Check out our new R/Bioconductor resource-sharing web-service on the Amazon Cloud

Here are some slides outlining CRdata. See also this review.

For examples of my group's past computational systems biology contributions, see BioTapestry, SBML, and Dizzy

We currently collaborate with the laboratories of Eric Davidson and Ellen Rothenberg at Caltech and Irwin Bernstein at the Fred Hutchinson Cancer Research Center.

PGPM book cover


My new book Personal Genomics and Personalized Medicine (Imperial College Press,2010) was recently reviewed in Nature, 1st April 2010, (464):680.

Table of Contents

Book description

Here are my slides from a talk on this topic at the 2009 annual meeting of the American College of Toxicologists.

Here are the Supplementary Data for my Feb 2010 Harvard Medical School Theory Lunch (see also these slides).


My other book Computational Modeling of Gene Regulatory Networks: a primerbook cover

was published by Imperial College Press in fall 2008.

Table of Contents

From the Introduction: "My aim throughout this book is to explain the how and why of modeling genetic regulatory networks (GRNs) in simple language that I hope will be accessible to all readers irrespective of their educational background."

Here are some of my course slides and associated models and lab exercises:


Here are some of my recent papers:

The gene regulatory network basis of the community effect, and analysis of a sea urchin embryo example, H Bolouri EH Davidson, Developmental Biology, 2010, (340):170-178. (article PDF), (Supplement)

A gene regulatory network armature for T lymphocyte specification, C Georgescu, WJ Longabaugh, DD Scripture-Adams, ES David-Fung, MA Yui, MA Zarnegar, H Bolouri, EV Rothenberg, Proc Natl Acad Sci USA, 2008 Dec 23, 105(51):20100-5. (article PDF), (Supplement)

Visualization, documentation, analysis, and communication of large-scale gene regulatory networks, WJ Longabaugh, EH Davidson, H Bolouri, Biochimica et Biophysica Acta, online 2008 Aug 6, print 2009, (1789):363-374. (PDF)

Inherent Gene Expression Variabilities and the need for Personalized Drug Dosage, H.Bolouri, Letters in Drug Design and Development, 2008 (5). (PDF)

The Innate Immune Database (IIDB), M. Korb#, A. G. Rust#, V. Thorsson, C. Battail, B. Li, D. Hwang, K. A. Kennedy, J. C. Roach, C. M. Rosenberger, M. Gilchrist, D. Zak, C. Johnson, B. Marzolf, A. Aderem, I. Shmulevich, H.Bolouri, BMC Immunology, 2008 9(7). (PDF)

Computational Challenges of Personal Genomics, Hamid Bolouri, Current Genomics, 2008, 9(1). (PDF)

Embryonic pattern formation without morphogens, Hamid Bolouri, BioEssays. 2008 3(5). (PDF)