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Fungal Phylogeny in the Age of Genomics: Insights Into Phylogenetic Inference From Genome-Scale Datasets.
Nagy LG, Szöllősi G. Nagy LG, et al. Adv Genet. 2017;100:49-72. doi: 10.1016/bs.adgen.2017.09.008. Epub 2017 Oct 20. Adv Genet. 2017. PMID: 29153404
The new era has also brought new challenges: systematic errors (resulting from, e.g., model violation) can be more pronounced in phylogenomic datasets and can lead to strongly supported incorrect relationships, creating significant incongruence among studies. ...
The new era has also brought new challenges: systematic errors (resulting from, e.g., model violation) can be more pronounced in phyl …
The maintenance of sex in bacteria is ensured by its potential to reload genes.
Szöllosi GJ, Derényi I, Vellai T. Szöllosi GJ, et al. Genetics. 2006 Dec;174(4):2173-80. doi: 10.1534/genetics.106.063412. Epub 2006 Oct 8. Genetics. 2006. PMID: 17028325 Free PMC article.
The inference of gene trees with species trees.
Szöllősi GJ, Tannier E, Daubin V, Boussau B. Szöllősi GJ, et al. Syst Biol. 2015 Jan;64(1):e42-62. doi: 10.1093/sysbio/syu048. Epub 2014 Jul 28. Syst Biol. 2015. PMID: 25070970 Free PMC article. Review.
Genome-scale phylogenetic analysis finds extensive gene transfer among fungi.
Szöllősi GJ, Davín AA, Tannier E, Daubin V, Boussau B. Szöllősi GJ, et al. Philos Trans R Soc Lond B Biol Sci. 2015 Sep 26;370(1678):20140335. doi: 10.1098/rstb.2014.0335. Philos Trans R Soc Lond B Biol Sci. 2015. PMID: 26323765 Free PMC article.
Gene transfers can date the tree of life.
Davín AA, Tannier E, Williams TA, Boussau B, Daubin V, Szöllősi GJ. Davín AA, et al. Nat Ecol Evol. 2018 May;2(5):904-909. doi: 10.1038/s41559-018-0525-3. Epub 2018 Apr 2. Nat Ecol Evol. 2018. PMID: 29610471 Free PMC article.
Megaphylogeny resolves global patterns of mushroom evolution.
Varga T, Krizsán K, Földi C, Dima B, Sánchez-García M, Sánchez-Ramírez S, Szöllősi GJ, Szarkándi JG, Papp V, Albert L, Andreopoulos W, Angelini C, Antonín V, Barry KW, Bougher NL, Buchanan P, Buyck B, Bense V, Catcheside P, Chovatia M, Cooper J, Dämon W, Desjardin D, Finy P, Geml J, Haridas S, Hughes K, Justo A, Karasiński D, Kautmanova I, Kiss B, Kocsubé S, Kotiranta H, LaButti KM, Lechner BE, Liimatainen K, Lipzen A, Lukács Z, Mihaltcheva S, Morgado LN, Niskanen T, Noordeloos ME, Ohm RA, Ortiz-Santana B, Ovrebo C, Rácz N, Riley R, Savchenko A, Shiryaev A, Soop K, Spirin V, Szebenyi C, Tomšovský M, Tulloss RE, Uehling J, Grigoriev IV, Vágvölgyi C, Papp T, Martin FM, Miettinen O, Hibbett DS, Nagy LG. Varga T, et al. Among authors: szollosi gj. Nat Ecol Evol. 2019 Apr;3(4):668-678. doi: 10.1038/s41559-019-0834-1. Epub 2019 Mar 18. Nat Ecol Evol. 2019. PMID: 30886374 Free PMC article.
Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models.
Borges R, Szöllősi GJ, Kosiol C. Borges R, et al. Among authors: szollosi gj. Genetics. 2019 Aug;212(4):1321-1336. doi: 10.1534/genetics.119.302074. Epub 2019 May 30. Genetics. 2019. PMID: 31147380 Free PMC article.
Zombi: a phylogenetic simulator of trees, genomes and sequences that accounts for dead linages.
Davín AA, Tricou T, Tannier E, de Vienne DM, Szöllősi GJ. Davín AA, et al. Among authors: szollosi gj. Bioinformatics. 2020 Feb 15;36(4):1286-1288. doi: 10.1093/bioinformatics/btz710. Bioinformatics. 2020. PMID: 31566657 Free PMC article.
Evolutionary games on minimally structured populations.
Szöllosi GJ, Derényi I. Szöllosi GJ, et al. Phys Rev E Stat Nonlin Soft Matter Phys. 2008 Sep;78(3 Pt 1):031919. doi: 10.1103/PhysRevE.78.031919. Epub 2008 Sep 23. Phys Rev E Stat Nonlin Soft Matter Phys. 2008. PMID: 18851077
Congruent evolution of genetic and environmental robustness in micro-RNA.
Szöllosi GJ, Derényi I. Szöllosi GJ, et al. Mol Biol Evol. 2009 Apr;26(4):867-74. doi: 10.1093/molbev/msp008. Epub 2009 Jan 23. Mol Biol Evol. 2009. PMID: 19168567
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