Thomas Manke

Summary

Affiliation: Max Planck Institute for Molecular Genetics
Country: Germany

Publications

  1. ncbi Quantifying the effect of sequence variation on regulatory interactions
    Thomas Manke
    Max Planck Institute for Molecular Genetics, Computational Biology, Ihnestrasse 73, Berlin, Germany
    Hum Mutat 31:477-83. 2010
  2. ncbi Lethality and entropy of protein interaction networks
    Thomas Manke
    Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Genome Inform 16:159-63. 2005
  3. ncbi An entropic characterization of protein interaction networks and cellular robustness
    Thomas Manke
    Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany
    J R Soc Interface 3:843-50. 2006
  4. ncbi Statistical modeling of transcription factor binding affinities predicts regulatory interactions
    Thomas Manke
    Max Planck Institute for Molecular Genetics, Berlin, Germany
    PLoS Comput Biol 4:e1000039. 2008
  5. ncbi Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters
    Hans Jörg Warnatz
    Department for Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63 73, 14195 Berlin, Germany
    Nucleic Acids Res 38:6112-23. 2010
  6. ncbi Predicting transcription factor affinities to DNA from a biophysical model
    Helge G Roider
    Max Planck Institute for Molecular Genetics Ihnestrasse 73, 14195 Berlin, Germany
    Bioinformatics 23:134-41. 2007
  7. ncbi Prioritization of gene regulatory interactions from large-scale modules in yeast
    Ho Joon Lee
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
    BMC Bioinformatics 9:32. 2008
  8. ncbi PASTAA: identifying transcription factors associated with sets of co-regulated genes
    Helge G Roider
    Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin
    Bioinformatics 25:435-42. 2009
  9. ncbi The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle
    Hans Jörg Warnatz
    Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
    J Biol Chem 286:23521-32. 2011
  10. ncbi MicroRNAs differentially expressed in postnatal aortic development downregulate elastin via 3' UTR and coding-sequence binding sites
    Claus Eric Ott
    Institute for Medical Genetics, Charite Universitatsmedizin Berlin, Berlin, Germany
    PLoS ONE 6:e16250. 2011

Collaborators

Detail Information

Publications17

  1. ncbi Quantifying the effect of sequence variation on regulatory interactions
    Thomas Manke
    Max Planck Institute for Molecular Genetics, Computational Biology, Ihnestrasse 73, Berlin, Germany
    Hum Mutat 31:477-83. 2010
    ..Given the good performance of our method, we developed a publicly available tool that can serve as an important starting point for routine analysis of disease-associated sequence regions...
  2. ncbi Lethality and entropy of protein interaction networks
    Thomas Manke
    Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin, Germany
    Genome Inform 16:159-63. 2005
    ..It is also applicable to networks in which the processes can be quantified and therefore serves as a link to study questions of structural and dynamical robustness in a unified way...
  3. ncbi An entropic characterization of protein interaction networks and cellular robustness
    Thomas Manke
    Max Planck Institute for Molecular Genetics, Ihnestr 73, 14195 Berlin, Germany
    J R Soc Interface 3:843-50. 2006
    ..One of its principal achievements is to provide a rationale to study proxies of cellular resilience and rank proteins according to their importance within the global network context...
  4. ncbi Statistical modeling of transcription factor binding affinities predicts regulatory interactions
    Thomas Manke
    Max Planck Institute for Molecular Genetics, Berlin, Germany
    PLoS Comput Biol 4:e1000039. 2008
    ..Its successful application to human promoter sequences serves as an encouraging example of how the method can be applied to other sequences...
  5. ncbi Functional analysis and identification of cis-regulatory elements of human chromosome 21 gene promoters
    Hans Jörg Warnatz
    Department for Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestrasse 63 73, 14195 Berlin, Germany
    Nucleic Acids Res 38:6112-23. 2010
    ..This study illustrates the modular functional architecture of chromosome 21 promoters and helps to reveal the complex mechanisms governing transcriptional regulation...
  6. ncbi Predicting transcription factor affinities to DNA from a biophysical model
    Helge G Roider
    Max Planck Institute for Molecular Genetics Ihnestrasse 73, 14195 Berlin, Germany
    Bioinformatics 23:134-41. 2007
    ..The question arises to what extent these two approaches converge. In this paper, we adopt a physical binding model to predict the relative binding affinity of a transcription factor for a given sequence...
  7. ncbi Prioritization of gene regulatory interactions from large-scale modules in yeast
    Ho Joon Lee
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
    BMC Bioinformatics 9:32. 2008
    ..In this work, we aim to prioritize regulator-target links within transcriptional modules based on three types of large-scale data sources...
  8. ncbi PASTAA: identifying transcription factors associated with sets of co-regulated genes
    Helge G Roider
    Max Planck Institute for Molecular Genetics, Ihnestrasse 73, 14195 Berlin
    Bioinformatics 25:435-42. 2009
    ..While, for a limited number of categories, the regulating TFs are already known, still for many functional categories the responsible factors remain to be elucidated...
  9. ncbi The BTB and CNC homology 1 (BACH1) target genes are involved in the oxidative stress response and in control of the cell cycle
    Hans Jörg Warnatz
    Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
    J Biol Chem 286:23521-32. 2011
    ....
  10. ncbi MicroRNAs differentially expressed in postnatal aortic development downregulate elastin via 3' UTR and coding-sequence binding sites
    Claus Eric Ott
    Institute for Medical Genetics, Charite Universitatsmedizin Berlin, Berlin, Germany
    PLoS ONE 6:e16250. 2011
    ..Our results demonstrate that multiple miR-29 and miR-15 family MREs are characteristic for some ECM genes and suggest that miR-29 and miR-15 family miRNAs are involved in the down-regulation of elastin in the adult aorta...
  11. ncbi Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs
    Morgane Thomas-Chollier
    Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany
    Nat Protoc 6:1860-9. 2011
    ..All of the tools are fully available online and do not need any additional installation. The complete protocol takes about 45 min, but each individual tool runs in a few minutes...
  12. ncbi Screening of human gene promoter activities using transfected-cell arrays
    Xi Cheng
    Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany
    Gene 450:48-54. 2010
    ..Moreover, this is the first large-scale functional study of regulatory sequences to use a high-throughput transfected-cell array technique...
  13. ncbi Integrating sequence, evolution and functional genomics in regulatory genomics
    Martin Vingron
    Computational Molecular Biology, Max Planck Institut fur Molekulare Genetik, Berlin, Germany
    Genome Biol 10:202. 2009
    ....
  14. ncbi Correlating protein-DNA and protein-protein interaction networks
    Thomas Manke
    Max-Planck-Institute for Molecular Genetics, Abt Bioinformatik, Ihnestr. 73, 14195 Berlin, Germany
    J Mol Biol 333:75-85. 2003
    ..In particular we find that directly interacting transcription factors and those which are members of a protein complex are more likely to occur together as putative DNA-binding modules...
  15. ncbi Promiscuous and depolarization-induced immediate-early response genes are induced by mechanical strain of osteoblasts
    Claus Eric Ott
    Institute for Medical Genetics, Charite Universitatsmedizin Berlin, Berlin, Germany
    J Bone Miner Res 24:1247-62. 2009
    ....
  16. ncbi Proteomic shifts in embryonic stem cells with gene dose modifications suggest the presence of balancer proteins in protein regulatory networks
    Lei Mao
    Institute for Human Genetics, Charite University Medicine Berlin, Germany
    PLoS ONE 2:e1218. 2007
    ..We propose that the "elasticity" of the proteomic regulatory network mediated by balancer proteins may compensate for changes that occur under diseased conditions...
  17. ncbi Control of replication initiation and heterochromatin formation in Saccharomyces cerevisiae by a regulator of meiotic gene expression
    Horst Irlbacher
    Otto Warburg Laboratorium and Department for Computational Molecular Biology, Max Planck Institut fur Molekulare Genetik, D 14195 Berlin, Germany
    Genes Dev 19:1811-22. 2005
    ..Full initiation activity of these origins required Sum1, and their origin activity was decreased upon removal of the Sum1-binding site. Thus, Sum1 constitutes a novel global regulator of replication initiation in yeast...