Tomas Vinar

Tomas Vinar

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Tomas Vinar

Tomas Vinar

Publications by authors named "Tomas Vinar"

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Genome Sequence of an Arthroconidial Yeast, Saprochaete fungicola CBS 625.85.

Microbiol Resour Announc 2019 Apr 11;8(15). Epub 2019 Apr 11.

Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova, Bratislava, Slovak Republic

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http://genomea.asm.org/lookup/doi/10.1128/MRA.00092-19
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http://dx.doi.org/10.1128/MRA.00092-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6460024PMC
April 2019

DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads.

PLoS One 2017 5;12(6):e0178751. Epub 2017 Jun 5.

Faculty of Mathematics, Physics and Informatics, Comenius University in Bratislava, Slovakia.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0178751PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5459436PMC
September 2017

Draft Genome Sequence of an Obligate Psychrophilic Yeast, NRRL Y-17665.

Genome Announc 2017 Aug 31;5(35). Epub 2017 Aug 31.

Departments of Biochemistry and Genetics, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovak Republic

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http://dx.doi.org/10.1128/genomeA.00851-17DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5578839PMC
August 2017

Isometric gene tree reconciliation revisited.

Algorithms Mol Biol 2017 13;12:17. Epub 2017 Jun 13.

Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia.

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http://dx.doi.org/10.1186/s13015-017-0108-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5470333PMC
June 2017

RNA motif search with data-driven element ordering.

BMC Bioinformatics 2016 May 18;17(1):216. Epub 2016 May 18.

Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, Bratislava, 842 48, Slovakia.

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http://dx.doi.org/10.1186/s12859-016-1074-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4870747PMC
May 2016

GAML: genome assembly by maximum likelihood.

Algorithms Mol Biol 2015 3;10:18. Epub 2015 Jun 3.

Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia.

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http://dx.doi.org/10.1186/s13015-015-0052-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4454275PMC
June 2015

Fast computation of a string duplication history under no-breakpoint-reuse.

Philos Trans A Math Phys Eng Sci 2014 May 21;372(2016):20130133. Epub 2014 Apr 21.

Faculty of Mathematics, Physics and Informatics, Comenius University, , Mlynská dolina, 842 48 Bratislava, Slovakia.

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http://link.springer.com/content/pdf/10.1007/978-3-642-24583
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http://rsta.royalsocietypublishing.org/content/roypta/372/20
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http://rsta.royalsocietypublishing.org/cgi/doi/10.1098/rsta.
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http://dx.doi.org/10.1098/rsta.2013.0133DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3996574PMC
May 2014

Massive programmed translational jumping in mitochondria.

Proc Natl Acad Sci U S A 2014 Apr 7;111(16):5926-31. Epub 2014 Apr 7.

Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montréal, QC, Canada H3T 1J4.

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http://dx.doi.org/10.1073/pnas.1322190111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4000857PMC
April 2014

Probabilistic approaches to alignment with tandem repeats.

Algorithms Mol Biol 2014 Mar 1;9(1). Epub 2014 Mar 1.

Department of Computer Science, Faculty of Mathematics, Physics, and Informatics, Comenius University, Mlynská dolina, 842 48 Bratislava, Slovakia.

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http://dx.doi.org/10.1186/1748-7188-9-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975930PMC
March 2014

Evolutionary genetics and implications of small size and twinning in callitrichine primates.

Proc Natl Acad Sci U S A 2014 Jan 30;111(4):1467-72. Epub 2013 Dec 30.

Departments of Obstetrics and Gynecology, Division of Maternal-Fetal Medicine and Molecular and Human Genetics, Human Genome Sequencing Center, and Department of Molecular and Cell Biology and the Reproductive Medicine Center, Baylor College of Medicine, Houston, TX 77030.

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http://dx.doi.org/10.1073/pnas.1316037111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3910650PMC
January 2014

The genome of the hydatid tapeworm Echinococcus granulosus.

Nat Genet 2013 Oct 8;45(10):1168-75. Epub 2013 Sep 8.

1] Shanghai-Ministry of Science and Technology Key Laboratory of Health and Disease Genomics, Chinese National Human Genome Center at Shanghai, Shanghai, China. [2].

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http://dx.doi.org/10.1038/ng.2757DOI Listing
October 2013

Sequencing the genome of Marssonina brunnea reveals fungus-poplar co-evolution.

BMC Genomics 2012 Aug 9;13:382. Epub 2012 Aug 9.

Jiangsu Key Laboratory for Poplar Germplasm Enhancement and Variety Improvement, Nanjing Forestry University, Nanjing, China.

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http://dx.doi.org/10.1186/1471-2164-13-382DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3484023PMC
August 2012

Discovery of RNA motifs using a computational pipeline that allows insertions in paired regions and filtering of candidate sequences.

Methods Mol Biol 2012 ;848:145-58

Department of Pharmaceutical Sciences, University of California, Irvine, CA, USA.

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http://dx.doi.org/10.1007/978-1-61779-545-9_10DOI Listing
May 2012

Evolution of linear chromosomes and multipartite genomes in yeast mitochondria.

Nucleic Acids Res 2011 May 25;39(10):4202-19. Epub 2011 Jan 25.

Department of Biochemistry, Comenius University, Mlynska dolina CH-1, 842 15 Bratislava, Slovak republic.

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http://dx.doi.org/10.1093/nar/gkq1345DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3105423PMC
May 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

CAGE: Combinatorial Analysis of Gene-cluster Evolution.

J Comput Biol 2010 Sep;17(9):1227-42

Center for Comparative Genomics and Bioinformatics, Penn State University, University Park, PA 16802, USA.

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http://www.bx.psu.edu/miller_lab/dist/CAGE.pdf
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http://www.liebertonline.com/doi/abs/10.1089/cmb.2010.0094
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http://dx.doi.org/10.1089/cmb.2010.0094DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3122889PMC
September 2010

Reconstructing histories of complex gene clusters on a phylogeny.

J Comput Biol 2010 Sep;17(9):1267-79

Faculty of Mathematics, Physics and Informatics, Comenius University , Bratislava, Slovakia.

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http://dx.doi.org/10.1089/cmb.2010.0090DOI Listing
September 2010

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

Evolutionary history reconstruction for Mammalian complex gene clusters.

J Comput Biol 2009 Aug;16(8):1051-70

Center for Comparative Genomics and Bioinformatics, Penn State University , University Park, PA 16802, USA.

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http://dx.doi.org/10.1089/cmb.2009.0040DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879273PMC
August 2009

Finding genes in Schistosoma japonicum: annotating novel genomes with help of extrinsic evidence.

Nucleic Acids Res 2009 Apr 5;37(7):e52. Epub 2009 Mar 5.

Department of Computer Science, Faculty of Mathematics, Physics, and Informatics, Comenius University, Bratislava, Slovakia.

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http://dx.doi.org/10.1093/nar/gkp052DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2673418PMC
April 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

Homology search for genes.

Bioinformatics 2007 Jul;23(13):i97-103

Cheriton School of Computer Science, University of Waterloo, Ontario, Canada N2L 3G1.

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http://dx.doi.org/10.1093/bioinformatics/btm225DOI 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

ExonHunter: a comprehensive approach to gene finding.

Bioinformatics 2005 Jun;21 Suppl 1:i57-65

School of Computer Science, University of Waterloo 200 University Avenue West, Waterloo, ON, Canada N2L 3G1.

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http://dx.doi.org/10.1093/bioinformatics/bti1040DOI Listing
June 2005

Optimal spaced seeds for homologous coding regions.

J Bioinform Comput Biol 2004 Jan;1(4):595-610

School of Computer Science, University of Waterloo, 200 University Ave West, Waterloo, ON N2L3G1, Canada.

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http://dx.doi.org/10.1142/s0219720004000326DOI Listing
January 2004