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 (access) is restricted to our local network and chosen collaborators. If you have problems accessing electronic information, please let us know:

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Publications of the bioinformatics group 2014

Energy-based RNA consensus secondary structure prediction in multiple sequence alignments.

Washietl, Stefan and Bernhart, Stephan H. and Kellis, Manolis
Methods in molecular biology (Clifton, N.J.) 1097: 125--141
PREPRINT 18-035: [ Abstract ]
[ Publishers's page ]

Design of Transcription Regulating Riboswitches

Findeiß, Sven and Wachsmuth, Manja and Mörl, Mario and Stadler, Peter F.
Methods Enzymol. 550: 1-22
PREPRINT 16-009:
[ Publishers's page ]

Comparative genomics reveals insights into avian genome evolution and adaptation

Zhang, Guojie and Li, Cai and Li, Qiye and Li, Bo and Larkin, Denis M. and Lee, Chu and Storz, Jay F. and Antunes, Agostinho and Greenwold, Matthew J. and Meredith, Robert W. and Ödeen, Anders and Cui, Jieand Zhou, Qi and Xu, Luohai and Pan, Hailin and Wang, Zongjiand Jin, Lijun and Zhang, Pei and Hu, Haofu and Yang, Weiand Hu, Jiang and Xiao, Jin and Yang, Zhikai and Liu, Yangand Xie, Qiaolin and Yu, Hao and Lian, Jinmin and Wen, Pingand Zhang, Fang and Li, Hui and Zeng, Yongli and Liu, Shipingand Zhou, Long and Huang, Zhiyong and An, Na and Wang, Jieand Zheng, Qiumei and Xiong, Yingqi and Wang, Guangbiao andWang, Bo and Wang, Jingjing and Fu, Yu and da Fonseca,Rute R. and Alfaro-Núñez, Alonzo and Schubert,Mikkel and Orlando, Ludovic and Mourier, Tobias and Howard, Jason T. and Ganapathy, Ganeshkumar and Pfenning,Andreas and Whitney, Osceola and Rivas, Miriam V. and Hara,Erina and Smith, Julia
Science. 2014 Dec 12;346(6215):1311-20
PREPRINT 15-035: [ Abstract ]
[ Publishers's page ]

plantDARIO: web based quantitative and qualitative analysis of small RNA-seq data in plants

Patra D, Fasold M, Langenberger D, Steger G, Grosse I, Stadler PF
Front Plant Sci. 2014 Dec 23;5:708
PREPRINT 15-034: [ Abstract ]
[ Publishers's page ]

Atom mapping with constraint programming

Mann M, Nahar F, Schnorr N, Backofen R, Stadler PF, Flamm C.
Algorithms Mol Biol. 2014 Nov 29;9(1):23
PREPRINT 15-033: [ Abstract ]
[ Publishers's page ]

Draft Genome Sequence of FT9, a Novel Bacillus cereus Strain Isolated from a Brazilian Thermal Spring.

Raiol T, De-Souza MT, Oliveira JV, Silva HS, Orem JC, Cavalcante DA, Almeida NF, Telles GP, Setubal JC, Brigido MM, Torres FA, Stadler PS, Walter ME, Moraes LM.
Genome Announc. 2014 Oct 9;2(5). pii: e01027-14
PREPRINT 15-032: [ Abstract ]
[ Publishers's page ]

Generic strategies for chemical space exploration.

Andersen JL, Flamm C, Merkle D, Stadler PF
Int J Comput Biol Drug Des. 2014;7(2-3):225-58
PREPRINT 15-031: [ Abstract ]
[ Publishers's page ]

Genome-Wide Identification of Non-coding RNAs in Komagatella pastoris str. GS115

Hugo Schneider, Sebastian Bartschat, Gero Doose, Lucas Maciel, Erick Pizani, Marcelo Bassani, Fernando Araripe Torres, Sebastian Will, Tainá Raiol, Marcelo Brígido, Maria Emília Walter, Peter Stadler
Lecture Notes in Computer Science Volume 8826, 2014, pp 115-122
PREPRINT 15-030: [ Abstract ]
[ Publishers's page ]

Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures

Qin J, Fricke M, Marz M, Stadler PF, Backofen R.
Algorithms Mol Biol. 2014 Sep 11;9:19
PREPRINT 15-029: [ Abstract ]
[ Publishers's page ]

A Common Framework for Linear and Cyclic Multiple Sequence Alignment Problems

Will, Sebastian and Stadler, Peter F.
Lecture Notes in Computer Science Volume 8701, 2014, pp 135-147
PREPRINT 15-028: [ Abstract ]
[ Publishers's page ]

Strong products of hypergraphs: Unique prime factorization theorems and algorithms

Hellmuth M, Ostermeier L, Noll M
Discrete Applied Mathematics 171 (2014): 60-71
PREPRINT 15-027: [ Abstract ]
[ Publishers's page ]

ExpaRNA-P: simultaneous exact pattern matching and folding of RNAs

Otto C, Möhl M, Heyne S, Amit M, Landau GM, Backofen R, Will S.
BMC Bioinformatics. 2014 Dec 31;15(1):6602
PREPRINT 15-026: [ Abstract ]
[ Publishers's page ]

Simultaneous alignment and folding of protein sequences

Waldispühl J, O'Donnell CW, Will S, Devadas S, Backofen R, Berger B.
J Comput Biol. 2014 Jul;21(7):477-91
PREPRINT 15-025: [ Abstract ]
[ Publishers's page ]

The role of gene regulatory factors in the evolutionary history of humans

Perdomo-Sabogal A, Kanton S, Walter MB, Nowick K
Curr Opin Genet Dev. 2014 Dec;29C:60-67
PREPRINT 15-023: [ Abstract ]
[ Publishers's page ]

Editorial overview: Genetics of human evolution: The genetics of human origins

Andrés AM, Nowick K
Curr Opin Genet Dev. 2014 Nov 22;29C:v-vii
PREPRINT 15-022:
[ Publishers's page ]

Multiple haplotype-resolved genomes reveal population patterns of gene and protein diplotypes

Hoehe MR, Church GM, Lehrach H, Kroslak T, Palczewski S, Nowick K, Schulz S, Suk EK, Huebsch T
Nat Commun. 2014 Nov 26;5:5569
PREPRINT 15-021: [ Abstract ]
[ Publishers's page ]

50 Shades of Rule Composition

Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Lecture Notes in Computer Science Volume 8738, 2014, pp 117-135
PREPRINT 15-020: [ Abstract ]
[ Publishers's page ]

Bioinformatics of prokaryotic RNAs

Backofen R, Amman F, Costa F, Findeiß S, Richter AS, Stadler PF
RNA Biol. 2014 May;11(5):470-83
PREPRINT 15-019: [ Abstract ]
[ Publishers's page ]

Structured RNAs and synteny regions in the pig genome

Anthon C, Tafer H, Havgaard JH, Thomsen B, Hedegaard J, Seemann SE, Pundhir S, Kehr S, Bartschat S, Nielsen M, Nielsen RO, Fredholm M, Stadler PF, Gorodkin J
BMC Genomics. 2014 Jun 10;15:459
PREPRINT 15-018: [ Abstract ]
[ Publishers's page ]

Challenges in RNA virus bioinformatics

Marz M, Beerenwinkel N, Drosten C, Fricke M, Frishman D, Hofacker IL, Hoffmann D, Middendorf M, Rattei T, Stadler PF, Töpfer A
Bioinformatics. 2014 Jul 1;30(13):1793-9
PREPRINT 15-016:
[ Publishers's page ]

GC Skew and Mitochondrial Origins of Replication

Sahyoun, Abdullah H. and Bernt, Matthias and Stadler, Peter F. and Tout, Kifah
Mitochondrion vol 17, pages 56-66
PREPRINT 15-014: [ Abstract ]
[ Publishers's page ]  paperID

Basin Hopping Graph: A computational framework

Kucharík, Marcel and Hofacker, Ivo and Stadler, Peter F. and Qin, Jing
Bioinformatics vol 30, pages 2009-2017
PREPRINT 15-013: [ Abstract ]
[ Publishers's page ]  paperID

Molecular morphology: Higher order characters derivable from sequence information

Donath, Alexander and Stadler, Peter F.
Deep Metazoan Phylogeny: The Backbone of the Tree of Life. New insights from analyses of molecules, morphology, and theory of data analysis, chapter 25, pages: 549-562
PREPRINT 15-012:
[ Publishers's page ]

Intron positions and near intron pairs

Lehmann, Jörg and Eisenhardt, Carina and Krauss, Veiko and Stadler, Peter F.
Deep Metazoan Phylogeny: The Backbone of the Tree of Life. New insights from analyses of molecules, morphology, and theory of data analysis, chapter 24, pages: 539–548
PREPRINT 15-011:
[ Publishers's page ]

RNA in phylogenetic reconstruction

Stocsits, Roman R. and Letsch, Harald and Meusemann, Karen and von Reumont, Böjrn M. and Misof, Bernhard and Hertel, Jana and Tafer, Hakim and Stadler, Peter F.
Deep Metazoan Phylogeny: The Backbone of the Tree of Life. New insights from analyses of molecules, morphology, and theory of data analysis, chapter 23, pages 531–538
PREPRINT 15-010:
[ Publishers's page ]

Computational methods for the analysis of mitochondrial genome rearrangements

Bernt, Matthias and Merkle, Daniel and Middendorf, Martin and Schierwater, Bernd and Schlegel, Martin and Stadler, Peter F
Deep Metazoan Phylogeny: The Backbone of the Tree of Life. New insights from analyses of molecules, morphology, and theory of data analysis, chapter 22, pages 515–530
PREPRINT 15-009:
[ Publishers's page ]

Deuterostome phylogeny: a molecular perspective

Schlegel, Martin and Weidhase, Michael and Stadler, Peter F.
Deep Metazoan Phylogeny: The Backbone of the Tree of Life. New insights from analyses of molecules, morphology, and theory of data analysis, chapter 17, pages: 413-424
PREPRINT 15-008:
[ Publishers's page ]

TSSAR: TSS annotation regime for dRNA-seq data

Amman, Fabian and Wolfinger, Michael T and Lorenz, Ronny and Hofacker, Ivo L and Stadler, Peter F and Findeiß
BMC Bioinformatics 2014, 15 :89
PREPRINT 15-007: [ Abstract ]
[ Publishers's page ]  paperID

Rugged and Elementary Landscapes

Klemm, Konstantin and Stadler, Peter F.
Theory and Principled Methods for the Design of Metaheuristics 978-3-642-33205-0 pages 41 to 61
PREPRINT 15-006: [ Abstract ]
[ Publishers's page ]

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

Steve Hoffmann, Christian Otto, Gero Doose, Andrea Tanzer, David Langenberger, Sabina Christ, Manfred Kunz, Lesca M. Holdt, Daniel Teupser, Jörg Hackermüller, Peter F. Stadler
Genome Biology 2014, 15:R34
PREPRINT 15-005: [ Abstract ]  [ Supplement ]  [ Software ]
[ Publishers's page ]  paperID

Unique square Property, equitable partitions, and product-like Graphs

Hellmuth, Marc and Ostermeier, Lydia and Stadler, Peter F.
Volume 320, 6 April 2014, Pages 92–103
PREPRINT 15-004: [ Abstract ]
[ Publishers's page ]  paperID

Long non-coding RNAs differentially expressed between normal versus primary breast tumor tissues disclose converse changes to breast cancer-related protein-coding genes.

Reiche K, Kasack K, Schreiber S, Lüders T, Due EU, Naume B, Riis M, Kristensen VN, Horn F, Børresen-Dale AL, Hackermüller J, Baumbusch LO
PLoS One. 2014 Sep 29;9(9):e106076
PREPRINT 15-003: [ Abstract ]
[ Publishers's page ]

CEM-Designer: Design of custom expression microarrays in the post-ENCODE Era.

Arnold C, Externbrink F, Hackermüller J, Reiche K
J Biotechnol. 2014 Nov 10;189:154-6
PREPRINT 15-002: [ Abstract ]
[ Publishers's page ]

Fast assembly of the mitochondrial genome of a plant parasitic nematode (Meloidogyne graminicola) using next generation sequencing

Guillaume Besnard, Frank Jühling, Élodie Chapuis, Loubab Zedane, Émeline Lhuillier, Thierry Mateille, Stéphane Bellafiore
Comptes Rendus Biologies Volume 337, Issue 5, May 2014, Pages 295–301
PREPRINT 15-001: [ Abstract ]
[ Publishers's page ]

The Coilin Interactome Identifies Hundreds of Small Noncoding RNAs that Traffic through Cajal Bodies

Martin Machyna, Stephanie Kehr, Korinna Straube, Dennis Kappei, Frank Buchholz, Falk Butter, Jernej Ule, Jana Hertel, Peter F. Stadler, Karla M. Neugebauer
Molecular Cell,Volume 56, Issue 3, 6 November 2014, Pages 389–399
PREPRINT 14-016: [ Abstract ]
[ Publishers's page ]  paperID

Dynamic Programming for Set Data Types

Christian Höner zu Siederdissen, Sonja J. Prohaska, and Peter F. Stadler
In Conference Proceedings of Brasilian Symposium on Bioinformatics BSB ’14, Belo Horizonte, MG, Brazil. Lect. Notes Comp Sci. 2014
PREPRINT 14-015: [ Abstract ]  [ Software ]
[ Publishers's page ]

A priori assessment of data quality in molecular phylogenetics

Bernhard Misof, Karen Meusemann, Björn M von Reumont, Patrick Kück, Sonja J Prohaska and Peter F Stadler
Algorithms for Molecular Biology 9.1 (2014): 22.
PREPRINT 14-014: [ Abstract ]
[ Publishers's page ]  paperID

Orthology detection combining clustering and synteny for very large datasets

Marcus Lechner, Maribel Hernandez-Rosales, Daniel Doerr, Nicolas Wieseke, Annelyse Thévenin, Jens Stoye, Roland K. Hartmann, Sonja J. Prohaska, Peter F. Stadler
PLoS ONE 9(8): e105015
PREPRINT 14-009: [ Abstract ]
[ Publishers's page ]  paperID

The CHR site: definition and genome-wide identification of a cell cycle transcriptional element

Gerd A. Müller, Axel Wintsche, Konstanze Stangner, Sonja J. Prohaska, Peter F. Stadler, and Kurt Engeland
Nucl. Acids Res. (2014)
PREPRINT 14-003: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

The HERMIT in the Stream

Andrew Farmer, Christian Höner zu Siederdissen, and Andy Gill
Proceedings of the ACM SIGPLAN 2014 workshop on Partial evaluation and program manipulation: 97--108
PREPRINT 14-002: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID

Product Grammars for Alignment and Folding

Christian Höner zu Siederdissen, Ivo L. Hofacker, Peter F. Stadler
IEEE/ACM Transactions on Computational Biology and Bioinformatics 99 (2014).
PREPRINT 13-048: [ Abstract ]  [ PDF ]

Convex Cycle Bases

Hellmuth, Marc and Leydold, Josef and Stadler, Peter F
Acta Math. Con- temp. 7:123–140 (2014)
PREPRINT 13-044: [ Abstract ]  [ PDF ]   paperID

Pitfalls of Ascertainment Biases in Genome Annotations —Computing Comparable Protein Domain Distributions in Eukarya

Arli Aditya Parikesit, Lydia Steiner, Peter F Stadler, Sonja J Prohaska
Malaysian Journal of Fundamental and Applied Sciences, Vol 10, No 2 (2014)
PREPRINT 13-033: [ Abstract ]  [ PDF ]   paperID

Computational prediction of microRNA genes

Jana Hertel, David Langenberger, and Peter F. Stadler
In Jan Gorodkin and Larry Ruzzo, editors, An introduction to RNA Bioinformatics , volume 1097 of Meth. Mol. Biol. Humana Press, New York, 2014. in press.
PREPRINT 13-029:
[ Publishers's page ]

Class-specific prediction of ncRNAs

Peter F. Stadler
In Jan Gorodkin and Larry Ruzzo, editors, An introduction to RNA Bioinformatics , volume 1097 of Meth. Mol. Biol. Humana Press, New York, 2014. in press.
PREPRINT 13-028: [ Abstract ]
[ Publishers's page ]

Geometry and Coarse-Grained Representations of Landscapes

Konstantin Klemm, Jing Qin, Peter F. Stadler
Recent Advances in the Theory and Application of Fitness Landscapes Emergence, Complexity and Computation Volume 6: 153-176 (2014)
PREPRINT 13-024: [ Abstract ]
[ Publishers's page ]

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Juliane C. Dohm, Andre E. Minoche, Daniela Holtgrawe, Salvador Capella Gutierrez, Falk Zakrzewski, Hakim Tafer, Oliver Rupp, Thomas Rosleff Sören sen, Ralf Stracke, Richard Reinhardt, Alexander Goesmann, Britta Schulz, Peter F. Stadler, Thomas Schmidt, Toni Gabaldon, Hans Lehrach, Bernd Weisshaar, and Heinz Himmelbauer
Nature 505: 546-549 (2014)
PREPRINT 13-023:
[ Publishers's page ]  paperID

Lacking alignments? The next-generation sequencing mapper segemehl revisited

Christian Otto, Peter F. Stadler, Steve Hoffmann
Bioinformatics. 2014 Jul 1;30(13):1837-43
PREPRINT 13-008: [ Abstract ]  [ PDF ]  [ Supplement ]  [ Software ]
[ Publishers's page ]  paperID

A First Glimpse at the Genome of the Baikalian Amphipod (Eulimnogammarus verrucosus)

Lorena Rivarola-Duarte, Christian Otto, Frank Jühling, Stephan Schreiber, Daria Bedulina, Lena Jakob, Anton Gurkov, Denis Axenov-Gribanov, Abdullah H. Sahyoun, Magnus Lucassen, Jörg Hackermüller, Steve Hoffmann, Franz Sartoris, Hans-Otto Pörtner, Maxim Timofeyev, Till Luckenbach, Peter F. Stadler
Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, Volume 322, Issue 3, pages 177–189, May 2014,DOI: 10.1002/jez.b.22560
PREPRINT 13-003: [ Abstract ]  [ PDF ]  [ Supplement ]
[ Publishers's page ]  paperID

Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro ncRNAs

Jörg Hackermüller, Kristin Reiche, Christian Otto, Nadine Hösler, Katja Brocke-Heidrich, Levin Böhlig, Katharina Kasack, Peter Ahnert, Wolfgang Krupp, Kurt Engeland, Peter F. Stadler, Friedemann Horn
Genome Biol. 2014 Mar 4;15(3):R48
PREPRINT 13-001: [ Abstract ]  [ Supplement ]
[ Publishers's page ]

Simulation of Gene Family Histories

BMC Bioinformatics 15(Suppl 3):A8 (2014)
PREPRINT 12-017: [ Abstract ]  [ PDF ]
[ Publishers's page ]  paperID