carrasco, Antonio Hermoso Pulido, Ionas Erb, Mara Dierssen, Julia V. Ponomarenko, Cédric Notredame
2018	—	`conf`	Nextflow integration for the Research Object Specification. RO Edgar Garriga Nogales, Paolo Di Tommaso, Cédric Notredame
2016	J	`jnl`	How should we measure proportionality on relative gene expression data? Theory Biosci. Ionas Erb, Cédric Notredame
2016	J	`jnl`	Multiple sequence alignment modeling: methods and applications. Briefings Bioinform. Maria Chatzou, Cedrik Magis, Jia-Ming Chang, Carsten Kemena, Giovanni Bussotti, Ionas Erb, Cédric Notredame
2016	J	`jnl`	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. Evan W. Floden, Paolo Di Tommaso, Maria Chatzou, Cedrik Magis, Cédric Notredame, Jia-Ming Chang
2015	J	`jnl`	High Performance computing improvements on bioinformatics consistency-based multiple sequence alignment tools. Parallel Comput. Miquel Orobitg, Fernando Guirado, Fernando Cores, Jordi Lladós, Cédric Notredame
2015	J	`jnl`	Recovering accuracy methods for scalable consistency library. J. Supercomput. Jordi Lladós, Fernando Guirado, Fernando Cores, Josep Lluís Lérida, Cédric Notredame
2015	J	`jnl`	TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction. Nucleic Acids Res. Jia-Ming Chang, Paolo Di Tommaso, Vincent Lefort, Olivier Gascuel, Cédric Notredame
2014	J	`jnl`	SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments. Nucleic Acids Res. Paolo Di Tommaso, Giovanni Bussotti, Carsten Kemena, Emidio Capriotti, Maria Chatzou, Pablo Prieto, Cédric Notredame
2013	J	`jnl`	Improving multiple sequence alignment biological accuracy through genetic algorithms. J. Supercomput. Miquel Orobitg, Fernando Cores, Fernando Guirado, Concepció Roig, Cédric Notredame
2013	J	`jnl`	Performance analysis of computational approaches to solve Multiple Sequence Alignment. J. Supercomput. Alberto Montañola, Concepció Roig, Fernando Guirado, Porfidio Hernández, Cédric Notredame
2013	C	`conf`	Scalability and accuracy improvements of consistency-based multiple sequence alignment tools. EuroMPI Miquel Orobitg, Jordi Lladós, Fernando Guirado, Fernando Cores, Cédric Notredame
2013	J	`jnl`	T-RMSD: a web server for automated fine-grained protein structural classification. Nucleic Acids Res. Cedrik Magis, Paolo Di Tommaso, Cédric Notredame
2013	J	`jnl`	Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package. Bioinform. Carsten Kemena, Giovanni Bussotti, Emidio Capriotti, Marc A. Martí-Renom, Cédric Notredame
2012	J	`jnl`	AMPA: an automated web server for prediction of protein antimicrobial regions. Bioinform. Marc Torrent, Paolo Di Tommaso, David Pulido, Victòria M. Nogués, Cédric Notredame, Ester Boix, David Andreu
2012	J	`jnl`	Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. BMC Bioinform. Jia-Ming Chang, Paolo Di Tommaso, Jean-François Taly, Cédric Notredame
2012	A	`conf`	Enhancing the Scalability of Consistency-based Progressive Multiple Sequences Alignment Applications. IPDPS Miquel Orobitg, Fernando Cores, Fernando Guirado, Carsten Kemena, Cédric Notredame, Ana Ripoll
2012	J	`jnl`	Epistasis as the primary factor in molecular evolution. Nat. Michael S. Breen, Carsten Kemena, Peter K. Vlasov, Cédric Notredame, Fyodor A. Kondrashov
2011	J	`jnl`	A user-friendly web portal for T-Coffee on supercomputers. BMC Bioinform. Josep Rius, Fernando Cores, Francesc Solsona, Jano I. van Hemert, Jos Koetsier, Cédric Notredame
2011	J	`jnl`	Exploiting parallelism on progressive alignment methods. J. Supercomput. Miquel Orobitg, Fernando Guirado, Cédric Notredame, Fernando Cores
2011	J	`jnl`	STRIKE: evaluation of protein MSAs using a single 3D structure. Bioinform. Carsten Kemena, Jean-François Taly, Jens Kleinjung, Cédric Notredame
2011	J	`jnl`	T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension. Nucleic Acids Res. Paolo Di Tommaso, Sébastien Moretti, Ioannis Xenarios, Miquel Orobitg, Alberto Montanyola, Jia-Ming Chang, Jean-François Taly, Cédric Notredame
2010	J	`jnl`	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. Paolo Di Tommaso, Miquel Orobitg, Fernando Guirado, Fernando Cores, Toni Espinosa, Cédric Notredame
2010	J	`jnl`	Predicting phenotypic traits of prokaryotes from protein domain frequencies. BMC Bioinform. Thomas Lingner, Stefanie Mühlhausen, Toni Gabaldón, Cédric Notredame, Peter Meinicke
2009	J	`jnl`	Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinform. Carsten Kemena, Cédric Notredame
2008	J	`jnl`	R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Res. Sébastien Moretti, Andreas Wilm, Desmond G. Higgins, Ioannis Xenarios, Cédric Notredame
2008	C	`conf`	Segment-based multiple sequence alignment. ECCB Tobias Rausch, Anne-Katrin Emde, David Weese, Andreas Döring, Cédric Notredame, Knut Reinert
2007	J	`jnl`	Recent Evolutions of Multiple Sequence Alignment Algorithms. PLoS Comput. Biol. Cédric Notredame
2007	J	`jnl`	The M-Coffee web server: a meta-method for computing multiple sequence alignments by combining alternative alignment methods. Nucleic Acids Res. Sébastien Moretti, Fabrice Armougom, Iain M. Wallace, Desmond G. Higgins, C. Victor Jongeneel, Cédric Notredame
2006	J	`jnl`	APDB: a web server to evaluate the accuracy of sequence alignments using structural information. Bioinform. Fabrice Armougom, Olivier Poirot, Sébastien Moretti, Desmond G. Higgins, Phillip Bucher, Vladimir Keduas, Cédric Notredame
2006	J	`jnl`	Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res. Fabrice Armougom, Sébastien Moretti, Olivier Poirot, Stéphane Audic, Pierre Dumas, Basile Schaeli, Vladimir Keduas, Cédric Notredame
2006	—	`conf`	Invited Talk: Combining Sequence Information with T-Coffee. German Conference on Bioinformatics Cédric Notredame
2006	J	`jnl`	PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. Nucleic Acids Res. Sébastien Moretti, Frédéric Reinier, Olivier Poirot, Fabrice Armougom, Stéphane Audic, Vladimir Keduas, Cédric Notredame
2006	—	`conf`	The iRMSD: a local measure of sequence alignment accuracy using structural information. ISMB (Supplement of Bioinformatics) Fabrice Armougom, Sébastien Moretti, Vladimir Keduas, Cédric Notredame
2004	J	`jnl`	3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Res. Olivier Poirot, Karsten Suhre, Chantal Abergel, Eamonn O'Toole, Cédric Notredame
2004	J	`jnl`	CaspR: a web server for automated molecular replacement using homology modelling. Nucleic Acids Res. Jean-Baptiste Claude, Karsten Suhre, Cédric Notredame, Jean-Michel Claverie, Chantal Abergel
2003	—	`conf`	APDB: a novel measure for benchmarking sequence alignment methods without reference alignments. ISMB (Supplement of Bioinformatics) Orla O'Sullivan, Mark Zehnder, Desmond G. Higgins, Philipp Bucher, Aurélien Grosdidier, Cédric Notredame
2003	J	`jnl`	Tcoffee add igs: a web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res. Olivier Poirot, Eamonn O'Toole, Cédric Notredame
2001	J	`jnl`	A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res. Sabine Dietmann, Jong-Chan Park, Cédric Notredame, Andreas Heger, Michael Lappe, Liisa Holm
2001	J	`jnl`	Mocca: semi-automatic method for domain hunting. Bioinform. Cédric Notredame
1998	J	`jnl`	COFFEE: an objective function for multiple sequence alignments. Bioinform. Cédric Notredame, Liisa Holm, Desmond G. Higgins
1998	J	`jnl`	Optimization of ribosomal RNA profile alignments. Bioinform. Emmet A. O'Brien, Cédric Notredame, Desmond G. Higgins