Zobrazeno 1 - 10
of 25
pro vyhledávání: '"Paolo Di Tommaso"'
Autor:
Paolo Di Tommaso, Emilio Palumbo, Maria Chatzou, Pablo Prieto, Michael L. Heuer, Cedric Notredame
Publikováno v:
PeerJ, Vol 3, p e1273 (2015)
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. Docker containers are emerg
Externí odkaz:
https://doaj.org/article/0e8cf15c6a164b10b92cabc7f498a043
Autor:
Andreas Wilm, Johannes Alneberg, Philip Ewels, Paolo Di Tommaso, Harshil Patel, Maxime Garcia, Sven Nahnsen, Alexander Peltzer, Sven Fillinger
Publikováno v:
Nature Biotechnology. 38:276-278
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::aa1f1f9e8841348b513e6ce12c163ba8
https://doi.org/10.1038/s41587-020-0439-x
https://doi.org/10.1038/s41587-020-0439-x
Autor:
Cedric Notredame, Paolo Di Tommaso, Cedrik Magis, Edgar Garriga, Leila Mansouri, Ionas Erb, Evan Floden, Athanasios Baltzis
Publikováno v:
Methods in Molecular Biology ISBN: 9781071610350
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 approximate solutions using heuristics so
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::c3f06c5f2d020024a5a49ed14765a81c
https://doi.org/10.1007/978-1-0716-1036-7_6
https://doi.org/10.1007/978-1-0716-1036-7_6
Autor:
Edgar, Garriga, Paolo, Di Tommaso, Cedrik, Magis, Ionas, Erb, Leila, Mansouri, Athanasios, Baltzis, Evan, Floden, Cedric, Notredame
Publikováno v:
Methods in molecular biology (Clifton, N.J.). 2231
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 approximate solutions using heuristics so
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=pmid________::1811ef5ef5b3adc3de963c75dc8d7bbf
https://pubmed.ncbi.nlm.nih.gov/33289888
https://pubmed.ncbi.nlm.nih.gov/33289888
Autor:
Matteo Carone, Evan Floden, Ola Spjuth, Pablo Moreno, Paolo Di Tommaso, Samuel Lampa, Stephanie Herman, Payam Emami Khoonsari, Morgan Ekmefjord, Jon Ander Novella, Marco Capuccini, Anders Larsson, Wesley Schaal, Kim Kultima, Oliver Stein, Cedric Notredame
Containers are gaining popularity in life science research as they provide a solution for encompassing dependencies of provisioned tools, simplify software installations for end users and offer a form of isolation between processes. Scientific workfl
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::2e9421a0a2da6bc17fb992990031961a
https://doi.org/10.20944/preprints202001.0378.v1
https://doi.org/10.20944/preprints202001.0378.v1
Autor:
Emilio Palumbo, Paolo Di Tommaso, Cedric Notredame, Pablo Prieto Barja, Evan Floden, Maria Chatzou
Publikováno v:
Nature Biotechnology. 35:316-319
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::e0c19d0422b5504f247629f6c5eb6471
https://doi.org/10.1038/nbt.3820
https://doi.org/10.1038/nbt.3820
Publikováno v:
Biologie Aujourd'hui. 211:233-237
La reproduction des analyses bio-informatiques de routine est difficile en raison d’une combinaison de facteurs difficiles a controler. Nextflow est un gestionnaire de flux (workflow manager ) qui utilise la technologie des conteneurs pour assurer
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_________::d25b32ab21706a34816161be558a5381
https://doi.org/10.1051/jbio/2017029
https://doi.org/10.1051/jbio/2017029
Autor:
Francesco Strozzi, Dominique Belhachemi, George Githinji, Steffen Möller, Pjotr Prins, Paolo Di Tommaso, Ricardo Wurmus, Roel Janssen, Geert Smant, Joep de Ligt, Michael R. Crusoe
Publikováno v:
Evolutionary Genomics
Evolutionary Genomics. Humana Press Inc.
Methods in Molecular Biology ISBN: 9781493990733
Evolutionary Genomics. Humana Press Inc.
Methods in Molecular Biology ISBN: 9781493990733
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 of data gene
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::f3f603d77bafdaaad9153e3ea1ebdae3
https://research.wur.nl/en/publications/scalable-workflows-and-reproducible-data-analysis-for-genomics
https://research.wur.nl/en/publications/scalable-workflows-and-reproducible-data-analysis-for-genomics
Autor:
Edgar Garriga, Cedric Notredame, Leila Mansouri, Hafid Laayouni, Athanasios Baltzis, Evan Floden, Paolo Di Tommaso, Cedrik Magis, Fyodor A. Kondrashov, Ionas Erb
Publikováno v:
Nature Biotechnology
Nature biotechnology
Nature biotechnology
Multiple sequence alignments (MSAs) are used for structural1,2 and evolutionary predictions1,2, but the complexity of aligning large datasets requires the use of approximate solutions3, including the progressive algorithm4. Progressive MSA methods st
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::61a91533710af045aef21280db06bc83
Autor:
Olivier Gascuel, Jia-Ming Chang, Evan Floden, Paolo Di Tommaso, Cedric Notredame, Javier Herrero
Publikováno v:
Bioinformatics
Bioinformatics, Oxford University Press (OUP), 2021, ⟨10.1093/bioinformatics/btz082⟩
Bioinformatics, 2021, ⟨10.1093/bioinformatics/btz082⟩
Bioinformatics, Oxford University Press (OUP), 2021, ⟨10.1093/bioinformatics/btz082⟩
Bioinformatics, 2021, ⟨10.1093/bioinformatics/btz082⟩
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 able to show that
Externí odkaz:
https://explore.openaire.eu/search/publication?articleId=doi_dedup___::7ef6a28519af84d0bec4c3245a5fa681
http://hdl.handle.net/10230/51908
http://hdl.handle.net/10230/51908