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publications [2025/04/17 14:10] – Dannie Durandpublications [2026/01/21 15:20] (current) – added first and last papers Natasha Glover
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 ====== Publications ======   ====== Publications ======  
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 +* [[ 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]] \\
 +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]] \\ * [[https://doi.org/10.1093/gbe/evae224| Quest for Orthologs in the Era of Biodiversity Genomics]] \\
-Felix Langschied, Nicola Bordin, Salvatore Cosentino, Diego Fuentes-Palacios, Natasha Glover, Michael Hiller, Yanhui Hu, Jaime Huerta-Cepas, Luis Pedro Coelho, Wataru Iwasaki, Sina Majidian, Saioa Manzano-Morales, Emma Persson, Thomas A Richards, Toni Gabaldón, Erik Sonnhammer, Paul D Thomas, Christophe Dessimoz, Ingo Ebersberger, +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 Genome Biology and Evolution, Volume 16, Issue 10, October 2024
 doi: 10.1093/gbe/evae224 doi: 10.1093/gbe/evae224
  
-* [[https://doi.org/10.1093/nar/gkac330| The Quest for Orthologs orthology benchmark service in 2022.]] \\+* [[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,. 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,
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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, 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.  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. 
  
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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. 
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 +*[[ 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