Martin Vingron

Better Tree Alignments through Near-Optimal Intermediates (2007)

. A formalization of the multiple sequence alignment problem that emphasizes the problem's evolutionary aspect is the Generalized Tree Alignment Problem. Given a set of sequences, this...

q-gram Based Database Searching Using a Suffix Array (QUASAR) (2007)

The reconstruction of hypothetical ancestral sequences is a widely used means to guide algorithms for multiple alignment and phylogeny reconstruction on the basis of an evolutionary tree. We identify...

Stefan Burkhardt, Andreas Crauser, Paolo Ferragina, Hans-peter Lenhof, Eric Rivals, Martin Vingron

With the increasing amount of DNA sequence information deposited in public databases, searching for similarity to a query sequence has become a basic operation in molecular biology. But even...

Attacking Generalized Tree Alignment By a Deferred Path Heuristic (2007)

Benno Schwikowski And Martin Vingron, Benno Schwikowski, Martin Vingron

Many multiple alignment methods implicitly or explicitly try to minimize the amount of biological change implied by an alignment. At the level of sequences, biological change is measured along a...

Identification of transcriptional modules in budding yeast (2007)

Thomas Manke, Ricardo Bringas, Martin Vingron

One focus of postgenomic research concerns the regulation of gene expression through signal transduction and combinatorial control of gene transcription. Protein-protein interactions and protein-DNA...

Limits of hornology detection by pairwise (2007)

Rainer Spang, Martin Vingron, Deutsches Krebsforschungszentrum, Theoretische Bioinformatik, Im Neuenheimer Feld

sequence comparison

Max-Planck-Institute for Molecular Genetics Computational Molecular Biology (2007)

Florian Markowetz, Martin Vingron

Knowledge of the three-dimensional structure of a protein is essential for describing and understanding its function. Today, a large number of known protein sequences faces a small number of identied...

Florian Markowetz et al.: Support Vector Machines for Protein Fold Class Prediction 1 Support Vector Machines for Protein Fold Class Prediction (2007)

Florian Markowetz, Martin Vingron

Abstract: Knowledge of the three-dimensional structure of a protein is essential for describing and understanding its function. Today, a large number of known protein sequences faces a small number...

Weighted sequence graphs: Boosting iterated dynamic programming using locally suboptimal solutions (2007)

Nicolas Pollet, Heiko A. Schmidt, Volker Gawantka, Martin Vingron, Christof Niehrs

Abstract: We present a novel technique for improving a fundamental aspect of iterated dynamic programming procedures on sequences, such as progressive sequence alignment.Instead of relying on the...

1 (2007)

Axeldb is a database storing and integrating gene expression patterns and DNA sequences identified in a large-scale in situ hybridization study in Xenopus laevis embryos. The data are organised in a...

Weighted sequence graphs: Boosting iterated dynamic programming using locally suboptimal solutions (2007)

Proteome Analysis Based on Motif Statistics Pierre Nicodeme (2007)

Abstract: We present a novel technique for improving a fundamental aspect of iterated dynamic programming procedures on sequences, such as progressive sequence alignment.Instead of relying on the...

Cnrs Genopole Evry, Tobias Doerks, Martin Vingron

Motivation: Even for the amino acid motifs collected in the Prosite database there may be chance occurences as opposed to those occurences where the motif is involved in fold or function of a...

Exonization of active mouse L1s: a driver of transcriptome evolution? (2007)

Zemojtel, Tomasz, Penzkofer, Tobias, Schultz, Jörg, Dandekar, Thomas, Badge, Richard, Vingron, Martin

Abstract Background Long interspersed nuclear elements (LINE-1s, L1s) have been recently implicated in the regulation of mammalian transcriptomes. Results Here, we show that members of the three...

Exonization of active mouse LIs: a driver of transcriptome evolution? (2007)

Zemojtel, Tomasz, Penzkofe, Tobias, Schultz, Jorg, Dandekar, Thomas, Badge, Richard, Vingron, Martin

This is the authors final draft of the paper published in BMC Genomics, 2007, vol. 8(392). The final publsihed version is available at http://www.biomedcentral.com/1471-2164/8/392

The Otto Warburg International Summer School and Workshop on Networks and Regulation (2007)

Arndt, Peter F, Vingron, Martin

Predicting transcription factor affinities to DNA from a biophysical model (2007)

Roider, Helge G., Kanhere, Aditi, Manke, Thomas, Vingron, Martin

Motivation: Theoretical efforts to understand the regulation of gene expression are traditionally centered around the identification of transcription factor binding sites at specific DNA positions....

Simultaneous alignment and annotation of cis-regulatory regions (2007)

Bais, Abha Singh, Grossmann, Steffen, Vingron, Martin

Motivation: Current methods that annotate conserved transcription factor binding sites in an alignment of two regulatory regions perform the alignment and annotation step separately and combine the...

Design and statistical properties of robust functional networks: A model study of biological signal transduction (2007)

Kaluza, Pablo, Ipsen, Mads, Vingron, Martin, Mikhailov, Alexander S.

A simple flow network model of biological signal transduction is investigated. Networks with prescribed signal processing functions, robust against random node or link removals, are designed through...

The Otto Warburg International Summer School and Workshop on Networks and Regulation. (2007)

Arndt, Peter F., Vingron, Martin

Simultaneous alignment and annotation of cis-regulatory regions. (2007)

Bais, Abha Singh, Grossmann, Steffen, Vingron, Martin

Motivation: Current methods that annotate conserved transcription factor binding sites in an alignment of two regulatory regions perform the alignment and annotation step separately and combine the...

Incorporating evolution of transcription factor binding sites into annotated alignments. (2007)

Bais, Abha Singh, Grossmann, Steffen, Vingron, Martin

Identifying transcription factor binding sites (TFBSs) is essential to elucidate putative regulatory mechanisms. A common strategy is to combine cross-species conservation with single sequence TFBS...

A physical model for tiling array analysis. (2007)

Chung, Ho-Ryun, Kostka, Dennis, Vingron, Martin

Motivation: Chromatin immunoprecipitation (ChIP) is a powerful experimental approach to identify in vivo binding sites of sequence-specific transcription factors (TFs). These experiments are designed...

Developments in CORG: a gene-centric comparative genomics resource. (2007)

Dieterich, C., Franz, M. W., Vingron, Martin

The CORG resource (Comparative Regulatory Genomics, http://corg.eb.tuebingen.mpg.de) provides extensive cross-species comparisons of promoter regions in particular and whole gene loci in general....

Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis. (2007)

Grossmann, Steffen, Bauer, Sebastian, Robinson, Peter N., Vingron, Martin

Motivation: High-throughput experiments such as microarray hybridizations often yield long lists of genes found to share a certain characteristic such as differential expression. Exploring Gene...

Design and statistical properties of robust functional networks: A model study of biological signal transduction. (2007)

Kaluza, Pablo, Ipsen, Mads, Vingron, Martin, Mikhailov, Alexander S.

A simple flow network model of biological signal transduction is investigated. Networks with prescribed signal processing functions, robust against random node or link removals, are designed through...

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...

Using Transcription Factor Binding Site Co-Occurrence to Predict Regulatory Regions. (2007)

Klein, Holger, Vingron, Martin

Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics. (2007)

Messer, Philipp W., Bundschuh, Ralf, Vingron, Martin, Arndt, Peter F.

Long-range correlations in genomic base composition are a ubiquitous statistical feature among many eukaryotic genomes. In this article, these correlations are shown to substantially influence the...

Predicting transcription factor affinities to DNA from a biophysical model (2007)

Roider, Helge G., Kanhere, Aditi, Manke, Thomas, Vingron, Martin

Motivation: Theoretical efforts to understand the regulation of gene expression are traditionally centered around the identification of transcription factor binding sites at specific DNA positions....

Exonization of active mouse L1s: a driver of transcriptome evolution? (2007)

Zemojtel, Tomasz, Penzkofer, Tobias, Schultz, Jörg, Dandekar, Thomas, Badge, Richard, Vingron, Martin

Background: Long interspersed nuclear elements (LINE-1s, L1s) have been recently implicated in the regulation of mammalian transcriptomes. Results: Here, we show that members of the three active...

Invited (2007)

Alexander Bockmayr Berlin, Hamid Bolouri Seattle, Hanspeter Herzel Berlin, Thomas Höfer Heidelberg, Steffen Klamt Magdeburg, Florian Markowetz Princeton, ...

The aim of this program is to bring together researchers and students from different backgrounds (including molecular biology, bioinformatics, biological physics) to discuss a topic of high current...

Exonization of active mouse L1s: a driver of transcriptome (2007)

Bmc Genomics, Tomasz Zemojtel, Tobias Penzkofer, Jörg Schultz, Thomas D, Richard Badge, ...

Research article

An inventory of yeast proteins associated with nucleolar and ribosomal components (2006)

Staub, Eike, Mackowiak, Sebastian, Vingron, Martin

Abstract Background Although baker's yeast is a primary model organism for research on eukaryotic ribosome assembly and nucleoli, the list of its proteins that are functionally associated with...

A joint model of regulatory and metabolic networks (2006)

Yeang, Chen-Hsiang, Vingron, Martin

Abstract Background Gene regulation and metabolic reactions are two primary activities of life. Although many works have been dedicated to study each system, the coupling between them is less well...

A joint model of regulatory and metabolic networks (2006)

Yeang, Chen-Hsiang, Vingron, Martin

Background: Gene regulation and metabolic reactions are two primary activities of life. Although many works have been dedicated to study each system, the coupling between them is less well...

An Improved Algorithm for the Macro-evolutionary Phylogeny Problem (2006)

Behzadi, Behshad, Vingron, Martin

Macro-evolutionary processes (e.g., gene duplication and loss) have rarely been incorporated into gene phylogeny reconstruction methods. Durand et al. [5] have proposed a polynomial time dynamic...

Reconstructing Domain Compositions of Ancestral Multi-Domain Proteins (2006)

Behzadi, Behshad, Vingron, Martin

A model for the evolution of multidomain proteins should encompass not only sequence divergence but also domain duplications and recombination of domains. Given a set of contemporary multidomain...

Horizontal Gene Transfer in Aminoacyl-tRNA Synthetases Including Leucine-Specific Subtypes (2006)

Dohm, Juliane C., Vingron, Martin, Staub, Eike

Aminoacyl-tRNA synthetases catalyze a fundamental reaction for the flow of genetic information from RNA to protein. Their presence in all organisms known today highlights their important role in the...

Family specific rates of protein evolution (2006)

Luz, Hannes, Vingron, Martin

Motivation: Amino acid changing mutations in proteins are contstrained by purifying selection and accumulate at different rates. We estimate evolutionary rates on multiple alignments of eukaryotic...

About the interrelation of evolutionary rate and protein age (2006)

Luz, Hannes, Staub, Eike, Vingron, Martin

Evolutionary rate and gene age are interrelated when the age of a gene is assessed by the taxonomic distribution in the gene family. This is because homology detection by sequence comparison is...

An entropic characterization of protein interaction networks and cellular robustness (2006)

Manke, Thomas, Demetrius, Lloyd, Vingron, Martin

The structure of molecular networks is believed to determine important aspects of their cellular function, such as the organismal resilience against random perturbations. Ultimately, however,...

Identification of highly specific localized sequence motifs in human ribosomal protein gene promoters (2006)

Roepcke, Stefan, Zhi, Degui, Vingron, Martin, Arndt, Peter F.

For ribosomal protein (RP) genes the start of transcription is rigidly controlled to maintain the 5′-TOP signal on the messenger RNA. The responsible regulatory mechanism is not yet fully...

An inventory of yeast proteins that are associated with nucleoli and ribosomal components (2006)

Staub, Eike, Mackowiak, Sebastian, Vingron, Martin

Background: Although baker's yeast is a primary model organism for research on eukaryotic ribosome assembly and nucleoli, the list of its proteins that are functionally associated with nucleoli or...

Review: Normalization and Quantification of Differential Expression (2006)

Steinhoff, Christine, Vingron, Martin

Array-based gene expression studies frequently serve to identify genes that are expressed differently under two or more conditions. The actual analysis of the data, however, may be hampered by a...

A joint model of regulatory and metabolic networks (2006)

Yeang, Chen-Hsiang, Vingron, Martin

Background: Gene regulation and metabolic reactions are two primary activities of life. Although many works have been dedicated to study each system, the coupling between them is less well...

Plant nitric oxide synthase: a never-ending story? (2006)

Zemojtel, Tomasz, Fröhlich, Andreas, Palmieri, M. Cristina, Kolanczyk, Mateusz, Mikula, Ivan, Wyrwicz, Lucjan S., ...

Plant nitric oxide synthase: a never-ending story? (2006)

Zemojtel, Tomasz, Fröhlich, Andreas, Palmieri, M. Cristina, Kolanczyk, Mateusz, Mikula, Ivan, Wyrwicz, Lucjan S., ...

Plant nitric oxide synthase: a never-ending story? (2006)

Zemojtel, Tomasz, Fröhlich, Andreas, Palmieri, M. Cristina, Kolanczyk, Mateusz, Mikula, Ivan, Wyrwicz, Lucjan S., ...

A new statistical model to select target sequences bound by transcription factors (2006)

Pape, Utz J., Grossmann, Steffen, Hammer, Stefanie, Sperling, Silke, Vingron, Martin

Transcription factors (TFs) play a key role in gene regulation by binding to target sequences. In silico prediction of potential binding to a sequence is a main task in computational biology....

Normalization and quantification (2006)

Christine Steinhoffand, Martin Vingron

of differential expression in gene expression microarrays

Exercise 1 (dnaml) [2 points] (2006)

Martin Vingron, Hannes Luz

Download an alignment of 5 mitochondrial ATPases in hominids from the lectures’ website at

BIOINFORMATICS Family specific rates of protein evolution (2006)

Hannes Luz, Martin Vingron, Thomas Lengauer

Motivation: Amino acid changing mutations in proteins are contstrained by purifying selection and accumulate at different rates. We estimate evolutionary rates on multiple alignments of eukaryotic...

05441 Executive Summary -- Managing and Mining Genome Information: Frontiers in Bioinformatics (2006)

Blazewicz, Jacek, Freytag, Johann Christoph, Vingron, Martin

This report summarizes the important aspects of the workshop on "Managing and Mining Genome Information: Frontiers in Bioinformatics" which took place October 31st until November 4th, 2005. Twenty...

05441 Abstracts Collection -- Managing and Mining Genome Information: Frontiers in Bioinformatics (2006)

Blazewicz, Jacek, Freytag, Johann Christoph, Vingron, Martin

From 30.10.05 to 04.11.05, the Dagstuhl Seminar 05441 ``Managing and Mining Genome Information: Frontiers in Bioinformatics'' was held in the International Conference and Research Center (IBFI),...

Family specific rates of protein evolution (2006)

Luz, Hannes, Vingron, Martin

Motivation: Amino acid changing mutations in proteins are contstrained by purifying selection and accumulate at different rates. We estimate evolutionary rates on multiple alignments of eukaryotic...

Normalization and quantification of differential expression in gene expression microarrays (2006)

Steinhoff, Christine, Vingron, Martin

Array-based gene expression studies frequently serve to identify genes that are expressed differently under two or more conditions. The actual analysis of the data, however, may be hampered by a...

An introduction to low-level analysis methods of DNA microarray data (2005)

Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin

This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of...

An introduction to low-level analysis methods of DNA microarray data (2005)

Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin

This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of...

An introduction to low-level analysis methods of DNA microarray data (2005)

Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin

This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of...

An introduction to low-level analysis methods of DNA microarray data (2005)

Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin

This article gives an overview over the methods used in the low--level analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of...

A gene expression map of Arabidopsis thaliana development (2005)

Schmid,Markus, Davison,Timothy S., Henz,Stefan R., Pape,Utz J., Demar,Monika, Vingron,Martin, ...

Genomic analysis of Drosophila chromosome underreplication reveals a link between replication control and transcriptional territories (2005)

Belyakin,Stepan N., Christophides,George K., Alekseyenko,Artyom A., Kriventseva,Evgenia V., Belyaeva,Elena S., Nanayev,Roman A., ...

In Drosophila polytene chromosomes, most late-replicating regions remain underreplicated. A loss-of-function mutant of the suppressor of underreplication [Su(UR)] gene suppresses underreplication...

Comparative promoter region analysis powered by CORG (2005)

Dieterich, Christoph, Grossmann, Steffen, Tanzer, Andrea, Röpcke, Stefan, Arndt, Peter F, Stadler, Peter F, ...

Abstract Background Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription initiation, which...

Comparative promoter region analysis powered by CORG (2005)

Dieterich,Christoph, Grossmann,Steffen, Tanzer,Andrea, Röpcke,Stefan, Arndt,Peter F, Stadler,Peter F, ...

Background Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription initiation, which largely...

Large scale hierarchical clustering of protein sequences (2005)

Krause, Antje, Stoye, Jens, Vingron, Martin

Abstract Background Searching a biological sequence database with a query sequence looking for homologues has become a routine operation in computational biology. In spite of the high degree of...

Large Scale Hierarchical Clustering of Protein Sequences (2005)

Krause,Antje, Stoye,Jens, Vingron,Martin

Background Searching a biological sequence database with a query sequence looking for homologues has become a routine operation in computational biology. In spite of the high degree of sophistication...

Comparative analysis of cell cycle regulated genes in eukaryotes (2005)

Dyczkowski,Jerzy, Vingron,Martin

We compared microarray experiments on cell cycle of three model eukaryotes: budding and fission yeast and human cells. Only 112 orthologous groups were cyclic in the three model organisms. The common...

T-STAG: resource and web-interface for tissue-specific transcripts and genes (2005)

Gupta,Shobhit, Vingron,Martin, Haas,Stefan A.

T-STAG (tissue-specific transcripts and genes) is a resource and web-interface, designated to analyze tissue/tumor-specific expression patterns in human and mouse transcriptomes. It integrates our...

A gene expression map of Arabidopsis thaliana development (2005)

Schmid, Markus, Davison, Timothy S., Henz, Stefan R., Pape, Utz J., Demar, Monika, Vingron, Martin, ...

Genomic analysis of Drosophila chromosome underreplication reveals a link between replication control and transcriptional territories (2005)

Belyakin, Stepan N., Christophides, George K., Alekseyenko, Artyom A., Kriventseva, Evgenia V., Belyaeva, Elena S., ...

In Drosophila polytene chromosomes, most late-replicating regions remain underreplicated. A loss-of-function mutant of the suppressor of underreplication [Su(UR)] gene suppresses underreplication...

Comparative promoter region analysis powered by CORG (2005)

Dieterich, Christoph, Grossmann, Steffen, Tanzer, Andrea, Röpcke, Stefan, Arndt, Peter F, Stadler, Peter F, ...

Background Promoters are key players in gene regulation. They receive signals from various sources (e.g. cell surface receptors) and control the level of transcription initiation, which largely...

Comparative analysis of cell cycle regulated genes in eukaryotes (2005)

Dyczkowski, Jerzy, Vingron, Martin

We compared microarray experiments on cell cycle of three model eukaryotes: budding and fission yeast and human cells. Only 112 orthologous groups were cyclic in the three model organisms. The common...

T-STAG: resource and web-interface for tissue-specific transcripts and genes (2005)

Gupta, Shobhit, Vingron, Martin, Haas, Stefan A.

T-STAG (tissue-specific transcripts and genes) is a resource and web-interface, designated to analyze tissue/tumor-specific expression patterns in human and mouse transcriptomes. It integrates our...

Large Scale Hierarchical Clustering of Protein Sequences (2005)

Krause, Antje, Stoye, Jens, Vingron, Martin

Background Searching a biological sequence database with a query sequence looking for homologues has become a routine operation in computational biology. In spite of the high degree of sophistication...

Lethality and entropy of protein interaction networks (2005)

Manke, Thomas, Demetrius, Lloyd, Vingron, Martin

We characterize protein interaction networks in terms of network entropy. This approach suggests a ranking principle, which strongly correlates with elements of functional importance, such as lethal...

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...

SVC: structured visualization of evolutionary sequence conservation (2005)

Roepcke, Stefen, Fiziev, P., Seeburg, P. H., Vingron, Martin

We have developed a web application for the detailed analysis and visualization of evolutionary sequence conservation in complex vertebrate genes. Given a pair of orthologous genes, the...

Gene Expression in Kidney Cancer Is Associated with Cytogenetic Abnormalities, Metastasis Formation, and Patient Survival (2005)

Sueltmann, Holger, Von Heydebreck, Anja, Huber, Wolfgang, Kuner, Ruprecht, Buness, Andreas, Vogt, Markus, ...

Current diagnosis of renal cancer consists of histopathologic examination of tissue sections and classification into tumor stages and grades of malignancy. Until recently, molecular differences...

Normalization strategies for microarray data analysis (2005)

Steinhoff, Christine, Vingron, Martin

Haplotype reconstruction for diploid populations (2005)

Zhang, Jian, Vingron, Martin, Hoehe, Margret R.

The inference of haplotype pairs directly from unphased genotype data is a key step in the analysis of genetic variation in relation to disease and pharmacogenetically relevant traits. Most popular...

Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression (2005)

Irlbacher, Horst, Franke, Jacqueline, Manke, Thomas, Vingron, Martin, Ehrenhofer-Murray, Ann E.

Heterochromatinization at the silent mating-type loci HMR and HML in Saccharomyces cerevisiae is achieved by targeting the Sir complex to these regions via a set of anchor proteins that bind to the...

Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression (2005)

Irlbacher, Horst, Franke, Jacqueline, Manke, Thomas, Vingron, Martin, Ehrenhofer-Murray, Ann E.

Heterochromatinization at the silent mating-type loci HMR and HML in Saccharomyces cerevisiae is achieved by targeting the Sir complex to these regions via a set of anchor proteins that bind to the...

SITEBLAST-rapid and sensitive local alignment of genomic sequences employing motif anchors (2005)

Michael, Morris, Dieterich, Christoph, Vingron, Martin

Motivation: Comparative sequence analysis is the essence of many approaches to genome annotation. Heuristic alignment algorithms utilize similar seed pairs to anchor an alignment. Some applications...

Haplotype reconstruction for diploid populations (2005)

Zhang, Jian, Vingron, Martin, Hoehe, Margret R.

The inference of haplotype pairs directly from unphased genotype data is a key step in the analysis of genetic variation in relation to disease and pharmacogenetically relevant traits. Most popular...

T-Reg Comparator: an analysis tool for the (2005)

Stefan Roepcke, Steffen Grossmann, Sven Rahmann, Martin Vingron

comparison of position weight matrices

Invited (2005)

David Arnosti, East Lansing, Luca Peliti Napoli, Alvis Brazma, Hinxton Nikolaus, Rajewsky New York, ...

The aim of this program is to bring together researchers and students from different backgrounds (including molecular biology, bioinformatics, biological physics) to discuss Networks and Regulation,...

BMC Bioinformatics Methodology article Large scale hierarchical clustering of protein sequences (2005)

Antje Krause, Jens Stoye, Martin Vingron

Background: Searching a biological sequence database with a query sequence looking for homologues has become a routine operation in computational biology. In spite of the high degree of...

Invited (2005)

Thomas Bartolomaeus Berlin, Laurent Duret Lyon, Simone Hoegg Konstanz, Martin Lercher Heidelberg, Julia Mixtacki Bielefeld, ...

The aim of this program is to bring together researchers and students from different backgrounds (including molecular biology, bioinformatics, biological physics) to discuss a topic of high current...

Comparative promoter region analysis powered by CORG (2005)

Dieterich, Christoph, Grossmann, Steffen, Tanzer, Andrea, Ropcke, Stefan, Arndt, Peter F, Stadler, Peter F, ...

The SYSTERS Protein Family Database in 2005 (2005)

Meinel, Thomas, Krause, Antje, Luz, Hannes, Vingron, Martin, Staub, Eike

The SYSTERS project aims to provide a meaningful partitioning of the whole protein sequence space by a fully automatic procedure. A refined two-step algorithm assigns each protein to a family and a...

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-STAG: resource and web-interface for tissue-specific transcripts and genes (2005)

Gupta, Shobhit, Vingron, Martin, Haas, Stefan A.

T-STAG (tissue-specific transcripts and genes) is a resource and web-interface, designated to analyze tissue/tumor-specific expression patterns in human and mouse transcriptomes. It integrates our...

Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression (2005)

Irlbacher, Horst, Franke, Jacqueline, Manke, Thomas, Vingron, Martin, Ehrenhofer-Murray, Ann E.

Heterochromatinization at the silent mating-type loci HMR and HML in Saccharomyces cerevisiae is achieved by targeting the Sir complex to these regions via a set of anchor proteins that bind to the...

SITEBLAST-rapid and sensitive local alignment of genomic sequences employing motif anchors (2005)

Michael, Morris, Dieterich, Christoph, Vingron, Martin

Motivation: Comparative sequence analysis is the essence of many approaches to genome annotation. Heuristic alignment algorithms utilize similar seed pairs to anchor an alignment. Some applications...

The SRF target gene Fhl2 antagonizes RhoA/MAL-dependent activation of SRF (2004)

Philippar,Ulrike, Schratt,Gerhard, Dieterich,Christoph, Müller,Judith M., Galgóczy,Petra, Engel,Felix B., ...

RhoA signaling regulates the activity of the transcription factor SRF (serum response factor) during muscle differentiation. How RhoA signaling is integrated at SRF target promoters to achieve...

Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing (2004)

Gupta, Shobhit, Zink, Dorothea, Korn, Bernhard, Vingron, Martin, Haas, Stefan A

Abstract Background Alternative splicing contributes significantly to the complexity of the human transcriptome and proteome. Computational prediction of alternative splice isoforms are usually based...

Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing (2004)

Gupta,Shobhit, Zink,Dorothea, Korn,Bernhard, Vingron,Martin, Haas,Stefan A

Background: Alternative splicing contributes significantly to the complexity of the human transcriptome and proteome. Computational prediction of alternative splice isoforms are usually based on EST...

Annotating significant pairs of transcription factor binding sites in regulatory DNA (2004)

Rateitschak,Katja, Mueller,Tobias, Vingron,Martin

In the presented work we search for transcription factor binding sites (BS) by including additional information about typical BS patterns. The new proposed score combines the ordinary profile score...

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...

Genome wide identification and classification of alternative splicing based on EST data (2004)

Gupta,Shobhit, Zink,D., Korn,B., Vingron,Martin, Haas,Stefan A.

Motivation: Alternative splicing is currently seen to explain the vast disparity between the number of predicted genes in the human genome and the highly diverse proteome. The mapping of expressed...

Huber,Wolfgang, Von Heydebreck,Anja, Vingron,Martin

We derive the additive-multiplicative error model for microarray intensities, and describe two applications. For the detection of differentially expressed genes, we obtain a statistic whose variance...

Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin

We derive the additive-multiplicative error model for microarray intensities, and describe two applications. For the detection of differentially expressed genes, we obtain a statistic whose variance...

Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin

We derive the additive-multiplicative error model for microarray intensities, and describe two applications. For the detection of differentially expressed genes, we obtain a statistic whose variance...

Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin

We derive the additive-multiplicative error model for microarray intensities, and describe two applications. For the detection of differentially expressed genes, we obtain a statistic whose variance...

Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin

We derive the additive-multiplicative error model for microarray intensities, and describe two applications. For the detection of differentially expressed genes, we obtain a statistic whose variance...

Functional inference from non-random distributions of conserved predicted transcription factor binding sites (2004)

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...

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources (2004)

Crass,T., Antes,I., Basekow,R., Bork,P., Buning,C., Christensen,M., ...

The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single...

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources (2004)

Crass,T., Antes,I., Basekow,R., Bork,P., Buning,C., Christensen,M., ...

The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single...

IntAct: an open source molecular interaction database (2004)

Hermjakob,Henning, Montecchi-Palazzi,Luisa, Lewington,Chris, Mudali,Sugath, Kerrien,Samuel, Orchard,Sandra, ...

IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...

Genexpressionsanalyse komplexer klinischer Phänotypen mittels cDNS-Arrays - Gene Expression Profiling of Complex Clinical Phenotypes using cDNA-Arrays (2004)

Von Heydebreck,Anja, Sperling,Silke, Kaynak,Bogac, Lehrach,Hans, Vingron,Martin

In a genome-wide gene expression study, normal and congenitally malformed human hearts were examined using cDNA arrays. Statistical and bioinformatic methods were used in order to identify tissue-...

A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift (2004)

Xue,Yongtao T., Haas,Stefan, Brino,Laurento, Gusnanto,Arief, Riemers,Mark, Talibi,Driss, ...

Completion of the fission yeast genome sequence has opened up possibilities for post-genomic approaches. We have constructed a DNA microarray for genome-wide gene expression analysis in fission...

A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift (2004)

Xue,Yongtao T., Haas,Stefan, Brino,Laurento, Gusnanto,Arief, Riemers,Mark, Talibi,Driss, ...

Completion of the fission yeast genome sequence has opened up possibilities for post-genomic approaches. We have constructed a DNA microarray for genome-wide gene expression analysis in fission...

Genexpressionsanalyse komplexer klinischer Phänotypen mittels cDNSArrays - Gene Expression Proﬁling of Complex Clinical Phenotypes using cDNA-Arrays (2004)

Heydebreck,Anja Von, Sperling,Silke, Kaynak,Bogac, Lehrach,Hans, Vingron,Martin

Zusammenfassung: In einer genomweiten Genexpressionsstudie wurden normale und fehlgebildete menschliche Herzen mittels cDNS-Arrays untersucht. Statistische und bioinformatische Methoden wurden...

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources (2004)

Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., ...

The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single...

IntAct: an open source molecular interaction database (2004)

Hermjakob, Henning, Montecchi-Palazzi, Luisa, Lewington, Chris, Mudali, Sugath, Kerrien, Samuel, Orchard, Sandra, ...

IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...

Genexpressionsanalyse komplexer klinischer Phänotypen mittels cDNSArrays - Gene Expression Proﬁling of Complex Clinical Phenotypes using cDNA-Arrays (2004)

Heydebreck, Anja Von, Sperling, Silke, Kaynak, Bogac, Lehrach, Hans, Vingron, Martin

Zusammenfassung: In einer genomweiten Genexpressionsstudie wurden normale und fehlgebildete menschliche Herzen mittels cDNS-Arrays untersucht. Statistische und bioinformatische Methoden wurden...

The Helmholtz Network for Bioinformatics: an integrative web portal for bioinformatics resources (2004)

Crass, T., Antes, I., Basekow, R., Bork, P., Buning, C., Christensen, M., ...

The Helmholtz Network for Bioinformatics (HNB) is a joint venture of eleven German bioinformatics research groups that offers convenient access to numerous bioinformatics resources through a single...

Functional inference from non-random distributions of conserved predicted transcription factor binding sites (2004)

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...

Genome wide identification and classification of alternative splicing based on EST data (2004)

Gupta, Shobhit, Zink, D., Korn, B., Vingron, Martin, Haas, Stefan A.

Motivation: Alternative splicing is currently seen to explain the vast disparity between the number of predicted genes in the human genome and the highly diverse proteome. The mapping of expressed...

Strengths and weaknesses of EST-based prediction of tissue-specific alternative splicing (2004)

Gupta, Shobhit, Zink, Dorothea, Korn, Bernhard, Vingron, Martin, Haas, Stefan A

Background: Alternative splicing contributes significantly to the complexity of the human transcriptome and proteome. Computational prediction of alternative splice isoforms are usually based on EST...

Genexpressionsanalyse komplexer klinischer Phänotypen mittels cDNS-Arrays - Gene Expression Profiling of Complex Clinical Phenotypes using cDNA-Arrays (2004)

Von Heydebreck, Anja, Sperling, Silke, Kaynak, Bogac, Lehrach, Hans, Vingron, Martin

In a genome-wide gene expression study, normal and congenitally malformed human hearts were examined using cDNA arrays. Statistical and bioinformatic methods were used in order to identify tissue-...

Huber, Wolfgang, Von Heydebreck, Anja, Vingron, Martin

We derive the additive-multiplicative error model for microarray intensities, and describe two applications. For the detection of differentially expressed genes, we obtain a statistic whose variance...

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...

The SRF target gene Fhl2 antagonizes RhoA/MAL-dependent activation of SRF (2004)

Philippar, Ulrike, Schratt, Gerhard, Dieterich, Christoph, Müller, Judith M., Galgóczy, Petra, Engel, Felix B., ...

RhoA signaling regulates the activity of the transcription factor SRF (serum response factor) during muscle differentiation. How RhoA signaling is integrated at SRF target promoters to achieve...

Annotating significant pairs of transcription factor binding sites in regulatory DNA (2004)

Rateitschak, Katja, Mueller, Tobias, Vingron, Martin

In the presented work we search for transcription factor binding sites (BS) by including additional information about typical BS patterns. The new proposed score combines the ordinary profile score...

A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift (2004)

Xue, Yongtao T., Haas, Stefan, Brino, Laurento, Gusnanto, Arief, Riemers, Mark, Talibi, Driss, ...

Completion of the fission yeast genome sequence has opened up possibilities for post-genomic approaches. We have constructed a DNA microarray for genome-wide gene expression analysis in fission...

A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift (2004)

Xue, Yongtao T., Haas, Stefan, Brino, Laurento, Gusnanto, Arief, Riemers, Mark, Talibi, Driss, ...

Completion of the fission yeast genome sequence has opened up possibilities for post-genomic approaches. We have constructed a DNA microarray for genome-wide gene expression analysis in fission...

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...

SITEBLAST - rapid and sensitive local alignment of genomic sequences employing motif anchors (2004)

Michael, Morris, Dieterich, Christoph, Vingron, Martin

Motivation: Comparative sequence analysis is the essence of many approaches to genome annotation. Heuristic alignment algorithms utilize similar seed pairs to anchor an alignment. Some applications...

Functional inference from non-random distributions of conserved predicted transcription factor binding sites (2004)

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...

IntAct: an open source molecular interaction database (2004)

Hermjakob, Henning, Montecchi-Palazzi, Luisa, Lewington, Chris, Mudali, Sugath, Kerrien, Samuel, Orchard, Sandra, ...

IntAct provides an open source database and toolkit for the storage, presentation and analysis of protein interactions. The web interface provides both textual and graphical representations of...

SITEBLAST - rapid and sensitive local alignment of genomic sequences employing motif anchors (2004)

Michael, Morris, Dieterich, Christoph, Vingron, Martin

Motivation: Comparative sequence analysis is the essence of many approaches to genome annotation. Heuristic alignment algorithms utilize similar seed pairs to anchor an alignment. Some applications...

An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome (2003)

Hild,M., Beckmann,B., Haas,Stefan. A., Koch,B., Solovyev,V., Busold,C., ...

Background While the genome sequences for a variety of organisms are now available, the precise number of the genes encoded is still a matter of debate. For the human genome several stringent...

On the Power of Profiles for Transcription Factor Binding Site Detection (2003)

On the Power of Profiles for Transcription Factor Binding Site Detection (2003)

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)

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)

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...

Correlating protein-DNA and protein-protein interaction networks (2003)

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...

Manke,Thomas, Bringas,Ricardo, Vingron,Martin

Here, we search protein–DNA binding data for prevalent pairs and higher-order tuples of co-occurring transcription factors (TF) in Saccharomyces cerevisiae. While the identification of such modules...

Genome-scale design of PCR primers and long oligomers for DNA microarrays (2003)

Haas,Stefan A., Hild,Marc, Wright,Anthony P. H., Hain,Torsten, Talibi,Driss, Vingron,Martin

During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost...

A genome-wide transcriptional fingerprint of normal and malformed human hearts (2003)

Kaynak,Bogac, Von Heydebreck,Anja, Mebas,Siegrun, Seelow,Dominic, Vogel,Jan, Sperling,Hans-Peter, ...

Background— We present the first genome-wide cDNA array analysis of human congenitally malformed hearts and attempted to partially elucidate these complex phenotypes. Most congential heart defects,...

Analysis of CREM-dependent gene expression during mouse spermatogenesis (2003)

Beißbarth,Tim, Borisevich,Igor, Hörlein,Andreas, Kenzelmann,Marc, Hergenhahn,Manfred, Klewe-Nebenius,Annette, ...

The transcription factors CREM, CREB, and ATF-1 constitute a subfamily of -Zip transcription factors. Several different kinase cascades regulate the activity of these proteins. The activator...

A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift (2003)

Xue,Yongtao T., Haas,Stefan, Brino,Laurento, Gusnanto,Arief, Riemers,Mark, Talibi,Driss, ...

Completion of the fission yeast genome sequence has opened up possibilities for post-genomic approaches. We have constructed a DNA microarray for genome-wide gene expression analysis in fission...

Molecular phylogenetics: parallelized parameter estimation and quartet puzzling (2003)

Schmidt,Heiko A., Petzold,E., Vingron,Martin, Von Haeseler,Arndt

Exponential growth of the data available for molecular sequence analysis causes eminent need for methods to analyze large datasets in reasonable time. In molecular phylogenetics maximum-likelihood...

Analysis of microarray gene expression data (2003)

Huber,Wolfgang, Heydebreck,Anja Von, Vingron,Martin

This article reviews the methods utilized in processing and analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of mRNA...

Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites (2003)

Dieterich,Christoph, Herwig,Ralf, Vingron,Martin

Many cellular signaling pathways induce gene expression by activating specific transcription factor complexes. Conventional approaches to the prediction of transcription factor binding sites lead to...

New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes (2003)

Panopoulou,Georgia, Hennig,Steffen, Groth,Detlef, Krause,Antje, Poustka,Albert J., Herwig,Ralf, ...

The 2R hypothesis predicting two genome duplications at the origin of vertebrates is highly controversial. Studies published so far include limited sequence data from organisms close to the...

Genome-wide array analysis of normal and malformed human hearts (2003)

Kaynak,Bogac, Von Heydebreck,Anja, Mebus,Sigrun, Seelow,Dominik, Hennig,Steffen, Vogel,Jan, ...

Background We present the first genome-wide cDNA array analysis of human congenitally malformed hearts and attempted to partially elucidate these complex phenotypes. Most congential heart defects,...

Parameter estimation for the calibration and variance stabilization of microarray data (2003)

Huber,Wolfgang, Von Heydebreck,Anja, Sültmann,Holger, Poustka,Annemarie, Vingron,Martin

We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances...

Parameter estimation for the calibration and variance stabilization of microarray data (2003)

Huber, Wolfgang, Von Heydebreck, Anja, Sueltmann, Holger, Poustka, Annemarie, Vingron, Martin

We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances...

Parameter estimation for the calibration and variance stabilization of microarray data (2003)

Huber, Wolfgang, Von Heydebreck, Anja, Sueltmann, Holger, Poustka, Annemarie, Vingron, Martin

We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances...

Parameter estimation for the calibration and variance stabilization of microarray data (2003)

Huber, Wolfgang, Von Heydebreck, Anja, Sueltmann, Holger, Poustka, Annemarie, Vingron, Martin

We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances...

Parameter estimation for the calibration and variance stabilization of microarray data (2003)

Huber, Wolfgang, Von Heydebreck, Anja, Sueltmann, Holger, Poustka, Annemarie, Vingron, Martin

We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances...

Weighted sequence graphs: boosting iterated dynamic programming using locally suboptimal solutions (2003)

Schwikowski,Benno, Vingron,Martin

We present a novel technique for improving a fundamental aspect of iterated dynamic programming procedures on sequences, such as progressive sequence alignment. Instead of relying on the unrealistic...

Increase of functional diversity by alternative splicing (2003)

Kriventseva,Evgenia V., Koch,Ina, Apweiler,Rolf, Vingron,Martin, Bork,Peer, Gelfand,Mikhail S., ...

A large-scale analysis of protein isoforms arising from alternative splicing shows that alternative splicing tends to insert or delete complete protein domains more frequently than expected by...

Gene expression profile of mouse bone marrow stromal cells determined by cDNA microarray analysis (2003)

Wieczorek,G., Steinhoff,C., Schulz,R., Scheller,M., Vingron,Martin, Ropers,Hans Hilger, ...

Gene expression profile of mouse bone marrow stromal cells determined by cDNA microarray analysis (2003)

Wieczorek,Georg, Steinhoff,Christine, Schulz,Ralph, Scheller,Marina, Vingron,Martin, Ropers,Hans-Hilger, ...

Bone marrow stromal cells (BMSC) have gained increased attention because of their multipotency and adult stem cell character. They have been shown to differentiate into other cell types of the...

CORG: a database for COmparative Regulatory Genomics (2003)

Dieterich,Christoph, Wang,H., Rateitschak,K., Luz,Hannes, Vingron,Martin

Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a...

Support vector machines for protein fold class prediction (2003)

Markowetz,Florian, Edler,Lutz, Vingron,Martin

Knowledge of the three-dimensional structure of a protein is essential for describing and understanding its function. Today, a large number of known protein sequences faces a small number of...

The SYSTERS protein family database: taxon-related protein family size distributions and singleton frequencies (2003)

Meinel,Thomas, Vingron,Martin, Krause,Antje

Based on the SYSTERS protein family database, we present taxon-related protein family frequencies and distributions. A set of taxon-related protein families is a subset of the whole family set with...

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...

Gaussian mixture density estimation applied to microarray data (2003)

Steinhoff,Christine, Müller,Tobias, Nuber,Ulrike A., Vingron,Martin

Several publications have focused on fitting a specific distribution to overall microarray data. Due to a number of biological features the distribution of overall spot intensities can take various...

A DNA microarray for fission yeast: minimal changes in global gene expression after temperature shift (2003)

Xue, Yongtao T., Haas, Stefan, Brino, Laurento, Gusnanto, Arief, Riemers, Mark, Talibi, Driss, ...

Completion of the fission yeast genome sequence has opened up possibilities for post-genomic approaches. We have constructed a DNA microarray for genome-wide gene expression analysis in fission...

A genome-wide transcriptional fingerprint of normal and malformed human hearts (2003)

Kaynak, Bogac, Von Heydebreck, Anja, Mebas, Siegrun, Seelow, Dominic, Vogel, Jan, Sperling, Hans-Peter, ...

Background— We present the first genome-wide cDNA array analysis of human congenitally malformed hearts and attempted to partially elucidate these complex phenotypes. Most congential heart defects,...

Gene expression profile of mouse bone marrow stromal cells determined by cDNA microarray analysis (2003)

Wieczorek, Georg, Steinhoff, Christine, Schulz, Ralph, Scheller, Marina, Vingron, Martin, Ropers, Hans-Hilger, ...

Bone marrow stromal cells (BMSC) have gained increased attention because of their multipotency and adult stem cell character. They have been shown to differentiate into other cell types of the...

Genome-scale design of PCR primers and long oligomers for DNA microarrays (2003)

Haas, Stefan A., Hild, Marc, Wright, Anthony P. H., Hain, Torsten, Talibi, Driss, Vingron, Martin

During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost...

An integrated gene annotation and transcriptional profiling approach towards the full gene content of the Drosophila genome (2003)

Hild, M., Beckmann, B., Haas, Stefan. A., Koch, B., Solovyev, V., Busold, C., ...

Background While the genome sequences for a variety of organisms are now available, the precise number of the genes encoded is still a matter of debate. For the human genome several stringent...

Genome-wide array analysis of normal and malformed human hearts (2003)

Kaynak, Bogac, Von Heydebreck, Anja, Mebus, Sigrun, Seelow, Dominik, Hennig, Steffen, Vogel, Jan, ...

Background We present the first genome-wide cDNA array analysis of human congenitally malformed hearts and attempted to partially elucidate these complex phenotypes. Most congential heart defects,...

Increase of functional diversity by alternative splicing (2003)

Kriventseva, Evgenia V., Koch, Ina, Apweiler, Rolf, Vingron, Martin, Bork, Peer, Gelfand, Mikhail S., ...

A large-scale analysis of protein isoforms arising from alternative splicing shows that alternative splicing tends to insert or delete complete protein domains more frequently than expected by...

Correlating protein-DNA and protein-protein interaction networks (2003)

Manke, Thomas, Bringas, Ricardo, Vingron, Martin

Here, we search protein–DNA binding data for prevalent pairs and higher-order tuples of co-occurring transcription factors (TF) in Saccharomyces cerevisiae. While the identification of such modules...

Support vector machines for protein fold class prediction (2003)

Markowetz, Florian, Edler, Lutz, Vingron, Martin

Knowledge of the three-dimensional structure of a protein is essential for describing and understanding its function. Today, a large number of known protein sequences faces a small number of...

CORG: a database for COmparative Regulatory Genomics (2003)

Dieterich, Christoph, Wang, H., Rateitschak, K., Luz, Hannes, Vingron, Martin

Sequence conservation in non-coding, upstream regions of orthologous genes from man and mouse is likely to reflect common regulatory DNA sites. Motivated by this assumption we have delineated a...

New evidence for genome-wide duplications at the origin of vertebrates using an amphioxus gene set and completed animal genomes (2003)

Panopoulou, Georgia, Hennig, Steffen, Groth, Detlef, Krause, Antje, Poustka, Albert J., Herwig, Ralf, ...

The 2R hypothesis predicting two genome duplications at the origin of vertebrates is highly controversial. Studies published so far include limited sequence data from organisms close to the...

Analysis of CREM-dependent gene expression during mouse spermatogenesis (2003)

Beißbarth, Tim, Borisevich, Igor, Hörlein, Andreas, Kenzelmann, Marc, Hergenhahn, Manfred, Klewe-Nebenius, Annette, ...

The transcription factors CREM, CREB, and ATF-1 constitute a subfamily of -Zip transcription factors. Several different kinase cascades regulate the activity of these proteins. The activator...

Exploring potential target genes of signaling pathways by predicting conserved transcription factor binding sites (2003)

Dieterich, Christoph, Herwig, Ralf, Vingron, Martin

Many cellular signaling pathways induce gene expression by activating specific transcription factor complexes. Conventional approaches to the prediction of transcription factor binding sites lead to...

Parameter estimation for the calibration and variance stabilization of microarray data (2003)

Huber, Wolfgang, Von Heydebreck, Anja, Sültmann, Holger, Poustka, Annemarie, Vingron, Martin

We derive and validate an estimator for the parameters of a transformation for the joint calibration (normalization) and variance stabilization of microarray intensity data. With this, the variances...

The SYSTERS protein family database: taxon-related protein family size distributions and singleton frequencies (2003)

Meinel, Thomas, Vingron, Martin, Krause, Antje

Based on the SYSTERS protein family database, we present taxon-related protein family frequencies and distributions. A set of taxon-related protein families is a subset of the whole family set with...

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...

Molecular phylogenetics: parallelized parameter estimation and quartet puzzling (2003)

Schmidt, Heiko A., Petzold, E., Vingron, Martin, Von Haeseler, Arndt

Exponential growth of the data available for molecular sequence analysis causes eminent need for methods to analyze large datasets in reasonable time. In molecular phylogenetics maximum-likelihood...

Weighted sequence graphs: boosting iterated dynamic programming using locally suboptimal solutions (2003)

Schwikowski, Benno, Vingron, Martin

We present a novel technique for improving a fundamental aspect of iterated dynamic programming procedures on sequences, such as progressive sequence alignment. Instead of relying on the unrealistic...

Gaussian mixture density estimation applied to microarray data (2003)

Steinhoff, Christine, Müller, Tobias, Nuber, Ulrike A., Vingron, Martin

Several publications have focused on fitting a specific distribution to overall microarray data. Due to a number of biological features the distribution of overall spot intensities can take various...

Analysis of microarray gene expression data (2003)

Huber, Wolfgang, Heydebreck, Anja Von, Vingron, Martin

This article reviews the methods utilized in processing and analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of mRNA...

Gene expression profile of mouse bone marrow stromal cells determined by cDNA microarray analysis (2003)

Wieczorek, G., Steinhoff, C., Schulz, R., Scheller, M., Vingron, Martin, Ropers, Hans Hilger, ...

SYSTERS Protein Family Database: Taxonomy Web Interface and (2003)

Thomas Meinel, Antje Krause, Martin Vingron

Introduction The SYSTERS [5] protein family database provides an automatically generated clustering of all publicly available protein sequences into disjoint family and superfamily clusters. The...

Analysis of Microarray Gene Expression Data (2003)

Wolfgang Huber, Anja Von Heydebreck, Martin Vingron

This article reviews the methods utilized in processing and analysis of gene expression data generated using DNA microarrays. This type of experiment allows to determine relative levels of mRNA...

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...

New Evidence for Genome-Wide Duplications at the Origin of Vertebrates Using an Amphioxus Gene Set and Completed Animal Genomes (2003)

Panopoulou, Georgia, Hennig, Steffen, Groth, Detlef, Krause, Antje, Poustka, Albert J., Herwig, Ralf, ...

The 2R hypothesis predicting two genome duplications at the origin of vertebrates is highly controversial. Studies published so far include limited sequence data from organisms close to the...

Genome-scale design of PCR primers and long oligomers for DNA microarrays (2003)

Haas, Stefan A., Hild, Marc, Wright, Anthony P. H., Hain, Torsten, Talibi, Driss, Vingron, Martin

During the last years, the demand for custom‐made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene‐specific primers/oligomers is of the...

Theoretical analysis of alternative splice forms using computational methods (2002)

Boué,Stéphanie, Vingron,Martin, Kriventseva,Evgenia, Koch,Ina

Nowadays understanding alternative splicing is one of the greatest challenges in biology, because it is a genetic process much more important than thought at the time of its discovery. In this paper,...

Variance stabilization applied to microarray data calibration and to the quantification of differential expression (2002)

Huber,Wolfgang, Von Heydebreck,Anja, Sültmann,Holger, Poustka,Annemarie, Vingron,Martin

We introduce a statistical model for microarray gene expression data that comprises data calibration, the quantification of differential expression, and the quantification of measurement error. In...

Annotating regulatory DNA based on man-mouse genomic comparison (2002)

Dieterich,Christoph, Cusack,Brian, Wang,Haiyan, Rateitschak,Katja, Krause,Antje, Vingron,Martin

Non-coding DNA segments that are conserved between the human and mouse genomic sequence are good indicators of possible regulatory sequences. Here we report on a systematic approach to delineate such...

Monitoring the Switch from Housekeeping to Pathogen Defense Metabolism in Arabidopsis thaliana Using cDNA Arrays (2002)

Scheideler,Marcel, Schlaich,Nikolaus L., Fellenberg,Kurt, Beissbarth,Tim, Hauser,Nicole C., Vingron,Martin, ...

Plants respond to pathogen attack by deploying several defense reactions. Some rely on the activation of preformed components, whereas others depend on changes in transcriptional activity. Using cDNA...

Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis (2002)

Fellenberg,Kurt, Hauser,Nicole C., Brors,Benedikt, Hoheisel,Jörg D., Vingron,Martin

Motivation: Microarray technology provides access to expression levels of thousands of genes at once, producing large amounts of data. These datasets are valuable only if they are annotated by...

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002)

Schmidt,Heiko A., Strimmer,Korbinian, Vingron,Martin, Von Haeseler,Arndt

Summary: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol. , 13, 964–969, 1996) that provides...

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002)

Schmidt, Heiko A., Strimmer, Korbinian, Vingron, Martin, Von Haeseler, Arndt

Summary: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol. , 13, 964-969, 1996) that provides...

SpliceNest: visualizing gene structure and alternative splicing based on EST clusters (2002)

Coward,Eivind, Haas,Stefan A., Vingron,Martin

Messenger RNA sequences, expressed sequence tags (ESTs), and, in particular, consensus sequences of clustered ESTs provide valuable information about splice variants of genes. We have mapped such...

SpliceNest: visualizing gene structure and alternative splicing based on EST clusters (2002)

Coward,Eivind, Haas,Stefan A., Vingron,Martin

Messenger RNA sequences, expressed sequence tags (ESTs), and, in particular, consensus sequences of clustered ESTs provide valuable information about splice variants of genes. We have mapped such...

SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein (2002)

Krause,Antje, Haas,Stefan A., Coward,Eivind, Vingron,Martin

We have integrated the protein families from SYSTERS and the expressed sequence tag (EST) clusters from our database GeneNest with SpliceNest, a new database mapping EST contigs into genomic DNA. The...

Estimating Amino Acid Substitution Models: A Comparison of Dayhoff's Estimator, the Resolvent Approach and a Maximum Likelihood Method (2002)

Müller,Tobias, Spang,Rainer, Vingron,Martin

Evolution of proteins is generally modeled as a Markov process acting on each site of the sequence. Replacement frequencies need to be estimated based on sequence alignments. Here we compare three...

Microarray Data Representation, Annotation and Storage (2002)

Brazma,Alvis, Sarkans,Ugis, Robinson,Allan, Jaak,Vilo, Vingron,Martin, Hoheisel,Jörg, ...

Management and analysis of the huge amounts of data produced by microarray experiments is becoming one of the major bottlenecks in the utilization of this high-throughput technology. We describe the...

Theoretical analysis of alternative splice forms using computational methods (2002)

Boué, Stéphanie, Vingron, Martin, Kriventseva, Evgenia, Koch, Ina

Nowadays understanding alternative splicing is one of the greatest challenges in biology, because it is a genetic process much more important than thought at the time of its discovery. In this paper,...

Microarray Data Representation, Annotation and Storage (2002)

Brazma, Alvis, Sarkans, Ugis, Robinson, Allan, Jaak, Vilo, Vingron, Martin, Hoheisel, Jörg, ...

Management and analysis of the huge amounts of data produced by microarray experiments is becoming one of the major bottlenecks in the utilization of this high-throughput technology. We describe the...

SpliceNest: visualizing gene structure and alternative splicing based on EST clusters (2002)

Coward, Eivind, Haas, Stefan A., Vingron, Martin

Messenger RNA sequences, expressed sequence tags (ESTs), and, in particular, consensus sequences of clustered ESTs provide valuable information about splice variants of genes. We have mapped such...

SpliceNest: visualizing gene structure and alternative splicing based on EST clusters (2002)

Coward, Eivind, Haas, Stefan A., Vingron, Martin

Messenger RNA sequences, expressed sequence tags (ESTs), and, in particular, consensus sequences of clustered ESTs provide valuable information about splice variants of genes. We have mapped such...

Annotating regulatory DNA based on man-mouse genomic comparison (2002)

Dieterich, Christoph, Cusack, Brian, Wang, Haiyan, Rateitschak, Katja, Krause, Antje, Vingron, Martin

Non-coding DNA segments that are conserved between the human and mouse genomic sequence are good indicators of possible regulatory sequences. Here we report on a systematic approach to delineate such...

Microarray data warehouse allowing for inclusion of experiment annotations in statistical analysis (2002)

Fellenberg, Kurt, Hauser, Nicole C., Brors, Benedikt, Hoheisel, Jörg D., Vingron, Martin

Motivation: Microarray technology provides access to expression levels of thousands of genes at once, producing large amounts of data. These datasets are valuable only if they are annotated by...

Variance stabilization applied to microarray data calibration and to the quantification of differential expression (2002)

Huber, Wolfgang, Von Heydebreck, Anja, Sültmann, Holger, Poustka, Annemarie, Vingron, Martin

We introduce a statistical model for microarray gene expression data that comprises data calibration, the quantification of differential expression, and the quantification of measurement error. In...

SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein (2002)

Krause, Antje, Haas, Stefan A., Coward, Eivind, Vingron, Martin

We have integrated the protein families from SYSTERS and the expressed sequence tag (EST) clusters from our database GeneNest with SpliceNest, a new database mapping EST contigs into genomic DNA. The...

Estimating Amino Acid Substitution Models: A Comparison of Dayhoff's Estimator, the Resolvent Approach and a Maximum Likelihood Method (2002)

Müller, Tobias, Spang, Rainer, Vingron, Martin

Evolution of proteins is generally modeled as a Markov process acting on each site of the sequence. Replacement frequencies need to be estimated based on sequence alignments. Here we compare three...

Monitoring the Switch from Housekeeping to Pathogen Defense Metabolism in Arabidopsis thaliana Using cDNA Arrays (2002)

Scheideler, Marcel, Schlaich, Nikolaus L., Fellenberg, Kurt, Beissbarth, Tim, Hauser, Nicole C., Vingron, Martin, ...

Plants respond to pathogen attack by deploying several defense reactions. Some rely on the activation of preformed components, whereas others depend on changes in transcriptional activity. Using cDNA...

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002)

Schmidt, Heiko A., Strimmer, Korbinian, Vingron, Martin, Von Haeseler, Arndt

Summary: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol. , 13, 964–969, 1996) that provides...

Pages S84–S90 Annotating regulatory DNA based on man-mouse genomic comparison (2002)

Christoph Dieterich, Brian Cusack, Haiyan Wang, Antje Krause, Martin Vingron

Non-coding DNA segments that are conserved between the human and mouse genomic sequence are good indicators of possible regulatory sequences. Here we report on a systematic approach to delineate such...

SYSTERS, GeneNest, SpliceNest: exploring sequence space from genome to protein (2002)

Krause, Antje, Haas, Stefan A., Coward, Eivind, Vingron, Martin

We have integrated the protein families from SYSTERS and the expressed sequence tag (EST) clusters from our database GeneNest with SpliceNest, a new database mapping EST contigs into genomic DNA. The...

TREE-PUZZLE: maximum likelihood phylogenetic analysis using quartets and parallel computing (2002)

Schmidt, Heiko A., Strimmer, Korbinian, Vingron, Martin, Von Haeseler, Arndt

Summary: TREE-PUZZLE is a program package for quartet-based maximum-likelihood phylogenetic analysis (formerly PUZZLE, Strimmer and von Haeseler, Mol. Biol. Evol. , 13, 964–969, 1996) that provides...

Estimating Amino Acid Substitution Models: A Comparison of Dayhoff's Estimator, the Resolvent Approach and a Maximum Likelihood Method (2002)

Müller, Tobias, Spang, Rainer, Vingron, Martin

Evolution of proteins is generally modeled as a Markov process acting on each site of the sequence. Replacement frequencies need to be estimated based on sequence alignments. Here we compare three...

Theoretical analysis of alternative splice forms using computational methods (2002)

Boué, Stéphanie, Vingron, Martin, Kriventseva, Evgenia, Koch, Ina

Nowadays understanding alternative splicing is one of the greatest challenges in biology, because it is a genetic process much more important than thought at the time of its discovery. In this paper,...

Annotating regulatory DNA based on man-mouse genomic comparison (2002)

Dieterich, Christoph, Cusack, Brian, Wang, Haiyan, Rateitschak, Katja, Krause, Antje, Vingron, Martin

Non-coding DNA segments that are conserved between the human and mouse genomic sequence are good indicators of possible regulatory sequences. Here we report on a systematic approach to delineate such...

Variance stabilization applied to microarray data calibration and to the quantification of differential expression (2002)

Huber, Wolfgang, Von Heydebreck, Anja, Sültmann, Holger, Poustka, Annemarie, Vingron, Martin

We introduce a statistical model for microarray gene expression data that comprises data calibration, the quantification of differential expression, and the quantification of measurement error. In...

On haplotype reconstruction for diploid populations (2001)

Zhang, Jian, Vingron, Martin, Hoehe, Margret R

Statistical tools for discovering pseudo-periodicities in biological sequences (2001)

Prum, Bernard, Turckheim, Élisabeth De, Vingron, Martin

Limits of homology detection by pairwise sequence comparison (2001)

Rainer Spang, Martin Vingron, Deutsches Krebsforschungszentrum, Theoretische Bioinformatik, Im Neuenheimer Feld

Motivation: Noise in database searches resulting from random sequences similarities increases as the databases expand rapidly. The noise problems are not a technical shortcoming of the database...

Concepts for the estimation of amino acid substitution models (2001)

Rainer Spang, Martin Vingron, Deutsches Krebsforschungszentrum

In a simple model, the evolution of proteins can be viewed as the accumulation of amino acid substitutions. Amino acids with similar chemical and physical properties are replaced by each other more...

Limits of homology detection by pairwise sequence comparison (2001)

Spang, Rainer, Vingron, Martin

Motivation: Noise in database searches resulting from random sequence similarities increases as the databases expand rapidly. The noise problems are not a technical shortcoming of the database search...

Bioinformatics needs to adopt statistical thinking (2001)

Vingron, Martin

Identifying splits with clear separation: a new class discovery method for gene expression data (2001)

Von Heydebreck, Anja, Huber, Wolfgang, Poustka, Annemarie, Vingron, Martin

We present a new class discovery method for microarray gene expression data. Based on a collection of gene expression profiles from different tissue samples, the method searches for binary class...

Identification and Classification of Differentially Expressed Genes in Renal Cell Carcinoma by Expression Profiling on a Global Human 31,500-Element cDNA Array (2001)

Boer, Judith M., Huber, Wolfgang K., Sültmann, Holger, Wilmer, Friederike, Von Heydebreck, Anja, Haas, Stefan, ...

Identification and Classification of Differentially Expressed Genes in Renal Cell Carcinoma by Expression Profiling on a Global Human 31,500-Element cDNA Array (2001)

Boer, Judith M., Huber, Wolfgang K., Sültmann, Holger, Wilmer, Friederike, Von Heydebreck, Anja, Haas, Stefan, ...

A polyhedral approach to sequence alignment problems (2000)

Kececioglu, John, Lenhof, Hans-Peter, Mehlhorn, Kurt, Mutzel, Petra, Reinert, Knut, Vingron, Martin

Axeldb: a Xenopus laevis database focusing on gene expression (2000)

Pollet, Nicolas, Schmidt, Heiko A., Gawantka, Volker, Vingron, Martin, Niehrs, Christof

Axeldb is a database storing and integrating gene expression patterns and DNA sequences identified in a large-scale in situ hybridization study in Xenopus laevis embryos. The data are organised in a...

Computational approaches to identify leucine zippers (1998)

Erich Bornberg-bauer, Eric Rivals, Martin Vingron

The leucine zipper is a dimerization domain occurring mostly in regulatory and thus in many oncogenic proteins. The leucine repeat in the sequence has been traditionally used for identification,...

Statistics of large scale sequence searching (1998)

Rainer Spang, Martin Vingron, Deutsches Krebsforschungszentrum (dkfz, Theorefische Bioinformafik, Im Neuenheimer Feld

Statistics of large scale sequence searching (1998)

Rainer Spang, Martin Vingron, Deutsches Krebsforschungszentrum (dkfz, Theoretische Bioinformatik, Im Neuenheimer Feld

A Polyhedral Approach to RNA Sequence Structure Alignment (1998)

Hans-peter Lenhof, Knut Reinert, Martin Vingron

Ribonucleic acid (RNA) is a polymer composed of four bases denoted A, C, G, and U. It generally is a single-stranded molecule where the bases form hydrogen bonds within the same molecule leading to...

Using Parallel Computing for Maximum Likelihood Phylogenetic Analysis (1998)

Heiko A. Schmidt, Martin Vingron

Introduction Phylogenetic reconstruction is used in several fields of genetic sequence analysis. It is applied not only for inferring relationships between species or within gene or protein families....

A Polyhedral Approach to Sequence Alignment Problems (1998)

John D. Kececioglu, Hans-peter Lenhof, Kurt Mehlhorn, Petra Mutzel, Knut Reinert, Martin Vingron

We study two new problems in sequence alignment both from a practical and a theoretical view, using tools from combinatorial optimization to develop branchand -cut algorithms. The Generalized Maximum...

Computational Approaches to Identify Leucine Zippers (1998)

Erich Bornberg-bauer, Eric Rivals, Martin Vingron, Deutsches Krebsforschungszentrum, Theoretische Bioinformatik

The leucine zipper is a dimerisation domain occurring mostly in regulatory and thus in many oncogenic proteins. The leucine repeat in the sequence has been traditionally used for identification,...

The Deferred Path Heuristic for the Generalized Tree Alignment Problem (1997)

The Deferred Path Heuristic for the Generalized Tree Alignment Problem (1997)

Many multiple alignment methods implicitly or explicitly try to minimize the amount of biological change implied by an alignment. At the level of sequences, biological change is measured along a...