Alejandro Schäffer's CS WWW Page

• Alejandro Schäffer (schaffer@nchgr.nih.gov)
• Computer Scientist
• National Institutes of Health

Current Research Interests

• Design and Analysis of Algorithms
• Software for Genetics
• Implementation and Evalautaion of Parallel Software

Ongoing Software Projects

FASTLINK

We are developing improved versions of the main programs in the LINKAGE package to do genetic linkage analysis. Genetic linkage analysis is a statistical technique used to map genes and find the approximate locations of disease genes. Our improved software is called FASTLINK. FASTLINK is significantly faster, more robust, and better documented than LINKAGE. FASTLINK is freely available via FTP to anybody who wants it. For more information see the FASTLINK home page

Past participants in the FASTLINK project include: Robert W. Cottingham Jr. (Baylor College of Medicine), Ramana M. Idury (USC), Sandeep Gupta (MIT), Shriram Krishnamurthi (Rice), Pete Keleher (Maryland). To see Sandeep's home page click here. To see Shriram's home page click here. Current collaborators on making parallel versions of FASTLINK include: Chris Hyams, Prof. Alan Cox, Dr. Sandhya Dwarkadas, and Prof. Willy Zwaenepoel (all from Rice University).

Polygenic Diseases

We are developing new software to do genetic analyses of polygenic diseases, such as diabetes, asthma, and some forms of cancer. In addition, we are using the software to assess the statistical usefulness of our analytic methods. Current participants in this project include Jeremy Buhler (undergraduate at Rice), Prof. Kenneth Gabbay (Baylor College of Medicine), Prof. Marek Kimmel (Department of Statistics at Rice), and Prof. David Owerbach (Baylor College of Medicine). To see Jeremy's home page click here.

MSA

In collaboration with Sandeep Gupta (now at MIT), we have developed a significantly faster and more space-efficient version of the program MSA to do multisequence alignment.

DECIDE

In collaboration with Dr. Leslie Biesecker (NIH), I have developed a software package to evaluate the prospects for detecting small chromsomal abnormalities by DNA genotyping. The current diagnostic method of choice is cytogenetics with Giemsa-banding (i.e., stick-figure- like pictures of the 23 chromosomes). Our software package is called DECIDE, which stands for DEtecting Chromosomal Insertions and DEletions.