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publications [2023/07/03 18:02] – Dannie Durandpublications [2025/04/17 14:10] (current) – Dannie Durand
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- ===== Publications =====  +====== Publications ======   
 +\\ 
 + 
 +* [[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,  
 +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.]] \\ * [[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,
 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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 E, Capella-Gutierrez S, Martin MJ, Dessimoz C, Altenhoff A. E, Capella-Gutierrez S, Martin MJ, Dessimoz C, Altenhoff A.
 Nucleic Acids Nucleic Acids
-Res. 2022 Jul 5;50(W1):W623-W632. doi: 10.1093/nar/gkac330. +Res. 2022 Jul 5;50(W1):W623-W632. doi: 10.1093/nar/gkac330.
  
  
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 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/gkac330| Advances and Applications in the Quest for Orthologs]] \\ +* [[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.  
 + 
 +* [[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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 Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830.  Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830. 
  
 +
 +*[[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.
 +
 +*[[https://dx.doi.org/10.1093/bioinformatics/bts050| 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.