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ORCIDBibTeX records: Salvador Capella-Gutiérrez
@inproceedings{DBLP:conf/cordi/GobleBSOEDMR0GL23,
author = {Carole A. Goble and
Finn Bacall and
Stian Soiland{-}Reyes and
Stuart Owen and
Ignacio Eguinoa and
Bert Droesbeke and
Herv{\'{e}} M{\'{e}}nager and
Laura Rodr{\'{\i}}guez{-}Navas and
Jos{\'{e}} Mar{\'{\i}}a Fern{\'{a}}ndez and
Bj{\"{o}}rn A. Gr{\"{u}}ning and
Simone Leo and
Luca Pireddu and
Michael R. Crusoe and
Johan Gustafsson and
Salvador Capella{-}Guti{\'{e}}rrez and
Frederik Coppens},
editor = {York Sure{-}Vetter and
Carole A. Goble},
title = {The EOSC-Life Workflow Collaboratory for the Life Sciences},
booktitle = {1st Conference on Research Data Infrastructure - Connecting Communities,
CoRDI 2023, Karlsruhe, Germany, September 12-14, 2023},
publisher = {{TIB} Open Publishing},
year = {2023},
url = {https://doi.org/10.52825/cordi.v1i.352},
doi = {10.52825/CORDI.V1I.352},
timestamp = {Sat, 21 Oct 2023 10:46:27 +0200},
biburl = {https://dblp.org/rec/conf/cordi/GobleBSOEDMR0GL23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/corr/abs-2312-07852,
author = {Simone Leo and
Michael R. Crusoe and
Laura Rodr{\'{\i}}guez{-}Navas and
Ra{\"{u}}l Sirvent and
Alexander Kanitz and
Paul De Geest and
Rudolf Wittner and
Luca Pireddu and
Daniel Garijo and
Jos{\'{e}} M. Fern{\'{a}}ndez and
Iacopo Colonnelli and
Matej Gallo and
Tazro Ohta and
Hirotaka Suetake and
Salvador Capella{-}Guti{\'{e}}rrez and
Renske de Wit and
Bruno de Paula Kinoshita and
Stian Soiland{-}Reyes},
title = {Recording provenance of workflow runs with RO-Crate},
journal = {CoRR},
volume = {abs/2312.07852},
year = {2023},
url = {https://doi.org/10.48550/arXiv.2312.07852},
doi = {10.48550/ARXIV.2312.07852},
eprinttype = {arXiv},
eprint = {2312.07852},
timestamp = {Mon, 08 Jan 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/corr/abs-2312-07852.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FuentesMCCMG22,
author = {Diego Fuentes and
Manuel Molina and
Uciel Chorostecki and
Salvador Capella{-}Guti{\'{e}}rrez and
Marina Marcet{-}Houben and
Toni Gabald{\'{o}}n},
title = {PhylomeDB {V5:} an expanding repository for genome-wide catalogues
of annotated gene phylogenies},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{D1}},
pages = {1062--1068},
year = {2022},
url = {https://doi.org/10.1093/nar/gkab966},
doi = {10.1093/NAR/GKAB966},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FuentesMCCMG22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/NeversJJYFPCCMV22,
author = {Yannis Nevers and
Tamsin E. M. Jones and
Dushyanth Jyothi and
Bethan Yates and
Meritxell Ferret and
Laura Portell{-}Silva and
Laia Cod{\'{o}} and
Salvatore Cosentino and
Marina Marcet{-}Houben and
Anna Vlasova and
Laetitia Poidevin and
Arnaud Kress and
Mark Hickman and
Emma Persson and
Ivana Pilizota and
Cristina Guijarro{-}Clarke and
Adrian M. Altenhoff and
Elspeth A. Bruford and
Christophe Dessimoz and
Ingo Ebersberger and
David M. Emms and
Toni Gabald{\'{o}}n and
Natasha M. Glover and
Yanhui Hu and
Wataru Iwasaki and
Odile Lecompte and
Benjamin Linard and
Mar{\'{\i}}a J. Mart{\'{\i}}n and
David S. Roos and
Erik Sonhammer and
Paul D. Thomas and
David Thybert and
Klaas Vandepoele and
Salvador Capella{-}Guti{\'{e}}rrez and
Asier Gonzalez{-}Uriarte and
Javier Garrayo{-}Ventas and
Dmitry Repchevsky and
Vicky Sundesha and
Erik L. L. Sonnhammer},
title = {The Quest for Orthologs orthology benchmark service in 2022},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{W1}},
pages = {623--632},
year = {2022},
url = {https://doi.org/10.1093/nar/gkac330},
doi = {10.1093/NAR/GKAC330},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/NeversJJYFPCCMV22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/works-ws/SirventCLERFCB22,
author = {Ra{\"{u}}l Sirvent and
Javier Conejero and
Francesc Lordan and
Jorge Ejarque and
Laura Rodr{\'{\i}}guez{-}Navas and
Jos{\'{e}} Mar{\'{\i}}a Fern{\'{a}}ndez and
Salvador Capella{-}Guti{\'{e}}rrez and
Rosa M. Badia},
title = {Automatic, Efficient and Scalable Provenance Registration for {FAIR}
{HPC} Workflows},
booktitle = {{IEEE/ACM} Workshop on Workflows in Support of Large-Scale Science,
WORKS@SC 2022, Dallas, TX, USA, November 13-18, 2022},
pages = {1--9},
publisher = {{IEEE}},
year = {2022},
url = {https://doi.org/10.1109/WORKS56498.2022.00006},
doi = {10.1109/WORKS56498.2022.00006},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/conf/works-ws/SirventCLERFCB22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/LamprechtPISMABACCCGGGGIJ21,
author = {Anna{-}Lena Lamprecht and
Magnus Palmblad and
Jon C. Ison and
Veit Schw{\"{a}}mmle and
Mohammad Sadnan Al Manir and
Ilkay Altintas and
Christopher J. O. Baker and
Ammar Ben Hadj Amor and
Salvador Capella{-}Guti{\'{e}}rrez and
Paulos Charonyktakis and
Michael R. Crusoe and
Yolanda Gil and
Carole A. Goble and
Timothy J. Griffin and
Paul Groth and
Hans Ienasescu and
Pratik D. Jagtap and
Mat{\'{u}}s Kalas and
Vedran Kasalica and
Alireza Khanteymoori and
Tobias Kuhn and
Hailiang Mei and
Herv{\'{e}} M{\'{e}}nager and
Steffen M{\"{o}}ller and
Robin A. Richardson and
Vincent Robert and
Stian Soiland{-}Reyes and
Robert Stevens and
Szaniszlo Szoke and
Suzan Verberne and
Aswin Verhoeven and
Katherine Wolstencroft},
title = {Perspectives on automated composition of workflows in the life sciences},
journal = {F1000Research},
volume = {10},
pages = {897},
year = {2021},
url = {https://doi.org/10.12688/f1000research.54159.1},
doi = {10.12688/F1000RESEARCH.54159.1},
timestamp = {Mon, 05 Feb 2024 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/f1000research/LamprechtPISMABACCCGGGGIJ21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/datasci/LamprechtGKMAPA20,
author = {Anna{-}Lena Lamprecht and
Leyla J. Garc{\'{\i}}a and
Mateusz Kuzak and
Carlos Martinez{-}Ortiz and
Ricardo Arcila and
Eva Martin Del Pico and
Victoria Dominguez Del Angel and
Stephanie van de Sandt and
Jon C. Ison and
Paula Andrea Mart{\'{\i}}nez and
Peter McQuilton and
Alfonso Valencia and
Jennifer L. Harrow and
Fotis E. Psomopoulos and
Josep Lluis Gelp{\'{\i}} and
Neil P. Chue Hong and
Carole A. Goble and
Salvador Capella{-}Guti{\'{e}}rrez},
title = {Towards {FAIR} principles for research software},
journal = {Data Sci.},
volume = {3},
number = {1},
pages = {37--59},
year = {2020},
url = {https://doi.org/10.3233/ds-190026},
doi = {10.3233/DS-190026},
timestamp = {Mon, 20 Sep 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/datasci/LamprechtGKMAPA20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/AltenhoffGCEGHN20,
author = {Adrian M. Altenhoff and
Javier Garrayo{-}Ventas and
Salvatore Cosentino and
David Emms and
Natasha M. Glover and
Ana Hern{\'{a}}ndez{-}Plaza and
Yannis Nevers and
Vicky Sundesha and
Damian Szklarczyk and
Jos{\'{e}} Mar{\'{\i}}a Fern{\'{a}}ndez and
Laia Cod{\'{o}} and
The Quest for Orthologs Consortium and
Josep Lluis Gelp{\'{\i}} and
Jaime Huerta{-}Cepas and
Wataru Iwasaki and
Steven Kelly and
Odile Lecompte and
Matthieu Muffato and
Maria Jesus Martin and
Salvador Capella{-}Guti{\'{e}}rrez and
Paul D. Thomas and
Erik L. L. Sonnhammer and
Christophe Dessimoz},
title = {The Quest for Orthologs benchmark service and consensus calls in 2020},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Webserver-Issue},
pages = {W538--W545},
year = {2020},
url = {https://doi.org/10.1093/nar/gkaa308},
doi = {10.1093/NAR/GKAA308},
timestamp = {Fri, 07 Jul 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/AltenhoffGCEGHN20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/SalgadoABBCCADFGCGGGHHHHJ20,
author = {David Salgado and
Irina M. Armean and
Michael Baudis and
Sergi Beltran and
Salvador Capella{-}Guti{\'{e}}rrez and
Denise Carvalho{-}Silva and
Victoria Dominguez Del Angel and
Joaqu{\'{\i}}n Dopazo and
Laura I. Furlong and
Bo Gao and
Leyla Jael Garc{\'{\i}}a Castro and
Dietlind Gerloff and
Ivo Gut and
Attila Gyenesei and
Nina Habermann and
John M. Hancock and
Marc Hanauer and
Eivind Hovig and
Lennart F. Johansson and
Thomas Keane and
Jan Korbel and
Katharina B. Lauer and
Steve Laurie and
Brane Leskosek and
David Lloyd and
Tom{\`{a}}s Marqu{\`{e}}s{-}Bonet and
Hailiang Mei and
Katalin Monostory and
Janet Pi{\~{n}}ero and
Krzysztof Poterlowicz and
Ana Rath and
Pubudu Samarakoon and
Ferran Sanz and
Gary Saunders and
Daoud Sie and
Morris A. Swertz and
Kirill Tsukanov and
Alfonso Valencia and
Marko Vidak and
Cristina Yenyxe Gonz{\'{a}}lez and
Bauke Ylstra and
Christophe B{\'{e}}roud},
title = {The {ELIXIR} Human Copy Number Variations Community: building bioinformatics
infrastructure for research},
journal = {F1000Research},
volume = {9},
pages = {1229},
year = {2020},
url = {https://doi.org/10.12688/f1000research.24887.1},
doi = {10.12688/F1000RESEARCH.24887.1},
timestamp = {Sun, 04 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/f1000research/SalgadoABBCCADFGCGGGHHHHJ20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/ForslundPCSAHMP18,
author = {Kristoffer Forslund and
C{\'{e}}cile Pereira and
Salvador Capella{-}Guti{\'{e}}rrez and
Alan W. Sousa da Silva and
Adrian M. Altenhoff and
Jaime Huerta{-}Cepas and
Matthieu Muffato and
Mateus Patricio and
Klaas Vandepoele and
Ingo Ebersberger and
Judith A. Blake and
Jesualdo Tom{\'{a}}s Fern{\'{a}}ndez{-}Breis and
The Quest for Orthologs Consortium and
Brigitte Boeckmann and
Toni Gabald{\'{o}}n and
Erik L. L. Sonnhammer and
Christophe Dessimoz and
Suzanna Lewis},
title = {Gearing up to handle the mosaic nature of life in the quest for orthologs},
journal = {Bioinform.},
volume = {34},
number = {2},
pages = {323--329},
year = {2018},
url = {https://doi.org/10.1093/bioinformatics/btx542},
doi = {10.1093/BIOINFORMATICS/BTX542},
timestamp = {Fri, 08 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/ForslundPCSAHMP18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CanadaCROVK17,
author = {Andr{\'{e}}s Ca{\~{n}}ada and
Salvador Capella{-}Guti{\'{e}}rrez and
Obdulia Rabal and
Julen Oyarzabal and
Alfonso Valencia and
Martin Krallinger},
title = {LimTox: a web tool for applied text mining of adverse event and toxicity
associations of compounds, drugs and genes},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Webserver-Issue},
pages = {W484--W489},
year = {2017},
url = {https://doi.org/10.1093/nar/gkx462},
doi = {10.1093/NAR/GKX462},
timestamp = {Thu, 23 Jun 2022 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CanadaCROVK17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/f1000research/JimenezKABBBCHC17,
author = {Rafael C. Jim{\'{e}}nez and
Mateusz Kuzak and
Monther Alhamdoosh and
Michelle Barker and
B{\'{e}}r{\'{e}}nice Batut and
Mikael Borg and
Salvador Capella{-}Guti{\'{e}}rrez and
Neil P. Chue Hong and
Martin Cook and
Manuel Corpas and
Madison Flannery and
Leyla J. Garc{\'{\i}}a and
Josep Lluis Gelp{\'{\i}} and
Simon L. Gladman and
Carole A. Goble and
Montserrat Gonz{\'{a}}lez Ferreiro and
Alejandra N. Gonz{\'{a}}lez{-}Beltr{\'{a}}n and
Philippa C. Griffin and
Bj{\"{o}}rn A. Gr{\"{u}}ning and
Jonas Hagberg and
Petr Holub and
Rob W. W. Hooft and
Jon C. Ison and
Daniel S. Katz and
Brane Leskosek and
Federico L{\'{o}}pez{-}G{\'{o}}mez and
Luis J. Oliveira and
David Mellor and
Rowland Mosbergen and
Nicola J. Mulder and
Yasset P{\'{e}}rez{-}Riverol and
Robert Pergl and
Horst Pichler and
Bernard J. Pope and
Ferran Sanz and
Maria Victoria Schneider and
Victoria Stodden and
Radoslaw Suchecki and
Radka Svobodov{\'{a}} Varekov{\'{a}} and
Harry{-}Anton Talvik and
Ilian T. Todorov and
Andrew E. Treloar and
Sonika Tyagi and
Maarten van Gompel and
Daniel Vaughan and
Allegra Via and
Xiaochuan Wang and
Nathan S. Watson{-}Haigh and
Steve Crouch},
title = {Four simple recommendations to encourage best practices in research
software},
journal = {F1000Research},
volume = {6},
pages = {876},
year = {2017},
url = {https://doi.org/10.12688/f1000research.11407.1},
doi = {10.12688/F1000RESEARCH.11407.1},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/f1000research/JimenezKABBBCHC17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/Huerta-CepasCPMG14,
author = {Jaime Huerta{-}Cepas and
Salvador Capella{-}Guti{\'{e}}rrez and
Leszek P. Pryszcz and
Marina Marcet{-}Houben and
Toni Gabald{\'{o}}n},
title = {PhylomeDB v4: zooming into the plurality of evolutionary histories
of a genome},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {897--902},
year = {2014},
url = {https://doi.org/10.1093/nar/gkt1177},
doi = {10.1093/NAR/GKT1177},
timestamp = {Tue, 21 Mar 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/Huerta-CepasCPMG14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nature/DohmMHCZTRSSRGK14,
author = {Juliane C. Dohm and
Andr{\'{e}} E. Minoche and
Daniela Holtgr{\"{a}}we and
Salvador Capella{-}Guti{\'{e}}rrez and
Falk Zakrzewski and
Hakim Tafer and
Oliver Rupp and
Thomas Rosleff S{\"{o}}rensen and
Ralf Stracke and
Richard Reinhardt and
Alexander Goesmann and
Thomas Kraft and
Britta Schulz and
Peter F. Stadler and
Thomas Schmidt and
Toni Gabald{\'{o}}n and
Hans Lehrach and
Bernd Weisshaar and
Heinz Himmelbauer},
title = {The genome of the recently domesticated crop plant sugar beet (\emph{Beta
vulgaris}) Open},
journal = {Nat.},
volume = {505},
number = {7484},
pages = {546--549},
year = {2014},
url = {https://doi.org/10.1038/nature12817},
doi = {10.1038/NATURE12817},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nature/DohmMHCZTRSSRGK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Capella-GutierrezG13,
author = {Salvador Capella{-}Guti{\'{e}}rrez and
Toni Gabald{\'{o}}n},
title = {Measuring guide-tree dependency of inferred gaps in progressive aligners},
journal = {Bioinform.},
volume = {29},
number = {8},
pages = {1011--1017},
year = {2013},
url = {https://doi.org/10.1093/bioinformatics/btt095},
doi = {10.1093/BIOINFORMATICS/BTT095},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Capella-GutierrezG13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/Huerta-CepasCPDKMG11,
author = {Jaime Huerta{-}Cepas and
Salvador Capella{-}Guti{\'{e}}rrez and
Leszek P. Pryszcz and
Ivan Andreevich Denisov and
Diego Kormes and
Marina Marcet{-}Houben and
Toni Gabald{\'{o}}n},
title = {PhylomeDB v3.0: an expanding repository of genome-wide collections
of trees, alignments and phylogeny-based orthology and paralogy predictions},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Database-Issue},
pages = {556--560},
year = {2011},
url = {https://doi.org/10.1093/nar/gkq1109},
doi = {10.1093/NAR/GKQ1109},
timestamp = {Mon, 12 Aug 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/Huerta-CepasCPDKMG11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SanchezSTMCPMCHGDD11,
author = {Rub{\'{e}}n S{\'{a}}nchez and
Fran{\c{c}}ois Serra and
Joaqu{\'{\i}}n T{\'{a}}rraga and
Ignacio Medina and
Jos{\'{e}} Carbonell and
Luis Pulido and
Alejandro de Mar{\'{\i}}a and
Salvador Capella{-}Guti{\'{e}}rrez and
Jaime Huerta{-}Cepas and
Toni Gabald{\'{o}}n and
Joaqu{\'{\i}}n Dopazo and
Hern{\'{a}}n Dopazo},
title = {Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics,
phylogenomics and hypotheses testing},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Web-Server-Issue},
pages = {470--474},
year = {2011},
url = {https://doi.org/10.1093/nar/gkr408},
doi = {10.1093/NAR/GKR408},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SanchezSTMCPMCHGDD11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/Capella-GutierrezSG09,
author = {Salvador Capella{-}Guti{\'{e}}rrez and
Jos{\'{e}} M. Silla{-}Mart{\'{\i}}nez and
Toni Gabald{\'{o}}n},
title = {trimAl: a tool for automated alignment trimming in large-scale phylogenetic
analyses},
journal = {Bioinform.},
volume = {25},
number = {15},
pages = {1972--1973},
year = {2009},
url = {https://doi.org/10.1093/bioinformatics/btp348},
doi = {10.1093/BIOINFORMATICS/BTP348},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/Capella-GutierrezSG09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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