Preprints and Peer-Reviewed Publications

53. Evaluating the robustness of current nucleic acid synthesis screening.

Edison R, Toner S, Esvelt KM.

In process (2024). PDF

52. Commitments for the responsible development of transmissible vaccines for control of animal infectious diseases.

Streicker DG, Griffiths ME, Antia R, Bergner L, Bowman P, de Moraes MVDS, Esvelt K, Famulare M, Gilbert A, He B, Jarvis MA, Kennedy DA, Kuzma J, Wanyonyi CN, Remien C, Rocke T, Rosenke K, Schreiner C, Sheen J, Simons D, Yordanova IA, Bull JJ, Nuismer SL.

Science (2024) 84:6693, 275-277. doi: 10.1126/science.adn323

51. A multiplexed, confinable CRISPR/Cas9 gene drive can propagate in caged Aedes aegypti populations. 

Anderson MAE, Gonzalez E, Edgington MP, Ang JXD, Purusothaman DK, Shackleford L, Nevard K, Verkuijl SAN, Harvey-Samuel T, Leftwich PT, Esvelt K, Alphey L.

Nat. Commun. (2024) 15 (1), 729. doi: 10.1038/s41467-024-44956-2

50. CRISPR-mediated germline mutagenesis for genetic sterilization of Anopheles gambiae males.

Smidler AL, Marrogi E, Kauffman J, Paton DG, Westervelt KA, Church GM, Esvelt KM, Shaw WR, Catteruccia F.

Scientific Reports (2024) 14 (1), 4057.  doi: 10.1038/s41598-024-54498-8

49. A framework for identifying fertility gene targets for mammalian pest control.

Clark AC, Edison R, Esvelt K, Kamau S, Dutoit L, Champer J, Champer SE, Messer PW, Alexander A, Gemmell NJ.

Mol. Ecology Res. (2024) 24 (2), e13901.  doi: 10.1111/1755-0998.13901

48. Assessing the safety of new germicidal Far-UVC technologies. 

Görlitz M, Justen L, Rochette PJ, Buonanno M, Welch D, Kleiman NJ, Eadie E, Kaidzu S, Bradshaw WJ, Javorsky E, Cridland N, Galor A, Guttmann M, Meinke MC, Schleusener J, Jensen P, Söderberg P, Yamano N, Nishigori C, O'Mahoney P, Manstein D, Croft R, Cole C, de Gruijl FR, Forbes PD, Trokel S, Marshall J, Brenner DJ, Sliney D, Esvelt K.

Photochem. & Photobiol. (2023) Nov 6. doi: 10.1111/php.13866

47. Securing civilisation against catastrophic pandemics.

         Gopal A, Bradshaw W, Sunil V, Esvelt KM.

         Geneva Paper (2023) 31.  PDF

46. Can large language models democratize access to dual-use biotechnology?

         Soice EH, Rocha R, Cordova K, Specter M, Esvelt KM.

         arXiv:2306.03809 (2023). PDF

45. PyLabRobot: An open-source, hardware-agnostic interface for liquid-handling robots and accessories.

Wierenga RP, Golas SM, Ho W, Coley CW, Esvelt KM.

Device (2023) doi: 10.1016/j.device.2023.100111

44. Insidious Insights: Implications of viral vector engineering for pathogen enhancement.

Sandbrink JB, Alley EC, Watson MC, Koblentz GD, Esvelt KM.

Gene Therapy (2023) 30 (5), 407-410. doi: 10.1038/s41434-021-00312-3

43. Exploring the value of a global gene drive project registry

Taitingfong RI, Triplett C, Vásquez VN, Rajagopalan RM, Raban R, Roberts A, Terradas G,

Baumgartner B, Emerson C, Gould F, Okumu F, Chairer C, Bossin H, Buchman L, Campbell K,

Clark A, Delborne J, Esvelt K, Fisher J, Friedman R, Gronvall G, Gurfield N, Heitman E, Kofler

N, Kuiken T, Kuzma J, Manrique P, Saide P, Marshall J, Montague M, Morrison A, Opesen C,

Phelan R, Piaggio A, Quemada H, Rudenko L, Sawadogo N, Smith R, Tuten H, Ullah A,

Vorsino A, Windichler N, Akbari O, Long K, Lavery J, Weiss Evans S, Tountas K, Bloss C

Nat. Biotechnol. (2023) 41, 9–13. doi: 10.1038/s41587-022-01591-w

42. Analysis of the first genetic engineering attribution challenge.

Crook OM, Warmbrod KL, Lipstein G, Chung C, Bakerlee CW, McKelvey G, Holland S,

Swett J, Esvelt K, Alley E, Bradshaw W.

Nat. Commun (2022) 13, 7374. doi: 10.1038/s41467-022-35032-8

41. Delay, Detect, Defend: Preparing for a future in which thousands can release new pandemics.

Esvelt KM.

Geneva Paper (2022) PDF

40. Direct and indirect impacts of synthetic biology on biodiversity conservation.

Macfarlane NBW, Adams J, Bennett EL, Brooks TM, Delborne JA, Eggermont H, Endy D, Esvelt K, Kolodziejczyk, B, Kuiken T, Oliva M, Moreno S, Slobodian L, Smith L, Thizy D, Tompkins D, Wei Wi, Redford K.

Iscience (2022) doi: 10.1016/j.isci.2022.105423

39. Measuring the tolerance of the genetic code to altered codon size.

        DeBenedictis EA, Söll D, Esvelt KM.

        Elife (2022) 11, e76941 doi: 10.7554/eLife.76941

38. A scalable solution for signaling face touches to reduce the spread of surface-based pathogens.

        Rojas C, Poulsen N, Van Tuy Ml, Vargas D, Cohen Z, Paradiso J, Maes P, Esvelt KM, Adib F.

        Proc. ACM Inter. Mobile Wear. Ubiq. Tech. (2022) 31, 1–22. doi: 10.1145/3448121

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 (2022) 19 (1), 55-64. doi: 10.1038/s41592-021-01348-4

bioRxiv 10.1101/2020.04.01.021022

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

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. 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.  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