{"id":23,"date":"2022-05-07T19:35:53","date_gmt":"2022-05-07T18:35:53","guid":{"rendered":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/?page_id=23"},"modified":"2022-05-09T09:38:42","modified_gmt":"2022-05-09T08:38:42","slug":"publications","status":"publish","type":"page","link":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/publications\/","title":{"rendered":"Publications"},"content":{"rendered":"

Co-evolving infectivity and expression patterns drive the diversification of endogenous retroviruses<\/span>
Senti, K.-A., Rafanel, B., Handler, D., Kosiol, C.<\/span>, Schl\u00f6tterer, C. & Brennecke, J., 16 Mar 2026<\/span>, In: EMBO Journal.<\/span><\/span> 45<\/span>, 6<\/span>, p. 1889-1908<\/span> 20 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Development and patterning of a highly versatile visual system in spiders<\/span>
Baudouin Gonzalez, L., Sch\u00f6nauer, A., Harper, A., Arif, S., Leite, D. J., Steinhoff, P. O. M., Pechmann, M., Telizhenko, V., Pande, A., Schultz, Z. X., Kosiol, C.<\/span>, Aase-Remedios, M., Sumner-Rooney, L. & McGregor, A. P., 12 Mar 2025<\/span>, In: Proceedings of the Royal Society B: Biological Sciences.<\/span><\/span> 292<\/span>, 2042<\/span>, 12 p.<\/span>, 20242069.
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Phylogenetic methods meet deep learning<\/span>
Braichenko, S., Borges, R.<\/span> & Kosiol, C.<\/span>, 11 Oct 2025<\/span>, In: Genome Biology and Evolution.<\/span><\/span> 17<\/span>, 10<\/span>, p. 1-9<\/span> 9 p.<\/span>, evaf177.
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Review article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Inference of genomic landscapes using ordered Hidden Markov Models with emission densities (oHMMed)<\/span>
Vogl, C., Karapetiants, M., Y\u0131ld\u0131r\u0131m, B., Kjartansd\u00f3ttir, H., Kosiol, C.<\/span>, Bergman, J., Majka, M. & Mikula, L. C., 16 Apr 2024<\/span>, In: BMC Bioinformatics.<\/span><\/span> 25<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Polymorphism-aware models in RevBayes: species trees, disentangling balancing selection and CG-biased gene conversion<\/span>
Braichenko, S.<\/span>, Borges, R. & Kosiol, C.<\/span>, 9 Jul 2024<\/span>, In: Molecular Biology and Evolution.<\/span><\/span> 41<\/span>, 7<\/span>, 16 p.<\/span>, msae138.
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Relaxed selection in evolution of genes regulating limb development gives clue to variation in forelimb morphology of cetaceans and other mammals<\/span>
Telizhenko, V., Kosiol, C.<\/span>, McGowen, M. R. & Gol'din, P., 9 Oct 2024<\/span>, In: Proceedings of the Royal Society B: Biological Sciences.<\/span><\/span> 291<\/span>, 2032<\/span>, 12 p.<\/span>, 20241106.
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

The patterns of codon usage between chordates and arthropods are different but co-evolving with mutational biases<\/span>
Kotari, I., Kosiol, C.<\/span> & Borges, R.<\/span>, May 2024<\/span>, In: Molecular Biology and Evolution.<\/span><\/span> 41<\/span>, 5<\/span>, 13 p.<\/span>, msae080.
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

UKCropDiversity\u2010HPC: a collaborative high\u2010performance computing resource approach for sustainable agriculture and biodiversity conservation<\/span>
Percival\u2010Alwyn, L., Barnes, I., Clark, M. D., Cockram, J., Coffey, M. P., Jones, S., Kersey, P. J., Kidner, C. A., Kosiol, C.<\/span>, Li, B., Marsh, W. A., Zhou, J., Caccamo, M. & Milne, I., 5 Dec 2024<\/span>, In: Plants, People, Planet.<\/span><\/span> 7<\/span>, 4<\/span>, p. 969-977<\/span> 9 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Bait-ER: a Bayesian method to detect targets of selection in Evolve-and-Resequence experiments<\/span>
Barata, C., Borges, R.<\/span> & Kosiol, C.<\/span>, 9 Jan 2023<\/span>, In: Journal of Evolutionary Biology.<\/span><\/span> 36<\/span>, 1<\/span>, p. 29-44<\/span> 16 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Selection on the fly: short-term adaptation to an altered sexual selection regime in Drosophila pseudoobscura<\/i><\/span>
Barata, C., Snook, R. R., Ritchie, M. G.<\/span> & Kosiol, C.<\/span>, 4 Jul 2023<\/span>, In: Genome Biology and Evolution.<\/span><\/span> 15<\/span>, 7<\/span>, 18 p.<\/span>, evad113.
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Nucleotide usage biases distort inferences of the species tree<\/span>
Borges, R., Boussau, B., Sz\u00f6ll\u0151si, G. J. & Kosiol, C.<\/span>, Jan 2022<\/span>, In: Genome Biology and Evolution.<\/span><\/span> 14<\/span>, 1<\/span>, 13 p.<\/span>, evab290.
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Polymorphism\u2010aware estimation of species trees and evolutionary forces from genomic sequences with RevBayes<\/span>
Borges, R.<\/span>, Boussau, B., H\u00f6hna, S., Pereira, R. J. & Kosiol, C.<\/span>, Nov 2022<\/span>, In: Methods in Ecology and Evolution.<\/span><\/span> 13<\/span>, 11<\/span>, p. 2339-2346<\/span> 8 p.<\/span>, 13980.
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Consistency and identifiability of the polymorphism-aware phylogenetic models<\/span>
Borges, R. & Kosiol, C.<\/span>, 7 Feb 2020<\/span>, In: Journal of Theoretical Biology.<\/span><\/span> 486<\/span>, p. 1-6<\/span> 6 p.<\/span>, 110074.
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Polymorphism-aware species trees with advanced mutation models, bootstrap and rate heterogeneity<\/span>
Schrempf, D.<\/span>, Minh, B. Q., von Haeseler, A. & Kosiol, C.<\/span>, Jun 2019<\/span>, In: Molecular Biology and Evolution.<\/span><\/span> 36<\/span>, 6<\/span>, p. 1294-1301<\/span> 8 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Quantifying GC-biased gene conversion in great ape genomes using polymorphism-aware models<\/span>
Borges, R., Sz\u00f6ll\u0151si, G. & Kosiol, C.<\/span>, 1 Aug 2019<\/span>, In: Genetics.<\/span><\/span> 212<\/span>, 4<\/span>, p. 1321-1336<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Selection acting on genomes<\/span>
Kosiol, C.<\/span> & Anisimova, M., 6 Jul 2019<\/span>, (E-pub ahead of print) Evolutionary genomics: statistical and computational methods.<\/em> Anisimova, M. (ed.). New York: Humana Press Inc.<\/span>, p. 373-397<\/span> 25 p.<\/span> (Methods in Molecular Biology; vol. 1910).
Research output: <\/span><\/span>Chapter in Book\/Report\/Conference proceeding \u203a <\/span><\/span>Chapter<\/span><\/span><\/p>

The comparative genomics and complex population history of Papio<\/i> baboons<\/span>
Rogers, J., Raveendran, M., Harris, R. A., Mailund, T., Lepp\u00e4l\u00e4, K., Athanasiadis, G., Schierup, M. H., Cheng, J., Munch, K., Walker, J. A., Konkel, M. K., Jordan, V., Steely, C. J., Beckstrom, T. O., Bergey, C., Burrell, A., Schrempf, D.<\/span>, Noll, A., Kothe, M. & Kopp, G. H. & 22 others<\/span><\/a>, Liu, Y., Murali, S., Billis, K., Martin, F. J., Muffato, M., Cox, L., Else, J., Disotell, T., Muzny, D. M., Phillips-conroy, J., Aken, B., Eichler, E. E., Marques-bonet, T., Kosiol, C.<\/span>, Batzer, M. A., Hahn, M. W., Tung, J., Zinner, D., Roos, C., Jolly, C. J., Gibbs, R. A. & Worley, K. C.<\/span>, 30 Jan 2019<\/span>, In: Science Advances.<\/span><\/span> 5<\/span>, 1<\/span>, 15 p.<\/span>, eaau6947.
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Inference in population genetics using forward and backward, discrete and continuous time processes<\/span>
Bergman, J., Schrempf, D.<\/span>, Kosiol, C.<\/span> & Vogl, C., 14 Feb 2018<\/span>, In: Journal of Theoretical Biology.<\/span><\/span> 439<\/span>, p. 166-180<\/span> 15 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Adaptive sequence evolution is driven by biotic stress in a pair of orchid species (Dactylorhiza<\/i>) with distinct ecological optima<\/span>
Balao, F., Trucchi, E., Wolfe, T., Hao, B.-H., Lorenzo, M. T., Baar, J., Sedman, L., Kosiol, C.<\/span>, Amman, F., Chase, M. W., Hedr\u00e9n, M. & Paun, O., 4 Jul 2017<\/span>, In: Molecular Ecology.<\/span><\/span> 26<\/span>, 14<\/span>, p. 3649-3662<\/span> 14 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Approximate maximum likelihood estimation for population genetic inference<\/span>
Bertl, J., Ewing, G., Kosiol, C.<\/span> & Futschik, A., 2 Nov 2017<\/span>, In: Statistical Applications in Genetics and Molecular Biology.<\/span><\/span> 16<\/span>, 5-6<\/span>, p. 291-312<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Estimating the effective population size from temporal allele frequency changes in experimental evolution<\/span>
J\u00f3n\u00e1s, \u00c1., Taus, T., Kosiol, C.<\/span>, Schl\u00f6tterer, C. & Futschik, A., 11 Oct 2016<\/span>, In: Genetics.<\/span><\/span> 204<\/span>, 2<\/span>, p. 723-735<\/span> 13 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Genetic diversity of species Fowl aviadenovirus<\/i> D and Fowl aviadenovirus<\/i> E<\/span>
Marek, A., Kaj\u00e1n, G. L., Kosiol, C.<\/span>, Benk\u0151, M., Schachner, A. & Hess, M., 1 Sept 2016<\/span>, In: Journal of General Virology.<\/span><\/span> 97<\/span>, 9<\/span>, p. 2323-32<\/span> 10 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Reversible polymorphism-aware phylogenetic models and their application to tree inference<\/span>
Schrempf, D.<\/span>, Minh, B. Q., De Maio, N., von Haeseler, A. & Kosiol, C.<\/span>, 21 Oct 2016<\/span>, In: Journal of Theoretical Biology.<\/span><\/span> 407<\/span>, p. 362-370<\/span> 9 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Gaussian process test for high-throughput sequencing time series: application to experimental evolution<\/span>
Topa, H., J\u00f3n\u00e1s, \u00c1., Kofler, R., Kosiol, C.<\/span> & Honkela, A., 1 Jun 2015<\/span>, In: Bioinformatics.<\/span><\/span> 31<\/span>, 11<\/span>, p. 1762-1770<\/span> 9 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

PoMo: an allele frequency-based approach for species tree estimation<\/span>
De Maio, N., Schrempf, D. & Kosiol, C.<\/span>, Nov 2015<\/span>, In: Systematic Biology.<\/span><\/span> 64<\/span>, 6<\/span>, p. 1018-1031<\/span> 14 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Complete genome sequences of pigeon adenovirus 1 and duck adenovirus 2 extend the number of species within the genus Aviadenovirus<\/span>
Marek, A., Kaj\u00e1n, G. L., Kosiol, C.<\/span>, Harrach, B., Schl\u00f6tterer, C. & Hess, M., Aug 2014<\/span>, In: Virology.<\/span><\/span> 462-463<\/span>, p. 107-14<\/span> 8 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

The common marmoset genome provides insight into primate biology and evolution<\/span>
The Marmoset Genome Sequencing and Analysis Consortium<\/span>, Aug 2014<\/span>, In: Nature Genetics.<\/span><\/span> 46<\/span>, 8<\/span>, p. 850-857<\/span> 8 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

The life cycle of Drosophila<\/i> orphan genes<\/span>
Palmieri, N., Kosiol, C.<\/span> & Schl\u00f6tterer, C., 19 Feb 2014<\/span>, In: eLife.<\/span><\/span> 3<\/span>, 21 p.<\/span>, e01311.
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Estimating empirical codon hidden Markov models<\/span>
De Maio, N., Holmes, I., Schl\u00f6tterer, C. & Kosiol, C.<\/span>, Mar 2013<\/span>, In: Molecular Biology and Evolution.<\/span><\/span> 30<\/span>, 3<\/span>, p. 725-36<\/span> 12 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models<\/span>
De Maio, N., Schl\u00f6tterer, C. & Kosiol, C.<\/span>, Oct 2013<\/span>, In: Molecular Biology and Evolution.<\/span><\/span> 30<\/span>, 10<\/span>, p. 2249-62<\/span> 14 p.<\/span>
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p>

Population genomic analysis reveals a rich speciation and demographic history of orang-utans (Pongo pygmaeus <\/i>and Pongo abelii<\/i>)<\/span>
Ma, X., Kelley, J. L., Eilertson, K., Musharoff, S., Degenhardt, J. D., Martins, A. L., Vinar, T., Kosiol, C.<\/span>, Siepel, A., Gutenkunst, R. N. & Bustamante, C. D., 23 Oct 2013<\/span>, In: PLoS One.<\/span><\/span> 8<\/span>, 10<\/span>, 11 p.<\/span>, e77175.
Research output: <\/span><\/span>Contribution to journal \u203a <\/span><\/span>Article<\/span> \u203a <\/span>peer-review<\/span><\/span><\/p><\/div>\n","protected":false},"excerpt":{"rendered":"","protected":false},"author":50,"featured_media":0,"parent":0,"menu_order":4,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-23","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/pages\/23","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/users\/50"}],"replies":[{"embeddable":true,"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/comments?post=23"}],"version-history":[{"count":0,"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/pages\/23\/revisions"}],"wp:attachment":[{"href":"https:\/\/biology.st-andrews.ac.uk\/kosiol-lab\/wp-json\/wp\/v2\/media?parent=23"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}