Baumbach, Jan, Rahmann, Sven, Tauch, Andreas
Abstract Background Transcriptional regulation of gene activity is essential for any living organism. Transcription factors therefore recognize specific binding sites within the DNA to regulate the...
Efficient exact motif discovery (2009)
Marschall, Tobias, Rahmann, Sven
Motivation: The motif discovery problem consists of finding over-represented patterns in a collection of biosequences. It is one of the classical sequence analysis problems, but still has not been...
Baumbach, Jan, Tauch, Andreas, Rahmann, Sven
To handle changing environmental surroundings and to manage unfavorable conditions, microbial organisms have evolved complex transcriptional regulatory networks. To comprehensively analyze these gene...
Detecting species-site dependencies in large multiple sequence alignments (2009)
Schwarz, Roland, Seibel, Philipp N., Rahmann, Sven, Schoen, Christoph, Huenerberg, Mirja, Müller-Reible, Clemens, ...
Multiple sequence alignments (MSAs) are one of the most important sources of information in sequence analysis. Many methods have been proposed to detect, extract and visualize their most significant...
Analyzing the Layout of Affymetrix Microarrays (2008)
Affymetrix microarrays have their probes synthesized in parallel, on the chip, in a series of repetitive steps. Each step appends the same nucleotide to selected regions of the chip. Selection occurs...
IMPROVING THE DESIGN OF GENECHIP ARRAYS BY COMBINING PLACEMENT AND EMBEDDING (2008)
The microarray layout problem is a generalization of the border length minimization problem and asks to distribute oligonucleotide probes on a microarray and to determine their embeddings in the...
am Fachbereich Mathematik und Informatik (2008)
Sven Rahmann, Prof Dr, Martin Vingron, Prof Dr, Knut Reinert, ...
Tag der Promotion:
cancer detection using ion mobility spectrometry data (2008)
Jan Baumbach, Er Bunkowski, Sita Lange, Timm Oberwahrenbrock, Sven Rahmann, Jörg Ingo Baumbach
IMS 2 – An integrated medical software system for early lung
Decoding non-unique oligonucleotide hybridization experiments of targets related by a phylogenetic tree
Stefan Wolfsheimer, Er K. Hartmann, Sven Rahmann
Abstract Statistics of pairwise local sequence alignment ("how probable is it to observe a certain align-ment score on two random sequences of given length?") mainly focuses on the...
Baumbach, Jan, Wittkop, Tobias, Weile, Jochen, Kohl, Thomas, Rahmann, Sven
Background. A precise experimental identification of transcription factor binding motifs (TFBMs), accurate to a single base pair, is time-consuming and diffcult. For several databases, TFBM...
Online abelian pattern matching (2008)
Ejaz, Tahir, Rahmann, Sven, Stoye, Jens
An abelian pattern describes the set of strings that comprise of the same combination of characters. Given an abelian pattern P and a text T [Epsilon] [Sigma]^n, the task is to find all occurrences...
Pape, Utz J., Rahmann, Sven, Vingron, Martin
Motivation: Transcription factors (TFs) play a key role in gene regulation by binding to target sequences. In silico prediction of potential binding of a TF to a binding site is a well-studied...
Pape, Utz J., Rahmann, Sven, Sun, Fengzhu, Vingron, Martin
Transcription factors play a key role in gene regulation by interacting with specific binding sites or motifs. Therefore, enrichment of binding motifs is important for genome annotation and efficient...
Pape, Utz J., Rahmann, Sven, Vingron, Martin
Motivation: Transcription factors (TFs) play a key role in gene regulation by binding to target sequences. In silico prediction of potential binding of a TF to a binding site is a well-studied...
Neuweger, Heiko, Baumbach, Jan, Albaum, Stefan, Bekel, Thomas, Dondrup, Michael, Hüser, Andrea T, ...
Abstract Background The introduction of high-throughput genome sequencing and post-genome analysis technologies, e.g. DNA microarray approaches, has created the potential to unravel and scrutinize...
Combinatorics of Periods in Strings Eric Rivals 1 (2007)
Abstract. We consider the set (n) of all period sets of strings of length n over a nite alphabet. We show that there is redundancy in period sets and introduce the notion of an irreducible period...
Wittkop, Tobias, Baumbach, Jan, Lobo, Francisco P, Rahmann, Sven
Abstract Background Detecting groups of functionally related proteins from their amino acid sequence alone has been a long-standing challenge in computational genome research. Several clustering...
Integer linear programming approaches for non-unique probe selection. (2007)
Klau, Gunnar W., Rahmann, Sven, Schliep, Alexander, Vingron, Martin, Reinert, Knut
In addition to their prevalent use for analyzing gene expression, DNA microarrays are an efficient tool for biological, medical, and industrial applications because of their ability to assess the...
Baumbach, Jan, Bunkowski, Alexander, Lange, Sita, Oberwahrenbrock, Timm, Kleinbölting, Nils, Rahmann, Sven, ...
IMS2 is an Integrated Medical Software system for the analysis of Ion Mobility Spectrometry (IMS) data. It assists medical staff with the following IMS data processing steps: acquisition,...
Bmc Bioinformatics, Tobias Wittkop, Jan Baumbach, Francisco P Lobo, Francisco P Lobo, Sven Rahmann
Research article Large scale clustering of protein sequences with FORCE-A layout based heuristic for weighted cluster editing
Baumbach, Jan, Brinkrolf, Karina, Czaja, Lisa F, Rahmann, Sven, Tauch, Andreas
Abstract Background The application of DNA microarray technology in post-genomic analysis of bacterial genome sequences has allowed the generation of huge amounts of data related to regulatory...
On common intervals with errors (2006)
Chauve, Cedric, Diekmann, Yoan, Heber, Steffen, Mixtacki, Julia, Rahmann, Sven, Stoye, Jens
The information that groups of genes co-occur in several genomes provides a basis for further comparative genomic analysis. The task of finding such constellations, mostly referred to as gene...
Baumbach, Jan, Brinkrolf, Karina, Wittkop, Tobias, Tauch, Andreas, Rahmann, Sven
CoryneRegNet is an ontology-based data warehouse of corynebacterial transcription factors and regulatory networks. Initially, it was designed to provide methods for the analysis and visualization of...
On Common Intervals with Errors (2006)
Abteilung Informationstechnik, Cedric Chauve, Yoan Diekmann, Steffen Heber, Julia Mixtacki, ...
The information that groups of genes co-occur in several genomes provides a basis for further comparative genomic analysis. The task of finding such constellations, mostly referred to as gene...
On Common Intervals with Errors (2006)
Abteilung Informationstechnik, Cedric Chauve, Yoan Diekmann, Steffen Heber, Julia Mixtacki, ...
The information that groups of genes co-occur in several genomes provides a basis for further comparative genomic analysis. The task of finding such constellations, mostly referred to as gene...
Jan Baumbach, Karina Brinkrolf, Lisa F Czaja, Sven Rahmann, Andreas Tauch, Lisa F Czaja, ...
corynebacterial transcription factors and regulatory networks
Schliep, Alexander, Rahmann, Sven
Motivation: The reliable identification of presence or absence of biological agents (“targets”), such as viruses or bacteria, is crucial for many applications from health care to biodiversity. If...
Statistics of cleavage fragments in random weighted strings (2005)
Kaltenbach, Hans-Michael, Sudek, Henner, Böcker, Sebastian, Rahmann, Sven
Peptide mass fingerprinting is an important technique that allows to identify a protein from its fragment masses obtained by mass spectrometry after enzymatic fragmentation: An experimental mass...
T-Reg Comparator: an analysis tool for the comparison of position weight matrices (2005)
Roepcke, Stefan, Grossmann, Steffen, Rahmann, Sven, Vingron, Martin
T-Reg Comparator is a novel software tool designed to support research into transcriptional regulation. Sequence motifs representing transcription factor binding sites are usually encoded as position...
T-Reg Comparator: an analysis tool for the (2005)
Stefan Roepcke, Steffen Grossmann, Sven Rahmann, Martin Vingron
comparison of position weight matrices
T-Reg Comparator: an analysis tool for the comparison of position weight matrices (2005)
Roepcke, Stefan, Grossmann, Steffen, Rahmann, Sven, Vingron, Martin
T-Reg Comparator is a novel software tool designed to support research into transcriptional regulation. Sequence motifs representing transcription factor binding sites are usually encoded as position...
Optimal robust non-unique probe selection using Integer Linear Programming (2004)
Klau,Gunnar W., Rahmann,Sven, Schliep,Alexander, Vingron,Martin, Reinert,Knut
Motivation: Besides their prevalent use for analyzing gene expression, microarrays are an efficient tool for biological, medical and industrial applications due to their ability to assess the...
Müller, Tobias, Rahmann, Sven, Dandekar, Thomas, Wolf, Matthias
Abstract Background In phylogenetic analysis we face the problem that several subclade topologies are known or easily inferred and well supported by bootstrap analysis, but basal branching patterns...
Dieterich,Christoph, Rahmann,Sven, Vingron,Martin
Motivation: Our understanding of how genes are regulated in a concerted fashion is still limited. Especially, complex phenomena like cell cycle regulation in multicellular organisms are poorly...
HMM Logos for visualization of protein families (2004)
Schuster-Böckler, Benjamin, Schultz, Jörg, Rahmann, Sven
Abstract Background Profile Hidden Markov Models (pHMMs) are a widely used tool for protein family research. Up to now, however, there exists no method to visualize all of their central aspects...
Dieterich, Christoph, Rahmann, Sven, Vingron, Martin
Motivation: Our understanding of how genes are regulated in a concerted fashion is still limited. Especially, complex phenomena like cell cycle regulation in multicellular organisms are poorly...
Optimal robust non-unique probe selection using Integer Linear Programming (2004)
Klau, Gunnar W., Rahmann, Sven, Schliep, Alexander, Vingron, Martin, Reinert, Knut
Motivation: Besides their prevalent use for analyzing gene expression, microarrays are an efficient tool for biological, medical and industrial applications due to their ability to assess the...
using Integer Linear Programming (2004)
Gunnar W. Klau, Sven Rahmann, Er Schliep, Martin Vingron, Knut Reinert
Vol. 20 Suppl. 1 2004, pages i186–i193
Optimal Robust Non-Unique Probe Selection Using Integer Linear Programming (2004)
Gunnar W. Klau, Sven Rahmann, Alexander Schliep, Er Schliep B, Martin Vingron, Knut Reinert
Motivation Besides their prevalent use for analyzing gene expression, microarrays are an efficient tool for biological, medical, and industrial applications due to their ability to assess the...
Tobias Müller, Sven Rahmann, Thomas D, Matthias Wolf, Thomas Dandekar, Matthias Wolf
Background: In phylogenetic analysis we face the problem that several subclade topologies are known or easily inferred and well supported by bootstrap analysis, but basal branching patterns cannot be...
BMC Bioinformatics Methodology article HMM Logos for visualization of protein families (2004)
Benjamin Schuster-böckler, Jörg Schultz, Sven Rahmann, Sven Rahmann
Hidden Markov ModelSequence LogoHMM Logoprofileinformation contenthitting probabilitydynamic programmingsmall GTPases Background: Profile Hidden Markov Models (pHMMs) are a widely used tool for...
Rahmann, Sven, Gräfe, Christine
Motivation: In order to assess the stability of DNA-DNA hybridizations--for example during PCR primer design or oligonucleotide selection for microarrays--one needs to predict the change in Gibbs...
Dieterich, Christoph, Rahmann, Sven, Vingron, Martin
Motivation: Our understanding of how genes are regulated in a concerted fashion is still limited. Especially, complex phenomena like cell cycle regulation in multicellular organisms are poorly...
Optimal robust non-unique probe selection using Integer Linear Programming (2004)
Klau, Gunnar W., Rahmann, Sven, Schliep, Alexander, Vingron, Martin, Reinert, Knut
Motivation: Besides their prevalent use for analyzing gene expression, microarrays are an efficient tool for biological, medical and industrial applications due to their ability to assess the...
Rahmann, Sven, Gräfe, Christine
Motivation: In order to assess the stability of DNA–DNA hybridizations—for example during PCR primer design or oligonucleotide selection for microarrays—one needs to predict the change in Gibbs...
Rahmann, Sven, Gräfe, Christine
Motivation: In order to assess the stability of DNA-DNA hybridizations--for example during PCR primer design or oligonucleotide selection for microarrays--one needs to predict the change in Gibbs...
On the Power of Profiles for Transcription Factor Binding Site Detection (2003)
Rahmann, Sven, Müller, Tobias, Vingron, Martin
Transcription factor binding site (TFBS) detection plays an important role in computational biology, with applications in gene finding and gene regulation. The sites are often modeled by gapless...
On the Power of Profiles for Transcription Factor Binding Site Detection (2003)
Rahmann, Sven, Müller, Tobias, Vingron, Martin
Transcription factor binding site (TFBS) detection plays an important role in computational biology, with applications in gene finding and gene regulation. The sites are often modeled by gapless...
On the Power of Profiles for Transcription Factor Binding Site Detection (2003)
Rahmann, Sven, Müller, Tobias, Vingron, Martin
Transcription factor binding site (TFBS) detection plays an important role in computational biology, with applications in gene finding and gene regulation. The sites are often modeled by gapless...
On the Power of Profiles for Transcription Factor Binding Site Detection (2003)
Rahmann, Sven, Müller, Tobias, Vingron, Martin
Transcription factor binding site (TFBS) detection plays an important role in computational biology, with applications in gene finding and gene regulation. The sites are often modeled by gapless...
Combinatorics of periods in strings (2003)
We consider the set Γn of all period sets of strings of length n over a finite alphabet. We show that there is redundancy in period sets and introduce the notion of an irreducible period set. We...
On the distribution of the number of missing words in random texts (2003)
Determining the distribution of the number of empty urns after a number of balls have been thrown randomly into the urns is a classical and well understood problem. We study a generalization: Given a...
On the power of profiles for transcription factor binding site detection (2003)
Rahmann,Sven, Müller,Tobias, Vingron,Martin
Transcription factor binding site (TFBS) detection plays an important role in computational biology, with applications in gene finding and gene regulation. The sites are often modeled by gapless...
Group testing with DNA chips: generating designs and decoding experiments (2003)
Schliep,Alexander, Torney,David C., Rahmann,Sven
DNA microarrays are a valuable tool for massively parallel DNA-DNA hybridization experiments. Currently, most applications rely on the existence of sequence-specific oligonucleotide probes. In large...
Robust estimation of the phylogeny of chlorophyceae (chlorophyta) based on profile distances (2003)
Müller, Tobias, Rahmann, Sven, Dandekar, Thomas, Wolf, Matthias
On the power of profiles for transcription factor binding site detection (2003)
Rahmann, Sven, Müller, Tobias, Vingron, Martin
Transcription factor binding site (TFBS) detection plays an important role in computational biology, with applications in gene finding and gene regulation. The sites are often modeled by gapless...
The shortest common supersequence problem in a microarray production setting (2003)
Motivation: During microarray production, several thousands of oligonucleotides (short DNA sequences) are synthesized in parallel, one nucleotide at a time. We are interested in finding the shortest...
Fast large scale oligonucleotide selection using the longest common factor approach (2003)
We present a fast method that selects oligonucleotide probes (such as DNA 25-mers) for microarray experiments on a truly large scale. For example, reliable oligos for human genes can be found within...
Fast Large Scale Oligonucleotide Selection Using the Longest Common Factor Approach (2003)
We present a fast method that selects oligonucleotide probes (such as DNA 25-mers) for microarray experiments on a truly large scale. For example, reliable oligos for human genes can be found within...
On the distribution of the number of missing words in Random texts (2003)
Determining the distribution of the number of empty urns after a number of balls have been thrown randomly into the urns is a classical and well understood problem. We study a generalization: Given a...
Fast and sensitive probe selection for DNA chips using jumps in matching statistics (2003)
The design of large scale DNA microarrays is a challenging problem. So far, probe selection algorithms must trade the ability to cope with large scale problems for a loss of accuracy in the...
Group testing with DNA chips: generating designs and decoding experiments (2003)
Schliep, Alexander, Torney, David C., Rahmann, Sven
DNA microarrays are a valuable tool for massively parallel DNA-DNA hybridization experiments. Currently, most applications rely on the existence of sequence-specific oligonucleotide probes. In large...
Combinatorics of periods in strings (2003)
We consider the set Γn of all period sets of strings of length n over a finite alphabet. We show that there is redundancy in period sets and introduce the notion of an irreducible period set. We...
Dynamic programming algorithms for two statistical problems in computational biology (2003)
We present dynamic programming algorithms for two exact statistical tests that frequently arise in computational biology. The first test concerns the decision whether an observed sequence stems from...
On the distribution of the number of missing words in random texts (2003)
Determining the distribution of the number of empty urns after a number of balls have been thrown randomly into the urns is a classical and well understood problem. We study a generalization: Given a...
On the Distribution of the Number of Missing Words in Random Texts (2003)
Introduction Let X be the ran[ mn umber of missin words of len th q (also called q-grams) a ran[' text of lenfi0 n+q-1 over an alphabet # of size #. Theun4' lyin probability space is (# P(#...
On the power of profiles for transcription factor binding site detection (2003)
Sven Rahmann, Tobias Müller, Martin Vingron
Test; Significance; Power; TRANSFAC. Abstract. Transcription factor binding site (TFBS) detection plays an important role in computational biology, with applications in gene finding and gene...
The shortest common supersequence problem in a microarray production setting (2003)
Motivation: During microarray production, several thousands of oligonucleotides (short DNA sequences) are synthesized in parallel, one nucleotide at a time. We are interested in finding the shortest...
A New Formulation of Evolutionary Models (2002)
RECOMB Poster Abstracts
Rapid Large-Scale Selection of Oligonucleotides for Microarrays (2002)
We present the first algorithm that selects oligonucleotide probes (e.g. 25-mers) for microarray experiments on a large scale. For example, oligos for human genes can be found within 50 hours. This...
Non-symmetric score matrices and the detection of homologous transmembrane proteins (2001)
Sven Rahmann, Marc Rehmsmeier, Theoretische Bioinformatik (tbi, Deutsches Krebsforschungszentrum Heidelberg
Key words: score matrix, transmembrane protein, database search. Abstract. Given a transmembrane protein, we wish to nd related ones by a database search. Due to the strongly hydrophobic amino acid...
Combinatorics of Periods in Strings (2001)
Eric Rivals And, Eric Rivals, Sven Rahmann, Rue Ada
We consider the set # (n) of all period sets of strings of length n over a finite alphabet. We show that there is redundancy in period sets and introduce the notion of an irreducible period set. We...
Non-symmetric score matrices and the detection of homologous transmembrane proteins (2001)
Müller, Tobias, Rahmann, Sven, Rehmsmeier, Marc
Given a transmembrane protein, we wish to find related ones by a database search. Due to the strongly hydrophobic amino acid composition of transmembrane domains, suboptimal results are obtained when...
The number of missing words (NMW) of length q in a text, and the number of common words (NCW) of two texts are useful text statistics. Knowing the distribution of the NMW in a random text is...
On the distribution of the number of missing words in random texts (1999)
The number of words of length q (q-grams) in a text or the number of common q-grams between two texts are used in pattern matching algorithms, as distance measure between texts or for testing the...
T-Reg Comparator: an analysis tool for the comparison of position weight matrices
Roepcke, Stefan, Grossmann, Steffen, Rahmann, Sven, Vingron, Martin
T-Reg Comparator is a novel software tool designed to support research into transcriptional regulation. Sequence motifs representing transcription factor binding sites are usually encoded as position...
T-Reg Comparator: an analysis tool for the comparison of position weight matrices
Roepcke, Stefan, Grossmann, Steffen, Rahmann, Sven, Vingron, Martin
T-Reg Comparator is a novel software tool designed to support research into transcriptional regulation. Sequence motifs representing transcription factor binding sites are usually encoded as position...
Neuweger, Heiko, Baumbach, Jan, Albaum, Stefan, Bekel, Thomas, Dondrup, Michael, Hüser, Andrea T, ...
On the Power of Profiles for Transcription Factor Binding Site Detection
Sven Rahmann, Tobias Müller, Martin Vingron
Transcription factor binding site (TFBS) detection plays an important role in computational biology, with applications in gene finding and gene regulation. The sites are often modeled by gapless...
Efficient exact motif discovery
Marschall, Tobias, Rahmann, Sven
Motivation: The motif discovery problem consists of finding over-represented patterns in a collection of biosequences. It is one of the classical sequence analysis problems, but still has not been...
Detecting species-site dependencies in large multiple sequence alignments
Schwarz, Roland, Seibel, Philipp N., Rahmann, Sven, Schoen, Christoph, Huenerberg, Mirja, Müller-Reible, Clemens, ...
Multiple sequence alignments (MSAs) are one of the most important sources of information in sequence analysis. Many methods have been proposed to detect, extract and visualize their most significant...