Currently:

I'm a second year Ph.D student with interests in probabilistic and machine learning techniques applied to large-scale biological data. I'm keen to find out how life works, and believe mathematical models with computational techniques and wetlab validation are the way forward. For the next 3 years my goals are to develop a good intuition of biology at the cell level (how things work), evolutionary level (how working things can and do change) and lab level (how do we learn about them). At the same time, I want to assemble a toolbox of mathematical and computational methods, and apply them to interesting problems. I started my Ph.D project looking at population genetics and population structure detection in yeast, and have now moved to detecting genotype-phenotype associations on the large scale.

Previously:

• Spring 2007 - rotation project with Andy Fraser's lab (Team 37). Played around in the lab a lot on C. elegans with help from Michelle and Sergey, found out there are a lot of ways to go wrong :) Hopefully will get some data to try out the image analysis techniques developed, and get some good football games with the lab team next season.
• Winter 2007 - rotation project with Anton Enright's group (Team 101). Again, nice and productive time doing large scale data mining and graph clustering on Medline data. Still working on it as a backburner project, as well as playing Go with Stijn, Cei, and Harpreet.
• Fall 2007 - rotation project with Team 118 on gene copy number variation in yeast (Yeast Resequencing Project). Noisy results from the ABI reads, hopefully comparing with the new Solexa sequencing technologies will yield better answers.
• Summer 2006 - working with Manolis Kellis's group in MIT, at the BIIT group at University of Tartu, on predicting miRNA genes from 12 Drosophila genomes. Nice and productive time, largely thanks to a good collaboration with Alex Stark and Pouya Kheradpour and support from Jaak Vilo. Resulted in 3 papers - hurrah!
• Summer 2005 - working at the Ensembl group in the European Bioinformatics Institute, comparing the Pest and Mopti strains of the mosquito Anopheles gambiae. Worked with Martin Hammond and Ewan Birney, and enjoyed the company of Ben, Karyn, Arne and Stefan as well. First proper look at doing science in computational biology, convinced me I should do science for living.

Life:

I play basketball for Cambridge University, and was coaxed into being the president of the Cambridge University Basketball Club for last year. I also play in a local volleyball league with the Genome Campus team, and go windsurfing whenever possible with the Cambridge University Windsurfing Club. I like playtime, outdoors, travelling, spending time with coursemates from Sanger (SCAMPS is coming up), and all the other good things. I try to learn guitar, French, cooking, and being less messy, but have failed spectacularly in each so far.

Education:

• 2006 - ... Cambridge University, Ph.D in Molecular Biology. This is what I do now.
• 2004 -
  2005 Cambridge - MIT exchange to Cambridge, England. Academically laid-back year with various courses around the university and time to think.
• 2003 - 2006 Massachusetts Institute of Technology, B. Sc. in Computer Science and Engineering, Mathematics. Very nice academic environment,
  always pushing forward for new results. But I prefer the other Cambridge as a place to live :)
• 2001 - 2003 University of Tartu, dept. of Computer Science. 2 years of nice uni life with plenty of basic undergrad classes.

Publications:

• Drosophila 12 Genomes Consortium. Evolution of genes and genomes on the Drosophila phylogeny.
  Nature, 2007.
• Alexander Stark, Michael F. Lin, Pouya Kheradpour, Jakob S. Pedersen, Leopold Parts et.al. Discovery of functional elements in 12 fly genomes using evolutionary signatures. Nature, 2007
  
• Alexander Stark, Pouya Kheradpour, Leopold Parts, Julius Brennecke, Emily Hodges,Gregory J. Hannon, and Manolis Kellis. Systematic discovery and characterization of fly
  microRNAs using 12 Drosophila genomes. Genome Research,
  2007
  
• I also have a blog in Estonian, mostly to keep up with friends and family from home and avoid writing long emails to individual people :), and a blog in
  English (local copy here as well), where I've started to write down cool math/cs/bio stuff I read and think about.