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: