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--- publications [2023/07/03 17:47] – created Dannie Durand
+++ publications [2023/07/10 09:49] (current) – Felix Langschied
@@ Line 1: / Line 1: @@
- ===== Publications =====
+====== Publications ======
+\\
-* [[https://doi.org/10.1093/nar/gkac330 Advances and Applications in the Quest for Orthologs]]
+* [[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,
+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.
-<br>
-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. &nbsp;
+* [[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.
+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. ]] \\
+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.
+* [[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.
 Mol Biol Evol. 2019 Oct 1;36(10):2157-2164. doi: 10.1093/molbev/msz150.
+* [[https://doi.org/10.1093/bioinformatics/btx542| 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:
+.1093/bioinformatics/btx542.
+* [[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,
+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.
+*[[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.