Publications - Published papers

Please find below publications of our group. Currently, we list 454 papers. Some of the publications are in collaboration with the group of Sonja Prohaska and are also listed in the publication list for her individual group. Access to published papers (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

©NOTICE: All papers are copyrighted by the authors; If you would like to use all or a portion of any paper, please contact the author.

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Publications of the bioinformatics group 2008

Process Flow for Classification and Clustering of Fruit Fly Gene Expression Patterns

Andreas Heffel, Peter F. Stadler, Sonja J. Prohaska, Gerhard Kauer, Jens-Peer Kuska
Proceedings of the 15'th IEEE International Conference on Image Processing, ICIP 2008. IEEE CD Proceedings ICIP'08, pp.721-724 (2008).
PREPRINT 08-027: [ Abstract ]
[ Publishers's page ]  paperID

Structural profiles of human miRNA families from pairwise clustering

Bogumil Kaczkowski, Elfar Torarinsson, Kristin Reiche, Jakob Hull Havgaard, Peter F. Stadler, Jan Gorodkin
Bioinformatics doi: 10.1093/bioinformatics/btn628
PREPRINT 08-026: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Early Replicons: Origin and Evolution

Peter Schuster and Peter F Stadler
Origin and Evolution of Viruses (Second Edition), Esteban Domingo, Colin R. Parrish, John J. Holland (eds); Academic press 2008, pp 1-41
PREPRINT 08-019: [ Abstract ]  [ PDF ]
[ Publishers's page ]

HLA-DRB1*0401 and HLA-DRB1*0408 are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis

Steve Hoffmann, Sabine Cepok, Verena Grummel, Klaus Lehmann-Horn, Jörg Hackermüller, Peter F. Stadler, Hans-Peter Hartung, Achim Berthele, Florian Deisenhammer, Ralf Wasmuth, Bernhard Hemmer
Am J Hum Genet. 83:219-227 (2008)
PREPRINT 08-016: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Universal Scaling in the Branching of the Tree of Life

E. Alejandro Herrada, Claudio J. Tessone, Konstantin Klemm, Victor M. Eguiluz, Emilio Hernandez-Garcia, Carlos M. Duarte
PLoS ONE 3(7):757. doi:10.1371/journal.pone.0002757
PREPRINT 08-015: [ Abstract ]
[ Publishers's page ]  paperID

Rate variations, phylogenetics, and partial orders.

Prohaska S J, Fritzsch G, Stadler P F
In Proceedings of the Fifth International Workshop on Computational Systems Biology, WCSB 2008. 375-391.
PREPRINT 08-013: [ Abstract ]  [ PDF ]   paperID

Noisy: identification of problematic columns in multiple sequence alignments

Dress A W M, Flamm Ch, Fritzsch G, Gruenewald St, Kruspe, M, Prohaska S J, Stadler P F
Alg. Mol. Biol. 3:7
PREPRINT 08-012: [ Abstract ]  [ PDF ]  [ Software ]
[ Publishers's page ]  paperID

Arthropod 7SK RNA

Andreas R. Gruber, Carsten Kilgus, Axel Mosig, Ivo L. Hofacker, Wolfgang Hennig, Peter F. Stadler
Mol.Biol.Evol. 25: 1923-1930 (2008)
PREPRINT 08-008: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Transcriptional regulation of the human CD97 promoter by Sp1/Sp3 in smooth muscle cells.

Wobus M, Wandel E, Prohaska S, Findeiß S, Tschöp K, Aust G.
Gene. 2008; 413(1-2):67-75
PREPRINT 08-007: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Translational Control by RNA-RNA Interaction: Improved Computation of RNA-RNA Binding Thermodynamics

Ulrike Mückstein, Hakim Tafer, Stephan H. Bernhart, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler, Ivo L. Hofacker
Bioinformatics Research and Development Second International Conference, BIRD 2008 Vienna, Austria, July 7-9, 2008 Proceedings;M. Elloumi, J. Küng, M. Linial, R.F. Murphy, K. Schneider, C. Toma (eds), CICS Vol 13, Springer, pp.114-127 (2008)
PREPRINT 08-005: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Genes

Sonja J. Prohaska, Peter F. Stadler
Theory Biosci . 127: 215-221 (2008)
PREPRINT 08-004: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Small ncRNA transcriptome analysis from <i>Aspergillus fumigatus</i> suggests a novel mechanism for regulation of protein-synthesis

Christoph Jöchl, Mathieu Rederstorff, Jana Hertel, Peter F. Stadler, Ivo L. Hofacker, Markus Schrettl, Hubertus Haas, Alexander Hüttenhofer
Nucleic Acids Res. 36: 2677-2689 (2008)
PREPRINT 08-003: [ Abstract ]
[ Publishers's page ]  paperID

SynBlast: Assisting the analysis of conserved synteny information

Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska
BMC Bioinformatics 9: 351 (2008)
PREPRINT 08-002: [ Abstract ]  [ PDF ]  [ Software ]
[ Publishers's page ]  paperID

Evolution of Spliceosomal snRNA Genes in Metazoan Animals

Manuela Marz, Toralf Kirsten, Peter F. Stadler
J.Mol.Evol.
PREPRINT 08-001: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

A Story of Growing Confusion: Genes and Their Regulation

Sonja J. Prohaska, Peter F. Stadler
In: Rubem P. Mondaini, Rui Dil„o Biomat 2007 - International Symposium on Mathematical and Computational Biology, World Scientific, Singapore 2008, pp.325-345
PREPRINT 07-030: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

The Amphioxus Hox Cluster: Characterization, Comparative Genomics, and Evolution

Chris T. Amemiya, Sonja J. Prohaska, Alicia Hill-Force, April Cooke, Jessica Wasserscheid, David E. K. Ferrier, Juan Pacual Anaya, Jordi Garcia-Fernàndez, Ken Dewar, Peter F. Stadler
J.Exp.Zool.MDE 310B: 465-477 (2008)
PREPRINT 07-029: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Folding Kinetics of Large RNAs

Michael Geis, Christoph Flamm, Michael T. Wolfinger, Ivo L. Hofacker, Martin Middendorf, Christian Mandl, Peter F. Stadler, Caroline Thurner
J.Mol.Biol. 379: 160-173 (2008)
PREPRINT 07-028: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Size Variation and Structural Conservation of Vertebrate Telomerase RNA

Mingyi Xie, Axel Mosig, Xiaodong Qi, Yang Li, Peter F. Stadler, Julian J.-L. Chen
J. Chem. Biol. 283: 2049-2059 (2008)
PREPRINT 07-025: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Duplicated RNA Genes in Teleost Fish Genomes

Dominic Rose, Julian Jöris, Jörg Hackermüller, Kristin Reiche, Qiang LI, Peter F. Stadler
J Bioinform Comput Biol. 2008 Dec;6(6):1157-75.
PREPRINT 07-024: [ Abstract ]  [ PDF ]  [ PS ]  [ Supplement ]
[ Publishers's page ]  paperID

Near Intron Positions Are Reliable Phylogenetic Markers: An Application to Holometabolous Insects

Veiko Krauss, Christian Thümmler, Franziska Georgi, Jörg Lehmann, Peter F. Stadler, Carina Eisenhardt
Mol Biol Evol 25 (5): 821-830
PREPRINT 07-022: [ Abstract ]
[ Publishers's page ]  paperID

Invertebrate 7SK snRNAs

Andreas R. Gruber, Dorota Koper-Emde, Manja Marz, Hakim Tafer, Stephan Bernhart, Gregor Obernosterer, Axel Mosig, Ivo L.Hofacker, Peter F. Stadler, Bernd-Joachim Benecke
J.Mol.Evol. 66:107-115 (2008)
PREPRINT 07-021: [ Abstract ]  [ PDF ]  [ PS ]  [ Supplement ]
[ Publishers's page ]  paperID

Evolution of Mitochondrial Gene Orders in Echinoderms

Marleen Perseke, Guido Fritzsch, Kai Ramsch, Matthias Bernt, Daniel Merkle, Martin Middendorf, Detlef Bernhard, Peter Stadler, Martin Schlegel
Mol.Phylog.Evol. 47: 855-864 (2008)
PREPRINT 07-017: [ Abstract ]  [ PDF ]  [ PS ]  [ Supplement ]
[ Publishers's page ]  paperID

<tt>SnoReport</tt>: Computational identification of snoRNAs with unknown targets

Jana Hertel, Ivo L. Hofacker, Peter F. Stadler
Bioinformatics 24: 158-164 (2008)
PREPRINT 07-015: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Funnels in Energy Landscapes

Konstantin Klemm, Christoph Flamm, Peter F. Stadler
Eur.J.Phys.B 63: 387-391
PREPRINT 07-013: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

PCR Survey of <i>Xenoturbella bocki</i> Hox Genes

Guido Fritzsch, Manja U. Böhme, Mike Thorndyke, Hiroaki Nakano, Olle Israelsson, Thomas Stach, Martin Schlegel, Thomas Hankeln, Thomas Stach, Peter F. Stadler
JEZ B: Mol. Dev. Evol. 310B: 278-284 (2008)
PREPRINT 07-012: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

<tt>NcDNAlign</tt>: Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences

Dominic Rose, Jana Hertel, Kristin Reiche, Jörg Hackermüller, Peter F. Stadler
Genomics 92: 65-74 (2008)
PREPRINT 07-007: [ Abstract ]  [ PDF ]  [ PS ]  [ Supplement ]
[ Publishers's page ]  paperID

Variations on RNA Folding and Alignment: Lessons from Benasque

Athanasius F. Bompfünewerer, Rolf Backofen, Stephan H. Berhart, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler, Sebastian Will
J Math Biol. 56: 129-144 (2008).
PREPRINT 06-014: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID