Research

Preprints and Peer-Reviewed Publications


37. Analysis of the first Genetic Engineering Attribution Challenge.

Crook OM, Warmbrod KL, Lipstein G, Chung C, Bakerlee CW, McKelvey TG, Holland SR, Swett JL, Esvelt KM, Alley EC, Bradshaw WJ.

arXiv 2110.11242 PDF


36. A Global Nucleic Acid Observatory for Biodefense and Planetary Health

The Nucleic Acid Observatory Consortium (2021)

arXiv:2108.02678. PDF


35. Systematic molecular evolution enables robust biomolecule discovery.

DeBenedictis EA*, Chory EJ*, Gretton D, Wang B, Golas S, Esvelt KM.

Nat. Methods (accepted)

bioRxiv 10.1101/2020.04.01.021022 PDF

34. The feasibility of targeted test-trace-isolate for the control of SARS-CoV-2 variants.

Bradshaw J, Huggins J, Lloyd AL, Esvelt KM.

F1000Research (2021) 10 (291). doi: 10.12688/f1000research.51164.1

33. Low-N protein engineering with data-efficient deep learning.

Biswas S, Khimulya G, Alley EC, Esvelt KM, Church GM.

Nat. Methods (2021) 8: 389-396. doi: 10.1038/s41592-021-01100-y

32. Enabling high-throughput biology with flexible open-source automation.

Chory EJ, Gretton DW, DeBenedictis EA, Esvelt KM.

Mol. Sys. Biol. (2021) 17(3) e9942. doi: 10.15252/msb.20209942 PDF

31. Safety and security concerns regarding transmissible vaccines.

Sandbrink JB, Watson MC, Hebbeler AM, Esvelt KM.

Nat. Ecol. Evol. (2021) doi:10.1038/s41559-021-01394-3

30. A Scalable Solution for Signaling Face Touches to Reduce the Spread of Surface-based Pathogens.

Rojas C, Poulsen N, Van Tuyl M, Vargas D, Cohen Z, Paradiso J, Maes P, , Adib F.

Proceedings of the ACM on Interactive, Mobile, Wearable and Ubiquitous Technologies

(2021) 5(1):1-22 doi: 10.1145/3448121

29. Bidirectional contact tracing could dramatically improve COVID-19 control.

Bradshaw WJ, Alley EC, Huggins JH, Lloyd AL, Esvelt KM.

Nat. Commun. (2021) 232. doi:10.1038/s41467-020-20325-7 PDF

28. Core commitments for field trials of gene drive organisms.

Long KC, Alphey L, Annas GJ, Bloss CS, Campbell KJ, Champer J, Chen C, Choudhary A, Church GM, Collins JP, Cooper KL, Delborne JA, Edwards OR, Emerson CI, Esvelt K, Evans SW, Friedman RM, Gantz VM, Gould F, Hartley S, Heitman E, Hemingway J, Kanuka H, Kuzma J, Lavery JV, Lee Y, Lorenzen M, Lunshof JE, Marshall JM, Messer PW, Montell C, Oye KA, Palmer MJ, Papathanos PA, Paradkar PN, Piagio AJ, Rasgon JL, Rašić G, Rudenko L, Saah JR, Scott MJ, Sutton JT, Vorsino AE, Akbari OS.

Science (2020) 370 (6523):1417-1419. doi:10.1038/s41467-020-19149-2

27. The biosecurity benefits of genetic engineering attribution.

Lewis G, Jordan JL, Relman DA, Koblentz GD, Leung J, Dafoe A, Nelson C, Epstein GL, Katz R, Montague M, Alley EC, Filone CM, Luby S, Church GM, Millett P, Esvelt KM, Cameron EE, Inglesby TV.

Nat. Commun. (2020) 6294. doi:10.1038/s41467-020-19149-2 PDF

26. A machine learning toolkit for genetic engineering attribution to facilitate biosecurity.

Alley EC, Turpin M, Liu AB, Kulp-McDowall T, Swett J, Edison R, Von Stetina SE, Church GM, Esvelt KM.

Nat. Commun. (2020) 6293. doi:10.1038/s41467-020-19612-0

25. Daisy-chain gene drive systems for the alteration of local populations.

Noble C, Min J, Olejarz J, Buchthal J, Chavez A, Smidler AL, DeBenedictis EA, Church GM, Nowak

MA, Esvelt KM.

Proc. Nat. Acad. Sci. USA (2019) 116(17):8275-8282. doi:10.1073/pnas.1716358116 PDF

bioRxiv preprint (2016) (10.1101/057307).

24. Mice Against Ticks: an experimental community-guided effort to prevent tick-borne disease by altering the shared environment.

Buchthal J, Evans SW, Lunshof JE, Telford SR III, Esvelt KM.

Phil. Trans. Roy. Soc. B (2019) 374(1772):20180105. doi:10.1098/rstb.2018.0105


23. Editing nature: local roots of global governance.

Kofler N, Collins JP, Kuzma J, Marris E, Esvelt KM, Nelson MP, Newhouse A, Rothschild LJ,

Vigliotti VS, Semenov M, Jacobsen R, Dahlman JE, Prince S, Caccone A, Brown T, Schmitz OJ.

Science (2018) 362(6414):527-529. doi:10.1126/science.aat4612

22. Inoculating science against potential pandemics and information hazards.

Esvelt KM.

PLoS Path. (2018) 14(10):e1007286. doi:10.1371/journal.ppat.1007286 PDF

21. Current CRISPR gene drives are likely to be highly invasive in wild populations.

Noble C, Adlam B, Church GM, Esvelt KM, Nowak MA.

Elife (2018) 7:e33423. doi:10.7554/eLife.33423

bioRxiv preprint, (10.1101/219022).

20. Harnessing gene drive.

Min J, Smidler AL, Najjar D, Esvelt KM.

J. Respon. Innov. (2017) 5(sup1):S40-65. doi:10.1080/23299460.2017.1415586 PDF


19. A roadmap for gene drives: using institutional analysis and development to frame research needs and governance in a systems context.

Kuzma J, Gould F, Brown Z, Collins J, Delborne J, Frow E, Esvelt KM, Guston D, Leitschuh C, Oye

K, Stauffer S.

J. Respon. Innov. (2017) 5(sup1):S13-39. doi:10.1080/23299460.2017.1410344


18. Driving towards ecotechnologies.

Najjar DA, Normandin AM, Strait EA, Esvelt KM°.

Path. Glob. Health. (2017) 111(8):448-458. doi:10.1080/20477724.2018.1452844 PDF


17. Conservation demands safe gene drive.

Esvelt KM, Gemmell NJ.

PLoS Biology. (2017) 15(11):e2003850. doi:10.1371/journal.pbio.2003850


16. Genome editing as a national security threat.

Esvelt KM, Millett PD.

Rev. Sci. Tech. (2017) 36(2):459-465. doi:10.20506/rst.36.2.2666


15. Evolutionary dynamics of CRISPR gene drives.

Noble C, Olejarz J, Esvelt KM°, Church GM, Nowak M°.

Science Adv. (2017) 3:e1601964. doi:10.1126/sciadv.1601964

bioRxiv preprint, (10.1101/057281).


14. Calls for caution in genome engineering should be a model for similar dialogue on pandemic pathogen research.

Lipsitch M, Esvelt K, Inglesby T°.

Ann. Intern. Med. (2015) 163(10):790-791. doi:10.7326/M15-1048.


13. Safeguarding CRISPR/Cas9 gene drives in yeast.

DiCarlo JE, Chavez A, Dietz SL, Esvelt KM°, Church GM°

Nat. Biotechnol. (2015) 33:1250-5. doi:10.1038/nbt.3412(bioRxiv 10.1101/013896). PDF

bioRxiv preprint, (10.1101/013896).


12. Safeguarding gene drive experiments in the laboratory.

Akbari AS, Bellen HJ, Bier E°, Bullock SL, Burt A, Church GM, Cook KR, Duchek P, Edwards OR, Esvelt KM°, Gantz VM, Golic KG, Gratz SJ, Harrison MM, Hayes KR, James AA, Kaufman TC, Knoblich J, Malik HS, Matthews KA, O'Connor-Giles KM, arks AL, Perrimon N, Port F, Russell S, Ueda R, Wildonger J

Science (2015) 349(6251):927-9. doi:10.1126/science.aac7932. PDF


11. Concerning RNA-guided gene drives for the alteration of wild populations.

Esvelt KM°, Smidler AL, Catteruccia F°, Church GM°.

eLife (2014) e03401. doi: 10.7554/eLife.03401 PDF

bioRxiv 10.1101/007203.


10. Regulating gene drives.

Oye KA*°, Esvelt KM*, Appleton E, Catteruccia F, Church GM, Kuiken T, Lightfoot SB, McNamara J, Smidler A, Collins JP.

Science (2014) 345(6197):626-8. doi: 10.1126/science.1254287. PDF


9. CRISPR/Cas9-mediated phage resistance is not impeded by the DNA modifications of phage T4.

Yaung SJ*, Esvelt KM*, Church GM°.

PLoS One (2014) 9:e98811. doi: 10.1371/journal.pone.0098811. PDF


8. Orthogonal Cas9 proteins for RNA-guided gene regulation and editing.

Esvelt KM*, Mali P*, Braff JL, Moosburner M, Yaung SJ, Church GM°.

Nat. Methods (2013) 10:1116-21. doi: 10.1038/nmeth.2681. PDF


7. Cas9 as a versatile tool for engineering biology.

Mali P*, Esvelt KM*, Church GM°.

Nat. Methods (2013) 10:957-63. doi: 10.1038/nmeth.2649. PDF


6. Cas9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering.

Mali P*, Aach J*, Stranges PB, Esvelt KM, Moosburner M, Kosuri S, Yang L, Church GM°.

Nat. Biotechnol. (2013) 9:833-8. doi: 10.1038/nbt.2675. PDF


5. Heritable genome editing in C. elegans via a CRISPR-Cas9 system.

Friedland AE, Tzur YB, Esvelt KM, Colaiácovo MP, Church GM°, Calarco JA°.

Nat. Methods (2013) 8:741-3. doi: 10.1038/nmeth.2532. PDF


4. Experimental interrogation of the path dependence and stochasticity of protein evolution using phage-assisted continuous evolution.

Dickinson BC, Leconte AM, Allen B, Esvelt KM°, Liu DR°.

Proc Natl Acad Sci USA (2013) 110:9007-12. doi: 10.1073/pnas.1220670110. PDF


3. Genome-scale engineering for systems and synthetic biology.

Esvelt KM°, Wang HH°.

Mol Syst Biol. (2013) 9:641. doi: 10.1038/msb.2012.66. Review.


2. 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) 339:823-6. doi: 10.1126/science.1232033.


1. A system for the continuous directed evolution of biomolecules.

Esvelt KM, Carlson JC, Liu DR°.

Nature (2011) 472:499-503. doi: 10.1038/nature09929. PDF


PDF versions provided for fair use.


Other Publications

On mitigating the cruelty of natural selection through humane genome editing

Edison R, Esvelt KM.

Neuroethics and Nonhuman Animals, 119-133. Spring, 2020.


Cryptographic Aspects of DNA Screening

Baum C, Cui H, Damgård I, Esvelt KM, Gao M, Gretton D, Paneth O, Rivest R, Vaikuntanathan V, Wichs D, Yao A, Yu Y.

SecureDNA technical manuscripts, 2020. (PDF)


Random adversarial threshold search enables specific, secure, and automated DNA synthesis screening

Gretton D, Wang B, DeBenedictis EA, Liu AB, Chory EJ, Cui H, Li X, Dong J, Fabre A, Dennison C, Don O, Ye T, Uberoy K, Rivest R, Gao M, Yu Y, Baum C, Yao AC, Esvelt KM.

SecureDNA technical manuscripts, 2020. (PDF)


The PACT Protocol Specification

Rivest RL, Callas J, Canetti R, Esvelt K, Gillmor DK, Kalai YT, Lysyanskaya A, Norige A, Raskar R, Shamir A, Shen E, Soibelman I, Specter M, Teague V, Trachtenberg A, Varia M, Viera M, Weitzner D, Wilkinson J, Zissman M.

Technical paper on the COVID-19 crisis, 2020.


Genetic frontiers for conservation: an assessment of synthetic biology and biodiversity conservation

Alphey L, Bennet E, Delborne J, Eggermont H, Esvelt K, Kingirl A, Kokotovich A, Kolodziejczyk B, Kuiken T, Mead A, Oliva M, Perello E, Slobodian L, Thizy D, Tompkins D, Winter G, Campbell K, Elsensohn J, Holmes N, Farmer C, Keitt B, Leftwich P, Maloney T, Masiga D, Newhouse A, Novak B, Phelan R, Powell W, Rollins-Smith L, van Oppen M

IUCN report, 2019


Rules for Sculpting Ecosystems: Gene drive and responsive science.

Esvelt KM.

Gene editing, law, and the environment, 20-37. Routledge, 17 July 2017.


Precaution: Open Gene Drive Research.

Esvelt KM (2017)

Science, (10.1126/science.aal5325); PDF


Gene Editing Can Drive Science to Openness.

Esvelt KM (2016)

Nature, (10.7326/M15-1048); open access