Learn More about GP-write

and the Field of Engineering Biology

GP-write Publications

Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof, J Maurano MT, Mitchell LA, Peterson T, Rine J, Rosser SJ, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L. The Genome Project-Write. Science. 2016; Epub ahead of print.

Boeke JD, Church G, Hessel A, Kelley NJ, Arkin A, Cai Y, Carlson R, Chakravarti A, Cornish VW, Holt L, Isaacs FJ, Kuiken T, Lajoie M, Lessor T, Lunshof, J Maurano MT, Mitchell LA, Peterson T, Rine J, Rosser SJ, Sanjana NE, Silver PA, Valle D, Wang H, Way JC, Yang L. Genome Project-write: A Grand Challenge Using Synthesis, Gene Editing and Other Technologies to Understand, Engineer and Test Living Systems (White Paper).

Boeke JD, Church, G, Hessel, A, Kelley NJ. HGP-write: Testing Large Genomes in Cells (May 10, 2016 Meeting Summary).

New Pilot Projects (Coming Soon)
Funding Opportunities: Requests for Proposals


HGP-write May 10, 2016 Meeting Videos

HGP-write: Testing Large Genomes in Cells.
Watch presentations that took place at the HGP-write organizing meeting on May 10th, 2016.

Additional Resources

Poll Results from the GP-write Meeting. May 2017.

4th Annual Sc2.0 and Synthetic Genomes Conference. Panel Discussion: Genome Engineering and Society. On July 16-17th, 2015, scientists from around the world convened in New York City at the New York Genome Center to discuss progress in synthetic yeast genome engineering as well as a broader discussion of other genome engineering efforts, CRISPRs, designer nucleases, and synthetic biology.

Engineering Biology for Science and Industry: Accelerating Progress. In April and July, 2015, emerging and established leaders of engineering biology came together in New York City to lay the groundwork for accelerating progress in this highly important field.
April 17, 2015 Meeting Summary
July 14-15, 2015 Meeting Summary

Woodrow Wilson International Center for Scholars, Synthetic Biology Project. The Synthetic Biology Project was established as an initiative of the Science and Technology Innovation Program of the Woodrow Wilson International Center for Scholars.

On the Promise and Challenges of Engineering Biology. View a short video series from leaders in the field providing their insights on the promises and challenges of engineering biology.

Engineering Biology to Address Global Problems: Synthetic Biology Markets, Needs, and Applications. This report reviews the development of synthetic biology from a historical perspective, within a global landscape of regulatory frameworks, funding initiatives, and social and ethical aspects.

The Promise and Challenge of Engineering Biology in the United States. This report reviews the role engineering biology will play in the U.S. bioeconomy and what needs to be done to move this important field forward safely and responsibly.

Time for Another Human Genome Project? Andrew Hessel for Huffpost Science; March 14, 2012


Bibliography


Below is a (non-comprehensive) sampling of precedents for projects that could take advantage of radical reduction in cost of genome-scale synthesis and high-throughput cellular/organismal testing of consequences. As with HGP-read, this is not restricted to human but could include mouse, pig, Drosophila, C.elegans, Arabidopsis, etc.


Genome-scale editing of repetitive elements (ERVs, LINEs, SINEs, Centromeres, Telomeres, etc.)

Genome-wide inactivation of porcine endogenous retroviruses (PERVs).
Yang L, Güell M, Niu D, George H, Lesha E, Grishin D, Aach J, Shrock E, Xu W, Poci J, Cortazio R, Wilkinson RA, Fishman JA, Church G.
Science. 2015 Nov 27,350(6264):1101-4.

Genome-wide change in protein sequences (humanization of mice and pigs)

Sachs DH, Sykes M, Yamada K. Transpl Immunol. 2009 21(2):101-5.
Achieving tolerance in pig-to-primate xenotransplantation: reality or fantasy.

Synthesis of common ancestral genomes

Blanchette M, Diallo AB, Green ED, Miller W, Haussler D. Methods Mol Biol. 2008,422:171-84. doi: 10.1007/978-1-59745-581-7_11.
Computational reconstruction of ancestral DNA sequences.

Jermann TM, Opitz JG, Stackhouse J, Benner SA.
Nature. 1995 Mar 2,374(6517):57-9.
Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily.

Use of genome-wide recoding for multi-viral resistance.

Lajoie, M.J., Rovner, A.J., Goodman, D.B., Aerni, H.R., Haimovich, A.D., Kuznetsov, G., Mercer, J.A., Wang, H.H., Carr, P.A., Mosberg, J.A., et al. (2013). Genomically recoded organisms expand biological functions. Science 342, 357-360.

Making haploid and homozygous mammalian genomes.

Zhou Q, Wang M, Yuan Y, Wang X, Fu R, Wan H, Xie M, Liu M, Guo X, Zheng Y, Feng G, Shi Q, Zhao XY, Sha J, Zhou Q. Cell Stem Cell. 2016 18(3):330-40. Complete Meiosis from Embryonic Stem Cell-Derived Germ Cells In Vitro.

Sagi I, Chia G, Golan-Lev T, Peretz M, Weissbein U, Sui L, Sauer MV, Yanuka O, Egli D, Benvenisty N. Nature. 2016 532(7597):107-11. Derivation and differentiation of haploid human embryonic stem cells.

Early history of custom de novo nucleic acid synthesis:

Grunberg-Manago M, Oritz Pj, Ochoa S. (1955) Science. 122(3176):907-10. Enzymatic synthesis of nucleic acidlike polynucleotides.

Kleppe K, Ohtsuka E, Kleppe R, Molineux I, Khorana HG (1971) J. Mol. Bio. 56: 341-361 Studies on Polynucleotides XCVI. Repair Replication of Short Synthetic DNA’s as catalyzed by DNA Polymerases

Simultaneous mutations genome-wide to test chromosome folding rules and readout. Simultaneous heterozygous mutations in cis-regulatory elements genome wide.

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states.
Boettiger AN, Bintu B, Moffitt JR, Wang S, Beliveau BJ, Fudenberg G, Imakaev M, Mirny LA, Wu CT, Zhuang X. Nature. 2016 529(7586):418-22.

Beliveau BJ, Boettiger AN, Avendaño MS, Jungmann R, McCole RB, Joyce EF, Kim-Kiselak C, Bantignies F, Fonseka CY, Erceg J, Hannan MA, Hoang HG, Colognori D, Lee JT, Shih WM, Yin P, Zhuang X, Wu CT. Nat Commun. 2015 6:7147. Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes.

Pinter SF, Colognori D, Beliveau BJ, Sadreyev RI, Payer B, Yildirim E, Wu CT, Lee JT.
Genetics. 2015 Jun;200(2):537-49. Allelic Imbalance Is a Prevalent and Tissue-Specific Feature of the Mouse Transcriptome.

Tests of prevention of cancer and aging in animals and human cells. Lists of cancer and aging related genes in animals and human cells:

Tomás-Loba A1, Flores I, Fernández-Marcos PJ, Cayuela ML, Maraver A, Tejera A, Borrás C, Matheu A, Klatt P, Flores JM, Viña J, Serrano M, Blasco MA. Cell. 2008 Nov 14;135(4):609-22. doi: 10.1016/j.cell.2008.09.034. Telomerase reverse transcriptase delays aging in cancer-resistant mice.

1207 Tumor Suppressors
bioinfo.mc.vanderbilt.edu/TSGene

233 Human onocogenes
uniprot.org

~3000 Haploinsufficient genes journals.plos.org/plosgenetics/article?id=10.1371/journal.pgen.1003484

GenAge Database of Cancer and Ageing-Related Genes
genomics.senescence.info/genes
genomics.senescence.info/cancer/


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