User:Alexander Wait Zaranek

Alexander (Sasha) Wait Zaranek

Education

• PhD Biophysics, Harvard (2009)
• BSc Computer Science, University of Toronto (1998)

Short Biography

I recently finished an exclusive, friendly, and flexible graduate program. I was a teaching fellow for classes on synthetic biology and personal genomics. I was lucky enough to be introduced to molecular biology in Jack Szostak's lab. Recently I've been a guest lecturer in HST508 and Biophysics 101.

I have been de-facto, director of informatics at the Personal Genome Project since 2005. The PGP is the only project worldwide that provides "open-access" to well integrated human tissue-samples, genetic data and phenotype data. We were one of the first users of CC0. The commitment to openness has also led to my longtime collaboration on the Polonator which is the only open-innovation instrument platform for DNA sequencing. The Polonator, and related technologies, is part of the revolution that brought DNA sequencing costs down by 10,000-fold in 4 years. More recently it has also served as a platform for synthetic chemistry and cell biology in the same open device. Finally, along with my colleagues at the PGP, I've spearheaded an open clinical genome sequence interpretation and evidence database.

In a past-life I was a contractor for a telecom equipment supplier. My team's software translated electronics design data into instructions for a medium volume, high-mix electronics factory. I am a contributor to the IPC-2511 (GenCAM) standard. That experience helped shape my thinking on open biological factories.

My professional interests include: personalized medicine, exascale computing, and free knowledge business models. When I can, I still enjoy tinkering with quantum lifeforms and synthetic biology.

Publications

1. Drmanac R, Sparks AB, Callow MJ, Halpern AL, Burns NL, Kermani BG, Carnevali P, Nazarenko I, Nilsen GB, Yeung G, Dahl F, Fernandez A, Staker B, Pant KP, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R, Curson B, Ebert JC, Hacker CR, Hartlage R, Hauser B, Huang S, Jiang Y, Karpinchyk V, Koenig M, Kong C, Landers T, Le C, Liu J, McBride CE, Morenzoni M, Morey RE, Mutch K, Perazich H, Perry K, Peters BA, Peterson J, Pethiyagoda CL, Pothuraju K, Richter C, Rosenbaum AM, Roy S, Shafto J, Sharanhovich U, Shannon KW, Sheppy CG, Sun M, Thakuria JV, Tran A, Vu D, Zaranek AW, Wu X, Drmanac S, Oliphant AR, Banyai WC, Martin B, Ballinger DG, Church GM, and Reid CA. Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays. Science. 2010 Jan 1;327(5961):78-81. DOI:10.1126/science.1181498 |
2. Kim JI, Ju YS, Park H, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Lee WC, Lee JS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Kim HJ, Yavartanoo M, Kwak M, Zheng Y, Lee MK, Park H, Kim JY, Gokcumen O, Mills RE, Zaranek AW, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Kim H, Yang KS, Park WY, Kim H, Church GM, Lee C, Kingsmore SF, and Seo JS. A highly annotated whole-genome sequence of a Korean individual. Nature. 2009 Aug 20;460(7258):1011-5. DOI:10.1038/nature08211 |
3. Whiteford N, Skelly T, Curtis C, Ritchie ME, Löhr A, Zaranek AW, Abnizova I, and Brown C. Swift: primary data analysis for the Illumina Solexa sequencing platform. Bioinformatics. 2009 Sep 1;25(17):2194-9. DOI:10.1093/bioinformatics/btp383 |
4. Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon JK, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, and Church GM. Multiplex padlock targeted sequencing reveals human hypermutable CpG variations. Genome Res. 2009 Sep;19(9):1606-15. DOI:10.1101/gr.092213.109 |

5. Zaranek AW, Clegg T, Vandewege W, Church GM: Free Factories: Unified Infrastructure for Data Intensive Web Services. USENIX Annual Technical Conference 2008: 391-404.