Paolo Di Tommaso
Paolo Di Tommaso
Comparative Bioinformatics at CRG
Verified email at crg.es
Title
Cited by
Cited by
Year
T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension
P Di Tommaso, S Moretti, I Xenarios, M Orobitg, A Montanyola, JM Chang, ...
Nucleic acids research 39 (suppl_2), W13-W17, 2011
8972011
Nextflow enables reproducible computational workflows
P Di Tommaso, M Chatzou, EW Floden, PP Barja, E Palumbo, ...
Nature biotechnology 35 (4), 316-319, 2017
6462017
TCS: a new multiple sequence alignment reliability measure to estimate alignment accuracy and improve phylogenetic tree reconstruction
JM Chang, P Di Tommaso, C Notredame
Molecular biology and evolution 31 (6), 1625-1637, 2014
1582014
The nf-core framework for community-curated bioinformatics pipelines
PA Ewels, A Peltzer, S Fillinger, H Patel, J Alneberg, A Wilm, MU Garcia, ...
Nature biotechnology 38 (3), 276-278, 2020
1422020
The impact of Docker containers on the performance of genomic pipelines
P Di Tommaso, E Palumbo, M Chatzou, P Prieto, ML Heuer, C Notredame
PeerJ 3, e1273, 2015
1312015
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee
JM Chang, P Di Tommaso, JF Taly, C Notredame
BMC bioinformatics 13 (4), 1-7, 2012
1152012
AMPA: an automated web server for prediction of protein antimicrobial regions
M Torrent, P Di Tommaso, D Pulido, MV Nogués, C Notredame, E Boix, ...
Bioinformatics 28 (1), 130-131, 2012
1152012
Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures
JF Taly, C Magis, G Bussotti, JM Chang, P Di Tommaso, I Erb, ...
Nature protocols 6 (11), 1669-1682, 2011
1022011
T-Coffee: tree-based consistency objective function for alignment evaluation
C Magis, JF Taly, G Bussotti, JM Chang, P Di Tommaso, I Erb, ...
Multiple Sequence Alignment Methods, 117-129, 2014
572014
Cloud-Coffee: implementation of a parallel consistency-based multiple alignment algorithm in the T-Coffee package and its benchmarking on the Amazon Elastic-Cloud
P Di Tommaso, M Orobitg, F Guirado, F Cores, T Espinosa, C Notredame
Bioinformatics 26 (15), 1903-1904, 2010
402010
PSI/TM-Coffee: a web server for fast and accurate multiple sequence alignments of regular and transmembrane proteins using homology extension on reduced databases
EW Floden, PD Tommaso, M Chatzou, C Magis, C Notredame, JM Chang
Nucleic acids research 44 (W1), W339-W343, 2016
382016
TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction
JM Chang, P Di Tommaso, V Lefort, O Gascuel, C Notredame
Nucleic acids research 43 (W1), W3-W6, 2015
302015
nf-core: Community curated bioinformatics pipelines
PA Ewels, A Peltzer, S Fillinger, J Alneberg, H Patel, A Wilm, MU Garcia, ...
BioRxiv, 610741, 2019
242019
Definition of visual processes in a language for expressing transitions
P Bottoni, M De Marsico, P Di Tommaso, S Levialdi, D Ventriglia
Journal of Visual Languages & Computing 15 (3-4), 211-242, 2004
162004
Scalable workflows and reproducible data analysis for genomics
F Strozzi, R Janssen, R Wurmus, MR Crusoe, G Githinji, P Di Tommaso, ...
Evolutionary Genomics, 723-745, 2019
132019
Large multiple sequence alignments with a root-to-leaf regressive method
E Garriga, P Di Tommaso, C Magis, I Erb, L Mansouri, A Baltzis, ...
Nature biotechnology 37 (12), 1466-1470, 2019
112019
Generalized bootstrap supports for phylogenetic analyses of protein sequences incorporating alignment uncertainty
M Chatzou, EW Floden, P Di Tommaso, O Gascuel, C Notredame
Systematic Biology 67 (6), 997-1009, 2018
112018
A novel tool for highly scalable computational pipelines
P DiTommaso, M Chatzou, PP Baraja, C Notredame
figshare, 2014
92014
SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments
P Di Tommaso, G Bussotti, C Kemena, E Capriotti, M Chatzou, P Prieto, ...
Nucleic acids research 42 (W1), W356-W360, 2014
72014
Fernado Cores, Toni Espinosa, Cedric Notredame," Cloud-Coffee: implementation of a parallel consistencybased multiple alignment algorithm in the T-Coffee package and its …
P Di Tommaso, M Orobitg, F Guirado
Bioinformatics 15 (26), 1903-1904, 2010
52010
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Articles 1–20