Amy Williams

Amy Williams


Assistant Professor, Cornell University

I am a population geneticist and computer scientist interested in leveraging large scale genetic data to understand human genetic history, evolution, and the genetic basis for human disease. My work focuses on developing computational methods to process large scale genetic datasets and on performing analyses of genetic data using my own and other software. I am interested in inferring haplotypes and understanding their evolution by recombination and mutation. In so doing, I aim to help reconstruct the ancestral recombination graph of humanity; i.e., the genealogical tree at each genomic position that relates human beings to each other.

I am currently a Postdoctoral Research Associate working with Molly Przeworski at the Howard Hughes Medical Institute (conducting work at Columbia University). I received a PhD (2010) and SM (2005) in Computer Science from Massachusetts Institute of Technology, and two BS (2003) degrees in Computer Science and Mathematics from the University of Utah. From 2009-2013 I worked as a Postdoctoral Research Fellow with David Reich and David Altshuler at Harvard Medical School.

Starting August, 2014, I will be an assistant professor at Cornell in the Biological Statistics and Computational Biology department. Job openings for a programmer and postdoctoral fellow will be posted soon! Send your CV if interested.

Education History

PhD, Massachusetts Institute of Technology
Computer Science

SM,  Massachusetts Institute of Technology
Computer Science

BS, University of Utah
Computer Science, Mathematics


Williams AL, Genovese G, Dyer T, Altemose N, Truax K, Jun G, Patterson N, Myers SR, Curran JE, Duggirala R, Blangero J, Reich D, Przeworski M. Non-crossover gene conversions show strong GC bias and unexpected clustering in humans. Elife. 2015 Mar 25;4. 

The SIGMA Type 2 Diabetes Consortium: Williams AL†, Jacobs SBR, Moreno-Macías H, et al.  Sequence variants in SLC16A11 are a common risk factor for type 2 diabetes in Mexico. Nature. 2014 Feb;506:97-101.

The 1000 Genomes Project Consortium♦.  An integrated map of genetic variation from 1,092 human genomes. Nature. 2012 Nov;491:56-65, Nov 2012.

Williams AL, Patterson N, Glessner J, Hakonarson H, Reich D.  Phasing Many Thousands of Genotyped Samples.  Am J Hum Genet. 2012 Aug;91:238-51.

Fejerman L, Chen GK, Eng C, Huntsman S, Hu D, Williams A, Pasaniuc B, John EM, Via M, Gignoux C, Ingles S, Monroe KR, Kolonel LN, Torres-Mejía G, Pérez-Stable EJ, Burchard EG, Henderson BE, Haiman CA, Ziv E. Admixture mapping identifies a locus on 6q25 associated with breast cancer risk in US Latinas. Hum Mol Genet. 2012 Apr;21:1907-17.

Williams AL, Housman DE, Rinard MC, Gifford DK.  Rapid haplotype inference for nuclear families. Genome Biol. 2012 Oct;11:R108.

Williams A, Thies W, Ernst MD. Static deadlock detection for Java libraries.  European Conference on Object-Oriented Programming (ECOOP).  Glasgow, Scotland, UK. Jul 2005.

Williams A, Barrus S, Morley K, Shirley P.  An efficient and robust ray-box intersection algorithm.  Journal of Graphics Tools. 2005 Jun;10:49-54.

† Led the genetics analysis and wrote the genetics portions of paper.

♦ Developed HAPMIX extension and applied it to the Latino populations.


Lab Staff