trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. - Salvador Capella-Gutiérrez; José M. Silla-Martínez; Toni Gabaldón (Bioinform., 2009)

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions. - Jaime Huerta-Cepas; Salvador Capella-Gutiérrez; Leszek P. Pryszcz; Ivan Andreevich Denisov; Diego Kormes; Marina Marcet-Houben; Toni Gabaldón (Nucleic Acids Res., 2011)

Phylemon 2.0: a suite of web-tools for molecular evolution, phylogenetics, phylogenomics and hypotheses testing. - Rubén Sánchez 002; François Serra; Joaquín Tárraga; Ignacio Medina; José Carbonell; Luis Pulido; Alejandro de María; Salvador Capella-Gutiérrez; Jaime Huerta-Cepas; Toni Gabaldón; Joaquín Dopazo; Hernán Dopazo (Nucleic Acids Res., 2011)

Measuring guide-tree dependency of inferred gaps in progressive aligners. - Salvador Capella-Gutiérrez; Toni Gabaldón (Bioinform., 2013)

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome. - Jaime Huerta-Cepas; Salvador Capella-Gutiérrez; Leszek P. Pryszcz; Marina Marcet-Houben; Toni Gabaldón (Nucleic Acids Res., 2014)

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris) Open. - Juliane C. Dohm; André E. Minoche; Daniela Holtgräwe; Salvador Capella-Gutiérrez; Falk Zakrzewski; Hakim Tafer; Oliver Rupp; Thomas Rosleff Sörensen; Ralf Stracke; Richard Reinhardt; Alexander Goesmann; Thomas Kraft; et al. (Nat., 2014)

Four simple recommendations to encourage best practices in research software. - Rafael C. Jiménez; Mateusz Kuzak; Monther Alhamdoosh; Michelle Barker; Bérénice Batut; Mikael Borg; Salvador Capella-Gutiérrez; Neil P. Chue Hong; Martin Cook; Manuel Corpas; Madison Flannery; Leyla J. García; et al. (F1000Research, 2017)

LimTox: a web tool for applied text mining of adverse event and toxicity associations of compounds, drugs and genes. - Andrés Cañada; Salvador Capella-Gutiérrez; Obdulia Rabal; Julen Oyarzabal; Alfonso Valencia; Martin Krallinger (Nucleic Acids Res., 2017)

Gearing up to handle the mosaic nature of life in the quest for orthologs. - Kristoffer Forslund; Cécile Pereira; Salvador Capella-Gutiérrez; Alan W. Sousa da Silva; Adrian M. Altenhoff; Jaime Huerta-Cepas; Matthieu Muffato; Mateus Patricio; Klaas Vandepoele; Ingo Ebersberger; Judith A. Blake; Jesualdo Tomás Fernández-Breis; et al. (Bioinform., 2018)

ECCB2020: the 19th European Conference on Computational Biology. - Salvador Capella-Gutiérrez; Eva Alloza; Edurne Gallastegui; Ioannis Kavakiotis; Jen Harrow; Alberto Langtry; Alfonso Valencia (Bioinform., 2020)

Towards FAIR principles for research software. - Anna-Lena Lamprecht; Leyla J. García; Mateusz Kuzak; Carlos Martinez-Ortiz; Ricardo Arcila; Eva Martin Del Pico; Victoria Dominguez Del Angel; Stephanie van de Sandt; Jon C. Ison; Paula Andrea Martínez; Peter McQuilton; Alfonso Valencia; et al. (Data Sci., 2020)

The ELIXIR Human Copy Number Variations Community: building bioinformatics infrastructure for research. - David Salgado; Irina M. Armean; Michael Baudis; Sergi Beltran; Salvador Capella-Gutiérrez; Denise Carvalho-Silva; Victoria Dominguez Del Angel; Joaquín Dopazo; Laura I. Furlong; Bo Gao; Leyla Jael García Castro; Dietlind Gerloff; et al. (F1000Research, 2020)

The Quest for Orthologs benchmark service and consensus calls in 2020. - Adrian M. Altenhoff; Javier Garrayo-Ventas; Salvatore Cosentino; David Emms; Natasha M. Glover; Ana Hernández-Plaza; Yannis Nevers; Vicky Sundesha; Damian Szklarczyk; José María Fernández 001; Laia Codó; Quest for Orthologs Consortium; et al. (Nucleic Acids Res., 2020)

Perspectives on automated composition of workflows in the life sciences. - Anna-Lena Lamprecht; Magnus Palmblad; Jon C. Ison; Veit Schwämmle; Mohammad Sadnan Al Manir; Ilkay Altintas; Christopher J. O. Baker; Ammar Ben Hadj Amor; Salvador Capella-Gutiérrez; Paulos Charonyktakis; Michael R. Crusoe; Yolanda Gil; et al. (F1000Research, 2021)

Automatic, Efficient and Scalable Provenance Registration for FAIR HPC Workflows. - Raül Sirvent; Javier Conejero; Francesc Lordan; Jorge Ejarque; Laura Rodríguez-Navas; José María Fernández 001; Salvador Capella-Gutiérrez; Rosa M. Badia (WORKS@SC, 2022)

ECCB2022: the 21st European Conference on Computational Biology. - Salvador Capella-Gutiérrez; Eva Alloza; Laura Rubinat-Ripoll; Ana Conesa; Alfonso Valencia (Bioinform., 2022)

PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies. - Diego Fuentes; Manuel Molina; Uciel Chorostecki; Salvador Capella-Gutiérrez; Marina Marcet-Houben; Toni Gabaldón (Nucleic Acids Res., 2022)

The Quest for Orthologs orthology benchmark service in 2022. - Yannis Nevers; Tamsin E. M. Jones; Dushyanth Jyothi; Bethan Yates; Meritxell Ferret; Laura Portell-Silva; Laia Codó; Salvatore Cosentino; Marina Marcet-Houben; Anna Vlasova; Laetitia Poidevin; Arnaud Kress; et al. (Nucleic Acids Res., 2022)

The EOSC-Life Workflow Collaboratory for the Life Sciences. - Carole A. Goble; Finn Bacall; Stian Soiland-Reyes; Stuart Owen; Ignacio Eguinoa; Bert Droesbeke; Hervé Ménager; Laura Rodríguez-Navas; José María Fernández 001; Björn A. Grüning; Simone Leo; Luca Pireddu; et al. (CoRDI, 2023)

Recording provenance of workflow runs with RO-Crate. - Simone Leo; Michael R. Crusoe; Laura Rodríguez-Navas; Raül Sirvent; Alexander Kanitz; Paul De Geest; Rudolf Wittner; Luca Pireddu; Daniel Garijo; José M. Fernández; Iacopo Colonnelli; Matej Gallo; et al. (CoRR, 2023)

WorkflowHub: a registry for computational workflows. - Johan Gustafsson 001; Sean R. Wilkinson; Finn Bacall; Luca Pireddu; Stian Soiland-Reyes; Simone Leo; Stuart Owen; Nick S. Juty; José María Fernández 001; Björn A. Grüning; Tom Brown; Hervé Ménager; et al. (CoRR, 2024)

Open and Sustainable AI: challenges, opportunities and the road ahead in the life sciences. - Gavin Farrell; Eleni Adamidi; Rafael Andrade Buono; Mihail Anton; Omar Abdelghani Attafi; Salvador Capella-Gutiérrez; Emidio Capriotti; Leyla Jael Castro; Davide Cirillo; Lisa C. Crossman; Christophe Dessimoz; Alexandros C. Dimopoulos; et al. (CoRR, 2025)

Identity resolution of software metadata using Large Language Models. - Eva Martin Del Pico; Josep Lluis Gelpí; Salvador Capella-Gutiérrez (CoRR, 2025)

PretoxTM: a text mining system for extracting treatment-related findings from preclinical toxicology reports. - Javier Corvi; Nicolás Díaz-Roussel; José M. Fernández; Francesco Ronzano; Emilio Centeno; Pablo Accuosto; Celine Ibrahim; Shoji Asakura; Frank Bringezu; Mirjam Fröhlicher; Annika Kreuchwig; Yoko Nogami; et al. (J. Cheminformatics, 2025)