Sven Bergmann

Summary

Affiliation: Weizmann Institute of Science
Country: Israel

Publications

  1. ncbi request reprint Iterative signature algorithm for the analysis of large-scale gene expression data
    Sven Bergmann
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Phys Rev E Stat Nonlin Soft Matter Phys 67:031902. 2003
  2. pmc The evolving doublecortin (DCX) superfamily
    Orly Reiner
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    BMC Genomics 7:188. 2006
  3. ncbi request reprint Rewiring of the yeast transcriptional network through the evolution of motif usage
    Jan Ihmels
    Department of Molecular Genetics and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
    Science 309:938-40. 2005
  4. pmc Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program
    Jan Ihmels
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Genet 1:e39. 2005
  5. ncbi request reprint Defining transcription modules using large-scale gene expression data
    Jan Ihmels
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Bioinformatics 20:1993-2003. 2004
  6. pmc Similarities and differences in genome-wide expression data of six organisms
    Sven Bergmann
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Biol 2:E9. 2004
  7. ncbi request reprint Revealing modular organization in the yeast transcriptional network
    Jan Ihmels
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
    Nat Genet 31:370-7. 2002
  8. ncbi request reprint Challenges and prospects in the analysis of large-scale gene expression data
    Jan H Ihmels
    Department of Molecular Genetics, Weizmann Institute, 76100 Rehovot, Israel
    Brief Bioinform 5:313-27. 2004
  9. ncbi request reprint Common and divergent roles for members of the mouse DCX superfamily
    Frédéric M Coquelle
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Cell Cycle 5:976-83. 2006
  10. pmc Pre-steady-state decoding of the Bicoid morphogen gradient
    Sven Bergmann
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Biol 5:e46. 2007

Collaborators

Detail Information

Publications13

  1. ncbi request reprint Iterative signature algorithm for the analysis of large-scale gene expression data
    Sven Bergmann
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot 76100, Israel
    Phys Rev E Stat Nonlin Soft Matter Phys 67:031902. 2003
    ..This result is confirmed by numerical analyses based on in silico expression data. We discuss briefly results obtained by applying our algorithm to expression data from the yeast Saccharomyces cerevisiae...
  2. pmc The evolving doublecortin (DCX) superfamily
    Orly Reiner
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    BMC Genomics 7:188. 2006
    ....
  3. ncbi request reprint Rewiring of the yeast transcriptional network through the evolution of motif usage
    Jan Ihmels
    Department of Molecular Genetics and Department of Physics of Complex Systems, Weizmann Institute of Science, Rehovot, Israel
    Science 309:938-40. 2005
    ..Our results shed new light on the genetic mechanisms underlying the large-scale evolution of transcriptional networks...
  4. pmc Comparative gene expression analysis by differential clustering approach: application to the Candida albicans transcription program
    Jan Ihmels
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Genet 1:e39. 2005
    ..Our study provides a comprehensive framework for comparative gene expression analysis and a rich source of hypotheses for uncharacterized open reading frames and putative cis-regulatory elements in C. albicans...
  5. ncbi request reprint Defining transcription modules using large-scale gene expression data
    Jan Ihmels
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Bioinformatics 20:1993-2003. 2004
    ..However, this approach is constrained by the comprehensiveness of relevant external data and its lacking ability to capture hierarchical modularity...
  6. pmc Similarities and differences in genome-wide expression data of six organisms
    Sven Bergmann
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Biol 2:E9. 2004
    ..Our results demonstrate the potential of combining sequence and expression data for improving functional gene annotation and expanding our understanding of how gene expression and diversity evolved...
  7. ncbi request reprint Revealing modular organization in the yeast transcriptional network
    Jan Ihmels
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, 76100, Israel
    Nat Genet 31:370-7. 2002
    ..Our results provide functional predictions for numerous genes, identify relations between modules and present a global view on the transcriptional network...
  8. ncbi request reprint Challenges and prospects in the analysis of large-scale gene expression data
    Jan H Ihmels
    Department of Molecular Genetics, Weizmann Institute, 76100 Rehovot, Israel
    Brief Bioinform 5:313-27. 2004
    ..Biological questions that have been addressed using the Signature Algorithm are highlighted and a summary of other important methods from the literature is provided...
  9. ncbi request reprint Common and divergent roles for members of the mouse DCX superfamily
    Frédéric M Coquelle
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    Cell Cycle 5:976-83. 2006
    ..The sub-specialization of some members due to confined intracellular localization, and protein interactions may explain the success of this superfamily...
  10. pmc Pre-steady-state decoding of the Bicoid morphogen gradient
    Sven Bergmann
    Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
    PLoS Biol 5:e46. 2007
    ..This can explain the surprisingly small shifts in gap and pair-rule gene expression domains observed in response to alterations in bcd dosage...
  11. doi request reprint A modular approach for integrative analysis of large-scale gene-expression and drug-response data
    Zoltan Kutalik
    Department of Medical Genetics, University of Lausanne, Rue de Bugnon 27 DGM 328, CH 1005 Lausanne, Switzerland
    Nat Biotechnol 26:531-9. 2008
    ..Co-modules provide insights into possible mechanisms of action for a wide range of drugs and suggest new targets for therapy...
  12. ncbi request reprint Investigations on the ORF 167L of lymphocystis disease virus (Iridoviridae)
    Sandra Essbauer
    Institute of Zoology, Fishery Biology and Fish Diseases, LMU University of Munich, Kaulbachstrasse 37, D 80539 Munich, Germany
    Virus Genes 28:19-39. 2004
    ..The myxomavirus M-T2 protein, a poxviral TNFR homologue, was also shown not to have TNFR-like functions but to be involved in the apoptosis signal cascade...
  13. ncbi request reprint Comparative genome hybridization reveals widespread aneuploidy in Candida albicans laboratory strains
    Anna Selmecki
    Department of Genetics, Cell Biology and Development, University of Minnesota, MN, USA
    Mol Microbiol 55:1553-65. 2005
    ..albicans strains. Furthermore, they highlight the high level of genome instability in C. albicans laboratory strains exposed to the stress of transformation and counterselection on 5-fluoro-orotic acid...