OMA, A Comprehensive, Automated Project for the Identification of Orthologs from Complete Genome Data: Introduction and First Achievements. - Christophe Dessimoz; Gina Cannarozzi; Manuel Gil; Daniel Margadant; Alexander C. J. Roth; Adrian Schneider; Gaston H. Gonnet (Comparative Genomics, 2005)

A Dimensionless Fit Measure for Phylogenetic Distance Trees. - Manuel Gil; Christophe Dessimoz; Gaston H. Gonnet (J. Bioinform. Comput. Biol., 2005)

Fast estimation of the difference between two PAM/JTT evolutionary distances in triplets of homologous sequences. - Christophe Dessimoz; Manuel Gil; Adrian Schneider; Gaston H. Gonnet (BMC Bioinform., 2006)

OMA Browser - Exploring orthologous relations across 352 complete genomes. - Adrian Schneider; Christophe Dessimoz; Gaston H. Gonnet (Bioinform., 2007)

DLIGHT - Lateral Gene Transfer Detection Using Pairwise Evolutionary Distances in a Statistical Framework. - Christophe Dessimoz; Daniel Margadant; Gaston H. Gonnet (RECOMB, 2008)

Alignments with non-overlapping moves, inversions and tandem duplications in O ( n 4) time. - Christian Ledergerber; Christophe Dessimoz (J. Comb. Optim., 2008)

Algorithm of OMA for large-scale orthology inference. - Alexander C. J. Roth; Gaston H. Gonnet; Christophe Dessimoz (BMC Bioinform., 2009)

The Microbe browser for comparative genomics. - Alexandre Gattiker; Christophe Dessimoz; Adrian Schneider; Ioannis Xenarios; Marco Pagni; Jacques Rougemont (Nucleic Acids Res., 2009)

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

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees. - Brigitte Boeckmann; Marc Robinson-Rechavi; Ioannis Xenarios; Christophe Dessimoz (Briefings Bioinform., 2011)

Editorial: Orthology and applications. - Christophe Dessimoz (Briefings Bioinform., 2011)

Comparative genomics approach to detecting split-coding regions in a low-coverage genome: lessons from the chimaera Callorhinchus milii (Holocephali, Chondrichthyes). - Christophe Dessimoz; Stefan Zoller; Tereza Manousaki; Huan Qiu; Axel Meyer; Shigehiro Kuraku (Briefings Bioinform., 2011)

Base-calling for next-generation sequencing platforms. - Christian Ledergerber; Christophe Dessimoz (Briefings Bioinform., 2011)

The what, where, how and why of gene ontology - a primer for bioinformaticians. - Louis du Plessis; Nives Skunca; Christophe Dessimoz (Briefings Bioinform., 2011)

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

Toward community standards in the quest for orthologs. - Christophe Dessimoz; Toni Gabaldón; David S. Roos; Erik L. L. Sonnhammer; Javier Herrero (Bioinform., 2012)

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)

Towards practical, high-capacity, low-maintenance information storage in synthesized DNA. - Nick Goldman; Paul Bertone; Siyuan Chen; Christophe Dessimoz; Emily M. LeProust; Botond Sipos; Ewan Birney (Nat., 2013)

Approximate Bayesian Computation. - Mikael Sunnåker; Alberto Giovanni Busetto; Elina Numminen; Jukka Corander; Matthieu Foll; Christophe Dessimoz (PLoS Comput. Biol., 2013)

Big data and other challenges in the quest for orthologs. - Erik L. L. Sonnhammer; Toni Gabaldón; Alan W. Sousa da Silva; Maria Jesus Martin; Marc Robinson-Rechavi; Brigitte Boeckmann; Paul D. Thomas; Christophe Dessimoz; Quest for Orthologs Consortium (Bioinform., 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)

Inferring Horizontal Gene Transfer. - Matt Ravenhall; Nives Skunca; Florent Lassalle; Christophe Dessimoz (PLoS Comput. Biol., 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)

RecPhyloXML: a format for reconciled gene trees. - Wandrille Duchemin; Guillaume Gence; Anne-Muriel Arigon Chifolleau; Lars Arvestad; Mukul S. Bansal; Vincent Berry; Bastien Boussau; François Chevenet; Nicolas Comte; Adrián A. Davín; Christophe Dessimoz; David Dylus; et al. (Bioinform., 2018)

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)

Prioritising candidate genes causing QTL using hierarchical orthologous groups. - Alex Warwick Vesztrocy; Christophe Dessimoz; Henning Redestig (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)

Submit a Topic Page to PLOS Computational Biology and Wikipedia. - Daniel Mietchen; Shoshana J. Wodak; Szymon Wasik; Natalia Szostak; Christophe Dessimoz (PLoS Comput. Biol., 2018)

VoIDext: Vocabulary and Patterns for Enhancing Interoperable Datasets with Virtual Links. - Tarcisio Mendes de Farias; Kurt Stockinger; Christophe Dessimoz (OTM Conferences, 2019)

How Much Does GenoGuard Really "Guard"?: An Empirical Analysis of Long-Term Security for Genomic Data. - Bristena Oprisanu; Christophe Dessimoz; Emiliano De Cristofaro (WPES@CCS, 2019)

Enabling semantic queries across federated bioinformatics databases. - Ana Claudia Sima; Tarcisio Mendes de Farias; Erich Zbinden; Maria Anisimova; Manuel Gil; Heinz Stockinger; Kurt Stockinger; Marc Robinson-Rechavi; Christophe Dessimoz (Database J. Biol. Databases Curation, 2019)

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)

Enhancing interoperable datasets with virtual links. - Tarcisio Mendes de Farias; Christophe Dessimoz (CoRR, 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)

A hands-on introduction to querying evolutionary relationships across multiple data sources using SPARQL. - Ana Claudia Sima; Christophe Dessimoz; Kurt Stockinger; Monique Zahn-Zabal; Tarcisio Mendes de Farias (F1000Research, 2019)

Parallel and Scalable Precise Clustering. - Stuart Byma; Akash Balasaheb Dhasade; Adrian M. Altenhoff; Christophe Dessimoz; James R. Larus (PACT, 2020)

Benchmarking gene ontology function predictions using negative annotations. - Alex Warwick Vesztrocy; Christophe Dessimoz (Bioinform., 2020)

A generalized Robinson-Foulds distance for labeled trees. - Samuel Briand; Christophe Dessimoz; Nadia El-Mabrouk; Manuel Lafond; Gabriela Lobinska (BMC Genom., 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)

Scalable phylogenetic profiling using MinHash uncovers likely eukaryotic sexual reproduction genes. - David Moi; Laurent Kilchoer; Pablo S. Aguilar; Christophe Dessimoz (PLoS Comput. Biol., 2020)

Bio-SODA: Enabling Natural Language Question Answering over Knowledge Graphs without Training Data. - Ana Claudia Sima; Tarcisio Mendes de Farias; Maria Anisimova; Christophe Dessimoz; Marc Robinson-Rechavi; Erich Zbinden; Kurt Stockinger (SSDBM, 2021)

ISMB/ECCB 2021 proceedings. - Christophe Dessimoz; Teresa M. Przytycka (Bioinform., 2021)

OMAmer: tree-driven and alignment-free protein assignment to subfamilies outperforms closest sequence approaches. - Victor Rossier; Alex Warwick Vesztrocy; Marc Robinson-Rechavi; Christophe Dessimoz (Bioinform., 2021)

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)

ISMB 2022 proceedings. - Christophe Dessimoz; Sushmita Roy (Bioinform., 2022)

OMAMO: orthology-based alternative model organism selection. - Alina Nicheperovich; Adrian M. Altenhoff; Christophe Dessimoz; Sina Majidian (Bioinform., 2022)

Federating and querying heterogeneous and distributed Web APIs and triple stores. - Tarcisio Mendes de Farias; Christophe Dessimoz; Aarón Ayllón-Benítez; Chen Yang; Jiao Long; Ana Claudia Sima (CoRR, 2022)

Bio-SODA UX: enabling natural language question answering over knowledge graphs with user disambiguation. - Ana Claudia Sima; Tarcisio Mendes de Farias; Maria Anisimova; Christophe Dessimoz; Marc Robinson-Rechavi; Erich Zbinden; Kurt Stockinger (Distributed Parallel Databases, 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)

Data in use for Alzheimer disease study: combining gene expression, orthology, bioresource and disease datasets. - Tarcisio Mendes de Farias; Tatsuya Kushida; Ana Claudia Sima; Christophe Dessimoz; Hirokazu Chiba; Frédéric B. Bastian; Hiroshi Masuya (SWAT4HCLS, 2023)

Towards predicting essential proteins via federated SPARQL queries. - Petros Liakopoulous; Borbala Banfalvi; Xinyi Wang; Sina Majidian; Tarcisio Mendes de Farias; Christophe Dessimoz; Ana Claudia Sima (SWAT4HCLS, 2023)

Federated SPARQL query performance evaluation for exploring disease model mouse: combining gene expression, orthology, and disease knowledge graphs. - Tatsuya Kushida; Tarcisio Mendes de Farias; Ana Claudia Sima; Christophe Dessimoz; Hirokazu Chiba; Frederic B. Bastian; Hiroshi Masuya (BMC Medical Informatics Decis. Mak., 2025)

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)