Harmen J. Bussemaker

Harmen J. Bussemaker

Fellow: Awarded 2010

Field of Study: Molecular and Cellular Biology

Competition: US & Canada

Born in Hengelo, Netherlands, Harmen J. Bussemaker studied music (B.A., 1989) and theoretical physics (M.Sc., 1991, Ph.D., 1995) at Utrecht University. His doctoral research, supervised by M. H. Ernst, on the properties of certain mathematical models for simulating complex fluid flows produced a number of articles, including “Long-range correlations in lattice gas automata,” written with Ernst and published in the Journal of Statistical Physics, 81 (1995), and “Analysis of a pattern forming lattice gas automaton: mean field theory and beyond,” which was published in Physical Review E, 53 (1996).

On completing his Ph.D., he accepted position as a postdoctoral research associate at the University of Maryland, College Park, where he investigated topics in mesoscopic physics with T. R. Kirkpatrick and protein folding with D. Thirumalai. But it was with his second postdoctoral appointment, at the lab of Eric Siggia at Rockefeller University, where he first worked in genomics, the field he has been exploring ever since. Applying techniques he had learned in working in theoretical physics and statistics to the problem of decoding gene sequences, he developed the MobyDick algorithm. When he, Eric Siggia, and Hao Li tested the algorithm on a non-coding part of the yeast genome, it revealed many DNA sequences that corresponded to known binding sites of a class of gene regulatory proteins. Their groundbreaking work was published as the cover article of Proceedings of the National Academy of Sciences U.S.A., 97 (2000).

He next developed a second algorithm named REDUCE. Using non-coding DNA sequence and messenger RNA expression levels in their test run, and again working with Siggia and Li, he showed that REDUCE allowed for direct integration of different types of genomics data and could directly predict expression from sequence. These findings showing the success of REDUCE, published in Nature Genetics, 27 (2001), firmly established Harmen Bussemaker as one of the world’s leaders in computational genomics.

After briefly returning to the Netherlands, where from 1999 to 2001 he worked as a Lecturer at the University of Amsterdam, he returned to the United States to take up an appointment as Assistant Professor in the Department of Biological Sciences at Columbia University. He was promoted to Associate Professor in 2007. There, working with a group of graduate students and postdocs in his own lab, he continued to make important advances. One of the most significant is MatrixREDUCE, an algorithm that he describes as “a biophysical approach to quantifying protein-DNA interactions . . . which is a more principled, simpler, and more accurate than existing methods for inferring so-called ‘weight matrices’ based on information theory.” An application of MatrixREDUCE to cross-species comparison earned him the ISMB’s Ian Lawson Van Toch Memorial Award in 2008.

His lab has also made important advances in biology, especially with gene expression regulation. Their investigations were recognized with the Insight Award, bestowed at the RECOMB 2005 conference held at MIT. During his Guggenheim Fellowship term, he will be continuing this work as a visiting scientist at Princeton University.

In addition to his research and supervision of graduate and postdoctoral students, Harmen Bussemaker has been a co-organizer of conferences at Cold Spring Harbor on “Systems Biology: Global Regulation of Gene Expression" (2008, 2010) and an instructor there in integrative data analysis for high-throughput biology. He is also since 2007 a member of the editorial board of BMC Systems Biology and an associate editor of PLoS Computational Biology. He also serves as an ad hoc reviewer for many important scientific journals, including Science, Nature, PNAS, Genome Research, and Nature Genetics, to name but a few.