Temporary Website for Computational Characterization and Exploitation of Biological Networks initiative at UCD

DRAFT OUTLINE FOR WEBSITE

Website for Computational Characterization and Exploitation of Biological Networks initiative at UCD.
We might use the URL cbn.ucdavis.edu, but that is not yet set ??

A. Introduction to the Computational Characterization and Exploitation of Biological Networks initiative at UCD

1. History of the Computational Characterization and Exploitation of Biological Networks initiative - may be short.

2. Initiative Proposal. Proposal Submitted in 2005

Result: The approved initiative now includes seven of the original eight proposed positions. The proposed position in Pharmacology has been removed.

3. Networks Biology v. Systems Biology - an intersection, but networks biology is broader.
see wikipedia definition of systems biology

4. UCD Strategic plan - under construction.

5. Responsibilities of the initiative committee: coordinate with the individual departments involved to assure that the fte hires are within the scope of the initiative; to build structures and programs to facilitate the growth of computational networks biology at UCD.

6. Initiative Committee Members - co-chairs Dan Gusfield, Oliver Feihn

Alexander Mogilner , Math
Craig Benham , Math, BME
David Neale
dbneale@ucdavis.edu, Plant Science
"Fiehn, Oliver" , MCB
gusfield, Computer Science
"Michelmore, Richard" , Genome Center
Neelima Sinha , Plant biology
"Plunkett, Lauren" , Genome Center
Sergey Nuzhdin , Evolution and Ecology
Subhadip Raychaudhuri BME

B. Plans for Storer Symposium on Computational Networks Biology (fall 2006).



C. Hiring Plans and fte searches.



D. *Illustrations* of activity in Networks Biology, both computational and wet-lab.

We need more suggestions here.
    ****Some Labs active in Networks Biology:
  1. Uri Alon's lab at Weizmann
  2. Trey Ideker's lab at UCSD.
  3. Another lab
  4. Another lab
  5. Another lab
  6. Another lab
  7. The concerns of this center are both broader than Networks Biology, and in with respect to Networks Biology, narrower than the full scope of Networks Biology.

    *****Illustrative Meetings, past, present and future:

  8. RECOMB sattelite meeting on Regulatory Genomics, July 17,18 2006
  9. A Dimacs meeting
  10. This meeting intersects Networks Biology because of the ``networked physiological processes involved".
  11. Oxford Statistics meeting
  12. Keystone meeting
  13. Another Dimacs meeting
  14. Inria meeting
  15. Inria sponsored meeting
  16. Another meeting

    ****Courses, Tutorials and Educational Material:

  17. site 1
  18. site 2
  19. site 3

    ****Research Publications illustrating Networks Biology (these need not be publications from UCD):
    Here will be citations that link to either the actual papers, or to the pubmed citation for that paper. The following were suggested by Alex Mogilner:

    Almaas E, Oltvai ZN, Barabasi AL. The Activity Reaction Core and Plasticity of Metabolic Networks. PLoS Comput Biol. 2005 Dec 16;1(7):e68 PMID: 16362071

    Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL. Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature. 2004 Feb 26;427(6977):839-43. PMID: 14985762

    Science. 2005 Apr 22;308(5721):523-9. Causal protein-signaling networks derived from multiparameter single-cell data. Sachs K, Perez O, Pe'er D, Lauffenburger DA, Nolan GP.

    TOWARD PREDICTIVE MODELS OF MAMMALIAN CELLS Avi Ma'ayan, Robert D. Blitzer, Ravi Iyengar Annual Review of Biophysics and Biomolecular Structure, Vol. 34: 319-349

    Stelling J, Gilles ED, Doyle FJ Robustness properties of circadian clock architectures. Proc Natl Acad Sci U S A. 2004 Sep 7;101(36):13210-5. PMID: 15340155

    von Dassow G, Meir E, Munro EM, Odell GM. The segment polarity network is a robust developmental module. Nature. 2000 Jul 13;406(6792):188-92. PMID: 10910359

    Alon U, Surette MG, Barkai N, Leibler S. Robustness in bacterial chemotaxis. Nature. 1999 Jan 14;397(6715):168-71.

    SIAM J. APPL. MATH. 2005 Vol. 65, No. 5, pp. 1526 MULTIPLE EQUILIBRIA IN COMPLEX CHEMICAL REACTION NETWORKS: I. THE INJECTIVITY PROPERTY GHEORGHE CRACIUN AND MARTIN FEINBERG

    Shmulevich I, Kauffman SA, Aldana M. Eukaryotic cells are dynamically ordered or critical but not chaotic. Proc Natl Acad Sci U S A. 2005 Sep 20;102(38):13439-44. PMID: 16155121

    Janes KA, Albeck JG, Gaudet S, Sorger PK, Lauffenburger DA, Yaffe MB. A systems model of signaling identifies a molecular basis set for cytokine-induced apoptosis. Science. 2005 Dec 9;310(5754):1646-53. PMID: 16339439

    Prill RJ, Iglesias PA, Levchenko A. Dynamic Properties of Network Motifs Contribute to Biological Network Organization. PLoS Biol. 2005 Oct 4;3(11):e343 PMID: 16187794

    Reconstruction of a Functional Human Gene Network, with an Application for Prioritizing Positional Candidate Genes Lude Franke, Harm van Bakel, Like Fokkens, Edwin D. de Jong, Michael Egmont-Petersen, and Cisca Wijmenga American J. of Human Genetics, Online publication, April 25, 2006

    Elucidating the murine brain transcriptional network in a segregating mouse population to identify core functional modules for obesity and diabetes Pek Yee Lum, Yanqing Chen, Jun Zhu, John Lamb, Shlomo Melmed, Susanna Wang, Tom A. Drake, Aldons J. Lusis, and Eric E. Schadt Journal of Neurochemistry, 2006, 97 (Suppl. 1).

    ****Journals

  20. Call for special issue on Network biology


    ****Powerpoints of Research talks:

    ****Illustrative jobs reflecting Networks Biology:

  21. job 1
  22. job 2
  23. job 3
  24. job 4

    *****Links to webpages with many links to network biology:

  25. links

E. Talks on Campus related to Computational Networks Biology

  1. Eric Schadt, April 24, 2006
  2. Chao Tang, April 24, 2006
  3. Mikael Savageau, April 28, 2006

F. Mailing list and input from web visitors

Here we want a window that allows a visitor to enter their email address in order to get further announcements on the initiative, and also a mechanism to allow the visitor to describe their activities and interests in the area.

G. Private working space for the intitiative committee

This is password protected and will contain information on: recruitment, discussions, review of drafts, information on committee meetings, minutes from committee meetings, something to help coordinate plans for meetings (committee members schedules), deligated tasks for symposium, coordinating visitor schedules etc. Presently it contains the minutes from the past meetings, the fte decision letter from the Provost, the draft Strategic Plan, and the draft Criteria statement.

Committee Work Space

Updated April 25, 2006