Welcome to the Laboratory of Harmen Bussemaker at Columbia University! We are a computational group interested in predictive modeling of gene expression regulation, driven by functional genomics data, and based on biophysical descriptions of the interactions between regulatory proteins and the DNA and mRNA molecules they bind. Our lab is located in the Department of Biological Sciences. We are also affiliated with the Center for Computational Biology and Bioinformatics at Columbia's Medical Center.

• Description of our research (slightly outdated, check back soon!)
• Publications in PubMed   |   Publications in Google Scholar
• Lab members, contact info, directions to our lab
• Positions available
• Software: MatrixREDUCE  |  TranscriptionDetector
• Web Tools: REDUCE  |  T-profiler
• Lab News
  1. At the ISMB 2008 conference in Toronto, Lucas Ward, one of the PhD students in our lab, was awarded the Ian Lawson Van Toch Outstanding Student Paper Award. Congratulations to Luke!
  2. The Yeast Transfactome database server is now available. The accompanying paper by Barrett Foat, Ron Tepper and Harmen Bussemaker has been published in the NAR 2008 Database issue.
  3. Our recent review article entitled "Predictive Modeling of Genome-Wide mRNA Expression: From Modules to Molecules" was published in Annual Review of Biophysics and Biomolecular Structure Vol. 36: 329-347 (Volume publication date June 2007) [HTML | PDF].
  4. Our 2006 PNAS paper by Moorman et al. entitled "Hotspots of transcription factor colocalization in the genome of Drosophila melanogaster" was highlighted in Nature [442(7103), August 2006]. It has also been listed as a "must read" on Faculty of 1000!
  5. Our 2004 BMC Bioinformatics paper by Gao et al. entitled "Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data" has been marked as "highly accessed". It has also been cited as a "paper of outstanding interest" in a review by Chua et al. (2004).
  6. The TranscriptionDetector software package is now available for download. A related paper was recently published in Genome Biol. 2006 July 19; 7(7):R59.
  7. The MatrixREDUCE software package is now available for download. A related paper was recently published in Bioinformatics as part of the ISMB 2006 proceedings.
  8. Our study on mRNA stability regulation in yeast was published in PNAS [abstract | pdf | supp info]. A poster about this work won us an "Insight Award" at RECOMB 2005.
  9. T-profiler provides a simple and intuitive of way of analyzing a single mRNA expression profile in terms of gene groups [paper in NAR | www.t-profiler.org]. We are currently extending this tool to other organisms than yeast.
  10. In collaboration with Kevin White's Lab at Yale, we analyzed the expression of intergenic regions in Drosophila melanogaster using genomic tiling arrays [Science paper | supp info/browser].