Alex Lancaster, Thomson Lab

Alex, with a friend.
(Photo by Jessica Garb)

Alex's research is focused on the evolution of the major histocompatibility complex (MHC), a gene family found in most vertebrates, and a major part of the adaptive immune system.

Dissertation

Alex is developing both computational tools and statistical techniques for detecting the operation of natural selection on the MHC genes in humans from large data sets collected from many different populations around the world.

Part of his thesis involves looking for patterns of selection at the protein sequence level (the individual amino acid sites that comprise the MHC proteins), and relating these patterns to structural and functional aspects of MHC proteins.

PyPop and Swarm

Alex's dissertation also includes the development of an open-source tool to assist biologists with large-scale population data analyses.

The tool, known as PyPop, operates on multi-locus genotype data, and performs many different population genetic analyses including tests for different modes of selection.

Alex is also interested in the evolution of genetic networks and cellular systems and in developing tools for modeling such networks: before starting the IB program, he worked on an open-source software package for modeling and simulation called Swarm, and recently worked on the Madonna differential equation solver package developed at Berkeley.

"I really enjoy the diversity of the backgrounds and interests of the faculty and students in IB. Not being trained originally as a biologist, I am always learning new neat stuff, and being in a biology program helps keeps my theoretical and computational studies firmly grounded."

"I also appreciate the flexibility within the program, allowing me to combine my various research interests of biology, math, and computer science."

Computational & Genomic Biology

Alex entered the IB program with a background in physics and electrical engineering.

His interest in the intersection of systems biology, bioinformatics and evolutionary biology led him to become a member of the recently-formed graduate group in Computational and Genomic Biology. He is enrolled in the "designated emphasis" program.

"Because of my background, one of the things that attracted me to Berkeley was the presence of a strong community of interdisciplinary researchers centering around computational biology and genomics."

For more information, visit:

Alex's Research Page

Computational and Genomics Biology Graduate Group

PyPop

Swarm

Berkeley Madonna

March 2006

Current Student Profile

IB Research News

IB Graduate Student Information