HARMEN BUSSEMAKER

Summary

Affiliation: Columbia University
Country: USA

Publications

  1. pmc TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors
    Barrett C Foat
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    Nucleic Acids Res 36:D125-31. 2008
  2. pmc Identifying the genetic determinants of transcription factor activity
    Eunjee Lee
    Department of Biological Sciences, Columbia University, New York, NY 10027, USA
    Mol Syst Biol 6:412. 2010
  3. pmc Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression
    Andre Boorsma
    Swammerdam Institute for Life Sciences, University of Amsterdam, BioCentrum Amsterdam, Amsterdam, The Netherlands
    PLoS ONE 3:e3112. 2008
  4. pmc Global chromatin domain organization of the Drosophila genome
    Elzo de Wit
    Department of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
    PLoS Genet 4:e1000045. 2008
  5. pmc Detecting transcriptionally active regions using genomic tiling arrays
    Gabor Halasz
    Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027, USA
    Genome Biol 7:R59. 2006
  6. pmc Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
    Feng Gao
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    BMC Bioinformatics 5:31. 2004
  7. ncbi request reprint Predictive modeling of genome-wide mRNA expression: from modules to molecules
    Harmen J Bussemaker
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    Annu Rev Biophys Biomol Struct 36:329-47. 2007
  8. pmc Dissecting complex transcriptional responses using pathway-level scores based on prior information
    Harmen J Bussemaker
    Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, MC 2441, New York, NY 10027, USA
    BMC Bioinformatics 8:S6. 2007
  9. pmc Profiling condition-specific, genome-wide regulation of mRNA stability in yeast
    Barrett C Foat
    Department of Biological Sciences, Columbia University, New York, NY 10027, USA
    Proc Natl Acad Sci U S A 102:17675-80. 2005
  10. pmc REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data
    Crispin Roven
    Department of Biological Sciences, Columbia University, New York, NY, USA
    Nucleic Acids Res 31:3487-90. 2003

Research Grants

Collaborators

Detail Information

Publications27

  1. pmc TransfactomeDB: a resource for exploring the nucleotide sequence specificity and condition-specific regulatory activity of trans-acting factors
    Barrett C Foat
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    Nucleic Acids Res 36:D125-31. 2008
    ..Our resource is freely available at http://bussemakerlab.org/TransfactomeDB/..
  2. pmc Identifying the genetic determinants of transcription factor activity
    Eunjee Lee
    Department of Biological Sciences, Columbia University, New York, NY 10027, USA
    Mol Syst Biol 6:412. 2010
    ..Our method has greatly improved statistical power over existing methods, is mechanism based, strictly causal, computationally efficient, and generally applicable...
  3. pmc Inferring condition-specific modulation of transcription factor activity in yeast through regulon-based analysis of genomewide expression
    Andre Boorsma
    Swammerdam Institute for Life Sciences, University of Amsterdam, BioCentrum Amsterdam, Amsterdam, The Netherlands
    PLoS ONE 3:e3112. 2008
    ....
  4. pmc Global chromatin domain organization of the Drosophila genome
    Elzo de Wit
    Department of Molecular Biology, Netherlands Cancer Institute, Amsterdam, The Netherlands
    PLoS Genet 4:e1000045. 2008
    ..Our results indicate that a substantial portion of the Drosophila genome is packaged into functionally coherent, multi-gene chromatin domains. This has broad mechanistic implications for gene regulation and genome evolution...
  5. pmc Detecting transcriptionally active regions using genomic tiling arrays
    Gabor Halasz
    Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, New York, NY 10027, USA
    Genome Biol 7:R59. 2006
    ..Our method also showed improved detection of transcriptional units when applied to high-density tiling array data for ten human chromosomes...
  6. pmc Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data
    Feng Gao
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    BMC Bioinformatics 5:31. 2004
    ..The challenge is to extract useful information about the global regulatory network from these data...
  7. ncbi request reprint Predictive modeling of genome-wide mRNA expression: from modules to molecules
    Harmen J Bussemaker
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    Annu Rev Biophys Biomol Struct 36:329-47. 2007
    ..As the ability of these models to represent complex cis-regulatory logic increases, the need for approaches based on cross-species conservation may diminish...
  8. pmc Dissecting complex transcriptional responses using pathway-level scores based on prior information
    Harmen J Bussemaker
    Department of Biological Sciences, Columbia University, 1212 Amsterdam Avenue, MC 2441, New York, NY 10027, USA
    BMC Bioinformatics 8:S6. 2007
    ....
  9. pmc Profiling condition-specific, genome-wide regulation of mRNA stability in yeast
    Barrett C Foat
    Department of Biological Sciences, Columbia University, New York, NY 10027, USA
    Proc Natl Acad Sci U S A 102:17675-80. 2005
    ..We provide computational and experimental evidence that regulation of mRNA stability by these factors is modulated in response to a variety of environmental stimuli...
  10. pmc REDUCE: An online tool for inferring cis-regulatory elements and transcriptional module activities from microarray data
    Crispin Roven
    Department of Biological Sciences, Columbia University, New York, NY, USA
    Nucleic Acids Res 31:3487-90. 2003
    ..bio.columbia.edu/reduce/. This web site provides functionality for the upload and management of microarray data. REDUCE analysis results can be viewed and downloaded, and optionally be shared with other users or made publicly accessible...
  11. pmc The RNA backbone plays a crucial role in mediating the intrinsic stability of the GpU dinucleotide platform and the GpUpA/GpA miniduplex
    Xiang Jun Lu
    Department of Biological Sciences, Columbia University, New York, NY 10027, USA
    Nucleic Acids Res 38:4868-76. 2010
    ..We propose that they may also provide a reason for the extreme conservation of GpU observed at most 5'-splice sites...
  12. ncbi request reprint Statistical mechanical modeling of genome-wide transcription factor occupancy data by MatrixREDUCE
    Barrett C Foat
    Department of Biological Sciences, Columbia University New York, NY 10027, USA
    Bioinformatics 22:e141-9. 2006
    ....
  13. pmc Predicting functional transcription factor binding through alignment-free and affinity-based analysis of orthologous promoter sequences
    Lucas D Ward
    Department of Biological Sciences, Columbia University, New York, NY 10027, USA
    Bioinformatics 24:i165-71. 2008
    ..Both of these approaches suffer from the inability to model and detect low-affinity binding sites, which have recently been shown to be abundant and functional...
  14. ncbi request reprint Identification of genes expressed in C. elegans touch receptor neurons
    Yun Zhang
    Department of Biological Sciences, Columbia University, New York, New York 10027, USA
    Nature 418:331-5. 2002
    ..Using regions 5' of the start codon of the first 20 genes, we have also identified an over-represented heptanucleotide, AATGCAT, that is needed for the expression of touch receptor genes...
  15. pmc The human transcriptome map reveals extremes in gene density, intron length, GC content, and repeat pattern for domains of highly and weakly expressed genes
    Rogier Versteeg
    Department of Human Genetics, Academic Medical Center, University of Amsterdam, 1100DE Amsterdam, The Netherlands
    Genome Res 13:1998-2004. 2003
    ..Ridges are therefore an integral part of a higher order structure in the genome related to transcriptional regulation...
  16. pmc Dissection of transient oxidative stress response in Saccharomyces cerevisiae by using DNA microarrays
    Marian Groot Koerkamp
    Department of Biochemistry, Academic Medical Center, University of Amsterdam, The Netherlands
    Mol Biol Cell 13:2783-94. 2002
    ..We ascribe the initiation of the oxidative stress response to a combination of poor redox flux and fatty acid-induced uncoupling of the respiratory chain during the metabolic reprogramming phase...
  17. pmc Hap4p overexpression in glucose-grown Saccharomyces cerevisiae induces cells to enter a novel metabolic state
    Romeo Lascaris
    Swammerdam Institute for Life Sciences, University of Amsterdam, 1098 SM Amsterdam, The Netherlands
    Genome Biol 4:R3. 2003
    ..To understand why overexpression of HAP4 is able to override the signals that normally result in glucose repression of mitochondrial function, we analyzed in detail the changes that occur in these cells...
  18. pmc T-profiler: scoring the activity of predefined groups of genes using gene expression data
    Andre Boorsma
    Swammerdam Institute for Life Sciences Microbiology, University of Amsterdam, BioCentrum Amsterdam, Nieuwe Achtergracht 166, 1018 WV Amsterdam, The Netherlands
    Nucleic Acids Res 33:W592-5. 2005
    ..Currently, gene expression data from Saccharomyces cerevisiae and Candida albicans are supported. Users can upload their microarray data for analysis on the web at http://www.t-profiler.org...
  19. pmc Genomewide analysis of Drosophila GAGA factor target genes reveals context-dependent DNA binding
    Bas van Steensel
    Netherlands Cancer Institute, 1066 CX, Amsterdam, The Netherlands
    Proc Natl Acad Sci U S A 100:2580-5. 2003
    ..Our approach for revealing determinants of context-dependent DNA binding will be applicable to many other transcription factors...
  20. pmc Revisiting the codon adaptation index from a whole-genome perspective: analyzing the relationship between gene expression and codon occurrence in yeast using a variety of models
    Ronald Jansen
    Department of Molecular Biophysics and Biochemistry, 266 Whitney Avenue, Yale University, PO Box 208114, New Haven, CT 06520, USA
    Nucleic Acids Res 31:2242-51. 2003
    ..More information is available at http://bioinfo.mbb.yale.edu/expression/codons...
  21. pmc Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster
    Celine Moorman
    Department of Molecular Biology, Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, The Netherlands
    Proc Natl Acad Sci U S A 103:12027-32. 2006
    ..Colocalization hotspots constitute a previously uncharacterized type of feature in the genome of Drosophila, and our results provide insights into the general targeting mechanisms of transcription regulators in a higher eukaryote...
  22. pmc Modeling gene expression control using Omes Law
    Harmen J Bussemaker
    Mol Syst Biol 2:2006.0013. 2006
  23. ncbi request reprint A gene expression map for the euchromatic genome of Drosophila melanogaster
    Viktor Stolc
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Science 306:655-60. 2004
    ..Our results provide a draft expression map for the entire nonrepetitive genome, which reveals a much more extensive and diverse set of expressed sequences than was previously predicted...
  24. pmc Genomic binding by the Drosophila Myc, Max, Mad/Mnt transcription factor network
    Amir Orian
    Division of Basic Sciences and Divison of Human Biology, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA
    Genes Dev 17:1101-14. 2003
    ..These results suggest that a fundamental aspect of Max network function involves widespread binding and regulation of gene expression...
  25. pmc Distinct HP1 and Su(var)3-9 complexes bind to sets of developmentally coexpressed genes depending on chromosomal location
    Frauke Greil
    Netherlands Cancer Institute, Amsterdam 1066 CX, The Netherlands
    Genes Dev 17:2825-38. 2003
    ..These results demonstrate that, depending on chromosomal location, the HP1 and Su(var)3-9 proteins form different complexes that associate with specific sets of developmentally coexpressed genes...
  26. pmc Comparative genome sequencing of Drosophila pseudoobscura: chromosomal, gene, and cis-element evolution
    Stephen Richards
    Human Genome Sequencing Center and Department of Molecular and Human Genetics, Baylor College of Medicine, Houston Texas 77030, USA
    Genome Res 15:1-18. 2005
    ..Overall, a pattern of repeat-mediated chromosomal rearrangement, and high coadaptation of both male genes and cis-regulatory sequences emerges as important themes of genome divergence between these species of Drosophila...

Research Grants7

  1. Inferring regulatory circuitry from microarray data
    HARMEN BUSSEMAKER; Fiscal Year: 2004
    ....
  2. Inferring regulatory circuitry from microarray data
    HARMEN BUSSEMAKER; Fiscal Year: 2005
    ....
  3. Inferring regulatory circuitry from microarray data
    HARMEN BUSSEMAKER; Fiscal Year: 2006
    ....
  4. Inferring regulatory circuitry from microarray data
    HARMEN BUSSEMAKER; Fiscal Year: 2007
    ....
  5. Inferring gene regulatory circuitry from functional genomics data
    HARMEN BUSSEMAKER; Fiscal Year: 2009
    ..Aberrant regulation of gene expression is often associated with disease. ..
  6. Inferring gene regulatory circuitry from functional genomics data
    Harmen J Bussemaker; Fiscal Year: 2010
    ..Aberrant regulation of gene expression is often associated with disease. ..
  7. Inferring gene regulatory circuitry from functional genomics data
    HARMEN BUSSEMAKER; Fiscal Year: 2009
    ..Aberrant regulation of gene expression is often associated with disease. ..