Integrating sequence, evolution and functional genomics in regulatory genomics (2009)
Vingron, Martin, Brazma, Alvis, Coulson, Richard, Van Helden, Jacques, Manke, Thomas, Palin, Kimmo, ...
Abstract With genome analysis expanding from the study of genes to the study of gene regulation, 'regulatory genomics' utilizes sequence information, evolution and functional genomics measurements to...
PASTAA: identifying transcription factors associated with sets of co-regulated genes (2009)
Roider, Helge G., Manke, Thomas, O'Keeffe, Sean, Vingron, Martin, Haas, Stefan A.
Motivation: A major challenge in regulatory genomics is the identification of associations between functional categories of genes (e.g. tissues, metabolic pathways) and their regulating transcription...
Supplementary Material For (2008)
Ho-joon Lee, Thomas Manke, Ricardo Bringas, Martin Vingron, Ho-joon Lee, Thomas Manke, ...
Prioritization of gene regulatory interactions from large-scale modules in yeast
Prioritization of gene regulatory interactions from large-scale modules in yeast (2008)
Lee, Ho-Joon, Manke, Thomas, Bringas, Ricardo, Vingron, Martin
Abstract Background The identification of groups of co-regulated genes and their transcription factors, called transcriptional modules, has been a focus of many studies about biological systems....
From gene expression profiling to gene regulation (2008)
Coulson, R., Manke, Thomas, Palin, K., Roider, H., Sand, O., Van Helden, J., ...
Manke, Thomas, Roider, Helge G., Vingron, Martin
Recent experimental and theoretical efforts have highlighted the fact that binding of transcription factors to DNA can be more accurately described by continuous measures of their binding affinities,...
A biophysical approach to large-scale protein-DNA binding data (2008)
Manke, Thomas, Roider, Helge G., Vingron, Martin
About this book * Cutting-edge genome analysis methods from leading bioinformaticians An accurate description of current scientific developments in the field of bioinformatics and computational...
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...
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....
Mao, Lei, Zabel, Claus, Herrmann, Marion, Nolden, Tobias, Mertes, Florian, Magnol, Laetitia, ...
Large numbers of protein expression changes are usually observed in mouse models for neurodegenerative diseases, even when only a single gene was mutated in each case. To study the effect of gene...
Mao, Lei, Zabel, Claus, Herrmann, Marion, Nolden, Tobias, Mertes, Florian, Magnol, Laetitia, ...
Large numbers of protein expression changes are usually observed in mouse models for neurodegenerative diseases, even when only a single gene was mutated in each case. To study the effect of gene...
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....
Two-flavor QCD Thermodynamics using Anisotropic Lattices (2006)
Levkova, Ludmila, Manke, Thomas, Mawhinney, Robert
Numerical simulations of full QCD on anisotropic lattices provide a convenient way to study QCD thermodynamics with fixed physics scales and reduced lattice spacing errors. We report results from...
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,...
Robustness and network evolution--an entropic principle (2005)
This article introduces the concept of network entropy as a characteristic measure of network topology. We provide computational and analytical support for the hypothesis that network entropy is a...
Robustness and network evolution--an entropic principle (2005)
Demetrius, Lloyd, Manke, Thomas
This article introduces the concept of network entropy as a characteristic measure of network topology. We provide computational and analytical support for the hypothesis that network entropy is a...
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...
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...
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...
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...
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...
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...
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...
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...
Mao, Lei, Zabel, Claus, Herrmann, Marion, Nolden, Tobias, Mertes, Florian, Magnol, Laetitia, ...
Large numbers of protein expression changes are usually observed in mouse models for neurodegenerative diseases, even when only a single gene was mutated in each case. To study the effect of gene...
Prioritization of gene regulatory interactions from large-scale modules in yeast
Lee, Ho-Joon, Manke, Thomas, Bringas, Ricardo, Vingron, Martin
An entropic characterization of protein interaction networks and cellular robustness
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,...
Statistical Modeling of Transcription Factor Binding Affinities Predicts Regulatory Interactions
Manke, Thomas, Roider, Helge G., Vingron, Martin
Recent experimental and theoretical efforts have highlighted the fact that binding of transcription factors to DNA can be more accurately described by continuous measures of their binding affinities,...
PASTAA: identifying transcription factors associated with sets of co-regulated genes
Roider, Helge G., Manke, Thomas, O'Keeffe, Sean, Vingron, Martin, Haas, Stefan A.
Motivation: A major challenge in regulatory genomics is the identification of associations between functional categories of genes (e.g. tissues, metabolic pathways) and their regulating transcription...
Integrating sequence, evolution and functional genomics in regulatory genomics
Vingron, Martin, Brazma, Alvis, Coulson, Richard, Van Helden, Jacques, Manke, Thomas, Palin, Kimmo, ...
Finding transcription factor binding sites in regulatory regions of the genome