Inst. f. Informatik



Uni Leipzig


Supplemental Material

[BIOINF 07-016 Supplemental Material]
Evolution of Mitochondrial Gene Orders in Echinoderms
Marleen Perseke, Guido Fritzsch, Kai Ramsch, Matthias Bernt, Daniel Merkle, Martin Middendorf, Detlef Bernhard, Peter F. Stadler, Martin Schlegel

[BIOINF 07-015 Supplemental Material]
snoReport: Computational identification of snoRNAs with unknown targets
Jana Hertel, Ivo L. Hofacker, Peter F. Stadler

[BIOINF 07-012 Supplemental Material]
PCR Survey of Xenoturbella bocki:
Evolution of Deuterostome Hox Genes
Guido Fritzsch, Manja U. Böhme, Olle Israelsson, Thomas Hankeln, Peter F. Stadler

[BIOINF 07-011 Supplemental Material]
Homology Search with Fragmented Nucleic Acid Sequence Patterns
Axel Mosig, Julian L. Chen, Peter F. Stadler

[BIOINF 07-010 Supplemental Material]
U7 snRNAs: A Computational Survey
Manja Lindemeyer, Axel Mosig, Bärbel M. R. Stadler, Peter F. Stadler

[BIOINF 07-009 Supplemental Material]
The Mitochondrial DNA of Xenoturbella bocki: Genomic Architecture and Phylogenetic Analysis
Marleen Perseke, Thomas Hankeln, Bettina Weich, Guido Fritzsch, Peter F. Stadler, Olle Israelson, Detlef Bernhard, Martin Schlegel

[BIOINF 07-008 Supplemental Material]
The complete mitochondrial genome of the Green Lizard Lacerta viridis viridis (Lacertidae) phylogenetic
implications and intraspecific variability
M. U. Böhme, G. Fritzsch, A. Tippmann, M. Schlegel, T.U. Berendonk

[BIOINF 07-007 Supplemental Material]
NcDNAlign: Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences
Dominic Rose, Jana Hertel, Kristin Reiche, Jörg Hackermüller, Peter F. Stadler

[BIOINF 07-004 Supplemental Material]
Evolution of the Vertebrate Y RNA Cluster
Axel Mosig, Meng Guofeng, Bärbel M. R. Stadler Peter F. Stadler

[BIOINF 07-001 Supplemental Material]
Computational RNomics of Drosophilids
Dominic Rose, Jörg Hackermüller, Stefan Washietl, Sven Findeiß, Kristin Reiche, Jana Hertel, Peter F. Stadler, Sonja J. Prohaska

[BIOINF 06-013 Supplemental Material]
Identification of Homoplastic Characters in Multiple Sequence Alignments: Supplemental Material
Andreas W. M. Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J. Prohaska and Peter F. Stadler

[BIOINF 06-012 Supplemental Material]
Inferring Non-Coding RNA Families and Classes by Means of Structure-Based Clustering: Supplemental Material
Sebastian Will, Kristin Missal, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen

[BIOINF 06-001 Supplemental Material]
Genome-Wide Analysis of Single Nucleotide Polymorphisms in Evolutionary Conserved DNA
Claudia Fried, Peter F. Stadler, Peter Ahnert

[BIOINF 05-023 Supplemental Material]
Prediction of Structured Non-Coding RNAs in the Genomes
of the Nematodes Caenorhabditis elegans and Caenorhabditis briggsae
Kristin Missal, Xiaopeng Zhu, Dominic Rose, Wei Deng, Geir Skogerbø, Runsheng Chen, Peter F. Stadler

[BIOINF 05-021 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,
ulian 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).

[BIOINF 05-008 Supplemental Material]
Noncoding RNA in Ciona Intestinalis
Kristin Missal, Dominic Rose, Peter F. Stadler

[BIOINF 05-007 Supplemental Material]
Evolution of the Vertebrate Parahox Clusters
Sonja J. Prohaska, Peter F. Stadler

[BIOINF 05-005 Supplemental Material]
Genome-wide mapping of conserved RNA Secondary Structures Reveals Evidence for Thousands of functional Non-Coding RNAs in Human
Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler

[BIOINF 05-003 Supplemental Material]
Fast and reliable prediction of noncoding RNAs
Stefan Washietl, Ivo L. Hofacker, Peter F. Stadler

[BIOINF 05-001 Supplemental Material]
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

[BIOINF 04-017 Supplemental Material]
Comparative promoter region analysis powered by CORG
Christoph Dieterich, Steffen Grossmann, Andrea Tanzer, Stefan Ropcke, Peter F Arndt, Peter F Stadler, Martin Vingron

[BIOINF 04-015 Supplemental Material]
Alignments of Mitochondrial Genome Arrangements:
Applications to Metazoan Phylogeny
Guido Fritzsch, Martin Schlegel, Peter F. Stadler

[BIOINF 04-014 Supplemental 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

[BIOINF 04-013 Supplemental Material]
Evolution of MicroRNAs Located Within Hox Gene Clusters
Andrea Tanzer, Chris T. Amemiya, Chang-Bae Kim, Peter F. Stadler

BIOINF 04-007 [Supplemental Material]
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., in press 2004

BIOINF 04-006 [Supplemental Material]
The Duplication of the Hox Gene Clusters in Teleost Fishes
Sonja J. Prohaska, Peter F. Stadler

BIOINF 04-002 [Supplemental Material]
Molecular Evolution of a microRNA Cluster
Andrea Tanzer, Peter F. Stadler

BIOINF 03-024 [Supplemental Material]
Evidence for independent Hox ene 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

BIOINF 03-023 [Supplemental Material]
Structural and evolutionary analysis of the transcribed sequence of Boudicca, a Schistosoma mansoni retrotransposon
Claudia S. Copeland, Oliver Heyers, Bernd H. Kalinna, Andreas Bachmair, Peter F. Stadler, Ivo L. Hofacker, Paul J. Brindley

BIOINF 03-010 [Supplemental Material]
The Shark HoxN cluster is homologous to the Human HoxD cluster
Sonja Prohaska, Claudia Fried, Chris T. Amemiya, Frank H. Ruddle, Günter P. Wagner, Peter F. Stadler

BIOINF 03-007 [Supplemental Material]
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).

BIOINF 03-002 [Supplemental Material]
Surveying Phylogenetic Footprints in Large Gene Clusters: Applications to Hox Cluster Duplications
Sonja Prohaska, Claudia Fried, Christoph Flamm, Günter P. Wagner, Peter F. Stadler

EXTERNAL Supplemental Material

This section contains material that we host for collaborators.

CHIU 2002 [Supplemental Material]
Molecular evolution of the HoxA cluster in the three major gnathostome lineages
Chiu, Chi-hua and Amemiya, Chris and Dewar, Ken and Kim, Chang-Bae and Ruddle, Frank H. and Wagner, Günter P. Proc.Natl.Acad.Sci.USA 99, 5492-5497 (2002).
Correspondence to: Chi-hua Chiu by mail

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