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 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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

<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 ]  paperID

Tanimoto&#039;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 ]

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 ]  paperID

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 ]   paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]

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:   paperID

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 ]  paperID

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 ]

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 ]  paperID

Progressive sequence alignments from Triplets

Matthias Kruspe, Peter F. Stadler
BMC Bioinformatics 8: 254 (2007)
PREPRINT 06-016: [ Abstract ]  [ PDF ]  [ Software ]
[ Publishers's page ]  paperID

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 ]   paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID

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 ]  paperID