Resumé

Publications

2011


Animal snoRNAs and scaRNAs with exceptional structures
Manja Marz, Andreas R Gruber, Christian Höner zu Siederdissen, Fabian Amman, Stefan Badelt, Sebastian Bartschat, Stephan H Bernhart, Wolfgang Beyer, Stephanie Kehr, Ronny Lorenz, Andrea Tanzer, Dilmurat Yusuf, Hakim Tafer, Ivo L Hofacker, and Peter F Stadler
RNA Biol. 2011 Nov-Dec; 8(6): 938–946
[Publisher's Page]

A user's guide to the encyclopedia of DNA elements (ENCODE).
ENCODE Project Consortium, Myers RM, Stamatoyannopoulos J, Snyder M, Dunham I, Hardison RC, Bernstein BE, Gingeras TR, Kent WJ, Birney E, Wold B, Crawford GE.
PLoS Biol. 2011 Apr;9(4):e1001046. Epub 2011 Apr 19.
[Publisher's Page]


2010


Nematode sbRNAs: homologs of vertebrate Y RNAs
Ilenia Boria, Andreas R. Gruber, Andrea Tanzer, Stephan H. Bernhart, Ronny Lorenz, Michael M. Mueller, Ivo L. Hofacker, Peter F. Stadler
J. Mol. Evol., (2010) 70(4): 346-58

RNPomics: Defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles
Rederstorff M, Bernhart SH, Tanzer A, Zywicki M, Perfler K, Lukasser M, Hofacker IL, Hüttenhofer A
Nucleic Acids Res. (2010) 38(10): e113
[Publisher's Page]

Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library
Lam HY, Mu XJ, Stütz AM, Tanzer A, Cayting PD, Snyder M, Kim PM, Korbel JO, Gerstein MB
Nat Biotechnol. 2010 Jan;28(1):47-55.
[Publisher's Page]

Evolutionary Genomics of microRNAs and Their Relatives
Andrea Tanzer, Markus Riester, Jana Hertel, Clara Isabel Bermudez-Santana, Jan Gorodkin and Ivo L. Hofacker, and Peter F. Stadler
in: Evolutionary Genomics and Systems Biology, ed Gustavo Caetano-Anolles, Wiley-Blackwell, Hoboken, 2010, pp 295-327


2009


Non-Coding RNA Annotation of the Genome of Trichoplax adhaerens
Jana Hertel, Danielle de Jong, Manja Marz, Dominic Rose, Hakim Tafer, Andrea Tanzer, Bernd Schierwater, Peter F. Stadler
Nucleic Acids Res. 37: 1602-1615 (2009)
[Abstract] [Supplement]
[Publisher's Page]

2008


Adaptive changes in the transcription factor HoxA-11 are essential for the evolution of pregnancy in mammals
Lynch VJ, Tanzer A, Wang Y, Leung FC, Gellersen B, Emera D, Wagner GP
Proc Natl Acad Sci U S A. 2008 Sep 30;105(39):14928-33. Epub 2008 Sep 22
[Publisher's Page]

Folding Kinetics of Large RNAs
Michael Geis, Christoph Flamm, Michael T. Wolfinger, Andrea Tanzer, Ivo L. Hofacker, Martin Middendorf, Christian Mandl, Peter F. Stadler and Caroline Thurner
J Mol Biol. 2008 May 23; 379(1): 160-73
[Abstract]
[Publisher's Page]


2007


Paired-End Mapping Reveals Extensive Structural Variation in the Human Genome.
Jan O. Korbel, Alexander Eckehart Urban, Jason P. Affourtit, Brian Godwin, Fabian Grubert, Jan
Fredrik Simons, Philip M. Kim, Dean Palejev, Nicholas J. Carriero, Lei Du, Bruce E. Taillon, Zhoutao Chen, Andrea
Tanzer, A. C. Eugenia Saunders, Jianxiang Chi, Fengtang Yang, Nigel P. Carter, Matthew E. Hurles, Sherman M. Weissman, Timothy T. Harkins, Mark B. Gerstein, Michael Egholm, Michael Snyder

Science. 2007 Oct 19; 318(5849): 420-6
[Publisher's Page]

Structured RNAs in the ENCODE selected regions of the human genome.
Washietl S, Pedersen JS, Korbel JO, Stocsits C, Gruber AR, Hackermüller J, Hertel J, Lindemeyer M, Reiche K, Tanzer A, Ucla C, Wyss C, Antonarakis SE, Denoeud F, Lagarde J, Drenkow J, Kapranov P, Gingeras TR, Guigó R, Snyder M, Gerstein MB, Reymond A, Hofacker IL, Stadler PF
Genome Res. 2007 Jun ; 17(6): 852-64
[Publisher's Page]
Preprint version:
[abstract]
preprint

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
The ENCODE Project Consortium
Nature 447: 799-816 (2007)
[Publisher's Page]

RNAs Everywhere: Genome-Wide Annotation of Structured RNAs
The Athanasius F. Bompfünewerer RNA Consortium: Rolf Backofen, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal Axel Mosig, Sonja J. Prohaska, Dominic Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Sebastian Will
J. Exp. Zool. B: Mol. Dev. Evol. 308B: 1-25 (2007).
[Publisher's page]


2006


Evolution of MicroRNAs
Andrea Tanzer, Peter F. Stadler
MicroRNA Protocols, Humana Press, Totowa, NJ, Methods in Molecular Biology 342: 335-350 (2006).
[Publisher's page]

The Expansion of the Metazoan MicroRNA Repertoire
Jana Hertel, Manuela Lindemeyer, Kristin Missal, Claudia Fried, Andrea Tanzer, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler, and The Students of Bioinformatics Computer Labs 2004 and 2005:

Sten Heinze, Alexander ''muppet'' Donath, Sven Findeß,
Stephanie Keller, Kevin Peter, Julian Jöris, Jokab Mühmel, Marco Dienelt (in Leipzig),
Martina Hödl, Bernhard Wurzinger, Camille Stephan-Otto Attolini, Ulrich Omasits, Sebastian Krüttner, Regina Anzengruber, Daniela Lenek, Gregor Neumayr, Reinhard Wohlfart (in Vienna).
BMC Genomics, 7: 15 (2006).
[Publisher's page]
Preprint version:
[abstract]
[ps]
[pdf]
[supplement]


2005


Evolutionary Patterns of Non-Coding RNAs
A.F. Bompfünewerer, Ch. Flamm, C. Fried, G. Fritzsch, I.L. Hofacker, J. Lehmann, K. Missal, A. Mosig, B. Müller, S.J. Prohaska, B.M.R. Stadler, P.F. Stadler, A. Tanzer, S. Washietl, Ch. Witwer
Th. Biosci. 123: 301-369 (2005).

[Publisher's Page]
Preprint version:
[abstract]
[ps]
[pdf]

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supplement]

Comparative promoter region analysis powered by CORG
Christoph Dieterich, Steffen Grossmann, Andrea Tanzer, Stefan Röpcke, Peter F Arndt, Peter F Stadler, Martin Vingron
BMC Genomics 6: 24 (2005).
[publisher's page]
Preprint version:
[abstract]
[pdf]
[supplement]

Evolution of MicroRNAs Located Within Hox Gene Clusters
Andrea Tanzer, Chris T. Amemiya, Chang-Bae Kim, Peter F. Stadler
J.Exp.Zool.(Mol.Dev.Evol.) 304B: 75-85 (2005).
[Publisher's Page]
Preprint version:
[abstract]
[ps]
[pdf]
[supplement]


2004


Molecular Evolution of a MicroRNA Cluster
Andrea Tanzer, Peter F. Stadler
J.Mol.Biol. 339: 327-335 (2004).
Preprint version:
[abstract]
[ps]
[pdf]
[supplement]

Andrea Tanzer

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