User:Alex K. Lancaster

I am a new member of OpenWetWare!

Contact Info

• Alex K. Lancaster
• Countway Library
• Harvard Medical School
• 10 Shattuck Street
• Boston, MA, 02115 USA
• Email me through OpenWetWare
• Website: http://scholar.harvard.edu/lancaster

I'm a computational and evolutionary systems biologist. I'm on the faculty at the Department of Pathology at Beth Israel Deaconess Medical Center and a research associate in the Center for Biomedical Informatics at Harvard Medical School (Faculty website, Catalyst profile). I joined OpenWetWare as an occasional participant in the Bioinformatics Interest Group meeting and because I am interested in open-source and open-science approaches to systems biology and genomics.

Education

• Ph.D., University of California, Berkeley
• B.Sc., B.E. (Hons), University of Sydney

Research interests

1. Systems biology
2. Evolutionary and population genomics
3. Mathematical biology

Publications

1. Lancaster A, Nelson MP, Meyer D, Single RM, and Thomson G. PyPop: a software framework for population genomics: analyzing large-scale multi-locus genotype data. Pac Symp Biocomput. 2003:514-25.
2. Williams F, Meenagh A, Single R, McNally M, Kelly P, Nelson MP, Meyer D, Lancaster A, Thomson G, and Middleton D. High resolution HLA-DRB1 identification of a Caucasian population. Hum Immunol. 2004 Jan;65(1):66-77. DOI:10.1016/j.humimm.2003.10.004 |
3. Cao K, Moormann AM, Lyke KE, Masaberg C, Sumba OP, Doumbo OK, Koech D, Lancaster A, Nelson M, Meyer D, Single R, Hartzman RJ, Plowe CV, Kazura J, Mann DL, Sztein MB, Thomson G, and Fernández-Viña MA. Differentiation between African populations is evidenced by the diversity of alleles and haplotypes of HLA class I loci. Tissue Antigens. 2004 Apr;63(4):293-325. DOI:10.1111/j.0001-2815.2004.00192.x |
4. Tu B, Mack SJ, Lazaro A, Lancaster A, Thomson G, Cao K, Chen M, Ling G, Hartzman R, Ng J, and Hurley CK. HLA-A, -B, -C, -DRB1 allele and haplotype frequencies in an African American population. Tissue Antigens. 2007 Jan;69(1):73-85. DOI:10.1111/j.1399-0039.2006.00728.x |
5. Lancaster AK, Single RM, Solberg OD, Nelson MP, and Thomson G. PyPop update--a software pipeline for large-scale multilocus population genomics. Tissue Antigens. 2007 Apr;69 Suppl 1(0 1):192-7. DOI:10.1111/j.1399-0039.2006.00769.x |
6. Single RM, Meyer D, Mack SJ, Lancaster A, Erlich HA, and Thomson G. 14th International HLA and Immunogenetics Workshop: report of progress in methodology, data collection, and analyses. Tissue Antigens. 2007 Apr;69 Suppl 1:185-7. DOI:10.1111/j.1399-0039.2006.00767.x |
7. Tang TF, Hou L, Chen M, Belle I, Mack S, Lancaster A, Ho GY, Hwang WY, Alsagoff F, Ng J, and Hurley CK. HLA haplotypes in Singapore: a study of mothers and their cord blood units. Hum Immunol. 2007 May;68(5):430-8. DOI:10.1016/j.humimm.2007.01.005 |
8. Solberg OD, Mack SJ, Lancaster AK, Single RM, Tsai Y, Sanchez-Mazas A, and Thomson G. Balancing selection and heterogeneity across the classical human leukocyte antigen loci: a meta-analytic review of 497 population studies. Hum Immunol. 2008 Jul;69(7):443-64. DOI:10.1016/j.humimm.2008.05.001 |
9. Mack SJ, Tu B, Lazaro A, Yang R, Lancaster AK, Cao K, Ng J, and Hurley CK. HLA-A, -B, -C, and -DRB1 allele and haplotype frequencies distinguish Eastern European Americans from the general European American population. Tissue Antigens. 2009 Jan;73(1):17-32. DOI:10.1111/j.1399-0039.2008.01151.x |
10. Lancaster AK and Masel J. The evolution of reversible switches in the presence of irreversible mimics. Evolution. 2009 Sep;63(9):2350-62. DOI:10.1111/j.1558-5646.2009.00729.x |
11. Lancaster AK, Bardill JP, True HL, and Masel J. The spontaneous appearance rate of the yeast prion [PSI+] and its implications for the evolution of the evolvability properties of the [PSI+] system. Genetics. 2010 Feb;184(2):393-400. DOI:10.1534/genetics.109.110213 |
12. Halfmann R, Jarosz DF, Jones SK, Chang A, Lancaster AK, and Lindquist S. Prions are a common mechanism for phenotypic inheritance in wild yeasts. Nature. 2012 Feb 15;482(7385):363-8. DOI:10.1038/nature10875 |
13. McLellan CA, Whitesell L, King OD, Lancaster AK, Mazitschek R, and Lindquist S. Inhibiting GPI anchor biosynthesis in fungi stresses the endoplasmic reticulum and enhances immunogenicity. ACS Chem Biol. 2012 Sep 21;7(9):1520-8. DOI:10.1021/cb300235m |
14. Holmes DL, Lancaster AK, Lindquist S, and Halfmann R. Heritable remodeling of yeast multicellularity by an environmentally responsive prion. Cell. 2013 Mar 28;153(1):153-65. DOI:10.1016/j.cell.2013.02.026 |
15. Tardiff DF, Jui NT, Khurana V, Tambe MA, Thompson ML, Chung CY, Kamadurai HB, Kim HT, Lancaster AK, Caldwell KA, Caldwell GA, Rochet JC, Buchwald SL, and Lindquist S. Yeast reveal a "druggable" Rsp5/Nedd4 network that ameliorates α-synuclein toxicity in neurons. Science. 2013 Nov 22;342(6161):979-83. DOI:10.1126/science.1245321 |
16. Clarke TH, Garb JE, Hayashi CY, Haney RA, Lancaster AK, Corbett S, and Ayoub NA. Multi-tissue transcriptomics of the black widow spider reveals expansions, co-options, and functional processes of the silk gland gene toolkit. BMC Genomics. 2014 May 23;15(1):365. DOI:10.1186/1471-2164-15-365 |
17. Lancaster AK, Nutter-Upham A, Lindquist S, and King OD. PLAAC: a web and command-line application to identify proteins with prion-like amino acid composition. Bioinformatics. 2014 Sep 1;30(17):2501-2. DOI:10.1093/bioinformatics/btu310 |
18. Gafni E, Luquette LJ, Lancaster AK, Hawkins JB, Jung JY, Souilmi Y, Wall DP, and Tonellato PJ. COSMOS: Python library for massively parallel workflows. Bioinformatics. 2014 Oct 15;30(20):2956-8. DOI:10.1093/bioinformatics/btu385 |

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