Research articles

Selected articles related to the PGP effort and/or using PGP resources.

PublicationTopics
Optimization of Scarless Human Stem Cell Genome Editing
Yang L, Guell M, Byrne S, Yang JL, De Los Angeles A, Mali P, Aach J, Kim-Kiselak C, Briggs AW, Rios X, Huang PY, Daley G, Church G. Nucleic Acids Res. 2013 Jul 31. (PDF)

Biotechnology

Our genomes today: time to be clear
Jeantine E Lunshof and Madeleine P Ball. Genome Med. 2013 Jun 27;5(6):52. (full text)

Bioethics

RNA-guided human genome engineering via Cas9
Mali P, Yang L, Esvelt KM, Aach J, Guell M, DiCarlo JE, Norville JE, Church GM. Science. 2013 Feb 15;339(6121):823-6. (PDF)

Biotechnology

Genetic Privacy Needs a More Nuanced Approach
Misha Angrist, Nature, February 6, 2013.

Bioethics

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells
Peters BA, Kermani BG, Sparks AB et al. Nature. 2012 Jul 11;487(7406):190-5. (pdf)

Biotechnology

A Public Resource Facilitating Clinical Use of Genomes
Ball MP, Thakuria JV, Zaranek AW, Clegg T, Rosenbaum AM, Wu X, Angrist M, Bhak J, Bobe J, Callow M, Cano C, Chou MF, Chung WK, Douglas SM, Estep P, Gore A, Hulick P, Labarga A, Lee J, Lunshof J, Kim BC, Kim JI, Li Z, Murray MF, Nilsen GB, Peters B, Raman AM, Reinhoff HY, Robasky K, Wheeler M, Vandewege W, Vorhaus D, 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. PNAS July 13, 2012. (pdf+html).

Computational

Health & Disease

Bioethics

Genomics and Privacy: Implications of the New Reality of Closed Data for the Field
Greenbaum D, Sboner A, Mu XJ, Gerstein M. PLoS Comput Biol. 2011 Dec;7(12):e1002278. (full text)

Computational

Bioethics

Neuronal maturation defect in induced pluripotent stem cells from patients with Rett syndrome
Kim KY, Hysolli E, Park IH. Proc Natl Acad Sci U S A. 2011 Aug 23;108(34):14169-74. (full text)

Biotechnology

Health & Disease

Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome
Shoemaker R, Deng J, Wang W, Zhang K. Genome Res. 2010 Jul;20(7):883-9. (full text)

Discovery

Biotechnology

Personal genomes in progress: From the Human Genome Project to the Personal Genome Project
Jeantine Lunshof, Jason Bobe, John Aach, Misha Angrist, Joseph Thakuria, Daniel Vorhaus, Margret Hoehe, George Church. Dialogues in Clinical Neuroscience. 12(1):47-60, 2010. article

Bioethics

Targeted and whole-genome methylomics reveals gene-body signatures in human cell lines
Ball MP, Li JB, Gao Y, Lee J, LeProust E, Park I-H, Xie B, Daley GQ, Church GM. Nature Biotechnol 27:361-8. (PDF)

Discovery

Biotechnology

Multiplex padlock capturing and sequencing reveal human hypermutable CpG variations
Li JB, Gao Y, Aach J, Zhang K, Kryukov GV, Xie B, Ahlford A, Yoon J-K, Rosenbaum AM, Zaranek AW, LeProust E, Sunyaev SR, Church GM. Genome Res 19(9):1606-15. (PDF)

Discovery

Biotechnology

Digital RNA Allelotyping Reveals Tissue-specific and Allele-specific Gene Expression in Human
Zhang K, Li JB, Gao Y, Egli D, Xie B, Lee JH, Aach J, LeProust E, Eggan K, Church GM (20-Jul-2009) Nature Methods 6, 613 - 618. (abstract)

Discovery

Biotechnology

Functional characterization of the antibiotic resistance reservoir in the human microflora
Sommer MO, Dantas G, Church GM. Science. 2009 Aug 28;325(5944):1128-31. (PDF)

Discovery

Biotechnology

Health & Disease

Generation of Functional Human Hepatic Endoderm from Human iPS cells
Sullivan GJ, Hay DC, Park IH, Fletcher J, Hannoun Z, Payne CM, Dalgetty D, Black JR, Ross J, Samuel K, Wang G, Daley GQ, Lee JH, Church GM, Forbes SJ, Iredale JP, Wilmut I. Hepatology. 2010 Jan;51(1):329-35. (full text)

Biotechnology

A robust approach to identifying tissue-specific gene expression regulatory variants using personalized human induced pluripotent stem cells
Lee JH, Park IH, Gao Y, Li JB, Li Z, Daley GQ, Zhang K, Church GM. PLoS Genet. 2009 Nov;5(11):e1000718. (full text)

Biotechnology

Human genome sequencing using unchained base reads on self-assembling DNA nanoarrays
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, Reid CA. Science. 2010 Jan 1;327(5961):78-81. (PDF)

Biotechnology

From genetic privacy to open consent.
Lunshof JE, Chadwick R, Vorhaus DB, Church GM (2008) From genetic privacy to open consent. Nat Rev Genet. 2008 May;9(5):406-11. PMID: 18379574 (PDF)

Bioethics

The Personal Genome Project
George Church. Molecular Systems Biology, Dec 2005. (full text)

Bioethics