Publications

* Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration
Majidian S, Hadziahmetovic A, Langschied F, Pascarelli S, Prieto-Baños S, Rojas-Vargas J, Quest for Orthologs Consortium, Braun EL, Dessimoz C, Diallo AB, Durand D, Fang G, Gabaldón T, Glover N, Liberles DA, McWhite C, Sonnhammer EL, Thomas PD, Ouangraoua A, & Julca I. J Mol Evol 93, 702–719 (2025). https://doi.org/10.1007/s00239-025-10272-6

* Quest for Orthologs in the Era of Biodiversity Genomics
Langschied F, Bordin N, Cosentino S, Fuentes-Palacios D, Glover N, Hiller M, Hu Y, Huerta-Cepas J, Coelho LP, Iwasaki W, Majidian S, Manzano-Morales S, Persson E, Richards TA, Gabaldón T, Sonnhammer E, Thomas PD, Dessimoz C & Ebersberger I. Genome Biology and Evolution, Volume 16, Issue 10, October 2024 doi: 10.1093/gbe/evae224

* The Quest for Orthologs orthology benchmark service in 2022
Nevers Y, Jones TEM, Jyothi D, Yates B, Ferret M, Portell-Silva L,. Codo L, Cosentino S, Marcet-Houben M, Vlasova A, Poidevin L, Kress A, Hickman M, Persson E, Piližota I, Guijarro-Clarke C; OpenEBench team the Quest for Orthologs Consortium; Iwasaki W, Lecompte O, Sonnhammer E, Roos DS, Gabaldón T, Thybert D, Thomas PD, Hu Y, Emms DM, Bruford E, Capella-Gutierrez S, Martin MJ, Dessimoz C, Altenhoff A. Nucleic Acids Res. 2022 Jul 5;50(W1):W623-W632. doi: 10.1093/nar/gkac330.

* Ten Years of Collaborative Progress in the Quest for Orthologs
Linard B, Ebersberger I, McGlynn SE, Glover N, Mochizuki T, Patricio M, Lecompte O, Nevers Y, Thomas PD, Gabaldón T, Sonnhammer E, Dessimoz C, Uchiyama I; QFO Consortium. Mol Biol Evol. 2021 Jul 29;38(8):3033-3045. doi: 10.1093/molbev/msab098.

* The Quest for Orthologs benchmark service and consensus calls in 2020
Altenhoff AM, Garrayo-Ventas J, Cosentino S, Emms D, Glover NM, Hernández-Plaza A, Nevers Y, Sundesha V, Szklarczyk D, Fernández JM, Codó L, the Quest For Orthologs Consortium, Gelpi JL, Huerta-Cepas J, Iwasaki W, Kelly S, Lecompte O, Muffato M, Martin MJ, Capella-Gutierrez S, Thomas PD, Sonnhammer E, Dessimoz C. Nucleic Acids Res. 2020 Jul 2;48(W1):W538-W545. doi: 10.1093/nar/gkaa308.

* Advances and Applications in the Quest for Orthologs
Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, da Silva AS, Wang Y, Sonnhammer E, Thomas PD. Mol Biol Evol. 2019 Oct 1;36(10):2157-2164. doi: 10.1093/molbev/msz150.

* Gearing up to handle the mosaic nature of life in the quest for orthologs.
Forslund K, Pereira C, Capella-Gutierrez S, da Silva AS, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT; Quest for Orthologs Consortium; Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S; Quest for Orthologs Consortium. Bioinformatics. 2018 Jan 15;34(2):323-329. doi: 10.1093/bioinformatics/btx542.

* Standardized benchmarking in the quest for orthologs
Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M; Quest for Orthologs consortium; Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C. Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830.

* Big data and other challenges in the quest for orthologs
Sonnhammer, E. L., Gabaldón, T., Sousa da Silva, A. W., Martin, M., Robinson-Rechavi, M., Boeckmann, B., Thomas, P. D., Dessimoz, C., & Quest for Orthologs consortium (2014). Bioinformatics (Oxford, England), 30(21), 2993–2998.

* Toward community standards in the quest for orthologs
Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J; Quest for Orthologs Consortium. Bioinformatics. 2012 Mar 15;28(6):900-4. doi: 10.1093/bioinformatics/bts050. Epub 2012 Feb 12.

* Joining forces in the quest for orthologs
Gabaldón T, Dessimoz C, Huxley-Jones J, Vilella AJ, Sonnhammer ELL & Lewis S. Genome Biol 10, 403 (2009). https://doi.org/10.1186/gb-2009-10-9-403