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Systems Biology Journal Club
Computational biology broadly falls into two main categories: bioinformatics and systems biology. Bioinformatics is concerned with relatively static aspects of biological information, such as sequence analyses, which change on an evolutionary time scale. In contrast, systems biology is concerned with processes that change on a physiological time scale, dealing integratively with topics such as signal transduction, inflammation, and homeostasis. The goals of the Systems Biology Journal Club are to:
- Broaden our knowledge of both the biological aspects and the theoretical aspects of this important field,
- Foster within-university collaborations,
- Stimulate discussion of relevant papers.
We began our meetings in July 2007. About half the participants are from other departments, and anyone interested in learning more about systems biology would be very welcome to join us. Our meetings are the 3rd Tuesday of the month at 4 PM in the Biostatistics Conference Room (G-11213) in MRBX. If you wish to be on the mailing list, please send e-mail to James S. Cavenaugh, Ph.D. at James_Cavenaugh@urmc.rochester.edu. We hope to strike a balance between theoretically oriented and biologically oriented presentations.
Suggested topics for presentation include papers dealing with biological feedback, networks (metabolic, transcriptional, signaling, etc.), immune system dynamics, pharmacodynamics, molecular or cellular interactions, etc. Immunological and signal transduction problems are especially welcome. Biological domains can be from sub-cellular or viral all the way up to mind-body interactions.
2007-2008 Presentations:
- 2008 March 18, Helene McMurray, "A Map of Human Cancer Signaling"; http://www.nature.com/msb/journal/v3/n1/full/msb4100200.html
- 2008 February 19, Kaja Abbas. "Modeling Influenza Immune Response".
- 2008 January 15, William Mowrey, “Ordered Phosphorylation Governs Oscillation of a Three-Protein Circadian Clock”; http://www.sciencemag.org/cgi/content/full/318/5851/809
- 2007 December 18, Gregory Warnes, "Statistical Modeling of Biochemical Pathways"; http://ieeexplore.ieee.org/xpls/abs_all.jsp?isnumber=4317450&arnumber=4317454&count=5&index=3
- 2007 November 20, Peter Salzman, “Introduction to Bayesian Networks for Genomic Analysis”; http://genomethods.org/sca/tutorial.pdf
- 2007 October 19, George Competillo, “Molecular Concepts Analysis Links Tumors, Pathways, Mechanisms, and Drugs”, http://www.pubmedcentral.nih.gov/articlerender.fcgi?&artinstid=1877973
- 2007 September 21, Joseph Miano, “Systematic Identification of cis-Regulatory Sequences Active in Mouse and Human Embryonic Stem Cells” (Grskovic et al., PLoS Genetics 3, 8, August 2007, e147, pp 1524-1540; http://genetics.plosjournals.org/perlserv/?request=get-document&doi=10.1371/journal.pgen.0030145&ct=1)
- 2007 September 7, Helene McMurray, “Prediction and Testing of Novel Transcriptional Networks Regulating Embryonic Stem Cell Self-Renewal and Commitment” (Walker et al., Cell Stem Cell 1, 71-86, July 2007 http://www.cellstemcell.com/content/article/abstract?uid=PIIS1934590907000069)
- 2007 August 17, Hongyu Miao, “Application of Mathematical Modeling in Biomedical Research”
- 2007 August 3, James S. Cavenaugh, "Kinetic Logic"
- 2007 July 27, Anthony Almuvedar, “Graphical Selection of Gene Perturbation Thresholds”
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