Our group member Jonathan Auerbach featured in NYT

For his award winning study on rats in NYC, our very own Jonathan Auerbach was featured in NYT last week.

Old data, new interactions, improved predictions

In our recent publication in Bioinformatics, we analyzed an eleven years old gene expression data set by Van't Veer et al (2002) and identified gene clusters that have demonstrated interaction associated with relapse risk of breast cancer patients. These newly identified gene clusters allowed us to improve the CV accuracy of prognosis prediction from ~30% to 8%.

Moving to wiki ...

For easy updating, we have decided to move (finally) our entire group website to our wikischolar website. The wikischolar website is a service provided by Columbia's CCNMTL center and adopts a simple-to-follow wiki format. Hopefully, we can now have a most up-to-date group website as we have always hoped for.

New Paper: Genome-wide meta-analysis increases to 71 the number of confirmed Crohn's disease susceptibility loci

Nature Genetics 42, 1118-1125.

NYTIMES: From one genome, many types of cells. But how?

This is a nice article in NYTIMES talking about the complex nature of genetics.

Some good readings on important trends in statistical genetics

I. OVERVIEW
1. Science 7 November 2008: Vol. 322. no. 5903, pp. 881 - 888
Genetic Mapping in Human Disease
2. Nature Reviews Genetics 10, 241-251 (April 2009)
Human genetic variation and its contribution to complex traits
II. Association Studies, especially GWAS
3. Nature Reviews Genetics 9, 356-369 (May 2008)
Genome-wide association studies for complex traits: consensus, uncertainty and challenges
4. Nature Reviews Cancer 4, 850-860 (November 2004)
Association studies for finding cancer-susceptibility genetic variants
III. Challenges of associations studies (interaction, population
stratification, etc)
5. Human Molecular Genetics, 2002, Vol. 11, No. 20 2463-2468
Epistasis: what it means, what it doesn't mean, and statistical methods to detect it in humans
6. Nature Genetics 37, 1243 - 1246 (2005)
Population structure, differential bias and genomic control in a large-scale, case-control association study
IV. LD and Haplotype block
7. The American Journal of Human Genetics, Volume 69, Issue 1, 1-14, 1 July 2001
Linkage Disequilibrium in Humans: Models and Data
8. Nature Reviews Genetics 4, 587-597 (August 2003)
Haplotype blocks and linkage disequilibrium in the human genome
V. Selected methodology reviews
9. The American Journal of Human Genetics, Volume 78, Issue 3, 437-450, 1 March 2006
A Comparison of Phasing Algorithms for Trios and Unrelated Individuals
10. The American Journal of Human Genetics, Volume 74, Issue 5, 979-1000, 1 May 2004
Methods for High-Density Admixture Mapping of Disease Genes

Reference for Tim's presentation

History of human genome project:
http://www.sciencemag.org/cgi/content/full/291/5507/1195

Science paper:
The sequence of human genome
http://www.sciencemag.org/cgi/content/full/291/5507/1195

The international hapmap project
http://www.hapmap.org/downloads/nature02168.pdf

Properties of linkage disequilibrium
http://www.pnas.org/cgi/content/full/99/26/17004

SNP discover (a presentation)
http://wheat.pw.usda.gov/ITMI/RafalskiXITMI2/index.htm

Let me know if you would like to know other topics along this line and I will find more references.