Hamid BolouriCheck out CRdata.org 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.
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My new book Personal Genomics and Personalized Medicine (Imperial College Press,2010) was recently reviewed in Nature, 1st April 2010, (464):680.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).
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My other book Computational Modeling of Gene Regulatory Networks: a primer
was published by Imperial College Press in fall 2008.
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:
- Course slides and Lab Notes (using CRdata.org) for my course on Gene Regulatory Networks at the Quantitative Systems Immunology summer school in San Antonio (July 2010)
- Course slides and model 1 and model 2 from the course I gave at Woods Hole (Oct 2009) about building Gene Regulatory Network models.
- slides about teaching intensive cross-disciplinary courses in computational systems biology (from a talk I gave at Iowa State)
- Course slides and simulation models from the Computational Immunology course I gave at Yale (Aug 2008). You will also need this data file).
- Course slides and simulation models from the course I gave at Woods Hole (Oct 2008) about Gene Regulatory Network building blocks.
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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)