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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.

Reading List 2: "Bacterial Regulation" Mini-workshop

J. Hoch

Stephenson, K. and J.A. Hoch. 2002. Evolution of signaling in the sporulation phosphorelay. Mol. Microbiol. 46(2):297-304.

Hoch, J.A. and K.I. Varughese. Keeping signals straight in phosphorelay signal transduction. J. Bacteriol. 183(17):4941-4949, 2001

S. Kustu

Zimmer DP, Soupene E, Lee HL, Wendisch VF, Khodursky AB, Peter BJ, Bender RA, Kustu S. 2000. Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation. Proc Natl Acad Sci U S A 2000 Dec 19;97(26):14674-9

Soupene E, King N, Feild E, Liu P, Niyogi KK, Huang CH, Kustu S. 2002. Rhesus expression in a green alga is regulated by CO(2). Proc Natl Acad Sci U S A 2002 May 28;99(11):7769-73

R.H Ebright

Benoff B, Yang H, Lawson CL, Parkinson G, Liu J, Blatter E, Ebright YW, Berman HM, Ebright RH.  Structural basis of transcription activation: the CAP-alpha CTD-DNA complex. Science. 2002 Aug 30;297(5586):1562-6.

Mekler V, Kortkhonjia E, Mukhopadhyay J, Knight J, Revyakin A, Kapanidis AN, Niu W, Ebright YW, Levy R, Ebright RH.  Structural organization of bacterial RNA polymerase holoenzyme and the RNA  polymerase-promoter open complex. Cell. 2002 Mar 8;108(5):599-614.

T.J. Silhavy

Rizzitello AE, Harper JR, Silhavy TJ.  Genetic evidence for parallel pathways of chaperone activity in the periplasm of Escherichia coli. J Bacteriol. 2001 Dec;183(23):6794-800.

Raivio TL, Silhavy TJ. Periplasmic stress and ECF sigma factors. Annu Rev Microbiol. 2001;55:591-624.

D. Low

Hernday A, Krabbe M, Braaten B, Low D. Self-perpetuating epigenetic pili switches in bacteria. Proc Natl Acad Sci U S A. 2002 Dec 10;99 Suppl 4:16470-6.

van der Woude M, Braaten B, Low D. Epigenetic phase variation of the pap operon in Escherichia coli. Trends Microbiol. 1996 Jan;4(1):5-9. Review.

K. Severinov

Borukhov S, Severinov K. Role of the RNA polymerase sigma subunit in transcription initiation. Res Microbiol. 2002 Nov;153(9):557-62. Review.

Nechaev S, Yuzenkova Y, Niedziela-Majka A, Heyduk T, Severinov K. A novel bacteriophage-encoded RNA polymerase binding protein inhibits transcription initiation and abolishes transcription termination by host RNA polymerase. J Mol Biol. 2002 Jun 28;320(1):11-22.

E.A. Groisman

Groisman EA. The pleiotropic two-component regulatory system PhoP-PhoQ. J Bacteriol. 2001 Mar;183(6):1835-42. Review.

Mouslim C, Groisman EA. Control of the Salmonella ugd gene by three two-component regulatory systems. Mol Microbiol. 2003 Jan;47(2):335-44.

M.A. Savageau

Savageau MA. Alternative designs for a genetic switch: analysis of switching times using the piecewise power-law representation. Math Biosci. 2002 Nov-Dec;180:237-53.

Savageau MA.Rules for the evolution of gene circuitry. Pac Symp Biocomput. 1998;:54-65.

N.S. Wingreen

K.C Huang  Y. Meir and N.S. Wingreen  to be submitted (pdf).

Some general references:

Regulation of gene expression in Escherichia coli / [edited by] E.C.C. Lin, A. Simon Lynch. New York : Chapman & Hall ; Austin : R.G. Landes Co., c1996. 

Two-component signal transduction  edited by James A. Hoch and Thomas J. Silhavy. Washington, D.C. : ASM Press, c1995.

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