Paolo Di Tommaso
Overview
Explore the profile of Paolo Di Tommaso including associated specialties, affiliations and a list of published articles.
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Articles
19
Citations
3265
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Recent Articles
1.
Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, et al.
Methods Mol Biol
. 2020 Dec;
2231:89-97.
PMID: 33289888
Many fields of biology rely on the inference of accurate multiple sequence alignments (MSA) of biological sequences. Unfortunately, the problem of assembling an MSA is NP-complete thus limiting computation to...
2.
Ewels P, Peltzer A, Fillinger S, Patel H, Alneberg J, Wilm A, et al.
Nat Biotechnol
. 2020 Feb;
38(3):276-278.
PMID: 32055031
No abstract available.
3.
Garriga E, Di Tommaso P, Magis C, Erb I, Mansouri L, Baltzis A, et al.
Nat Biotechnol
. 2019 Dec;
37(12):1466-1470.
PMID: 31792410
Multiple sequence alignments (MSAs) are used for structural and evolutionary predictions, but the complexity of aligning large datasets requires the use of approximate solutions, including the progressive algorithm. Progressive MSA...
4.
Strozzi F, Janssen R, Wurmus R, Crusoe M, Githinji G, Di Tommaso P, et al.
Methods Mol Biol
. 2019 Jul;
1910:723-745.
PMID: 31278683
Biological, clinical, and pharmacological research now often involves analyses of genomes, transcriptomes, proteomes, and interactomes, within and between individuals and across species. Due to large volumes, the analysis and integration...
5.
Chang J, Floden E, Herrero J, Gascuel O, Di Tommaso P, Notredame C
Bioinformatics
. 2019 Feb;
37(11):1506-1514.
PMID: 30726875
Motivation: Most evolutionary analyses are based on pre-estimated multiple sequence alignment. Wong et al. established the existence of an uncertainty induced by multiple sequence alignment when reconstructing phylogenies. They were...
6.
Chatzou M, Floden E, Di Tommaso P, Gascuel O, Notredame C
Syst Biol
. 2018 Oct;
67(6):997-1009.
PMID: 30295908
Phylogenetic reconstructions are essential in genomics data analyses and depend on accurate multiple sequence alignment (MSA) models. We show that all currently available large-scale progressive multiple alignment methods are numerically...
7.
Di Tommaso P, Floden E, Magis C, Palumbo E, Notredame C
Biol Aujourdhui
. 2018 Feb;
211(3):233-237.
PMID: 29412134
Reproducing routine bioinformatics analysis is challenging owing to a combination of factors hard to control for. Nextflow is a flow management framework that uses container technology to insure efficient deployment...
8.
Di Tommaso P, Chatzou M, Floden E, Prieto Barja P, Palumbo E, Notredame C
Nat Biotechnol
. 2017 Apr;
35(4):316-319.
PMID: 28398311
No abstract available.
9.
Di Tommaso P, Palumbo E, Chatzou M, Prieto P, Heuer M, Notredame C
PeerJ
. 2015 Oct;
3:e1273.
PMID: 26421241
Genomic pipelines consist of several pieces of third party software and, because of their experimental nature, frequent changes and updates are commonly necessary thus raising serious deployment and reproducibility issues....
10.
Chang J, Di Tommaso P, Lefort V, Gascuel O, Notredame C
Nucleic Acids Res
. 2015 Apr;
43(W1):W3-6.
PMID: 25855806
This article introduces the Transitive Consistency Score (TCS) web server; a service making it possible to estimate the local reliability of protein multiple sequence alignments (MSAs) using the TCS index....