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Cédric Notredame
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2020 – today
- 2022
- [j37]Athanasios Baltzis
, Leila Mansouri, Suzanne Jin
Highly significant improvement of protein sequence alignments with AlphaFold2. Bioinform. 38(22): 5007-5011 (2022) - 2021
- [j36]Jia-Ming Chang
Incorporating alignment uncertainty into Felsenstein's phylogenetic bootstrap to improve its reliability. Bioinform. 37(11): 1506-1514 (2021) - [i2]Ola Spjuth
Approaches for containerized scientific workflows in cloud environments with applications in life science. F1000Research 10: 513 (2021)
2010 – 2019
- 2019
- [j35]Jose Espinosa-Carrasco
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): W600-W604 (2019) - 2018
- [i1]Edgar Garriga Nogales
Nextflow integration for the Research Object Specification. RO 2018 - 2016
- [j34]Maria Chatzou, Cedrik Magis, Jia-Ming Chang
Multiple sequence alignment modeling: methods and applications. Briefings Bioinform. 17(6): 1009-1023 (2016) - [j33]Evan W. Floden
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): W339-W343 (2016) - [j32]Ionas Erb
How should we measure proportionality on relative gene expression data? Theory Biosci. 135(1-2): 21-36 (2016) - 2015
- [j31]Jia-Ming Chang
TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction. Nucleic Acids Res. 43(Webserver-Issue): W3-W6 (2015) - [j30]Miquel Orobitg, Fernando Guirado
High Performance computing improvements on bioinformatics consistency-based multiple sequence alignment tools. Parallel Comput. 42: 18-34 (2015) - [j29]Jordi Lladós
Recovering accuracy methods for scalable consistency library. J. Supercomput. 71(5): 1833-1845 (2015) - 2014
- [j28]Paolo Di Tommaso
SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments. Nucleic Acids Res. 42(Webserver-Issue): 356-360 (2014) - 2013
- [j27]Carsten Kemena
Using tertiary structure for the computation of highly accurate multiple RNA alignments with the SARA-Coffee package. Bioinform. 29(9): 1112-1119 (2013) - [j26]Cedrik Magis
T-RMSD: a web server for automated fine-grained protein structural classification. Nucleic Acids Res. 41(Webserver-Issue): 358-362 (2013) - [j25]Alberto Montañola, Concepció Roig
Performance analysis of computational approaches to solve Multiple Sequence Alignment. J. Supercomput. 64(1): 69-78 (2013) - [j24]Miquel Orobitg
Improving multiple sequence alignment biological accuracy through genetic algorithms. J. Supercomput. 65(3): 1076-1088 (2013) - [c6]Miquel Orobitg
Scalability and accuracy improvements of consistency-based multiple sequence alignment tools. EuroMPI 2013: 259-264 - 2012
- [j23]Marc Torrent
AMPA: an automated web server for prediction of protein antimicrobial regions. Bioinform. 28(1): 130-131 (2012) - [j22]Jia-Ming Chang
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee. BMC Bioinform. 13(S-4): S1 (2012) - [j21]Michael S. Breen, Carsten Kemena
Epistasis as the primary factor in molecular evolution. Nat. 490(7421): 535-538 (2012) - [c5]Miquel Orobitg
Enhancing the Scalability of Consistency-based Progressive Multiple Sequences Alignment Applications. IPDPS 2012: 71-82 - 2011
- [j20]Carsten Kemena
STRIKE: evaluation of protein MSAs using a single 3D structure. Bioinform. 27(24): 3385-3391 (2011) - [j19]Josep Rius
A user-friendly web portal for T-Coffee on supercomputers. BMC Bioinform. 12: 150 (2011) - [j18]Paolo Di Tommaso
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): 13-17 (2011) - [j17]Miquel Orobitg
Exploiting parallelism on progressive alignment methods. J. Supercomput. 58(2): 186-194 (2011) - 2010
- [j16]Paolo Di Tommaso
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): 1903-1904 (2010) - [j15]Thomas Lingner, Stefanie Mühlhausen
Predicting phenotypic traits of prokaryotes from protein domain frequencies. BMC Bioinform. 11: 481 (2010)
2000 – 2009
- 2009
- [j14]Carsten Kemena
Upcoming challenges for multiple sequence alignment methods in the high-throughput era. Bioinform. 25(19): 2455-2465 (2009) - 2008
- [j13]Sébastien Moretti
R-Coffee: a web server for accurately aligning noncoding RNA sequences. Nucleic Acids Res. 36(Web-Server-Issue): 10-13 (2008) - [c4]Tobias Rausch
Segment-based multiple sequence alignment. ECCB 2008: 187-192 - 2007
- [j12]Sébastien Moretti
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): 645-648 (2007) - [j11]Cédric Notredame
Recent Evolutions of Multiple Sequence Alignment Algorithms. PLoS Comput. Biol. 3(8) (2007) - 2006
- [j10]Fabrice Armougom, Olivier Poirot
APDB: a web server to evaluate the accuracy of sequence alignments using structural information. Bioinform. 22(19): 2439-2440 (2006) - [j9]Sébastien Moretti
PROTOGENE: turning amino acid alignments into bona fide CDS nucleotide alignments. Nucleic Acids Res. 34(Web-Server-Issue): 600-603 (2006) - [j8]Fabrice Armougom, Sébastien Moretti
Expresso: automatic incorporation of structural information in multiple sequence alignments using 3D-Coffee. Nucleic Acids Res. 34(Web-Server-Issue): 604-608 (2006) - [c3]Cédric Notredame:
Invited Talk: Combining Sequence Information with T-Coffee. German Conference on Bioinformatics 2006: 103 - [c2]Fabrice Armougom, Sébastien Moretti
The iRMSD: a local measure of sequence alignment accuracy using structural information. ISMB (Supplement of Bioinformatics) 2006: 35-39 - 2004
- [j7]Olivier Poirot
3DCoffee@igs: a web server for combining sequences and structures into a multiple sequence alignment. Nucleic Acids Res. 32(Web-Server-Issue): 37-40 (2004) - [j6]Jean-Baptiste Claude
CaspR: a web server for automated molecular replacement using homology modelling. Nucleic Acids Res. 32(Web-Server-Issue): 606-609 (2004) - 2003
- [j5]Olivier Poirot
Tcoffee add igs: a web server for computing, evaluating and combining multiple sequence alignments. Nucleic Acids Res. 31(13): 3503-3506 (2003) - [c1]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 - 2001
- [j4]Cédric Notredame:
Mocca: semi-automatic method for domain hunting. Bioinform. 17(4): 373-374 (2001) - [j3]Sabine Dietmann
A fully automatic evolutionary classification of protein folds: Dali Domain Dictionary version 3. Nucleic Acids Res. 29(1): 55-57 (2001)
1990 – 1999
- 1998
- [j2]Emmet A. O'Brien, Cédric Notredame, Desmond G. Higgins:
Optimization of ribosomal RNA profile alignments. Bioinform. 14(4): 332-341 (1998) - [j1]Cédric Notredame, Liisa Holm, Desmond G. Higgins:
COFFEE: an objective function for multiple sequence alignments. Bioinform. 14(5): 407-422 (1998)
Coauthor Index
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