Andrea Tanzer

Andrea Tanzer

UNVERIFIED PROFILE

Are you Andrea Tanzer?   Register this Author

Register author
Andrea Tanzer

Andrea Tanzer

Publications by authors named "Andrea Tanzer"

Are you Andrea Tanzer?   Register this Author

37Publications

1210Reads

36Profile Views

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.

View Article

Download full-text PDF

Source
https://linkinghub.elsevier.com/retrieve/pii/S10462023183019
Publisher Site
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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:

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

Source
http://www.nature.com/articles/nbt.1600
Publisher Site
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
http://www.pnas.org/cgi/doi/10.1073/pnas.0802355105
Publisher Site
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.

View Article

Download full-text PDF

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

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

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

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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

Source
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.

View Article

Download full-text PDF

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