A stochastic boundary forcing for dissipative particle dynamics. - Adrian M. Altenhoff; Jens H. Walther; Petros Koumoutsakos (J. Comput. Phys., 2007)

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods. - Adrian M. Altenhoff; Christophe Dessimoz (PLoS Comput. Biol., 2009)

OMA 2011: orthology inference among 1000 complete genomes. - Adrian M. Altenhoff; Adrian Schneider; Gaston H. Gonnet; Christophe Dessimoz (Nucleic Acids Res., 2011)

Resolving the Ortholog Conjecture: Orthologs Tend to Be Weakly, but Significantly, More Similar in Function than Paralogs. - Adrian M. Altenhoff; Romain A. Studer; Marc Robinson-Rechavi; Christophe Dessimoz (PLoS Comput. Biol., 2012)

Quality of Computationally Inferred Gene Ontology Annotations. - Nives Skunca; Adrian M. Altenhoff; Christophe Dessimoz (PLoS Comput. Biol., 2012)

Orthology inference: Methods, benchmarking and applications. - Adrian M. Altenhoff (2012)

Fifteen years SIB Swiss Institute of Bioinformatics: life science databases, tools and support. - Heinz Stockinger; Adrian M. Altenhoff; Konstantin Arnold; Amos Bairoch; Frederic B. Bastian; Sven Bergmann; Lydie Bougueleret; Philipp Bucher; Mauro Delorenzi; Lydie Lane; Philippe Le Mercier; Frédérique Lisacek; et al. (Nucleic Acids Res., 2014)

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements. - Adrian M. Altenhoff; Nives Skunca; Natasha M. Glover; Clément-Marie Train; Anna Sueki; Ivana Pilizota; Kevin Gori; Bartlomiej Tomiczek; Steven Müller; Henning Redestig; Gaston H. Gonnet; Christophe Dessimoz (Nucleic Acids Res., 2015)

Orthologous Matrix (OMA) algorithm 2.0: more robust to asymmetric evolutionary rates and more scalable hierarchical orthologous group inference. - Clément-Marie Train; Natasha M. Glover; Gaston H. Gonnet; Adrian M. Altenhoff; Christophe Dessimoz (Bioinform., 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)

The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces. - Adrian M. Altenhoff; Natasha M. Glover; Clément-Marie Train; Klara Kaleb; Alex Warwick Vesztrocy; David Dylus; Tarcisio M. Farias; Karina Zile; Charles Stevenson; Jiao Long; Henning Redestig; Gaston H. Gonnet; et al. (Nucleic Acids Res., 2018)

Phylogenetic approaches to identifying fragments of the same gene, with application to the wheat genome. - Ivana Pilizota; Clément-Marie Train; Adrian M. Altenhoff; Henning Redestig; Christophe Dessimoz (Bioinform., 2019)

iHam and pyHam: visualizing and processing hierarchical orthologous groups. - Clément-Marie Train; Miguel Pignatelli; Adrian M. Altenhoff; Christophe Dessimoz (Bioinform., 2019)

Parallel and Scalable Precise Clustering for Homologous Protein Discovery. - Stuart Byma; Akash Balasaheb Dhasade; Adrian M. Altenhoff; Christophe Dessimoz; James R. Larus (CoRR, 2019)

Expanding the Orthologous Matrix (OMA) programmatic interfaces: REST API and the OmaDB packages for R and Python. - Klara Kaleb; Alex Warwick Vesztrocy; Adrian M. Altenhoff; Christophe Dessimoz (F1000Research, 2019)

Parallel and Scalable Precise Clustering. - Stuart Byma; Akash Balasaheb Dhasade; Adrian M. Altenhoff; Christophe Dessimoz; James R. Larus (PACT, 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)

OMA orthology in 2021: website overhaul, conserved isoforms, ancestral gene order and more. - Adrian M. Altenhoff; Clément-Marie Train; Kimberly J. Gilbert; Ishita Mediratta; Tarcisio Mendes de Farias; David Moi; Yannis Nevers; Hale-Seda Radoykova; Victor Rossier; Alex Warwick Vesztrocy; Natasha M. Glover; Christophe Dessimoz (Nucleic Acids Res., 2021)

OMAMO: orthology-based alternative model organism selection. - Alina Nicheperovich; Adrian M. Altenhoff; Christophe Dessimoz; Sina Majidian (Bioinform., 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)

A large collection of bioinformatics question-query pairs over federated knowledge graphs: methodology and applications. - Jerven T. Bolleman; Vincent Emonet; Adrian M. Altenhoff; Amos Bairoch; Marie-Claude Blatter; Alan J. Bridge; Severine Duvaud; Elisabeth Gasteiger; Dmitry Kuznetsov; Sébastien Moretti; Pierre-André Michel; Anne Morgat; et al. (CoRR, 2024)