Carolin Kosiol

Carolin Kosiol

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Carolin Kosiol

Carolin Kosiol

Publications by authors named "Carolin Kosiol"

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Quantifying GC-Biased Gene Conversion in Great Ape Genomes Using Polymorphism-Aware Models.

Genetics 2019 08 30;212(4):1321-1336. Epub 2019 May 30.

Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Wien, Austria

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http://dx.doi.org/10.1534/genetics.119.302074DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6707462PMC
August 2019

Polymorphism-Aware Species Trees with Advanced Mutation Models, Bootstrap, and Rate Heterogeneity.

Mol Biol Evol 2019 06;36(6):1294-1301

Centre for Biological Diversity, University of St Andrews, St Andrews, United Kingdom.

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http://dx.doi.org/10.1093/molbev/msz043DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6526911PMC
June 2019

Selection Acting on Genomes.

Methods Mol Biol 2019 ;1910:373-397

Institute of Applied Simulation, School of Life Sciences and Facility Management, Zurich University of Applied Sciences (ZHAW), Wädenswil, Switzerland.

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http://dx.doi.org/10.1007/978-1-4939-9074-0_12DOI Listing
January 2019

Inference in population genetics using forward and backward, discrete and continuous time processes.

J Theor Biol 2018 02 9;439:166-180. Epub 2017 Dec 9.

Institut für Tierzucht und Genetik, Vetmeduni Vienna, Veterinärplatz 1, Wien, A-1210, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2017.12.008DOI Listing
February 2018

Reversible polymorphism-aware phylogenetic models and their application to tree inference.

J Theor Biol 2016 10 29;407:362-370. Epub 2016 Jul 29.

Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.jtbi.2016.07.042DOI Listing
October 2016

Estimating the Effective Population Size from Temporal Allele Frequency Changes in Experimental Evolution.

Genetics 2016 Oct 19;204(2):723-735. Epub 2016 Aug 19.

†Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Vienna, Austria ‡Department of Applied Statistics, Johannes Kepler Universität Linz, 4040 Linz, Austria

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http://dx.doi.org/10.1534/genetics.116.191197DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5068858PMC
October 2016

Genetic diversity of species Fowl aviadenovirus D and Fowl aviadenovirus E.

J Gen Virol 2016 09 6;97(9):2323-2332. Epub 2016 Jun 6.

Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, Vetmeduni Vienna, Vienna, Austria.

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http://dx.doi.org/10.1099/jgv.0.000519DOI Listing
September 2016

PoMo: An Allele Frequency-Based Approach for Species Tree Estimation.

Syst Biol 2015 Nov 23;64(6):1018-31. Epub 2015 Jul 23.

Institut für Populationsgenetik, Vetmeduni Vienna, Wien 1210, Austria;

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http://dx.doi.org/10.1093/sysbio/syv048DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4604832PMC
November 2015

Gaussian process test for high-throughput sequencing time series: application to experimental evolution.

Bioinformatics 2015 Jun 21;31(11):1762-70. Epub 2015 Jan 21.

Helsinki Institute for Information Technology (HIIT), Department of Information and Computer Science, Aalto University, Espoo, Finland, Institut für Populationsgenetik, Vetmeduni Vienna, 1210 Wien, Austria, Vienna Graduate School of Population Genetics, Wien, Austria and Helsinki Institute for Information Technology (HIIT), Department of Computer Science, University of Helsinki, Helsinki, Finland.

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http://dx.doi.org/10.1093/bioinformatics/btv014DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4443671PMC
June 2015

Complete genome sequences of pigeon adenovirus 1 and duck adenovirus 2 extend the number of species within the genus Aviadenovirus.

Virology 2014 Aug 25;462-463:107-14. Epub 2014 Jun 25.

Clinic for Poultry and Fish Medicine, Department for Farm Animals and Veterinary Public Health, Vetmeduni Vienna, Veterinärplatz 1, 1210 Vienna, Austria. Electronic address:

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https://linkinghub.elsevier.com/retrieve/pii/S00426822140015
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http://dx.doi.org/10.1016/j.virol.2014.04.033DOI Listing
August 2014

The life cycle of Drosophila orphan genes.

Elife 2014 Feb 19;3:e01311. Epub 2014 Feb 19.

Institut für Populationsgenetik, Vetmeduni Vienna, Vienna, Austria.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3927632PMC
http://dx.doi.org/10.7554/eLife.01311DOI Listing
February 2014

Whole-genome sequences of two turkey adenovirus types reveal the existence of two unknown lineages that merit the establishment of novel species within the genus Aviadenovirus.

J Gen Virol 2014 Jan 28;95(Pt 1):156-70. Epub 2013 Sep 28.

Clinic for Avian, Reptile and Fish Medicine, Department for Farm Animals and Veterinary Public Health, University of Veterinary Medicine, Vienna, Austria.

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http://jgv.microbiologyresearch.org/content/journal/jgv/10.1
Publisher Site
http://dx.doi.org/10.1099/vir.0.057711-0DOI Listing
January 2014

Linking great apes genome evolution across time scales using polymorphism-aware phylogenetic models.

Mol Biol Evol 2013 Oct 1;30(10):2249-62. Epub 2013 Aug 1.

Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria.

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http://dx.doi.org/10.1093/molbev/mst131DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3773373PMC
October 2013

The first whole genome sequence of a Fowl adenovirus B strain enables interspecies comparisons within the genus Aviadenovirus.

Vet Microbiol 2013 Sep 14;166(1-2):250-6. Epub 2013 Jun 14.

Clinic for Avian, Reptile and Fish Medicine, Department for Farm Animals and Veterinary Public Health, Vetmeduni Vienna, Vienna, Austria.

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http://dx.doi.org/10.1016/j.vetmic.2013.05.017DOI Listing
September 2013

Estimating empirical codon hidden Markov models.

Mol Biol Evol 2013 Mar 27;30(3):725-36. Epub 2012 Nov 27.

Institut für Populationsgenetik, Vetmeduni Vienna, Wien, Austria.

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http://dx.doi.org/10.1093/molbev/mss266DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3563974PMC
March 2013

Selection on the protein-coding genome.

Methods Mol Biol 2012 ;856:113-40

Institute of Population Genetics, Vetmeduni Vienna, Austria.

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http://dx.doi.org/10.1007/978-1-61779-585-5_5DOI Listing
July 2012

Markovian and non-Markovian protein sequence evolution: aggregated Markov process models.

J Mol Biol 2011 Aug 21;411(4):910-23. Epub 2011 Jun 21.

Institut für Populationsgenetik, Vetmeduni Vienna, Veterinärplatz 1, A-1210 Wien, Austria.

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http://dx.doi.org/10.1016/j.jmb.2011.06.005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3157587PMC
August 2011

Comparative and demographic analysis of orang-utan genomes.

Authors:
Devin P Locke LaDeana W Hillier Wesley C Warren Kim C Worley Lynne V Nazareth Donna M Muzny Shiaw-Pyng Yang Zhengyuan Wang Asif T Chinwalla Pat Minx Makedonka Mitreva Lisa Cook Kim D Delehaunty Catrina Fronick Heather Schmidt Lucinda A Fulton Robert S Fulton Joanne O Nelson Vincent Magrini Craig Pohl Tina A Graves Chris Markovic Andy Cree Huyen H Dinh Jennifer Hume Christie L Kovar Gerald R Fowler Gerton Lunter Stephen Meader Andreas Heger Chris P Ponting Tomas Marques-Bonet Can Alkan Lin Chen Ze Cheng Jeffrey M Kidd Evan E Eichler Simon White Stephen Searle Albert J Vilella Yuan Chen Paul Flicek Jian Ma Brian Raney Bernard Suh Richard Burhans Javier Herrero David Haussler Rui Faria Olga Fernando Fleur Darré Domènec Farré Elodie Gazave Meritxell Oliva Arcadi Navarro Roberta Roberto Oronzo Capozzi Nicoletta Archidiacono Giuliano Della Valle Stefania Purgato Mariano Rocchi Miriam K Konkel Jerilyn A Walker Brygg Ullmer Mark A Batzer Arian F A Smit Robert Hubley Claudio Casola Daniel R Schrider Matthew W Hahn Victor Quesada Xose S Puente Gonzalo R Ordoñez Carlos López-Otín Tomas Vinar Brona Brejova Aakrosh Ratan Robert S Harris Webb Miller Carolin Kosiol Heather A Lawson Vikas Taliwal André L Martins Adam Siepel Arindam Roychoudhury Xin Ma Jeremiah Degenhardt Carlos D Bustamante Ryan N Gutenkunst Thomas Mailund Julien Y Dutheil Asger Hobolth Mikkel H Schierup Oliver A Ryder Yuko Yoshinaga Pieter J de Jong George M Weinstock Jeffrey Rogers Elaine R Mardis Richard A Gibbs Richard K Wilson

Nature 2011 Jan;469(7331):529-33

The Genome Center at Washington University, Washington University School of Medicine, 4444 Forest Park Avenue, Saint Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature09687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3060778PMC
January 2011

Positive selection on apoptosis related genes.

FEBS Lett 2010 Feb 22;584(3):469-76. Epub 2009 Dec 22.

Department of Integrative Biology, UC-Berkeley, Berkeley, CA 94720, USA.

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http://dx.doi.org/10.1016/j.febslet.2009.12.022DOI Listing
February 2010

The sequence and de novo assembly of the giant panda genome.

Nature 2010 Jan 13;463(7279):311-7. Epub 2009 Dec 13.

BGI-Shenzhen, Shenzhen 518083, China.

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http://dx.doi.org/10.1038/nature08696DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3951497PMC
January 2010

Investigating protein-coding sequence evolution with probabilistic codon substitution models.

Mol Biol Evol 2009 Feb 14;26(2):255-71. Epub 2008 Oct 14.

Institute of Computational Science, Swiss Federal Institute of Technology, Zurich, Switzerland.

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http://dx.doi.org/10.1093/molbev/msn232DOI Listing
February 2009

Patterns of positive selection in six Mammalian genomes.

PLoS Genet 2008 Aug 1;4(8):e1000144. Epub 2008 Aug 1.

Department of Biological Statistics and Computational Biology, Cornell University, Ithaca, New York, United States of America.

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http://dx.doi.org/10.1371/journal.pgen.1000144DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2483296PMC
August 2008

An empirical codon model for protein sequence evolution.

Mol Biol Evol 2007 Jul 30;24(7):1464-79. Epub 2007 Mar 30.

EMBL-European [corrected] Bioinformatics Institute, Hinxton, United Kingdom.

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http://i122server.vu-wien.ac.at/pop/Kosiol_website/pdfs/Kosi
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http://mbe.oxfordjournals.org/cgi/doi/10.1093/molbev/msm064
Publisher Site
http://dx.doi.org/10.1093/molbev/msm064DOI Listing
July 2007

Evolutionary and biomedical insights from the rhesus macaque genome.

Authors:
Richard A Gibbs Jeffrey Rogers Michael G Katze Roger Bumgarner George M Weinstock Elaine R Mardis Karin A Remington Robert L Strausberg J Craig Venter Richard K Wilson Mark A Batzer Carlos D Bustamante Evan E Eichler Matthew W Hahn Ross C Hardison Kateryna D Makova Webb Miller Aleksandar Milosavljevic Robert E Palermo Adam Siepel James M Sikela Tony Attaway Stephanie Bell Kelly E Bernard Christian J Buhay Mimi N Chandrabose Marvin Dao Clay Davis Kimberly D Delehaunty Yan Ding Huyen H Dinh Shannon Dugan-Rocha Lucinda A Fulton Ramatu Ayiesha Gabisi Toni T Garner Jennifer Godfrey Alicia C Hawes Judith Hernandez Sandra Hines Michael Holder Jennifer Hume Shalini N Jhangiani Vandita Joshi Ziad Mohid Khan Ewen F Kirkness Andrew Cree R Gerald Fowler Sandra Lee Lora R Lewis Zhangwan Li Yih-Shin Liu Stephanie M Moore Donna Muzny Lynne V Nazareth Dinh Ngoc Ngo Geoffrey O Okwuonu Grace Pai David Parker Heidie A Paul Cynthia Pfannkoch Craig S Pohl Yu-Hui Rogers San Juana Ruiz Aniko Sabo Jireh Santibanez Brian W Schneider Scott M Smith Erica Sodergren Amanda F Svatek Teresa R Utterback Selina Vattathil Wesley Warren Courtney Sherell White Asif T Chinwalla Yucheng Feng Aaron L Halpern Ladeana W Hillier Xiaoqiu Huang Pat Minx Joanne O Nelson Kymberlie H Pepin Xiang Qin Granger G Sutton Eli Venter Brian P Walenz John W Wallis Kim C Worley Shiaw-Pyng Yang Steven M Jones Marco A Marra Mariano Rocchi Jacqueline E Schein Robert Baertsch Laura Clarke Miklós Csürös Jarret Glasscock R Alan Harris Paul Havlak Andrew R Jackson Huaiyang Jiang Yue Liu David N Messina Yufeng Shen Henry Xing-Zhi Song Todd Wylie Lan Zhang Ewan Birney Kyudong Han Miriam K Konkel Jungnam Lee Arian F A Smit Brygg Ullmer Hui Wang Jinchuan Xing Richard Burhans Ze Cheng John E Karro Jian Ma Brian Raney Xinwei She Michael J Cox Jeffery P Demuth Laura J Dumas Sang-Gook Han Janet Hopkins Anis Karimpour-Fard Young H Kim Jonathan R Pollack Tomas Vinar Charles Addo-Quaye Jeremiah Degenhardt Alexandra Denby Melissa J Hubisz Amit Indap Carolin Kosiol Bruce T Lahn Heather A Lawson Alison Marklein Rasmus Nielsen Eric J Vallender Andrew G Clark Betsy Ferguson Ryan D Hernandez Kashif Hirani Hildegard Kehrer-Sawatzki Jessica Kolb Shobha Patil Ling-Ling Pu Yanru Ren David Glenn Smith David A Wheeler Ian Schenck Edward V Ball Rui Chen David N Cooper Belinda Giardine Fan Hsu W James Kent Arthur Lesk David L Nelson William E O'brien Kay Prüfer Peter D Stenson James C Wallace Hui Ke Xiao-Ming Liu Peng Wang Andy Peng Xiang Fan Yang Galt P Barber David Haussler Donna Karolchik Andy D Kern Robert M Kuhn Kayla E Smith Ann S Zwieg

Science 2007 Apr;316(5822):222-34

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

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http://dx.doi.org/10.1126/science.1139247DOI Listing
April 2007

XRate: a fast prototyping, training and annotation tool for phylo-grammars.

BMC Bioinformatics 2006 Oct 3;7:428. Epub 2006 Oct 3.

Department of Bioengineering, University of California, Berkeley CA, USA.

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http://dx.doi.org/10.1186/1471-2105-7-428DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1622757PMC
October 2006

Phylogenetics by likelihood: evolutionary modeling as a tool for understanding the genome.

J Biomed Inform 2006 Feb 15;39(1):51-61. Epub 2005 Sep 15.

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK.

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http://dx.doi.org/10.1016/j.jbi.2005.08.003DOI Listing
February 2006

Different versions of the Dayhoff rate matrix.

Mol Biol Evol 2005 Feb 13;22(2):193-9. Epub 2004 Oct 13.

EMBL-European Bioinformatics Institute, Hinxton, UK.

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http://dx.doi.org/10.1093/molbev/msi005DOI Listing
February 2005

A new criterion and method for amino acid classification.

J Theor Biol 2004 May;228(1):97-106

School of Mathematics, Trinity College, University of Dublin, Dublin 2, Ireland.

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http://dx.doi.org/10.1016/j.jtbi.2003.12.010DOI Listing
May 2004

Simulating the hydrodynamic conditions in the United States Pharmacopeia paddle dissolution apparatus.

AAPS PharmSciTech 2003 ;4(2):E22

Department of Pharmaceutics and Pharmaceutical Technology, Trinity College Dublin, Ireland.

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http://dx.doi.org/10.1208/pt040222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2750600PMC
October 2003