Paolo Di Tommaso - Publications, H-index & Citations

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Paolo Di Tommaso

Pompeu Fabra University

18H-index

67Paper Count

1.0WCitation Count

Published Papers 13

Publication Date

An nf-core framework for the systematic comparison of alternative modeling tools: the multiple sequence alignment case study

NAR GENOMICS AND BIOINFORMATICS

IF2.8

2025-09-01

OAAI

Santus, Luisa; Espinosa-Carrasco, Jose; Rauschning, Leon; Mir-Pedrol, Julia; Trujnara, Igor; Vignoli, Alessio; Mansouri, Leila; Baltzis, Athanasios; Floden, Evan W.; Di Tommaso, Paolo; Garriga, Edgar; Gudys, Adam; Deorowicz, Sebastian; Gilchrist, Cameron; Steinegger, Martin; Notredame, Cedric

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A terminology for scientific workflow systems

Future Generation Computer Systems

IF0

2025-06-24

PREAI

Frédéric Suter; Tainã Coleman; İlkay Altintaş; Rosa M. Badia; Bartosz Balis; Kyle Chard; Iacopo Colonnelli; Ewa Deelman; Paolo Di Tommaso; Thomas Fahringer; Carole Goble; Shantenu Jha; Daniel S. Katz; Johannes Köster; Ulf Leser; Kshitij Mehta; Hilary Oliver; J.-Luc Peterson; Giovanni Pizzi; Loïc Pottier; Rafael Ferreira da Silva

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The nf-core framework for community-curated bioinformatics pipelines

NATURE BIOTECHNOLOGY

IF41.7

2020-02-13

943

PREAI

Ewels, Philip A.; Peltzer, Alexander; Fillinger, Sven; Patel, Harshil; Alneberg, Johannes; Wilm, Andreas; Garcia, Maxime Ulysse; Di Tommaso, Paolo; Nahnsen, Sven

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Large multiple sequence alignments with a root-to-leaf regressive method

NATURE BIOTECHNOLOGY

IF41.7

2019-12-02

OAAI

Garriga, Edgar; Di Tommaso, Paolo; Magis, Cedrik; Erb, Ionas; Mansouri, Leila; Baltzis, Athanasios; Laayouni, Hafid; Kondrashov, Fyodor; Floden, Evan; Notredame, Cedric

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Generalized Bootstrap Supports for Phylogenetic Analyses of Protein Sequences Incorporating Alignment Uncertainty

SYSTEMATIC BIOLOGY

IF5.7

2018-03-29

OAAI

Chatzou, Maria; Floden, Evan W.; Di Tommaso, Paolo; Gascuel, Olivier; Notredame, Cedric

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Nextflow enables reproducible computational workflows

NATURE BIOTECHNOLOGY

IF41.7

2017-04-11

1.2K

PREAI

Di Tommaso, Paolo; Chatzou, Maria; Floden, Evan W.; Prieto Barja, Pablo; Palumbo, Emilio; Notredame, Cedric

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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 RESEARCH

IF13.1

2016-04-22

OAAI

Floden, Evan W.; Tommaso, Paolo D.; Chatzou, Maria; Magis, Cedrik; Notredame, Cedric; Chang, Jia-Ming

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TCS: a web server for multiple sequence alignment evaluation and phylogenetic reconstruction

NUCLEIC ACIDS RESEARCH

IF13.1

2015-04-08

OAAI

Chang, Jia-Ming; Di Tommaso, Paolo; Lefort, Vincent; Gascuel, Olivier; Notredame, Cedric

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SARA-Coffee web server, a tool for the computation of RNA sequence and structure multiple alignments

NUCLEIC ACIDS RESEARCH

IF13.1

2014-06-27

OAAI

Tommaso, Paolo Di; Bussotti, Giovanni; Kemena, Carsten; Capriotti, Emidio; Chatzou, Maria; Prieto, Pablo; Notredame, Cedric

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TCS: A New Multiple Sequence Alignment Reliability Measure to Estimate Alignment Accuracy and Improve Phylogenetic Tree Reconstruction

MOLECULAR BIOLOGY AND EVOLUTION

IF5.3

2014-04-01

156

OAAI

Chang, Jia-Ming; Di Tommaso, Paolo; Notredame, Cedric

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T-RMSD: a web server for automated fine-grained protein structural classification

NUCLEIC ACIDS RESEARCH

IF13.1

2013-05-28

OAAI

Magis, Cedrik; Di Tommaso, Paolo; Notredame, Cedric

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Using the T-Coffee package to build multiple sequence alignments of protein, RNA, DNA sequences and 3D structures

NATURE PROTOCOLS

IF16

2011-10-06

PREAI

Taly, Jean-Francois; Magis, Cedrik; Bussotti, Giovanni; Chang, Jia-Ming; Di Tommaso, Paolo; Erb, Ionas; Espinosa-Carrasco, Jose; Kemena, Carsten; Notredame, Cedric

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T-Coffee: a web server for the multiple sequence alignment of protein and RNA sequences using structural information and homology extension

NUCLEIC ACIDS RESEARCH

IF13.1

2011-05-09

854

OAAI

Di Tommaso, Paolo; Moretti, Sebastien; Xenarios, Ioannis; Orobitg, Miquel; Montanyola, Alberto; Chang, Jia-Ming; Taly, Jean-Francois; Notredame, Cedric

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Research Directions