User:Alexander Wait Zaranek

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==Publications==
==Publications==
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#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  
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<biblio>
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#'''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 (in production)  
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#Ashley2010 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, Zaranek AW, Church GM, Greely HT, Quake SR, Altman RB (2010) Clinical assessment incorporating a personal genome. Lancet 375: 1525-35
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#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 (2009) ''Human Genome Sequencing Using Unchained Base Reads on Self-assembling DNA Nanoarrays.'' Science 2010 Jan 1;327(5961):78-81. Epub 2009 Nov 5;
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#Zaranek2010 Zaranek AW, 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 (in production)  
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#Whiteford2009 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.
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#Drmanac2010 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, Zaranek AW, Drmanac S, Oliphant AR, Banyai WC, Martin B, Ballinger DG, Church GM, Reid CA (2009) Human Genome Sequencing Using Unchained Base Reads on Self-assembling DNA Nanoarrays. Science 2010 Jan 1;327(5961):78-81. Epub 2009 Nov 5;
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#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
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#Whiteford2009 Whiteford N, Skelly T, Curtis C, Ritchie M, Lohr A, Zaranek AW, Abnizove I, Brown C, (2009) Swift: Primary Data Analysis for the Illumina Solexa Sequencing Platform. Bioinformatics 25(17):2194-2199.  
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#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.
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#Li2009 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, Zaranek AW, 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
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#'''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.
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#Zaranek2008 Zaranek AW, Clegg T, Vandewege W, Church GM: ''Free Factories: Unified Infrastructure for Data Intensive Web Services.'' USENIX Annual Technical Conference 2008: 391-404.
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</biblio>
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[http://www.ncbi.nlm.nih.gov/pubmed?term=Zaranek%2C%20Alexander%20Wait PubMed]
[http://www.ncbi.nlm.nih.gov/pubmed?term=Zaranek%2C%20Alexander%20Wait PubMed]

Revision as of 08:53, 4 May 2010

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-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 the last four 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 and helped set the foundation for SCE.

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. 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
  2. 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 (in production)
  3. 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 (2009) Human Genome Sequencing Using Unchained Base Reads on Self-assembling DNA Nanoarrays. Science 2010 Jan 1;327(5961):78-81. Epub 2009 Nov 5;
  4. Whiteford2009 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.
  5. 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
  6. 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.
  7. 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

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