Publications by authors named "Andrea Tanzer"

37Publications

RNA modifications in structure prediction - Status quo and future challenges.

Methods 2019 03 30;156:32-39. Epub 2018 Oct 30.

Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria.

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https://linkinghub.elsevier.com/retrieve/pii/S10462023183019
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http://dx.doi.org/10.1016/j.ymeth.2018.10.019DOI Listing
March 2019

RNA Structure Elements Conserved between Mouse and 59 Other Vertebrates.

Genes (Basel) 2018 Aug 1;9(8). Epub 2018 Aug 1.

Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währingerstraße 17, 1090 Wien, Austria.

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http://dx.doi.org/10.3390/genes9080392DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6116022PMC
August 2018

Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity.

Genome Biol 2016 10 25;17(1):220. Epub 2016 Oct 25.

Department of Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Vienna, A-1090, Austria.

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http://dx.doi.org/10.1186/s13059-016-1083-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5080714PMC
October 2016

Predicting RNA secondary structures from sequence and probing data.

Methods 2016 07 5;103:86-98. Epub 2016 Apr 5.

University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria; University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstr. 29, 1090 Vienna, Austria. Electronic address:

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http://dx.doi.org/10.1016/j.ymeth.2016.04.004DOI Listing
July 2016

AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements.

Nucleic Acids Res 2016 Jan 23;44(D1):D90-5. Epub 2015 Nov 23.

Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, A-1090 Vienna, Austria Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währingerstraße 29, A-1090 Vienna, Austria Center for non-coding RNA in Technology and Health, University of Copenhagen, Grønnegårdsvej 3, DK-1870 Frederiksberg C, Denmark.

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http://dx.doi.org/10.1093/nar/gkv1238DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4702876PMC
January 2016

A comparative encyclopedia of DNA elements in the mouse genome.

Authors:
Feng Yue Yong Cheng Alessandra Breschi Jeff Vierstra Weisheng Wu Tyrone Ryba Richard Sandstrom Zhihai Ma Carrie Davis Benjamin D Pope Yin Shen Dmitri D Pervouchine Sarah Djebali Robert E Thurman Rajinder Kaul Eric Rynes Anthony Kirilusha Georgi K Marinov Brian A Williams Diane Trout Henry Amrhein Katherine Fisher-Aylor Igor Antoshechkin Gilberto DeSalvo Lei-Hoon See Meagan Fastuca Jorg Drenkow Chris Zaleski Alex Dobin Pablo Prieto Julien Lagarde Giovanni Bussotti Andrea Tanzer Olgert Denas Kanwei Li M A Bender Miaohua Zhang Rachel Byron Mark T Groudine David McCleary Long Pham Zhen Ye Samantha Kuan Lee Edsall Yi-Chieh Wu Matthew D Rasmussen Mukul S Bansal Manolis Kellis Cheryl A Keller Christapher S Morrissey Tejaswini Mishra Deepti Jain Nergiz Dogan Robert S Harris Philip Cayting Trupti Kawli Alan P Boyle Ghia Euskirchen Anshul Kundaje Shin Lin Yiing Lin Camden Jansen Venkat S Malladi Melissa S Cline Drew T Erickson Vanessa M Kirkup Katrina Learned Cricket A Sloan Kate R Rosenbloom Beatriz Lacerda de Sousa Kathryn Beal Miguel Pignatelli Paul Flicek Jin Lian Tamer Kahveci Dongwon Lee W James Kent Miguel Ramalho Santos Javier Herrero Cedric Notredame Audra Johnson Shinny Vong Kristen Lee Daniel Bates Fidencio Neri Morgan Diegel Theresa Canfield Peter J Sabo Matthew S Wilken Thomas A Reh Erika Giste Anthony Shafer Tanya Kutyavin Eric Haugen Douglas Dunn Alex P Reynolds Shane Neph Richard Humbert R Scott Hansen Marella De Bruijn Licia Selleri Alexander Rudensky Steven Josefowicz Robert Samstein Evan E Eichler Stuart H Orkin Dana Levasseur Thalia Papayannopoulou Kai-Hsin Chang Arthur Skoultchi Srikanta Gosh Christine Disteche Piper Treuting Yanli Wang Mitchell J Weiss Gerd A Blobel Xiaoyi Cao Sheng Zhong Ting Wang Peter J Good Rebecca F Lowdon Leslie B Adams Xiao-Qiao Zhou Michael J Pazin Elise A Feingold Barbara Wold James Taylor Ali Mortazavi Sherman M Weissman John A Stamatoyannopoulos Michael P Snyder Roderic Guigo Thomas R Gingeras David M Gilbert Ross C Hardison Michael A Beer Bing Ren

Nature 2014 Nov;515(7527):355-64

Ludwig Institute for Cancer Research and University of California, San Diego School of Medicine, 9500 Gilman Drive, La Jolla, California 92093, USA.

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http://dx.doi.org/10.1038/nature13992DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4266106PMC
November 2014

Comparative analysis of the transcriptome across distant species.

Nature 2014 Aug;512(7515):445-8

1] Department of Genome Sciences and University of Washington School of Medicine, William H. Foege Building S350D, 1705 Northeast Pacific Street, Box 355065 Seattle, Washington 98195-5065, USA [2].

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http://dx.doi.org/10.1038/nature13424DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4155737PMC
August 2014

2D meets 4G: G-quadruplexes in RNA secondary structure prediction.

IEEE/ACM Trans Comput Biol Bioinform 2013 Jul-Aug;10(4):832-44

University of Leipzig, Leipzig, Max Planck Institute for Mathematics in the Sciences, Leipzig, Fraunhofer Institute for CellTherapy and Immunology and University of Copenhagen.

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http://dx.doi.org/10.1109/TCBB.2013.7DOI Listing
August 2014

Landscape of transcription in human cells.

Nature 2012 Sep;489(7414):101-8

Centre for Genomic Regulation and UPF, Doctor Aiguader 88, Barcelona 08003, Catalonia, Spain.

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http://dx.doi.org/10.1038/nature11233DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3684276PMC
September 2012

The GENCODE pseudogene resource.

Genome Biol 2012 Sep 26;13(9):R51. Epub 2012 Sep 26.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/gb-2012-13-9-r51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491395PMC
September 2012

Nematode sbRNAs: homologs of vertebrate Y RNAs.

J Mol Evol 2010 Apr 27;70(4):346-58. Epub 2010 Mar 27.

Department of Medical Sciences and Interdisciplinary Research Centre for Autoimmune Diseases, Università del Piemonte Orientale, via Solaroli 17, 28100 Novara, Italy.

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http://dx.doi.org/10.1007/s00239-010-9332-4DOI Listing
April 2010

RNPomics: defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles.

Nucleic Acids Res 2010 Jun 11;38(10):e113. Epub 2010 Feb 11.

Division of Genomics and RNomics, Innsbruck Biocentre, Innsbruck Medical University, Innsbruck and Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1093/nar/gkq057DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2879528PMC
June 2010

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library.

Nat Biotechnol 2010 Jan 27;28(1):47-55. Epub 2009 Dec 27.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, Connecticut, USA.

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http://www.nature.com/articles/nbt.1600
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http://dx.doi.org/10.1038/nbt.1600DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2951730PMC
January 2010

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

Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals.

Proc Natl Acad Sci U S A 2008 Sep 22;105(39):14928-33. Epub 2008 Sep 22.

Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT 06511, USA.

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http://www.pnas.org/cgi/doi/10.1073/pnas.0802355105
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http://dx.doi.org/10.1073/pnas.0802355105DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2567470PMC
September 2008

Folding kinetics of large RNAs.

J Mol Biol 2008 May 6;379(1):160-73. Epub 2008 Mar 6.

Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany.

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http://dx.doi.org/10.1016/j.jmb.2008.02.064DOI Listing
May 2008

Evolutionary patterns of non-coding RNAs.

Theory Biosci 2005 Apr;123(4):301-69

Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Wien, Austria.

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http://dx.doi.org/10.1016/j.thbio.2005.01.002DOI Listing
April 2005

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

Evolution of microRNAs.

Methods Mol Biol 2006 ;342:335-50

Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1385/1-59745-123-1:335DOI Listing
September 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

Comparative promoter region analysis powered by CORG.

BMC Genomics 2005 Feb 21;6:24. Epub 2005 Feb 21.

Computational Molecular Biology Department, Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany.

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http://dx.doi.org/10.1186/1471-2164-6-24DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC555765PMC
February 2005

Evolution of microRNAs located within Hox gene clusters.

J Exp Zool B Mol Dev Evol 2005 Jan;304(1):75-85

Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Kreuzstrasse 7b, D 04103 Leipzig, Germany.

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http://dx.doi.org/10.1002/jez.b.21021DOI Listing
January 2005

Molecular evolution of a microRNA cluster.

J Mol Biol 2004 May;339(2):327-35

Lehrstuhl für Bioinformatik am Institut für Informatik und Interdisziplinäres, Zentrum für Bioinformatik, Universität Leipzig, Germany.

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http://dx.doi.org/10.1016/j.jmb.2004.03.065DOI Listing
May 2004