Paolo Di Tommaso
Paolo Di Tommaso
Seqera Labs
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Cited by
Cited by
Nextflow enables reproducible computational workflows
P Di Tommaso, M Chatzou, EW Floden, PP Barja, E Palumbo, ...
Nature biotechnology 35 (4), 316-319, 2017
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
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
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
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
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
Accurate multiple sequence alignment of transmembrane proteins with PSI-Coffee
JM Chang, P Di Tommaso, JF Taly, C Notredame
BMC bioinformatics 13, 1-7, 2012
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
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
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
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
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
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
Scalable workflows and reproducible data analysis for genomics
F Strozzi, R Janssen, R Wurmus, MR Crusoe, G Githinji, P Di Tommaso, ...
Evolutionary Genomics: Statistical and Computational Methods, 723-745, 2019
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
Workflows community summit: Bringing the scientific workflows community together
RF da Silva, H Casanova, K Chard, D Laney, D Ahn, S Jha, C Goble, ...
arXiv preprint arXiv:2103.09181, 2021
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
Incorporating alignment uncertainty into Felsenstein’s phylogenetic bootstrap to improve its reliability
JM Chang, EW Floden, J Herrero, O Gascuel, P Di Tommaso, ...
Bioinformatics 37 (11), 1506-1514, 2021
A novel tool for highly scalable computational pipelines
P Di Tommaso, M Chatzou, PP Baraja, C Notredame
figshare, 2014
Multiple sequence alignment computation using the t-coffee regressive algorithm implementation
E Garriga, P Di Tommaso, C Magis, I Erb, L Mansouri, A Baltzis, E Floden, ...
Multiple Sequence Alignment: Methods and Protocols, 89-97, 2021
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