Stefan Washietl

Stefan Washietl

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Stefan Washietl

Stefan Washietl

Publications by authors named "Stefan Washietl"

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Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.

Methods Mol Biol 2014 ;1097:125-41

Computer Science and Artificial Intelligence Lab, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1007/978-1-62703-709-9_7DOI Listing
November 2014

Evolutionary dynamics and tissue specificity of human long noncoding RNAs in six mammals.

Genome Res 2014 Apr 15;24(4):616-28. Epub 2014 Jan 15.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts 02140, USA;

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http://dx.doi.org/10.1101/gr.165035.113DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3975061PMC
April 2014

Genome-wide probing of RNA structure reveals active unfolding of mRNA structures in vivo.

Nature 2014 Jan 15;505(7485):701-5. Epub 2013 Dec 15.

Department of Cellular and Molecular Pharmacology, California Institute of Quantitative Biology, Center for RNA Systems Biology, Howard Hughes Medical Institute, University of California, San Francisco, California 94158, USA.

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http://dx.doi.org/10.1038/nature12894DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3966492PMC
January 2014

RNAz 2.0: improved noncoding RNA detection.

Pac Symp Biocomput 2010 :69-79

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://www.mdpi.com/2073-4425/9/8/392/pdf
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November 2013

Computational analysis of noncoding RNAs.

Wiley Interdiscip Rev RNA 2012 Nov-Dec;3(6):759-78. Epub 2012 Sep 18.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA, USA.

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http://dx.doi.org/10.1002/wrna.1134DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3472101PMC
February 2013

RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction.

Nucleic Acids Res 2012 May 28;40(10):4261-72. Epub 2012 Jan 28.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, 32 Vassar Street, Cambridge, MA 02139, USA.

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http://dx.doi.org/10.1093/nar/gks009DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3378861PMC
May 2012

Locating protein-coding sequences under selection for additional, overlapping functions in 29 mammalian genomes.

Genome Res 2011 Nov 12;21(11):1916-28. Epub 2011 Oct 12.

Department of Electrical Engineering and Computer Science, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, USA.

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http://dx.doi.org/10.1101/gr.108753.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205576PMC
November 2011

New families of human regulatory RNA structures identified by comparative analysis of vertebrate genomes.

Genome Res 2011 Nov 12;21(11):1929-43. Epub 2011 Oct 12.

The Bioinformatics Centre, Department of Biology, University of Copenhagen, DK-2200 Copenhagen, Denmark.

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http://dx.doi.org/10.1101/gr.112516.110DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3205577PMC
November 2011

A high-resolution map of human evolutionary constraint using 29 mammals.

Nature 2011 Oct 12;478(7370):476-82. Epub 2011 Oct 12.

Broad Institute of Harvard and Massachusetts Institute of Technology, 7 Cambridge Center, Cambridge, Massachusetts 02142, USA.

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http://dx.doi.org/10.1038/nature10530DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3207357PMC
October 2011

RNAcode: robust discrimination of coding and noncoding regions in comparative sequence data.

RNA 2011 Apr 28;17(4):578-94. Epub 2011 Feb 28.

EMBL-European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire CB101SD, United Kingdom.

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http://dx.doi.org/10.1261/rna.2536111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3062170PMC
April 2011

Optimization of parameters for coverage of low molecular weight proteins.

Anal Bioanal Chem 2010 Dec 28;398(7-8):2867-81. Epub 2010 Aug 28.

Department of Proteomics, UFZ, Helmholtz-Centre for Environmental Research, Permoserstraße 15, 04318 Leipzig, Germany.

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http://dx.doi.org/10.1007/s00216-010-4093-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990009PMC
December 2010

Identification of functional elements and regulatory circuits by Drosophila modENCODE.

Science 2010 Dec 22;330(6012):1787-97. Epub 2010 Dec 22.

Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology (MIT), Cambridge, MA 02139, USA.

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http://compbio.mit.edu/publications/46_modENCODE_Science_10.
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http://www.sciencemag.org/cgi/doi/10.1126/science.1198374
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http://dx.doi.org/10.1126/science.1198374DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3192495PMC
December 2010

Nucleic acid sequence and structure databases.

Methods Mol Biol 2010 ;609:3-15

Department of Theoretical Chemistry, University of Vienna, Wien, Austria.

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http://dx.doi.org/10.1007/978-1-60327-241-4_1DOI Listing
May 2010

Sequence and structure analysis of noncoding RNAs.

Authors:
Stefan Washietl

Methods Mol Biol 2010 ;609:285-306

Department of Theoretical Chemistry, University of Vienna, Vienna, Wien, Austria.

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http://dx.doi.org/10.1007/978-1-60327-241-4_17DOI Listing
May 2010

Evolutionary footprints of nucleosome positions in yeast.

Trends Genet 2008 Dec 24;24(12):583-7. Epub 2008 Oct 24.

European Molecular Biology Laboratory - European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridgeshire, CB10 1SD, UK.

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http://dx.doi.org/10.1016/j.tig.2008.09.003DOI Listing
December 2008

Dinucleotide controlled null models for comparative RNA gene prediction.

BMC Bioinformatics 2008 May 27;9:248. Epub 2008 May 27.

Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria.

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http://dx.doi.org/10.1186/1471-2105-9-248DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2453142PMC
May 2008

Prediction of structural noncoding RNAs with RNAz.

Authors:
Stefan Washietl

Methods Mol Biol 2007 ;395:503-26

Department of Theoretical Chemistry, University of Vienna.

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http://dx.doi.org/10.1007/978-1-59745-514-5_32DOI Listing
March 2008

Strategies for measuring evolutionary conservation of RNA secondary structures.

BMC Bioinformatics 2008 Feb 26;9:122. Epub 2008 Feb 26.

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

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http://dx.doi.org/10.1186/1471-2105-9-122DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2335298PMC
February 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

Identifying structural noncoding RNAs using RNAz.

Curr Protoc Bioinformatics 2007 Sep;Chapter 12:Unit 12.7

University of Vienna, Vienna, Austria.

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http://dx.doi.org/10.1002/0471250953.bi1207s19DOI Listing
September 2007

The RNAz web server: prediction of thermodynamically stable and evolutionarily conserved RNA structures.

Nucleic Acids Res 2007 Jul 22;35(Web Server issue):W335-8. Epub 2007 Apr 22.

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

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
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http://dx.doi.org/10.1093/nar/gkm222DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1933143PMC
July 2007

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

miRNAMap: genomic maps of microRNA genes and their target genes in mammalian genomes.

Nucleic Acids Res 2006 Jan;34(Database issue):D135-9

Institute of Bioinformatics, National Chiao Tung University, Hsin-Chu 300, Taiwan, ROC.

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http://dx.doi.org/10.1093/nar/gkj135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1347497PMC
January 2006

Mapping of conserved RNA secondary structures predicts thousands of functional noncoding RNAs in the human genome.

Nat Biotechnol 2005 Nov;23(11):1383-90

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

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http://www.nature.com/articles/nbt1144
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http://dx.doi.org/10.1038/nbt1144DOI Listing
November 2005

A benchmark of multiple sequence alignment programs upon structural RNAs.

Nucleic Acids Res 2005 28;33(8):2433-9. Epub 2005 Apr 28.

Department of Evolutionary Biology, University of Copenhagen Universitetsparken 15, 2100 Copenhagen Ø, Denmark.

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http://dx.doi.org/10.1093/nar/gki541DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1087786PMC
May 2005

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

Fast and reliable prediction of noncoding RNAs.

Proc Natl Acad Sci U S A 2005 Feb 21;102(7):2454-9. Epub 2005 Jan 21.

Department of Theoretical Chemistry and Structural Biology, University of Vienna, Währingerstrasse 17, A-1090 Wien, Austria.

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http://dx.doi.org/10.1073/pnas.0409169102DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC548974PMC
February 2005

Consensus folding of aligned sequences as a new measure for the detection of functional RNAs by comparative genomics.

J Mol Biol 2004 Sep;342(1):19-30

Institut für Theoretische Chemie und Molekulare Strukturbiologie, Universität Wien, Währingerstrasse 17, A-1090, Austria.

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http://dx.doi.org/10.1016/j.jmb.2004.07.018DOI Listing
September 2004

Reannotation of the CELO genome characterizes a set of previously unassigned open reading frames and points to novel modes of host interaction in avian adenoviruses.

BMC Bioinformatics 2003 Nov 7;4:55. Epub 2003 Nov 7.

Research Institute of Molecular Pathology, Dr, Bohrgasse 7, A-1030 Vienna, Austria.

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http://dx.doi.org/10.1186/1471-2105-4-55DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC302110PMC
November 2003

Protein prenyltransferases: anchor size, pseudogenes and parasites.

Biol Chem 2003 Jul;384(7):977-89

Research Institute of Molecular Pathology, Dr. Bohr-Gasse 7, A-1030 Vienna, Austria.

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http://dx.doi.org/10.1515/BC.2003.110DOI Listing
July 2003

Protein prenyltransferases.

Genome Biol 2003 1;4(4):212. Epub 2003 Apr 1.

Research Institute of Molecular Pathology, Dr Bohr-Gasse 7, A-1030 Vienna, Austria.

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http://www.ncbi.nlm.nih.gov/pmc/articles/PMC154572PMC
http://dx.doi.org/10.1186/gb-2003-4-4-212DOI Listing
May 2003