Publications - Published papers
Please find below publications of our group. Currently, we list 565 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 (
) is restricted to our local network and chosen collaborators.
If you have problems accessing electronic information, please let us know:
) 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 2007
Information Feedback and Mass Media Effects in Cultural Dynamics
Juan Carlos Gonzalez-Avella, Mario G. Cosenza, Konstantin Klemm, Víctor M. Eguiluz and Maxi San Miguel
Journal of Artificial Societies and Social Simulation 10(3)9
PREPRINT 07-032: [ Abstract ]
[ Publishers's page ]
Journal of Artificial Societies and Social Simulation 10(3)9
PREPRINT 07-032: [ Abstract ]
[ Publishers's page ]
Synchroma grande spec. nov. (Synchromophyceae class. nov., Heterokontophyta): An Amoeboid Marine Alga with Unique Plastid Complexes
Horn S, Ehlers K, Fritzsch G, Candelaria Gil-Rodríguez M, Wilhelm Ch and Schnetter R.
Protist. 158: 277-293.
PREPRINT 07-031: [ Abstract ]
[ Publishers's page ]
Protist. 158: 277-293.
PREPRINT 07-031: [ Abstract ]
[ Publishers's page ]
Evolution of genes and genomes on the Drosophila phylogeny
Drosophila 12 Genomes Consortium (featuring Sven Findeiß)
Nature 450, 203-218
PREPRINT 07-027: [ Abstract ]
[ Publishers's page ]
Nature 450, 203-218
PREPRINT 07-027: [ Abstract ]
[ Publishers's page ]
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, <b>Andrea Tanzer</b>, 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 318:420-426 (2007)
PREPRINT 07-026: [ Abstract ]
[ Publishers's page ]
Science 318:420-426 (2007)
PREPRINT 07-026: [ Abstract ]
[ Publishers's page ]
Interleukin-6–dependent survival of multiple myeloma cells involves the Stat3-mediated induction of microRNA-21 through a highly conserved enhancer
D. Löffler, K. Brocke-Heidrich, G. Pfeifer, C. Stocsits, J. Hackermüller, A. Kretzschmar, R. Burger, M. Gramatzki, C. Blumert, K. Bauer, H. Cvijic, P. F. Stadler, and F. Horn
Blood
PREPRINT 07-020: [ Abstract ] [ PDF ]
[ Publishers's page ]
Blood
PREPRINT 07-020: [ Abstract ] [ PDF ]
[ Publishers's page ]
RNA maps reveal new RNA classes and a possible function for pervasive transcription
Kapranov P, Cheng J, Dike S, Nix DA, Duttagupta R, Willingham AT, Stadler PF, Hertel J, Hackermüller J, Hofacker IL, Bell I, Cheung E, Drenkow J, Dumais E, Patel S, Helt G, Ganesh M, Ghosh S, Piccolboni A, Sementchenko V, Tammana H, Gingeras TR.
Science 316: 1484-1488 (2007)
PREPRINT 07-019: [ Abstract ] [ Supplement ]
[ Publishers's page ]
Science 316: 1484-1488 (2007)
PREPRINT 07-019: [ Abstract ] [ Supplement ]
[ Publishers's page ]
<tt>CREx</tt>: Inferring Genomic Rearrangements Based on Common Intervals
Matthias Bernt, Daniel Merkle, Kai Ramsch, Guido Fritzsch, Marleen Perseke, Detlef Bernhard, Martin Schlegel, Peter Stadler, Martin Middendorf
Bioinformatics. 2007 Nov 1;23(21):2957-2958. Epub 2007 Sep 25.
PREPRINT 07-018: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Bioinformatics. 2007 Nov 1;23(21):2957-2958. Epub 2007 Sep 25.
PREPRINT 07-018: [ Abstract ] [ PDF ] [ PS ]
[ Publishers's page ]
Tanimoto's Best Barbecue: Discovering Regulatory Modules using Tanimoto Scores
Peter Menzel, Peter F. Stadler, Axel Mosig
In "German Confernce on Biocomputing (GCB 2007)", C.Falter, A.Schliep, J.Selbig, M.Vingron, D.Walther (eds), Lect.Notes Informatik 115: 68-77 (2007)
PREPRINT 07-016: [ Abstract ] [ PDF ]
In "German Confernce on Biocomputing (GCB 2007)", C.Falter, A.Schliep, J.Selbig, M.Vingron, D.Walther (eds), Lect.Notes Informatik 115: 68-77 (2007)
PREPRINT 07-016: [ Abstract ] [ PDF ]
Detection of RNA structures in porcine EST data and related mammals
Stefan E. Seemann, Michael J. Gilchrist, Ivo L. Hofacker, Peter F. Stadler, Jan Gorodkin
BMC Genomics 8: 316 (2007)
PREPRINT 07-014: [ Abstract ]
[ Publishers's page ]
BMC Genomics 8: 316 (2007)
PREPRINT 07-014: [ Abstract ]
[ Publishers's page ]
Homology Search with Fragmented Nucleic Acid Sequence Patterns
Axel Mosig, Julian L. Chen, Peter F. Stadler
WABI 2007 (R. Giancarlo & S. Hannehalli, eds.), Springer Verlag, Berlin, LNBI 4645, pp. 335-345 (2007).
PREPRINT 07-011: [ Abstract ] [ Supplement ]
WABI 2007 (R. Giancarlo & S. Hannehalli, eds.), Springer Verlag, Berlin, LNBI 4645, pp. 335-345 (2007).
PREPRINT 07-011: [ Abstract ] [ Supplement ]
U7 snRNAs: A Computational Survey
Manja Marz, Axel Mosig, Bärbel M. R. Stadler, Peter F. Stadler
Geno.Prot.Bioinf. 5: 187-195 (2007)
PREPRINT 07-010: [ Abstract ] [ PDF ] [ Supplement ]
[ Publishers's page ]
Geno.Prot.Bioinf. 5: 187-195 (2007)
PREPRINT 07-010: [ Abstract ] [ PDF ] [ Supplement ]
[ Publishers's page ]
The Mitochondrial DNA of Xenoturbella bocki: Genomic Architecture and Phylogenetic Analysis
Marlen Perseke, Thomas Hankeln, Bettina Weich, Guido Fritzsch, Peter F. Stadler, Olle Israelson, Detlef Bernhard, Martin Schlegel
Th Biosci. 126: 35-42 (2007)
PREPRINT 07-009: [ Abstract ] [ PDF ] [ Supplement ]
[ Publishers's page ]
Th Biosci. 126: 35-42 (2007)
PREPRINT 07-009: [ Abstract ] [ PDF ] [ Supplement ]
[ Publishers's page ]
The complete mitochondrial genome of the Green Lizard Lacerta viridis viridis (Reptilia: Lacertidae) phylogenetic implications and intraspecific variability
M. U. Böhme, G. Fritzsch, A. Tippmann, M Schlegel, T. U. Berendonk
Gene, Volume 394, Issues 1-2, 1 June 2007, Pages 69-77 (2007)
PREPRINT 07-008: [ Supplement ]
[ Publishers's page ]
Gene, Volume 394, Issues 1-2, 1 June 2007, Pages 69-77 (2007)
PREPRINT 07-008: [ Supplement ]
[ Publishers's page ]
A stochastic model for the evolution of transcription factor binding site abundance
Günter P. Wagner, Wolfgang Otto, Vincent Lynch, Peter F. Stadler
J.Theor.Biol. 247:544-553 (2007)
PREPRINT 07-006: [ Abstract ]
[ Publishers's page ]
J.Theor.Biol. 247:544-553 (2007)
PREPRINT 07-006: [ Abstract ]
[ Publishers's page ]
Evolution of the Vertebrate Y RNA Cluster
Axel Mosig, Meng Guofeng, Bärbel M. R. Stadler, Peter F. Stadler
Th Biosci. 126: 9-14 (2007)
PREPRINT 07-004: [ Abstract ] [ PDF ] [ Supplement ]
[ Publishers's page ]
Th Biosci. 126: 9-14 (2007)
PREPRINT 07-004: [ Abstract ] [ PDF ] [ Supplement ]
[ Publishers's page ]
A Particle Swarm Optimizer for Finding Minimum Free Energy RNA Secondary Structures
Michael Geis and Martin Middendorf
Proceedings of the IEEE Swarm Intelligence Symposium 2007, pp 1-8 (2007)
PREPRINT 07-002:
[ Publishers's page ]
Proceedings of the IEEE Swarm Intelligence Symposium 2007, pp 1-8 (2007)
PREPRINT 07-002:
[ Publishers's page ]
Computational RNomics of Drosophilids
Dominic Rose, Jörg Hackermüller, Stefan Washietl, Sven Findeiß, Kristin Reiche, Jana Hertel, Peter F. Stadler, Sonja J. Prohaska
BMC Genomics 2007, 8:406.
PREPRINT 07-001: [ Abstract ] [ PDF ] [ Supplement ]
[ Publishers's page ]
BMC Genomics 2007, 8:406.
PREPRINT 07-001: [ Abstract ] [ PDF ] [ Supplement ]
[ Publishers's page ]
Regulatory Signals in Genomic Sequences
Sonja J. Prohaska, Axel Mosig, Peter F. Stadler
In "Networks: From Biology to Theory", J.Feng, J.Jost, M.Qian (eds), Springer, New York, 2007, pp. 191-220
PREPRINT 06-030: [ PDF ]
In "Networks: From Biology to Theory", J.Feng, J.Jost, M.Qian (eds), Springer, New York, 2007, pp. 191-220
PREPRINT 06-030: [ PDF ]
Modeling Conformational Flexibility and Evolution of Structure: RNA as an Example
Peter Schuster and Peter F. Stadler
In "Structural Approaches to Sequence Evolution: Molecules, Networks, Populations", U.Bastolla, M.Porto, H.E.Roman, M.Vendruscolo (eds), Springer Verlag, Berlin, 2007, pp. 3-26
PREPRINT 06-029:
In "Structural Approaches to Sequence Evolution: Molecules, Networks, Populations", U.Bastolla, M.Porto, H.E.Roman, M.Vendruscolo (eds), Springer Verlag, Berlin, 2007, pp. 3-26
PREPRINT 06-029:
Analysis of attachment models for directory and file trees
K. Klemm, V. M. Eguiluz, M. San Miguel
Physica D 224, 149 (2006)
PREPRINT 06-020: [ Abstract ]
[ Publishers's page ]
Physica D 224, 149 (2006)
PREPRINT 06-020: [ Abstract ]
[ Publishers's page ]
RNA Secondary Structures
Ivo L. Hofacker, Peter F. Stadler
In: Bioinformatics: From Genomes to Therapies, T. Lengauer (ed), Wiley-VCH, Weinheim, Germany, 2007, pp.439-489.
PREPRINT 06-018:
[ Publishers's page ]
In: Bioinformatics: From Genomes to Therapies, T. Lengauer (ed), Wiley-VCH, Weinheim, Germany, 2007, pp.439-489.
PREPRINT 06-018:
[ Publishers's page ]
Comparative Analysis of Structured RNAs in S. cerevisiae Indicates a Multitude of Different Functions
Stephan Steigele, Wolfgang Huber, Claudia Stocsits, Peter F. Stadler, Kay Nieselt
BMC Biol. 5:25 (2007)
PREPRINT 06-017: [ Abstract ]
[ Publishers's page ]
BMC Biol. 5:25 (2007)
PREPRINT 06-017: [ Abstract ]
[ Publishers's page ]
Progressive sequence alignments from Triplets
Matthias Kruspe, Peter F. Stadler
BMC Bioinformatics 8: 254 (2007)
PREPRINT 06-016: [ Abstract ] [ PDF ] [ Software ]
[ Publishers's page ]
BMC Bioinformatics 8: 254 (2007)
PREPRINT 06-016: [ Abstract ] [ PDF ] [ Software ]
[ Publishers's page ]
Saddles and Barrier in Landscapes of Generalized Search Operators
Christoph Flamm, Bärbel M. R. Stadler, Peter F. Stadler
In: "Foundations of Genetic Algorithms IX", C. Stephens, M.Toussaint, D.Whitely, PF Stadler (eds). Springer, Berlin. Lect.Notes Comp.Sci. 4436: 194-212 (2007)
PREPRINT 06-015: [ Abstract ] [ PDF ]
In: "Foundations of Genetic Algorithms IX", C. Stephens, M.Toussaint, D.Whitely, PF Stadler (eds). Springer, Berlin. Lect.Notes Comp.Sci. 4436: 194-212 (2007)
PREPRINT 06-015: [ Abstract ] [ PDF ]
Inferring Non-Coding RNA Families and Classes by Means of Structure-Based Clustering
Sebastian Will, Kristin Missal, Ivo L. Hofacker, Peter F. Stadler, Rolf Backofen
PLoS Comp. Biol., 3: e65 (2007)
PREPRINT 06-012: [ Abstract ] [ PDF ] [ Supplement ]
[ Publishers's page ]
PLoS Comp. Biol., 3: e65 (2007)
PREPRINT 06-012: [ Abstract ] [ PDF ] [ Supplement ]
[ Publishers's page ]
Structured RNAs in the ENCODE Selected Regions of the Human Genome
Stefan Washietl, Jakob S. Pedersen, Jan O. Korbel, Claudia Fried, Andreas R. Gruber, Jöorg 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
Genome Res., 17:852-864 (2007)
PREPRINT 06-010: [ Abstract ]
[ Publishers's page ]
Genome Res., 17:852-864 (2007)
PREPRINT 06-010: [ Abstract ]
[ Publishers's page ]
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)
PREPRINT 06-009: [ Abstract ]
[ Publishers's page ]
Nature 447: 799-816 (2007)
PREPRINT 06-009: [ Abstract ]
[ Publishers's page ]
PCR Survey of Hox Genes in the Goldfish <i>Carassius auratus auratus</i>
Jing Luo, Peter F. Stadler, Shunping He, Axel Meyer
J.Exp.Zool.B: Mol.Dev.Evol. 308B: 250-258 (2007)
PREPRINT 06-007: [ Abstract ] [ Supplement ]
[ Publishers's page ]
J.Exp.Zool.B: Mol.Dev.Evol. 308B: 250-258 (2007)
PREPRINT 06-007: [ Abstract ] [ Supplement ]
[ Publishers's page ]
RNAstrand: Reading Direction of Structured RNAs in Multiple Sequence Alignments
Kristin Missal, Peter F. Stadler
Alg.Mol.Biol. 2:6 (2007)
PREPRINT 06-006: [ Abstract ] [ PDF ]
[ Publishers's page ]
Alg.Mol.Biol. 2:6 (2007)
PREPRINT 06-006: [ Abstract ] [ PDF ]
[ Publishers's page ]
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
J.Exp.Zool.B: Mol.Dev.Evol, 308B: 1-25 (2007).
PREPRINT 06-005: [ Abstract ] [ PDF ]
[ Publishers's page ]
J.Exp.Zool.B: Mol.Dev.Evol, 308B: 1-25 (2007).
PREPRINT 06-005: [ Abstract ] [ PDF ]
[ Publishers's page ]
RNase MRP and the RNA Processing Cascade in the Eukaryotic Ancestor
Michael D. Woodhams, Peter F. Stadler, David Penny, Lesley J. Collins
BMC Evol. Biol. 7(Suppl 1): S13 (2007)
PREPRINT 06-003: [ Abstract ] [ PDF ]
[ Publishers's page ]
BMC Evol. Biol. 7(Suppl 1): S13 (2007)
PREPRINT 06-003: [ Abstract ] [ PDF ]
[ Publishers's page ]
Modeling amino acid substitution patterns in orthologous and paralogous genes
Gavin C. Conant, Günter P. Wagner, Peter F. Stadler
Mol. Phylog. Evol. 42: 298-307 (2007)
PREPRINT 05-011: [ Abstract ]
[ Publishers's page ]
Mol. Phylog. Evol. 42: 298-307 (2007)
PREPRINT 05-011: [ Abstract ]
[ Publishers's page ]