Adrian Heilbut

research | teaching | background | publications | resumé | links



aheilbut [at] gmail [dot} on {dot] com
617-512-6124

current address:
10 Dana Street, Apt 8
Cambridge, MA 02138
USA
Moved to empiricist.ca

I'm currently a graduate student in the Department of Biochemistry at the University of Toronto. I work in computational biology and bioinformatics at the Samuel Lunenfeld Research Institute at Mount Sinai Hospital, Toronto.

Biochemical network dynamics

I'm interested in understanding the function, evolution, and design principles of biochemical networks and cells by modeling their dynamics. In particular, I am interested in methods for automatically constructing models of biochemical networks that perform a desired function or exhibit desired (ie. experimentally observed) dynamics. My current project is investigating the simulated evolution of simple biochemical networks, such as switches and oscillators, building on work done by Francois and Hakim as well as some earlier efforts by Koza.

Functional genomics and proteomics

I am also interested in practical issues involved in generating and analyzing high-throughput functional genomics and proteomics data. High-throughput interaction datasets generated to date contain a significant amount of false-positive data, and miss many known interactions. Despite a lot of work on clever statistical approaches to filter interaction data, the quality of high-throughput data could be improved immensely by doing simple things to design experiments better, and by focussing more attention on reproducibility. Experimental designs also need to balance ideals with the economics of data generation. Working with MDS Proteomics and Dr. Gregg Morin, I analyzed a large set of immunoprecipitation data to determine some of the parameters needed to better design mass-spec based protein complex identification experiments. Some of that work was presented in a poster at HUPO2003, and a manuscript is currently in preparation.

Teaching
I taught the bioinformatics segment of a tutorial on
Protein-Protein Interactions at the PENCE/CPI conference. [Slides]
Background

Prior to starting grad school, I worked for two years at MDS Proteomics. I did my undergraduate work at University College in the University of Toronto in Neuroscience and Computer Science.

I'm a lindyhopper.
Resumé [pdf]
Recent Courses
JRX1124H Structure-based Drug Design
CSC2515H Machine learning
Recent conferences
May 13-16, 2004CPI and ETP Proteomics conference, Montreal.
May 17-28, 2004 Systems Biology / Nonlinear Dynamics Summer School, McGill
June 10-12, 2004 Synthetic Biology Conference 1.0, MIT
August 2004 ISMB/ECCB,Glasgow, Scotland
Papers

Bader GD, Heilbut A, Andrews B, Tyers M, Hughes T, Boone C. Functional genomics and proteomics: charting a multidimensional map of the yeast cell. Trends Cell Biol. 2003 Jul;13(7):344-56. Review. PMID: 12837605

Ho Y, Gruhler A, Heilbut A, Bader GD, Moore L, Adams SL, Millar A, Taylor P, Bennett K, Boutilier K, Yang L, Wolting C, Donaldson I, Schandorff S, Shewnarane J, Vo M, Taggart J, Goudreault M, Muskat B, Alfarano C, Dewar D, Lin Z, Michalickova K, Willems AR, Sassi H, Nielsen PA, Rasmussen KJ, Andersen JR, Johansen LE, Hansen LH, Jespersen H, Podtelejnikov A, Nielsen E, Crawford J, Poulsen V, Sorensen BD, Matthiesen J, Hendrickson RC, Gleeson F, Pawson T, Moran MF, Durocher D, Mann M, Hogue CW, Figeys D, Tyers M.
Systematic identification of protein complexes in Saccharomyces cerevisiae by mass spectrometry. Nature.2002 Jan 10;415(6868):180-3. PMID: 11805837

[pdf]

Cowan KN, Heilbut A, Humpl T, Lam C, Ito S, Rabinovitch M. Complete reversal of fatal pulmonary hypertension in rats by a serine elastase inhibitor. Nature Medicine. 2000 Jun;6(6):698-702. PMID: 10835689

Posters and Abstracts

[abstract] [pdf]
Optimizing Experimental Design in High-Throughput Interaction Proteomics
HUPO/IUBMB World Congress, Montreal, October 2003.