Sven Rahmann's Publications

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Journal Publications

[1] Johannes H. Schulte, Tobias Marschall, Marcel Martin, Philipp Rosenstiel, Pieter Mestdagh, Stefanie Schlierf, Theresa Thor, Jo Vandesompele, Angelika Eggert, Stefan Schreiber, Sven Rahmann, and Alexander Schramm.
Deep sequencing reveals differential expression of microRNAs in favorable versus unfavorable neuroblastoma.
Nucleic Acids Res, 2010.
In press; available online at http://nar.oxfordjournals.org/cgi/content/abstract/gkq342. Featured article (top 5% of NAR articles).
[2] Tobias Wittkop, Dorothea Emig, Sita Lange, Sven Rahmann, Mario Albrecht, John H. Morris, Sebastian Böcker, Jens Stoye, and Jan Baumbach.
Partitioning biological data with transitivity clustering.
Nature Methods, 7(6):419-420, Jun 2010.
[3] Tobias Wittkop, Sven Rahmann, and Jan Baumbach.
Efficient online transcription factor binding site adjustment by integrating transitive graph projection with MoRAine 2.0.
Journal of Integrative Bioinformatics, 7(3):Article 117, 2010.
[4] E. Fritzilas, M. Milanic, S. Rahmann, and Y.A. Rios-Solis.
Structural identifiability in low-rank matrix factorization.
Algorithmica, 53(3):313-332, 2010.
[5] Roland Schwarz, Philipp N. Seibel, Sven Rahmann, Christoph Schön, Mirja Hünerberg, Clemens Müller-Reible, Thomas Dandekar, Rachel Karchin, Jörg Schultz, and Tobias Müller.
Detecting species-site dependencies in large multiple sequence alignments.
Nucleic Acids Research, 7(18):5959-5968, 2009.
[6] Tobias Marschall and Sven Rahmann.
Efficient exact motif discovery.
Bioinformatics, 25(12):i356-i364, 2009.
[7] Michael Zeschnigk, Marcel Martin, Gisela Betzl, Andreas Kalbe, Caroline Sirsch, Karin Buiting, Stephanie Gross, Epameinondas Fritzilas, Bruno Frey, Sven Rahmann, and Bernhard Horsthemke.
Massive parallel bisulfite sequencing of CG-rich DNA fragments reveals that methylation of many X-chromosomal CpG islands in female blood DNA is incomplete.
Hum Mol Genet, 18(8):1439-1448, 2009.
[8] Jan Baumbach, Sven Rahmann, and Andreas Tauch.
Reliable transfer of transcriptional gene regulatory networks between taxonomically related organisms.
BMC Syst Biol, 3:8, 2009.
[9] Jan Baumbach, Andreas Tauch, and Sven Rahmann.
Towards the integrated analysis, visualization and reconstruction of microbial gene regulatory networks.
Brief Bioinform, 10(1):75-83, 2009.
[10] Julia C. Engelmann, Sven Rahmann, Matthias Wolf, Jörg Schultz, Epameinondas Fritzilas, Susanne Kneitz, Thomas Dandekar, and Tobias Müller.
Modeling cross-hybridization on phylogenetic rDNA microarrays increases the detection power of closely related species.
Molecular Ecology Resources, 9(1):83-93, 2009.
[11] Cees Elzinga, Sven Rahmann, and Hui Wang.
Algorithms for subsequence combinatorics.
Theoretical Computer Science, 409(3):394-404, 2008.
[12] Utz J. Pape, Sven Rahmann, Fengzhu Sun, and Martin Vingron.
Compound poisson approximation of the number of occurrences of a position frequency matrix (PFM) on both strands.
J Comput Biol, 15(6):547-564, 2008.
[13] Sérgio A. de Carvalho Jr. and Sven Rahmann.
Better GeneChip microarray layouts by combining probe placement and embedding.
J Bioinform Comput Biol, 6(3):623-641, Jun 2008.
[14] Jan Baumbach, Tobias Wittkop, Jochen Weile, Thomas Kohl, and Sven Rahmann.
MoRAine - a web server for fast computational transcription factor binding motif re-annotation.
Journal of Integrative Bioinformatics, 5(2):Article 91, 2008.
[15] Utz J Pape, Sven Rahmann, and Martin Vingron.
Natural similarity measures between position frequency matrices with an application to clustering.
Bioinformatics, 24(3):350-357, Feb 2008.
[16] Heiko Neuweger, Jan Baumbach, Stefan Albaum, Thomas Bekel, Michael Dondrup, Andrea T. Hüser, Jörn Kalinowski, Sebastian Oehm, Alfred Pühler, Sven Rahmann, Jochen Weile, and Alexander Goesmann.
CoryneCenter - an online resource for the integrated analysis of corynebacterial genome and transcriptome data.
BMC Systems Biology, 1:Article 55, 2007.
[17] Tobias Wittkop, Jan Baumbach, Francisco P. Lobo, and Sven Rahmann.
Large scale clustering of protein sequences with FORCE - a layout based heuristic for weighted cluster editing.
BMC Bioinformatics, 8:Article 396, 2007.
[18] Jan Baumbach, Alexander Bunkowski, Sita Lange, Timm Oberwahrenbrock, Nils Kleinbölting, Sven Rahmann, and Jörg Ingo Baumbach.
IMS2 - an integrated medical software system for early lung cancer detection using ion mobility spectrometry data of human breath.
Journal of Integrative Bioinformatics, 4:Article 75, 2007.
[19] Daniel Gerlach, Matthias Wolf, Thomas Dandekar, Tobias Müller, Andreas Pokorny, and Sven Rahmann.
Deep metazoan phylogeny.
In Silico Biology, 7:Article 15, 2007.
[20] Jan Baumbach, Tobias Wittkop, Sven Rahmann, Karina Brinkrolf, and Andreas Tauch.
CoryneRegNet 3.0 - an interactive bioinformatics platform for the analysis of gene regulatory networks in corynebacteria and escherichia coli.
Journal of Biotechnology, 129:279-289, 2007.
[21] Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, and Knut Reinert.
Integer linear programming approaches for non-unique probe selection.
Discrete Applied Mathematics, 155(6-7):840-856, 2007.
[22] Jan Baumbach, Karina Brinkrolf, Tobias Wittkop, Andreas Tauch, and Sven Rahmann.
CoryneRegNet 2: An integrative bioinformatics approach for reconstruction and comparison of transcriptional regulatory networks in prokaryotes.
Journal of Integrative Bioinformatics, 3(2):24, 2006.
[23] Alexander Schliep and Sven Rahmann.
Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree.
Bioinformatics, 22(14):e424-e430, 2006.
[24] Jan Baumbach, Karina Brinkrolf, Lisa Czaja, Sven Rahmann, and Andreas Tauch.
CoryneRegNet: An ontology-based data warehouse of corynebacterial transcription factors and regulatory networks.
BMC Genomics, 7:Article 24, 2006.
[25] Stefan Röpcke, Steffen Grossmann, Sven Rahmann, and Martin Vingron.
T-Reg Comparator: an analysis tool for the comparison of position weight matrices.
Nucleic Acids Research, 33:W438-W441, 2005.
[26] Hans-Helmut Niller, D. Salamon, Sven Rahmann, K. Ilg, A. Koroknai, F. Banati, F. Schwarzmann, H. Wolf, and J. Minarovits.
A 30 kb region of the Epstein-Barr virus genome is colinear with the rearranged human immunoglobulin gene loci: implications for a "ping-pong evolution" model for persisting viruses and their hosts. A review.
Acta Microbiol. Immunol. Hung., 51(4):469-484, 2004.
[27] Christoph Dieterich, Sven Rahmann, and Martin Vingron.
Functional inference from non-random distributions of conserved predicted transcription factor binding sites.
Bioinformatics, 20(Suppl.1):i109-i115, 2004.
[28] Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Martin Vingron, and Knut Reinert.
Optimal robust non-unique probe selection using integer linear programming.
Bioinformatics, 20(Suppl.1):i186-i193, 2004.
[29] Sven Rahmann and Christine Gräfe.
Mean and variance of the Gibbs free energy of oligonucleotides in the nearest neighbor model under varying conditions.
Bioinformatics, 20(17):2928-2933, 2004.
[30] Tobias Müller, Sven Rahmann, Thomas Dandekar, and Matthias Wolf.
Accurate and robust phylogeny estimation based on profile distances: a study of the Chlorophyceae (Chlorophyta).
BMC Evolutionary Biology, 4:Article 20, 2004.
[31] Benjamin Schuster-Böckler, Jörg Schultz, and Sven Rahmann.
HMM Logos for visualization of protein families.
BMC Bioinformatics, 5:Article 7, 2004.
[32] Sven Rahmann.
The shortest common supersequence problem in a microarray production setting.
Bioinformatics, 19(Suppl.2):ii156-ii161, 2003.
[33] Eric Rivals and Sven Rahmann.
Combinatorics of periods in strings.
Journal of Combinatorial Theory Series A, 104(1):95-113, 2003.
[34] Sven Rahmann, Tobias Müller, and Martin Vingron.
On the power of profiles for transcription factor binding site detection.
Statistical Applications in Genetics and Molecular Biology, 2(1):Article 7, 2003.
[35] Sven Rahmann.
Fast large-scale oligonucleotide selection using the longest common factor approach.
Journal of Bioinformatics and Computational Biology, 1(2):343-361, 2003.
[36] Sven Rahmann and Eric Rivals.
On the distribution of the number of missing words in random texts.
Combinatorics, Probability and Computing, 12:73-87, 2003.
[37] Tobias Müller, Sven Rahmann, and Marc Rehmsmeier.
Non-symmetric score matrices and the detection of homologous transmembrane proteins.
Bioinformatics, 17(Suppl.1):S182-S189, 2001.

Refereed Conference Publications

[1] Markus Chimani, Sven Rahmann, and Sebastian Böcker.
Exact ILP solutions for phylogenetic minimum flip problems.
In ACM-BCB'10. ACM, 2010.
To appear.
[2] Tobias Marschall and Sven Rahmann.
Exact analysis of Horspool's and Sunday's pattern matching algorithms with Probabilistic Arithmetic Automata.
In Henning Fernau and Carlos Martin-Vide, editors, LATA 2010, LNCS. Springer, 2010.
To appear.
[3] Sven Rahmann, Tobias Marschall, Frank Behler, and Oliver Kramer.
Modeling evolutionary fitness for DNA motif discovery.
In Franz Rothlauf, editor, Genetic and Evolutionary Computation Conference (GECCO) 2009, pages 225-232. ACM, 2009.
[4] Inke Herms and Sven Rahmann.
Computing alignment seed sensitivity with probabilistic arithmetic automata.
In Keith Crandall and Jens Lagergren, editors, Algorithms in Bioinformatics (WABI'08), LNCS, pages 318-329. Springer, 2008.
[5] Epameinondas Fritzilas, Yasmin A. Rios-Solis, and Sven Rahmann.
Structural identifiability in low-rank matrix factorization.
In Xiaodong Hu and Jie Wang, editors, COCOON (Computing and Combinatorics), volume 5092 of LNCS, pages 140-148. Springer, 2008.
[6] Tobias Marschall and Sven Rahmann.
Probabilistic arithmetic automata and their application to pattern matching statistics.
In Paolo Ferragina and Gad Landau, editors, Combinatorial Pattern Matching (CPM'08), volume 5029 of LNCS, pages 95-106. Springer, 2008.
[7] Sven Rahmann, Tobias Wittkop, Jan Baumbach, Marcel Martin, Anke Truß, and Sebastian Böcker.
Exact and heuristic algorithms for weighted cluster editing.
In Computational Systems Bioinformatics Conference, pages 391-401, 2007.
[8] Sérgio Anibal de Carvalho Jr. and Sven Rahmann.
Improving the design of GeneChip arrays by combining placement and embedding.
In Computational Systems Bioformatics Conference, pages 417-427, 2007.
[9] Christian Höner zu Siederdissen, Susanne Ragg, and Sven Rahmann.
Discovering biomarkers for myocardial infarction from SELDI-TOF spectra.
In R. Decker and H.-J. Lenz, editors, Advances in Data Analysis - Proceedings of the 30th Annual Conference of the Gesellschaft für Klassifikation e.V., Studies in Classification, Data Analysis, and Knowledge Organization, pages 569-576. Springer, 2007.
[10] Hans-Michael Kaltenbach, Sebastian Böcker, and Sven Rahmann.
Markov additive chains and applications to fragment statistics for peptide mass fingerprinting.
In Proceedings of the RECOMB Satellite Conference on Systems Biology and Computational Proteomics 2006, volume 4532 of LNBI, pages 29-41. Springer, 2007.
[11] Sven Rahmann and Gunnar W. Klau.
Integer linear programs for discovering approximate gene clusters.
In Philipp Bucher and Bernard Moret, editors, Proceedings of the 6th Workshop on Algorithms in Bioinformatics (WABI), volume 4175 of LNBI, pages 298-309. Springer, 2006.
[12] Sérgio A. de Carvalho Jr. and Sven Rahmann.
Improving the layout of oligonucleotide microarrays: Pivot Partitioning.
In Philipp Bucher and Bernard Moret, editors, Proceedings of the 6th Workshop of Algorithms in Bioinformatics (WABI'06), volume 4175 of LNBI, pages 321-332. Springer, 2006.
[13] Sérgio A. de Carvalho Jr. and Sven Rahmann.
Microarray layout as a quadratic assignment problem.
In Daniel Huson, Oliver Kohlbacher, Andrei Lupas, Kay Nieselt, and Andreas Zell, editors, Proceedings of the German Conference on Bioinformatics (GCB), volume P-83 of Lecture Notes in Informatics, pages 11-20. GI, 2006.
[14] Sven Rahmann.
Subsequence combinatorics and applications to microarray production, DNA sequencing and chaining algorithms.
In Moshe Lewenstein and Gabriel Valiente, editors, Combinatorial Pattern Matching (CPM), volume 4009 of LNCS, pages 153-164, 2006.
[15] Tobias Müller, Sven Rahmann, Thomas Dandekar, and Matthias Wolf.
Robust estimation of the phylogeny of Chlorophyceae (Chlorophyta) based on profile distances.
In H.-W. Mewes, D. Frishman, V. Heun, and S. Kramer, editors, Proceedings of the German Conference on Bioinformatics (GCB'03), volume 1, pages 97-101, Munich, October 2003. belleville.
[16] Sven Rahmann.
Dynamic programming algorithms for two statistical problems in computational biology.
In Proceedings of the 3rd Workshop of Algorithms in Bioinformatics (WABI), volume 2812 of LNCS, pages 151-164. Springer, 2003.
[17] Sven Rahmann.
Fast and sensitive probe selection for DNA chips using jumps in matching statistics.
In Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference (CSB 2003), pages 57-64. IEEE, 2003.
[18] Alexander Schliep, David C. Torney, and Sven Rahmann.
Group testing with DNA chips: Generating designs and decoding experiments.
In Proceedings of the 2nd IEEE Computer Society Bioinformatics Conference (CSB 2003), pages 84-93. IEEE, 2003.
[19] Sven Rahmann.
Rapid large-scale oligonucleotide selection for microarrays.
In Proceedings of the First IEEE Computer Society Bioinformatics Conference (CSB 2002), pages 54-63. IEEE, 2002.
An abstract of this work also appeared in Proceedings of WABI 2002, LNCS vol. 2452, p. 434. Springer, 2002.
[20] Eric Rivals and Sven Rahmann.
Combinatorics of periods in strings.
In P. Orejas, P. G. Spirakis, and J. van Leuween, editors, Proceedings of the 28th International Colloquium on Automata, Languages, and Programming (ICALP 2001), volume 2076 of LNCS, pages 615-626. Springer, 2001.
[21] Sven Rahmann and Eric Rivals.
Exact and efficient computation of the expected number of missing and common words in random texts.
In David Sankoff and Raffaele Giancarlo, editors, Proceedings of the 11th Symposium on Combinatorial Pattern Matching (CPM 2000), volume 1848 of LNCS, pages 375-387. Springer, 2000.

Books and Book Chapters

[1] Tobias Marschall, Marcel Martin, and Sven Rahmann.
Extending SeqAn with a BWT-based suffix array construction.
In Andreas Gogol-Döring and Knut Reinert, editors, Biological Sequence Analysis Using the SeqAn C++ Library, CRC Mathematical & Computational Biology. Chapman & Hall, 2009.
[2] Sérgio A. de Carvalho Jr. and Sven Rahmann.
Modeling and optimizing oligonucleotide microarray layout.
In Ion Mandoiu and Alexander Zelikowsky, editors, Bioinformatics Algorithms: Techniques and Applications, Wiley Book Series on Bioinformatics, chapter 13, pages 279-302. Wiley, 2008.
[3] Sven Rahmann and Gunnar W. Klau.
Integer linear programming techniques for discovering approximate gene clusters.
In Ion Mandoiu and Alexander Zelikovsky, editors, Bioinformatics Algorithms: Techniques and Applications, Wiley Series on Bioinformatics: Computational Techniques and Engineering, chapter 9, pages 203-222. Wiley, 2008.
[4] Sven Rahmann, Tobias Müller, Thomas Dandekar, and Matthias Wolf.
Efficient and robust analysis of large phylogenetic datasets.
In Hui-Huang Hsu, editor, Advanced Data Mining Techonolgies in Bioinformatics, chapter VI, pages 104-117. Idea Group Publising, 2006.
[5] Sven Rahmann.
Algorithmen für das Design von DNA-Microarrays.
In Dorthea Wagner et al., editors, Ausgezeichnete Informatikdissertationen 2004, volume D-5 of Lecture Notes in Informatics, pages 145-154. GI, 2005.

Selected Unrefereed Conference Contributions and Poster Abstracts

[1] Sven Rahmann, Tobias Müller, and Martin Vingron.
Non-unique probe selection by matrix condition optimization.
In Currents in Computational Molecular Biology 2004. San Diego Supercomputing Center, San Diego, USA, 2004.
[2] Sven Rahmann and Tobias Müller.
The embedding problem for evolutionary Markov processes.
In Proceedings of the Karlsruher Stochastik-Tage. Universität Karlsruhe, March 2004.
[3] Sven Rahmann and Tobias Müller.
A new formulation of evolutionary models.
In Liliana Florea, Brian Walenz, and Sridhar Hannenhalli, editors, Currents in Computational Molecular Biology 2002, pages 156-157. RECOMB 2002, Washington D.C., USA, 2002.
[4] Sven Rahmann, Eric Rivals, and Martin Vingron.
A generalization of Jokinen's and Ukkonen's fundamental q-gram lemma.
In ISMB'99 poster abstracts. GI, Heidelberg, 1999.

Technical Reports and Miscellanies

[1] Cedric Chauve, Yoan Diekmann, Steffen Heber, Julia Mixtacki, Sven Rahmann, and Jens Stoye.
On common intervals with errors.
Technical Report 2006-02, Abteilung Informationstechnik, Technische Fakultät, Universität Bielefeld, 2006.
ISSN 0946-7831.
[2] Hans-Michael Kaltenbach, Henner Sudek, Sebastian Böcker, and Sven Rahmann.
Statistics of cleavage fragments in random weighted strings.
Technical Report 2005-06, Abteilung Informationstechnik, Technische Fakultät, Universität Bielefeld, 2005.
[3] Sérgio A. de Carvalho Jr. and Sven Rahmann.
Searching for the shortest common supersequence.
Technical Report 2005-03, Abteilung Informationstechnik, Technische Fakultät, Universität Bielefeld, 2005.
[4] Sven Rahmann.
Algorithms for probe selection and DNA microarray design.
PhD thesis, Freie Universität Berlin, February 2004.
[5] Sven Rahmann.
Word statistics in random texts and applications to computational molecular biology.
Diplomarbeit (Master's Thesis), Universität Heidelberg, July 2000.
[6] Sven Rahmann.
Spezielle Methoden und Anwendungen der Statistik in der Bioinformatik.
Lecture notes for a course given at the Akademie für Weiterbildung der Universitäten Heidelberg und Mannheim. In German, May 2003.
[7] Mathew J. Palakal, Sven Rahmann, and Birong Liao.
Editorial message: special track on bioinformatics.
In Proceedings of the ACM Symposium on Applied Computing (SAC), page 99. ACM, 2005.
[8] Sven Rahmann.
Using and designing generalized regular expressions to discover bad diction in scientific writing.
Unpublished manuscript, 2002-2004.
[9] Betty Lazareva, Sven Rahmann, and David Haussler.
Towards an accurate EST consensus.
Unpublished manuscript, 1999.

   (c) Sven Rahmann. Back to homepage and imprint.