CS/PB/BSCB 726 : Problems and perspective in computational molecular biology

Note: Regular meeting time is Monday 4:30 Place:RH 484

Next meeting: Monday December 1st, 4:30PM, Lecturer: Sung-Wook Chi

Wednesday September 10: Doug Knipple will present
"Evolution of the integral membrane desaturase gene family in moths and flies."
by Knipple, D. C., C.-L. Rosenfield, R. Nielsen, K. M. You and S. E. Jeong
Genetics 162, 1737-1752, 2002. It is accessible via the Cornell Library Gateway.

Monday, Spetember 15: Ron Elber will present
"Coupling the folding of homologous proteins"
by C. Keasar, D. Tobi, R. Elber and J. Skolnick
Proc. Natl. Acad. Sci. USA 95,5880-5883(1998)

Monday September 22: Liviu Popescu will present
"Statistical significance for genomewide studies"
by John D. Storey and Robert Tibshirani
PNAS, August 5, 2003; 100(16): 9440 - 9445

Monday September 29: Niranjan Nagarajan will present
"Module networks: identifying regulatory modules and their condition-specific regulators from gene expression data"
by Eran Segal, Michael Shapira, Aviv Regev, Dana Pe'er, David Botstein, Daphne Koller and Nir Friedman
Nature Genetics, volume 34 no. 2 pp 166 - 176
, May 2003.

Monday October 6: Steve Fairchild will present
"Reducing the computational complexity of protein folding via fragment folding and assembly"
by Haspel N., Tsai C., Wolfson H. and Nussinov R.
Protein Science. 2003 Jun;12(6):1177-87
Steve will also be covering portions of the following papers which go into more detail about some aspects of the primary paper: (1) (2)

Friday October 17: Helgi Ingolfsson will present
"Sequencing and comparison of yeast species to identify genes and regulatory elements"
by Kellis M., Patterson N., Endrizzi M., Birren B., and Lander ES.
Nature. 2003 May 15;423(6937):241-54.

Monday October 20: Anat Maoz will present
"How spike synchronization among olfactory neurons can contribute to sensory discrimination"
by Linster C, Cleland TA.
J Comput Neurosci. 2001 Mar-Apr;10(2):187-93.

Monday October 27: Shobhit Varshney will present
"What is the minimum number of letters required to fold a protein?"
by Fan K, Wang W.
J Mol Biol. 2003 May 9;328(4):921-6.

Monday November 3: Leonid Meyerguz will present
"Linking the genes: inferring quantitative gene networks from microarray data"
by de la Fuente A, Brazhnik P, Mendes P.
Trends Genet. 2002 Aug;18(8):395-8.
Leonid will also be talking about this related paper.

Monday November 10: Yonatan Ben Shimon will present
"A Novel Approach to Decoy Set Generation: Designing a Physical Energy Function Having Local Minima with Native Structure Characteristics"
by Keasar C, Levitt M.
J Mol Biol. 2003 May 23;329(1):159-74.

Monday November 17: Jian Qiu will present
"Using a neural network and spatial clustering to predict the location of active sites in enzymes"
by Gutteridge A, Bartlett GJ, Thornton JM
J Mol Biol. 2003 Jul 18;330(4):719-34.

Monday November 24: Amrita Basu will present
"Improved detection of homologous membrane proteins by inclusion of information from topology predictions"
by Hedman M, Deloof H, Von Heijne G, Elofsson A.
Protein Sci. 2002 Mar;11(3):652-8.

Monday December 1: Sung-Wook Chi will present
"MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network
by Bhalla US, Ram PT, Iyengar R.
Science. 2002 Aug 9;297(5583):1018-23.
The presentation will also draw on papers 1 & 2.

Instructors: Uri Keich Douglas C. Knipple and Ron Elber

Suggested papers by:

Uri Keich

Doug Knipple

Ron Elber