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KITP Program: Bio-Molecular Networks (Jan 6 - Mar 28, 2003)
Coordinators: D.Fygenson, A.Ruckenstein, B.Shraiman, L.Wolpert

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KITP Program: Bio-Molecular Networks (Jan 6 - Mar 28, 2003)
Coordinators: D.Fygenson, A.Ruckenstein, B.Shraiman, L.Wolpert

Reading List 1: "Modules and Evolvability" Mini-Workshop

Andrew Murray

Hartwell, L.H., Hopfield, J.J., Leibler, S., and Murray, A.W. (1999). "From molecular to modular cell biology" 402, C47-52.

Kirschner, M. and J. Gerhart (1998). "Evolvability." Proc.Natl Acad Sci USA 95 (15): 8420-7. An introduction to the idea of evolvability (explored at much greater Length) in their book: Cells, Embryos, And Evolution, 1997,Blackwell Science

Two shortish texts that provide a good introduction to population genetics: Maynard Smith's is more elegant, Hartl's more thorough:

Maynard Smith, J. Evolutionary Genetics, Oxford University Press.

Hartl, D. L. A primer of population genetics, Sinauer


Naama Barkai

Ihmels, J, Friedlander, G., Bergmann, S., Sarig, O., Ziv, Y., and Barkai, N., (2002). "Revealing Modular Organization in the Yeast Transcription Network". Nature Genetics, 31


Wen-Hsiung Li

Gu, Z., D. Nicolae, H. H.-S Lu, and W.-H. Li (2002). "Rapid divergence in expression between duplicate genes inferred from microarray gene expression data", Trend Genetics 18:609-613.

Gu, Z., L. M. Steinmetz, X. Gu, C. Scharfe, R. W. Davis, and W.-H. Li (2003). "Role of duplicate genes in genetic robustness against null mutations", Nature 421:63-66.


Marie-Anne Felix

Felix, M.-A. (1999). "Evolution of developmental mechanisms in nematodes", J. Exp. Zool. (Mol. Dev. Evol.) 285, 3-18.

Delattre, M. and Felix, M.-A. (2001). "Microevolutionary studies in nematodes: a beginning", Bioessays 23, 807-819.


Erin O'Shea

Komeili, A., and O'Shea, E.K. (2001). "New Perspectives on Nuclear Transport", Ann. Rev. Genetics, 35, 341-364.

Wykoff, D.D., and O'Shea, E.K., (2002). "Phosphate transport and sensing in Saccharomyces cerevisiae", Genetics, 159, 1491-1499.


Jonathan Weissman

Santoso, A, Chien, P, Osherovich, LZ, and Weissman, J (2000). "Molecular Basis of a Yeast Prion Species Barrier", Cell 100(1) 1-20

DePace, A. H., Santoso, A, Hillner, P., and Weissman, J. S. (1998). "A critical role for amino-terminal glutamine/asparagine repeats in the formation and propagation of a yeast prion", Cell, 93, 1241-1252.

Rutherford, S. L., and S. Lindquist (1998). "Hsp90 as a capacitor for morphological evolution", Nature, 396: 336-42.


Adam Arkin

Synthetic Cell Biology Current Opinion in Biotechnology (preprint).

Rao CV, Arkin AP.,(2001). "Control motifs for intracellular regulatory networks" Rev. Biomed. 3:391-419.

McAdams HH, Arkin A., (2000). "Towards a circuit engineering discipline" Curr. Biol.10(8):R318-20.
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