User:Alexander Wait Zaranek

Alexander (Sasha) Wait Zaranek

a.k.a. Sasha - awaitz @ post.harvard.edu

Education

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

Short Biography

As a biophysics student at Harvard, I received my introduction to molecular biology in Jack Szostak's lab and learned computational biology with George Church. I was a teaching fellow for classes on synthetic biology and personal genomics and, more recently, I've continued to teach in these areas as a guest lecturer for HST508 and Biophysics 101.

I have been 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 and other 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 reduced human DNA sequencing costs by a million-fold since the completion of the Human Genome Project. More recently it has also served as a platform for synthetic chemistry and cell biology in the same open device.

My current research focus is the development of Arvados -- an open-source platform for data-management, analysis and sharing of large biomedical data sets spanning millions of individual humans across numerous organizations and eventually encompassing exabytes of data. As an example of an Arvados application, along with my colleagues at the PGP, I've launched an open, genome interpretation system, GET-Evidence and the study management system Tapestry.

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. Ball MP, Thakuria JV, Alexander Wait Zaranek, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow MJ, Cano C, Chou MF, Chung WK, Douglas SM, Estep PW, Gore A, Hulick P, Labarga A, Lee JH, Lunshof JE, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters BA, Raman AM, Rienhoff HY, Robasky K, Wheeler MT, Vandewege W, Vorhaus DB, Yang JL, Yang L, Aach J, Ashley EA, Drmanac R, Kim SJ, Li JB, Peshkin L, Seidman CE, Seo JS, Zhang K, Rehm HL, Church GM. (2012) A public resource facilitating clinical use of genomes. Proc Natl Acad Sci U S A. Jul 24;109(30):11920-7. Epub 2012 Jul 13. PMID: 22797899
2. Peters BA, Kermani BG, Sparks AB, Alferov O, Hong P, Alexeev A, Jiang Y, Dahl F, Tang YT, Haas J, Robasky K, Alexander Wait Zaranek, Lee JH, Ball MP, Peterson JE, Perazich H, Yeung G, Liu J, Chen L, Kennemer MI, Pothuraju K, Konvicka K, Tsoupko-Sitnikov M, Pant KP, Ebert JC, Nilsen GB, Baccash J, Halpern AL, Church GM, Drmanac R. (2012) Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells. Nature. Jul 11;487(7406):190-5. doi: 10.1038/nature11236. PMID: 22785314
3. Thakuria JV, Alexander Wait Zaranek, Church GM, Berry GT. (2012) Back to the future: from genome to metabolome. Hum Mutat. May;33(5):809-12. doi: 10.1002/humu.22073.
4. Dewey FE, Chen R, Cordero SP, Ormond KE, Caleshu C, Karczewski KJ, Whirl-Carrillo M, Wheeler MT, Dudley JT, Byrnes JK, Cornejo OE, Knowles JW, Woon M, Sangkuhl K, Gong L, Thorn CF, Hebert JM, Capriotti E, David SP, Pavlovic A, West A, Thakuria JV, Ball MP, Alexander Wait Zaranek, Rehm HL, Church GM, West JS, Bustamante CD, Snyder M, Altman RB, Klein TE, Butte AJ, Ashley EA. (2011) Phased whole-genome genetic risk in a family quartet using a major allele reference sequence. PLoS Genetics 7(9):e1002280. doi:10.1371/journal.pgen.1002280
5. Alexander Wait Zaranek, Levanon EY, Zecharia T, Clegg T, Church GM (2010) A Survey of Genomic Traces Reveals a Common Sequencing Error, RNA Editing and DNA Editing. PLoS Genetics 6(5): e1000954. doi:10.1371/journal.pgen.1000954
6. Ashley EA, Butte AJ, Wheeler MT, Chen R, Klein TE, Dewey FE, Dudley JT, Ormond KE, Pavlovic A, Morgan AA, Pushkarev D,Neff NF ,Hudgins L, Gong L, Hodges LM, Berlin DS, Thorn CF, Sangkuhl K, Hebert JM, Woon M, Sagreiya H, Whaley R, Knowles JW, Chou MF, Thakuria JV, Rosenbaum AM, Alexander Wait Zaranek, Church GM, Greely HT, Quake SR, Altman RB (2010) Clinical assessment incorporating a personal genome. Lancet 375: 1525-35
7. Drmanac R, Burns NL, Callow MJ, Carnevali P, Dahl F, Fernandez A, Halpern AL, Kermani BG, Nazarenko I, Nilsen GB, Pant KP, Sparks AB, Staker B, Yeung G, Baccash J, Borcherding AP, Brownley A, Cedeno R, Chen L, Chernikoff D, Cheung A, Chirita R, Curson B, Ebert J, 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, Shananhovich V, Shannon KW, Sheppy CG, Sun M, Thakuria JV, Tran A, Vu D, Wu X, Alexander Wait Zaranek, Drmanac S, Oliphant AR, Banyai WC, Martin B, Ballinger DG, Church GM, Reid CA (2010) Human Genome Sequencing Using Unchained Base Reads on Self-assembling DNA Nanoarrays. Science 2010 Jan 1;327(5961):78-81.
8. Whiteford N, Skelly T, Curtis C, Ritchie M, Lohr A, Alexander Wait Zaranek, Abnizove I, Brown C, (2009) Swift: Primary Data Analysis for the Illumina Solexa Sequencing Platform. Bioinformatics 25(17):2194-2199.
9. Kim JI, Ju YS, Park HS, Kim S, Lee S, Yi JH, Mudge J, Miller NA, Hong D, Bell CJ, Kim HS, Chung IS, Seo SH, Yun JY, Woo HN, Lee H, Suh D, Lee S, Park H, Kim JY, Gokcumen O, Mills RE, Alexander Wait Zaranek, Thakuria J, Wu X, Kim RW, Huntley JJ, Luo S, Schroth GP, Wu TD, Yang KS, Kim H, Church GM, Lee C, Kingsmore SF, Seo JS (2009) A highly annotated whole genome sequence of a Korean Individual. Nature Jul 8; 195
10. Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon J-K, Rosenbaum AM, Alexander Wait Zaranek, LeProust E, Sunyaev SR, Church GM (2009) Multiplex padlock capturing and sequencing reveal human hypermutable CpG variations. Genome Research Sep;19(9):1606-15.
11. Alexander Wait Zaranek, Clegg T, Vandewege W, Church GM: Free Factories: Unified Infrastructure for Data Intensive Web Services. USENIX Annual Technical Conference 2008: 391-404.

PubMed