List of Publications


Induction of microRNA-21 contributes to the oncogenic potential of Stat3
Dennis Löller, Katja Brocke-Heidrich, Gabriele Pfeifer, Claudia Fried, Jörg Hackermüller, Antje K. Kretzschmar, Renate Burger, Martin Gramatzki, Conny Blumert, Kay Bauer, Helena Cvijic, Peter F. Stadler, Friedemann Horn
submitted

Structured RNAs in the ENCODE Selected Regions of the Human Genome
Stefan Washietl, Jakob S. Pedersen, Jan O. Korbel, Claudia Fried, Andreas R. Gruber, Jörg Hackermüller, Jana Hertel, Manja Lindemeyer, Kristin Missal, Andrea Tanzer, Catherine Ucla, Stylianos E. Antonarakis, Alexandre Reymond, France Denoeud, Julien Lagarde, Jorg Drenkow, Philipp Kapranov, Thomas R. Gingeras, Michael Snyder, Mark B. Gerstein, Ivo L. Hofacker, Peter F. Stadler
Submitted [Abstract]

Long Distance and Global Transcription Networks Characterize ENCODE Regions
ENCODE Project Consortium
Roderic Guigó, 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, Paul Flicek, Sujit Dike, Jill Cheng, 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, Xiao-Dong Zhao, K.G. Srinivasan, Wing-Kin Sung, Hong Sain Ooi, Kuo Ping Chiu, Sylvain Foissac, Tyler Alioto, Siew Woh Choo, Chiou Yu Choo, Catherine Ucla, Caroline Manzano, Carine Wyss, Evelyn Cheung, Taane Clarke, 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 M. Weissman, Emmanouil Dermitzakis, Elliott H. Margulies, Tim Hubbard, Richard M. Myers, Jane Rogers, Peter F. Stadler, Todd M. Lowe, Chia-Lin Wei, Yijun Ruan, Michael Snyder, Ewan Birney, Mark Gerstein, Stylianos E. Antonarakis, Thomas R. Gingeras

Submitted. [Abstract]
RNAs Everywhere: Genome-Wide Annotation of Structured RNAs
Athanasius F. Bompfünewerer, Rolf Backofen, Stephan H. Bernhart, 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
in print (J.Exp.Zool.)
Preprint version: [PDF]
Genome-Wide Analysis of Single Nucleotide Polymorphisms in Evolutionary Conserved DNA
Claudia Fried, Peter F. Stadler, Peter Ahnert
submitted
Preprint version: [Abstract] [PDF] [Supplemental Material]
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 Findeiß, Stephanie Keller, Kevin Peter,
Julian Jöris, Jakob Mühmel, Marco Dienelt, Lisa aus Jena, Maiko Lohet, Holger Schmidtchen,
Nick Jagiella, Andrej Aderhold, Paul-Robert Kästerer, Thomas Skodawessely (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 2006, 7:25 [epub] (2006)
Preprint version: [Abstract] [PS] [PDF]
[Supplementary Material]
Molecular Evolution of Duplicated Ray Finned Fisch HoxA Clusters:
Increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences

Günter P. Wagner, Kazuhiko Takahashi, Vincent Lynch, Sonja J. Prohaska, Claudia Fried, Peter F. Stadler, Chris T. Amemiya
J.Mol.Evol. 60: 665-676 (2005).
[Publisher's Page]
Preprint version: [
Abstract] [PDF] [Supplement]
Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences
Roman R. Stocsits, Ivo L. Hofacker, Claudia Fried, Peter F. Stadler
BMC Bioinformatics 6: 160 [epub] (2005).
[Publisher's Page]
Preprint version: [
Abstract] [Postscript] [PDF]
[Software]

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] [Postscript] [PDF]
[Supplement]

Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests
Günter P. Wagner, Claudia Fried, Sonja J. Prohaska, Peter F. Stadler
Mol.Biol.Evol. 21: 2116-2121 (2004)
[Publisher's Page]
[Supplement]


Exclusion of Repetitive DNA Elements from Gnathostome Hox Clusters
Claudia Fried, Sonja J. Prohaska, Peter F. Stadler
J.Exp.Zool., Mol.Dev.Evol.302B: 165-173 (2004)

Evidence for independent Hox gene duplications in the hagfish lineage: A PCR-based gene inventory of Eptatretus stoutii
Peter F. Stadler, Claudia Fried, Sonja J. Prohaska, Wendy J. Bailey, Bernhard Y. Misof, Frank H. Ruddle, Günter P. Wagner
Mol.Phylog.Evol. 32: 686-694 (2004)
[Publisher's Page]

The Footprint Sorting Problem
Claudia Fried, Wim Hordijk, Sonja J. Prohaska, Claus R. Stadler, Peter F. Stadler
J.Chem.Inf.Comput.Sci 44: 332-338 (2004).
The Shark HoxN cluster is homologous to the Human HoxD cluster
Sonja J. Prohaska, Claudia Fried, Chris T. Amemiya, Frank H. Ruddle, Günter P. Wagner, Peter F. Stadler
J.Mol.Evol. 58 (2): 212-217 (2004)
Bichir HoxA cluster sequence reveals surprising trends in ray-finned fish genomic evolution
Chi-Hua Chiu, Ken Dewar, Günter P. Wagner, Kazuhiko Takahashi, Frank Ruddle, Christina Ledje, Peter Bartsch, Jean-Luc Scemama, Edmund Stellwag, Claudia Fried, Sonja J. Prohaska, Peter F. Stadler, Chris T. Amemiya
Genome Res. 14: 11-17 (2004).
[Publisher's Page]

Independent Hox-Cluster Duplications in Lampreys
Claudia Fried, Sonja J. Prohaska, Peter F. Stadler
J.Exp.Zool., Mol. Dev. Evol 299B: 18-25 (2003).
[Publisher's Page]

Surveying Phylogenetic Footprints in Large Gene Clusters:
Applications to Hox Cluster Duplications

Sonja Prohaska, Claudia Fried, Christoph Flamm, Günter P. Wagner, Peter F. Stadler
Mol.Evol.Phylog., 31(2): 581-604 (2004).
[Supplement]


Last modified: 2004-04-05 13:58:35 claudia