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publications [2023/07/03 18:16] – Dannie Durandpublications [2026/01/21 15:20] (current) – added first and last papers Natasha Glover
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-* [[https://doi.org/10.1093/nar/gkac330| The Quest for Orthologs orthology benchmark service in 2022.]] \\ +* [[ https://link.springer.com/article/10.1007/s00239-025-10272-6| Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration]] \\ 
-Nevers Y, Jones TEM, Jyothi D, Yates B, Ferret M, Portell-Silva L,+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 
 + 
 +* [[https://doi.org/10.1093/gbe/evae224| 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 
 + 
 +* [[https://doi.org/10.1093/nar/gkac330| 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, Codo L, Cosentino S, Marcet-Houben M, Vlasova A, Poidevin L, Kress A,
 Hickman M, Persson E, Piližota I, Guijarro-Clarke C; OpenEBench team Hickman M, Persson E, Piližota I, Guijarro-Clarke C; OpenEBench team
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-* [[https://doi.org/10.1093/molbev/msab098|Ten Years of Collaborative Progress in the Quest for Orthologs.]] \\+* [[https://doi.org/10.1093/molbev/msab098|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. 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. Mol Biol Evol. 2021 Jul 29;38(8):3033-3045. doi: 10.1093/molbev/msab098.
  
-* [[https://doi.org/10.1093/nar/gkaa308| The Quest for Orthologs benchmark service and consensus calls in 2020. ]] \\  +* [[https://doi.org/10.1093/nar/gkaa308| 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, For Orthologs Consortium TQ, 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. +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. 
  
-* [[https://doi.org/10.1093/nar/gkac330| Advances and Applications in the Quest for Orthologs]] \\ +* [[https://doi.org/10.1093/molbev/msz150| 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.  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.  Mol Biol Evol. 2019 Oct 1;36(10):2157-2164. doi: 10.1093/molbev/msz150. 
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 10.1093/bioinformatics/btx542. 10.1093/bioinformatics/btx542.
  
-* [[https://dx.doi.org/10.1038/nmeth.3830|  Standardized benchmarking in the quest for orthologs.]] \\+* [[https://dx.doi.org/10.1038/nmeth.3830|  Standardized benchmarking in the quest for orthologs]] \\
 Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T,
 Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber
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-*[[https://doi.org/10.1093/bioinformatics/btu492|   Big data and other challenges in the quest for orthologs.]] \\+*[[https://doi.org/10.1093/bioinformatics/btu492|   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. 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.
  
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 Dessimoz C, Gabaldón T, Roos DS, Sonnhammer EL, Herrero J; Quest for 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.  Orthologs Consortium.  Bioinformatics. 2012 Mar 15;28(6):900-4. doi: 10.1093/bioinformatics/bts050. Epub 2012 Feb 12. 
 +
 +*[[ https://link.springer.com/article/10.1186/gb-2009-10-9-403| 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