Bartek Wilczynski

Summary

Affiliation: Warsaw University
Country: Poland

Publications

  1. pmc Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state
    Bartek Wilczynski
    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Comput Biol 8:e1002798. 2012
  2. pmc Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs
    Bartek Wilczynski
    Institute of Informatics, University of Warsaw, Warsaw, Poland
    BMC Bioinformatics 10:82. 2009
  3. doi request reprint Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
    Stefan Bonn
    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Genet 44:148-56. 2012
  4. pmc Using local gene expression similarities to discover regulatory binding site modules
    Bartek Wilczynski
    lnstitute of Mathematics, Polish Academy of Sciences, Warsaw, Poland
    BMC Bioinformatics 7:505. 2006
  5. pmc BNFinder: exact and efficient method for learning Bayesian networks
    Bartek Wilczynski
    Institute of Informatics, University of Warsaw, Poland
    Bioinformatics 25:286-7. 2009
  6. pmc BNFinder2: Faster Bayesian network learning and Bayesian classification
    Norbert Dojer
    Institute of Informatics, University of Warsaw, Warsaw, Poland
    Bioinformatics 29:2068-70. 2013
  7. pmc Applying dynamic Bayesian networks to perturbed gene expression data
    Norbert Dojer
    Institute of Informatics, Warsaw University, Banacha 2, 02 097 Warszawa, Poland
    BMC Bioinformatics 7:249. 2006
  8. pmc Dynamic CRM occupancy reflects a temporal map of developmental progression
    Bartek Wilczynski
    Department of Genome Biology, European Molecular Biology Laboratory EMBL, Heidelberg, Germany
    Mol Syst Biol 6:383. 2010
  9. doi request reprint Challenges for modeling global gene regulatory networks during development: insights from Drosophila
    Bartek Wilczynski
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Dev Biol 340:161-9. 2010
  10. ncbi request reprint Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis
    Lucia Ciglar
    European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany
    Development 141:2633-43. 2014

Collaborators

Detail Information

Publications10

  1. pmc Predicting spatial and temporal gene expression using an integrative model of transcription factor occupancy and chromatin state
    Bartek Wilczynski
    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    PLoS Comput Biol 8:e1002798. 2012
    ..While this is, to our knowledge, the first genome-wide approach to predict tissue-specific gene expression in metazoan development, our results suggest that integrative models of this type will become more prevalent in the future...
  2. pmc Finding evolutionarily conserved cis-regulatory modules with a universal set of motifs
    Bartek Wilczynski
    Institute of Informatics, University of Warsaw, Warsaw, Poland
    BMC Bioinformatics 10:82. 2009
    ..This makes the problem of finding regions significantly enriched in binding sites difficult...
  3. doi request reprint Tissue-specific analysis of chromatin state identifies temporal signatures of enhancer activity during embryonic development
    Stefan Bonn
    Genome Biology Unit, European Molecular Biology Laboratory, Heidelberg, Germany
    Nat Genet 44:148-56. 2012
    ..This cell type-specific view identifies dynamic enhancer usage, an essential step in deciphering developmental networks...
  4. pmc Using local gene expression similarities to discover regulatory binding site modules
    Bartek Wilczynski
    lnstitute of Mathematics, Polish Academy of Sciences, Warsaw, Poland
    BMC Bioinformatics 7:505. 2006
    ..The novel aspects include local expression similarity clustering and an exact IF-THEN rule inference algorithm. We also provide a method of rule generalization to include genes with unknown expression profiles...
  5. pmc BNFinder: exact and efficient method for learning Bayesian networks
    Bartek Wilczynski
    Institute of Informatics, University of Warsaw, Poland
    Bioinformatics 25:286-7. 2009
    ..Moreover, they usually require at least basic programming abilities, which restricts their potential user base. Our goal was to provide software which would be freely available, efficient and usable to non-programmers...
  6. pmc BNFinder2: Faster Bayesian network learning and Bayesian classification
    Norbert Dojer
    Institute of Informatics, University of Warsaw, Warsaw, Poland
    Bioinformatics 29:2068-70. 2013
    ..net/bnfinder, together with a user's manual, introductory tutorial and supplementary methods...
  7. pmc Applying dynamic Bayesian networks to perturbed gene expression data
    Norbert Dojer
    Institute of Informatics, Warsaw University, Banacha 2, 02 097 Warszawa, Poland
    BMC Bioinformatics 7:249. 2006
    ..For example, dynamic Bayesian networks (DBN) apply to time series microarray data. To our knowledge the DBN technique has not been applied in the context of perturbation experiments...
  8. pmc Dynamic CRM occupancy reflects a temporal map of developmental progression
    Bartek Wilczynski
    Department of Genome Biology, European Molecular Biology Laboratory EMBL, Heidelberg, Germany
    Mol Syst Biol 6:383. 2010
    ..Systematic measurement of dynamic CRM occupancy may therefore serve as a powerful method to decode dynamic changes in gene expression driving developmental progression...
  9. doi request reprint Challenges for modeling global gene regulatory networks during development: insights from Drosophila
    Bartek Wilczynski
    European Molecular Biology Laboratory, D 69117 Heidelberg, Germany
    Dev Biol 340:161-9. 2010
    ..We focus on two very well-studied examples from Drosophila, which likely represent typical developmental regulatory modules across metazoans...
  10. ncbi request reprint Coordinated repression and activation of two transcriptional programs stabilizes cell fate during myogenesis
    Lucia Ciglar
    European Molecular Biology Laboratory, Genome Biology Unit, Heidelberg 69117, Germany
    Development 141:2633-43. 2014
    ..Lineage-specific factors are therefore not sufficient to maintain FCM identity. Instead, their identity appears more plastic, requiring the combination of instructive repressive and activating programs to stabilize cell fate. ..