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Alex Lancaster

Alex LancasterPostdoctoral Research Associate

alexlanc@u.arizona.edu
Ph. 520 626 1727
Office BSW121



I am interested in the evolution of evolvability specifically the notion of capacitance and how these ideas apply to the evolution of genetic and biochemical networks. I use a combination of theoretical population genetics, computer simulation and bioinformatics to investigate these questions in the context of the [PSI+] yeast prion system. I have previously investigated how the evolution of epigenetic inheritance systems (EIS) is affected by the presence of genetic mutations that mimic inherited epigenetically-controlled phenotypes. I am currently developing a realistic, yet tractable model of stochastic gene regulation in Saccharomyces cerevisiae to explore the evolution of the genotype-phenotype map.

Some of my previous work was on the evolution of the immune system, specifically the major histocompatibility complex (MHC), a gene family found in most vertebrates, and a major part of the adaptive immune system. I looked for patterns of selection at the protein sequence level, and related these patterns to structural and functional aspects of MHC proteins.

I also developed a population genetics bioinformatics pipeline, PyPop, which operates on multi-locus genotype data, and performs many different population genetic analyses including tests for different modes of selection (Lancaster et al. 2007, 2003).

Previously I was a primary developer of the agent-based modeling software package, Swarm, and recently worked on the Madonna differential equation solver package developed at University of California, Berkeley.

Links

Software:

Publications:

  • Lancaster, A. K., Bardill, J. P., True, H. L., Masel, J. (in prep.). The spontaneous appearance rates of both the yeast prion [PSI+] and of other [PSI+]-like phenotypes.
  • Lancaster, A. K., Masel, J. (Forthcoming). The evolution of reversible switches in the presence of irreversible mimics. Evolution.
  • Solberg, O. D., Mack, S. J., Lancaster, A. K., Single, R. M., Tsai, Y., Sanchez-Mazas, A., Thomson, G. (2008). Balancing selection and heterogeneity across the classical human leukocyte antigen loci: A meta-analytic review of 497 population studies. Hum Immunol, 69(7), 443-64. (PubMed)Go to document (doi)Go to document
  • Mack, S. J., Tu, B., Lazaro, A., Yang, R., Lancaster, A. K., Cao, K., et al. (2008). HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies distinguish Eastern European Americans from the general European American population. Tissue Antigens. (doi)Go to document
  • Tu, B., Mack, S. J., Lazaro, A., Lancaster, A., Thomson, G., Cao, K., et al. (2007). HLA-A, -B, -C, -DRB1 allele and haplotype frequencies in an African American population. Tissue Antigens, 69(1), 73-85. (PubMed)Go to document (doi)Go to document
  • Tang, T. F., Hou, L., Chen, M., Belle, I., Mack, S., Lancaster, A., et al. (2007). HLA haplotypes in Singapore: a study of mothers and their cord blood units. Hum Immunol, 68(5), 430-8. (PubMed)Go to document (doi)Go to document
  • Meyer, D., Single, R. M., Mack, S. J., Lancaster, A. K., Nelson, M. P., Erlich, H. A., et al. (2007). Single locus polymorphism of classical HLA genes. In J. A. Hansen (Ed.), (Vol. I, pp. 653-704). Seattle, WA: IHWG Press.
  • Single, R. M., Meyer, D., Mack, S. J., Lancaster, A. K., Nelson, M. P., Erlich, H. A., et al. (2007). Haplotype frequencies and linkage disequilibrium among classical HLA genes. In J. A. Hansen (Ed.), (Vol. I, pp. 705-746). Seattle, WA: IHWG Press.
  • Lancaster, A. K., Nelson, M. P., Single, R. M., Meyer, D., Thomson, G. (2007). Software framework for the Biostatistics Core of the International Histocompatibility Working Group. In J. A. Hansen (Ed.), (Vol. I, pp. 510-517). Seattle, WA: IHWG Press.
  • Single, R. M., Meyer, D., Mack, S. J., Lancaster, A., Erlich, H. A., Thomson, G. (2007). 14th International HLA and Immunogenetics Workshop: report of progress in methodology, data collection, and analyses. Tissue Antigens, 69 Suppl 1, 185-7. (PubMed)Go to document (doi)Go to document
  • Lancaster, A. K., Single, R. M., Solberg, O. D., Nelson, M. P., Thomson, G. (2007). PyPop update–a software pipeline for large-scale multilocus population genomics. Tissue Antigens, 69 Suppl 1, 192-7. (PubMed)Go to document (doi)Go to document
  • Lancaster, A. K., Nelson, M. P., Meyer, D., Single, R. M., Solberg, O. (2006). PyPop User Guide: User Guide for Python for Population Genetics Berkeley, California. (PubMed)Go to document
  • Lancaster, A. K. ((2006). Identifying associations between natural selection and molecular function in human MHC genes.). Unpublished PhD Thesis.
  • Williams, F., Meenagh, A., Single, R., McNally, M., Kelly, P., Nelson, M. P., et al. (2004). High resolution HLA-DRB1 identification of a caucasian population. Hum Immunol, 65(1), 66-77. (PubMed)Go to document
  • Cao, K., Moormann, A. M., Lyke, K. E., Masaberg, C., Sumba, O. P., Doumbo, O. K., et al. (2004). Differentiation between African populations is evidenced by the diversity of alleles and haplotypes of HLA class I loci. Tissue Antigens, 63(4), 293-325. (PubMed)Go to document
  • Lancaster, A., Nelson, M. P., Meyer, D., Single, R. M., Thomson, G. (2003). PyPop: a software framework for population genomics: analyzing large-scale multi-locus genotype data. Pac Symp Biocomput, 514-25. (PubMed)Go to document
  • Qutub, A., Lancaster, A., Hunt, A. C. (2001). Therapeutic engineering: Models of individual variability in drug systems.. Paper presented at the Computers and Their Applications.