Publications by authors named "Jana Hertel"

33Publications

SnoReport 2.0: new features and a refined Support Vector Machine to improve snoRNA identification.

BMC Bioinformatics 2016 Dec 15;17(Suppl 18):464. Epub 2016 Dec 15.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Haertelstraße 16-18, Leipzig, D-04107, Germany.

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http://dx.doi.org/10.1186/s12859-016-1345-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5249026PMC
December 2016

Evolution of Fungal U3 snoRNAs: Structural Variation and Introns.

Noncoding RNA 2017 Jan 5;3(1). Epub 2017 Jan 5.

Helmholtz Centre for Environmental Research-UFZ, Young Investigators Group Bioinformatics and Transcriptomics Permoserstraße 15, D-04318 Leipzig, Germany.

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http://dx.doi.org/10.3390/ncrna3010003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5832005PMC
January 2017

Phylogenetic distribution of plant snoRNA families.

BMC Genomics 2016 11 24;17(1):969. Epub 2016 Nov 24.

Bioinformatics Group, Dept. Computer Science, and artin-Luther-Universität Halle-Wittenberg, Leipzig, D-04107, Germany.

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http://dx.doi.org/10.1186/s12864-016-3301-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5122169PMC
November 2016

An updated human snoRNAome.

Nucleic Acids Res 2016 06 12;44(11):5068-82. Epub 2016 May 12.

Computational and Systems Biology, Biozentrum, University of Basel and Swiss Institute of Bioinformatics, Basel CH-4056, Switzerland

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http://dx.doi.org/10.1093/nar/gkw386DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4914119PMC
June 2016

U6 snRNA intron insertion occurred multiple times during fungi evolution.

RNA Biol 2016 ;13(2):119-27

a Bioinformatics Group , Department of Computer Science,and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18 , D-04107 Leipzig , Germany.

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http://dx.doi.org/10.1080/15476286.2015.1132139DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4829304PMC
November 2016

Third Report on Chicken Genes and Chromosomes 2015.

Authors:
Michael Schmid Jacqueline Smith David W Burt Bronwen L Aken Parker B Antin Alan L Archibald Chris Ashwell Perry J Blackshear Clarissa Boschiero C Titus Brown Shane C Burgess Hans H Cheng William Chow Derrick J Coble Amanda Cooksey Richard P M A Crooijmans Joana Damas Richard V N Davis Dirk-Jan de Koning Mary E Delany Thomas Derrien Takele T Desta Ian C Dunn Matthew Dunn Hans Ellegren Lél Eöry Ionas Erb Marta Farré Mario Fasold Damarius Fleming Paul Flicek Katie E Fowler Laure Frésard David P Froman Valerie Garceau Paul P Gardner Almas A Gheyas Darren K Griffin Martien A M Groenen Thomas Haaf Olivier Hanotte Alan Hart Julien Häsler S Blair Hedges Jana Hertel Kerstin Howe Allen Hubbard David A Hume Pete Kaiser Darek Kedra Stephen J Kemp Christophe Klopp Kalmia E Kniel Richard Kuo Sandrine Lagarrigue Susan J Lamont Denis M Larkin Raman A Lawal Sarah M Markland Fiona McCarthy Heather A McCormack Marla C McPherson Akira Motegi Stefan A Muljo Andrea Münsterberg Rishi Nag Indrajit Nanda Michael Neuberger Anne Nitsche Cedric Notredame Harry Noyes Rebecca O'Connor Elizabeth A O'Hare Andrew J Oler Sheila C Ommeh Helio Pais Michael Persia Frédérique Pitel Likit Preeyanon Pablo Prieto Barja Elizabeth M Pritchett Douglas D Rhoads Charmaine M Robinson Michael N Romanov Max Rothschild Pierre-François Roux Carl J Schmidt Alisa-Sophia Schneider Matthew G Schwartz Steve M Searle Michael A Skinner Craig A Smith Peter F Stadler Tammy E Steeves Claus Steinlein Liang Sun Minoru Takata Igor Ulitsky Qing Wang Ying Wang Wesley C Warren Jonathan M D Wood David Wragg Huaijun Zhou

Cytogenet Genome Res 2015 14;145(2):78-179. Epub 2015 Jul 14.

Department of Human Genetics, University of Würzburg, Würzburg, Germany.

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http://dx.doi.org/10.1159/000430927DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5120589PMC
October 2015

Conservation and losses of non-coding RNAs in avian genomes.

PLoS One 2015 30;10(3):e0121797. Epub 2015 Mar 30.

Bioinformatics Group, Department of Computer Science; and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany; Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany; Fraunhofer Institute for Cell Therapy and Immunology, Perlickstrasse 1, D-04103 Leipzig, Germany; Department of Theoretical Chemistry of the University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria; Center for RNA in Technology and Health, Univ. Copenhagen, Grønnegårdsvej 3, Frederiksberg C, Denmark; Santa Fe Institute, 1399 Hyde Park Road, Santa Fe NM 87501, USA; German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Germany.

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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0121797PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4378963PMC
April 2016

The Expansion of Animal MicroRNA Families Revisited.

Life (Basel) 2015 Mar 13;5(1):905-20. Epub 2015 Mar 13.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.3390/life5010905DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4390885PMC
March 2015

The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies.

Mol Cell 2014 Nov 6;56(3):389-99. Epub 2014 Nov 6.

Max Planck Institute of Molecular Cell Biology and Genetics, Pfotenhauerstrasse 108, 01307 Dresden, Germany; Department of Molecular Biophysics & Biochemistry, Yale University, 333 Cedar Street, New Haven, CT 06520, USA. Electronic address:

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http://dx.doi.org/10.1016/j.molcel.2014.10.004DOI Listing
November 2014

Computational prediction of microRNA genes.

Methods Mol Biol 2014 ;1097:437-56

Bioinformatics Group, Department of Computer Science, University of Leipzig, Leipzig, Germany.

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http://link.springer.com/10.1007/978-1-62703-709-9_20
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http://dx.doi.org/10.1007/978-1-62703-709-9_20DOI Listing
November 2014

snoStrip: a snoRNA annotation pipeline.

Bioinformatics 2014 Jan 29;30(1):115-6. Epub 2013 Oct 29.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btt604DOI Listing
January 2014

Matching of Soulmates: coevolution of snoRNAs and their targets.

Mol Biol Evol 2014 Feb 24;31(2):455-67. Epub 2013 Oct 24.

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1093/molbev/mst209DOI Listing
February 2014

Evolution of the let-7 microRNA family.

RNA Biol 2012 Mar 1;9(3):231-41. Epub 2012 Mar 1.

Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.4161/rna.18974DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3384580PMC
March 2012

RNAsnoop: efficient target prediction for H/ACA snoRNAs.

Bioinformatics 2010 Mar 16;26(5):610-6. Epub 2009 Dec 16.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Vienna, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btp680DOI Listing
March 2010

Homology-based annotation of non-coding RNAs in the genomes of Schistosoma mansoni and Schistosoma japonicum.

BMC Genomics 2009 Oct 8;10:464. Epub 2009 Oct 8.

Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.1186/1471-2164-10-464DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2770079PMC
October 2009

Accurate and efficient reconstruction of deep phylogenies from structured RNAs.

Nucleic Acids Res 2009 Oct 1;37(18):6184-93. Epub 2009 Sep 1.

Zoologisches Forschungsmuseum Alexander Koenig, Bonn, Germany.

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http://dx.doi.org/10.1093/nar/gkp600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2764418PMC
October 2009

Evidence for human microRNA-offset RNAs in small RNA sequencing data.

Bioinformatics 2009 Sep 6;25(18):2298-301. Epub 2009 Jul 6.

Department of Computer Science, University of Leipzig, Leipzig, Germany.

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http://dx.doi.org/10.1093/bioinformatics/btp419DOI Listing
September 2009

Non-coding RNA annotation of the genome of Trichoplax adhaerens.

Nucleic Acids Res 2009 Apr 16;37(5):1602-15. Epub 2009 Jan 16.

Bioinformatics Group, Department of Computer Science, Interdisciplinary Center for Bioinformatics, University of Leipzig, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.1093/nar/gkn1084DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2655684PMC
April 2009

NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences.

Genomics 2008 Jul 3;92(1):65-74. Epub 2008 Jun 3.

Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.1016/j.ygeno.2008.04.003DOI Listing
July 2008

Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein synthesis.

Nucleic Acids Res 2008 May 16;36(8):2677-89. Epub 2008 Mar 16.

Innsbruck Biocenter, Division of Genomics and RNomics - Innsbruck Medical University, Fritz-Pregl-Strasse 3, 6020 Innsbruck, Austria.

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http://dx.doi.org/10.1093/nar/gkn123DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2377427PMC
May 2008

Computational RNomics of drosophilids.

BMC Genomics 2007 Nov 8;8:406. Epub 2007 Nov 8.

Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16-18, Leipzig, Germany.

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http://dx.doi.org/10.1186/1471-2164-8-406DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2216035PMC
November 2007

SnoReport: computational identification of snoRNAs with unknown targets.

Bioinformatics 2008 Jan 25;24(2):158-64. Epub 2007 Sep 25.

Institute for Theoretical Chemistry, University of Vienna, Währingerstrasse 17, A-1090 Wien, Austria.

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http://dx.doi.org/10.1093/bioinformatics/btm464DOI Listing
January 2008

Variations on RNA folding and alignment: lessons from Benasque.

J Math Biol 2008 Jan 5;56(1-2):129-44. Epub 2007 Jul 5.

Zentralfriedhof Wien, 3. Tor Simmeringer Haupstrasse, Wien, Austria.

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http://dx.doi.org/10.1007/s00285-007-0107-5DOI Listing
January 2008

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors:
Ewan Birney John A Stamatoyannopoulos Anindya Dutta Roderic Guigó Thomas R Gingeras Elliott H Margulies Zhiping Weng Michael Snyder Emmanouil T Dermitzakis Robert E Thurman Michael S Kuehn Christopher M Taylor Shane Neph Christoph M Koch Saurabh Asthana Ankit Malhotra Ivan Adzhubei Jason A Greenbaum Robert M Andrews Paul Flicek Patrick J Boyle Hua Cao Nigel P Carter Gayle K Clelland Sean Davis Nathan Day Pawandeep Dhami Shane C Dillon Michael O Dorschner Heike Fiegler Paul G Giresi Jeff Goldy Michael Hawrylycz Andrew Haydock Richard Humbert Keith D James Brett E Johnson Ericka M Johnson Tristan T Frum Elizabeth R Rosenzweig Neerja Karnani Kirsten Lee Gregory C Lefebvre Patrick A Navas Fidencio Neri Stephen C J Parker Peter J Sabo Richard Sandstrom Anthony Shafer David Vetrie Molly Weaver Sarah Wilcox Man Yu Francis S Collins Job Dekker Jason D Lieb Thomas D Tullius Gregory E Crawford Shamil Sunyaev William S Noble Ian Dunham France Denoeud Alexandre Reymond Philipp Kapranov Joel Rozowsky Deyou Zheng Robert Castelo Adam Frankish Jennifer Harrow Srinka Ghosh Albin Sandelin Ivo L Hofacker Robert Baertsch Damian Keefe Sujit Dike Jill Cheng Heather A Hirsch Edward A Sekinger Julien Lagarde Josep F Abril Atif Shahab Christoph Flamm Claudia Fried Jörg Hackermüller Jana Hertel Manja Lindemeyer Kristin Missal Andrea Tanzer Stefan Washietl Jan Korbel Olof Emanuelsson Jakob S Pedersen Nancy Holroyd Ruth Taylor David Swarbreck Nicholas Matthews Mark C Dickson Daryl J Thomas Matthew T Weirauch James Gilbert Jorg Drenkow Ian Bell XiaoDong Zhao K G Srinivasan Wing-Kin Sung Hong Sain Ooi Kuo Ping Chiu Sylvain Foissac Tyler Alioto Michael Brent Lior Pachter Michael L Tress Alfonso Valencia Siew Woh Choo Chiou Yu Choo Catherine Ucla Caroline Manzano Carine Wyss Evelyn Cheung Taane G Clark James B Brown Madhavan Ganesh Sandeep Patel Hari Tammana Jacqueline Chrast Charlotte N Henrichsen Chikatoshi Kai Jun Kawai Ugrappa Nagalakshmi Jiaqian Wu Zheng Lian Jin Lian Peter Newburger Xueqing Zhang Peter Bickel John S Mattick Piero Carninci Yoshihide Hayashizaki Sherman Weissman Tim Hubbard Richard M Myers Jane Rogers Peter F Stadler Todd M Lowe Chia-Lin Wei Yijun Ruan Kevin Struhl Mark Gerstein Stylianos E Antonarakis Yutao Fu Eric D Green Ulaş Karaöz Adam Siepel James Taylor Laura A Liefer Kris A Wetterstrand Peter J Good Elise A Feingold Mark S Guyer Gregory M Cooper George Asimenos Colin N Dewey Minmei Hou Sergey Nikolaev Juan I Montoya-Burgos Ari Löytynoja Simon Whelan Fabio Pardi Tim Massingham Haiyan Huang Nancy R Zhang Ian Holmes James C Mullikin Abel Ureta-Vidal Benedict Paten Michael Seringhaus Deanna Church Kate Rosenbloom W James Kent Eric A Stone Serafim Batzoglou Nick Goldman Ross C Hardison David Haussler Webb Miller Arend Sidow Nathan D Trinklein Zhengdong D Zhang Leah Barrera Rhona Stuart David C King Adam Ameur Stefan Enroth Mark C Bieda Jonghwan Kim Akshay A Bhinge Nan Jiang Jun Liu Fei Yao Vinsensius B Vega Charlie W H Lee Patrick Ng Atif Shahab Annie Yang Zarmik Moqtaderi Zhou Zhu Xiaoqin Xu Sharon Squazzo Matthew J Oberley David Inman Michael A Singer Todd A Richmond Kyle J Munn Alvaro Rada-Iglesias Ola Wallerman Jan Komorowski Joanna C Fowler Phillippe Couttet Alexander W Bruce Oliver M Dovey Peter D Ellis Cordelia F Langford David A Nix Ghia Euskirchen Stephen Hartman Alexander E Urban Peter Kraus Sara Van Calcar Nate Heintzman Tae Hoon Kim Kun Wang Chunxu Qu Gary Hon Rosa Luna Christopher K Glass M Geoff Rosenfeld Shelley Force Aldred Sara J Cooper Anason Halees Jane M Lin Hennady P Shulha Xiaoling Zhang Mousheng Xu Jaafar N S Haidar Yong Yu Yijun Ruan Vishwanath R Iyer Roland D Green Claes Wadelius Peggy J Farnham Bing Ren Rachel A Harte Angie S Hinrichs Heather Trumbower Hiram Clawson Jennifer Hillman-Jackson Ann S Zweig Kayla Smith Archana Thakkapallayil Galt Barber Robert M Kuhn Donna Karolchik Lluis Armengol Christine P Bird Paul I W de Bakker Andrew D Kern Nuria Lopez-Bigas Joel D Martin Barbara E Stranger Abigail Woodroffe Eugene Davydov Antigone Dimas Eduardo Eyras Ingileif B Hallgrímsdóttir Julian Huppert Michael C Zody Gonçalo R Abecasis Xavier Estivill Gerard G Bouffard Xiaobin Guan Nancy F Hansen Jacquelyn R Idol Valerie V B Maduro Baishali Maskeri Jennifer C McDowell Morgan Park Pamela J Thomas Alice C Young Robert W Blakesley Donna M Muzny Erica Sodergren David A Wheeler Kim C Worley Huaiyang Jiang George M Weinstock Richard A Gibbs Tina Graves Robert Fulton Elaine R Mardis Richard K Wilson Michele Clamp James Cuff Sante Gnerre David B Jaffe Jean L Chang Kerstin Lindblad-Toh Eric S Lander Maxim Koriabine Mikhail Nefedov Kazutoyo Osoegawa Yuko Yoshinaga Baoli Zhu Pieter J de Jong
June 2007

RNAs everywhere: genome-wide annotation of structured RNAs.

J Exp Zool B Mol Dev Evol 2007 Jan;308(1):1-25

Bioinformatics Group, Department of Computer Science, University of Freiburg, D-79110 Freiburg, Germany.

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http://dx.doi.org/10.1002/jez.b.21130DOI Listing
January 2007

Hairpins in a Haystack: recognizing microRNA precursors in comparative genomics data.

Bioinformatics 2006 Jul;22(14):e197-202

Bioinformatics Group, Department of Computer Science and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btl257DOI Listing
July 2006

The expansion of the metazoan microRNA repertoire.

BMC Genomics 2006 Feb 15;7:25. Epub 2006 Feb 15.

Bioinformatics Group, Department of Computer Science, University of Leipzig, Härtelstrasse 16-18, D-04107 Leipzig, Germany.

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http://dx.doi.org/10.1186/1471-2164-7-25DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1388199PMC
February 2006