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Quantitative Biology Journal Club

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12 noon, NB11.120

Date

Presenter

Journal

9/8/2008

Bong-Hyun Kim

L. Breiman 2001 machine learning
http://www.springerlink.com/content/u0p06167n6173512 RF in microarray
http://www.biomedcentral.com/1471-2105/9/319
http://www.biomedcentral.com/1471-2105/7/3

9/15/2008

Jacob Schwartz

"Distinct role of long 3' UTR BDNF mRNA in spine morphology and synaptic plasticity in hippocampal neurons." Cell 2008 Jul 11; 134(1):175-87.

9/22/2008

Cristi Galindo

Work in Progress "Microsatellites: Potential Facilitators of Evolutionary Change and Cancer"

9/29/2008

Jimin Pei

An Alternative Menaquinone Biosynthetic Pathway Operating in Microorganisms by Tomoshige Hiratsuka, Kazuo Furihata, Jun Ishikawa, Haruyuki Yamashita,Nobuya Itoh, Haruo Seto, and Tohru Dairi; Science 19 September 2008: 1670-1673.

10/6/2008

Discussion Group-

Dana Pe'er, Ph.D., Assistant Professor, Columbia University "Genetic Regulatory Complexity, Lessons from Yeast and Cancer"

10/13/2008

No Journal Club

 

10/20/2008

Dominika Borek

"High-resolution structure prediction and the crystallographic phase problem." Nature (8 November 2007) doi:10.1038/nature06249 450:259-264

10/27/2008

Yong Wang

Work in progress "ProCAIn: protein Profile-profile Comparison with Assisting Information -- a new protein sequence similarity search method."

11/3/2008

Lisa Kinch

"Emergence of symetry in homooligomeric biological assemblies."PMID:18849473http://www.pnas.org/content/105/42/16148.abstract

11/10/2008

Discussion Group

Jim Feader, Ph.D.,  -CANCELLED

11/17/2008

Shuoyong Shi

Alternative splicing and protein structure evolutionJournal:  Nucleic Acids Research, 2008, Vol. 36, No. 2 550-558link:  http://nar.oxfordjournals.org/cgi/content/abstract/36/2/550

12/1/2008

Juan Mendoza

"Improved residue contact prediction using support vector machines and a large feature set." BMC Bioinformatics, 2007,8:113, http://www.biomedcentral.com/1471-2105/8/113

12/8/2008

Discussion Group

Jim Feader, Ph.D., Associate Professor, Biological Sciences, University of Pittsburgh "Rule-based modeling of biological signal transduction"

1/12/2009

Chalam Chitturi

Work in progress

1/26/2009

Sasha Safronova

"Markov Additive Processes and Repeats in Sequences." J. Appl. Prob.44, 514-527 (2007)

2/2/2009

Discussion Group

Matthew A. Lewis, Ph.D., Assistant Professor, Radiology, UT Southwestern Medical Center "An Introduction to Compressive Sensing and Other State-of-the-Art Data Analyses"

2/9/2009

No Journal Club

No Journal Club

2/23/2009

Ruslan Sadreyev

Visel et al. Ultraconservation identifies a small subset of extremely constrained developmental enhancershttp://www.nature.com/ng/journal/v40/n2/abs/ng.2007.55.html

3/2/2009

Discussion Group

Ned Wingreen, Ph.D., Professor Princeton University
"Modeling adaptation in E. coli chemotaxis: precise, robust and optimized"

3/9/2009

Spring Break

No Journal Club

3/16/2009

Nishanth Marthandan

"Global variation in copy number in the human genome", Nature 444, 444-454 (23 November 2006) | doi:10.1038/nature05329; Received 13 June 2006; Accepted 10 October 2006 http://www.nature.com/nature/journal/v444/n7118/full/nature05329.html

3/23/2009

Yuxiao Wang

unpublished data

3/30/2009

Betsy Goldsmith

"NLP Search of MEDLINE Based on Cognition CSIR"

4/6/2009

 

No Journal Club

4/13/2009

Jing Tong

 "Detection of protein catalytic residues at high precision using local network properties" (http://www.biomedcentral.com/1471-2105/9/517) .

4/20/2009

Juan Mendoza

Phenylalanine-508 mediates a cytoplasmic-membrane domain contact in the CFTR 3D structure crucial to assembly and channel function by Serohijos, A. W., et al. (2008) Proc Natl Acad Sci U S A. 105, 3256-61. http://www.pubmedcentral.nih.gov/picrender.fcgi?artid=2265173&blobtype=pdf

4/27/2009

Yang Xie

"Statistical methods for integrating multiple types of genomic data"

5/4/2009

Nassim Sohaee

Work in progress "Clustering Algorithms for Protein Interaction Networks"