Publications

Chory lab members designated in bold.

View the full publication list on Google Scholar Open ›

Preprints

  1. Hamrick GS, Son H, Maddamsetti R, Zhou Z, Lok K, Chen X, Yip A, Qian J, Villalobos C, Ma Q, Moghimianavval H, Shyti I, Shende AR, Chory EJ, Dunlop MJ, You L. Gene circuit-driven amplified selection enables evolution of fast-growing Escherichia coli. bioRxiv. 2026.
  2. Boileau RM*, Golas SM*, Ma Q, Jiang B, Jia M, Ilieva N, Baydush A, Fu H, Chory EJ. An autonomous system for multi-objective continuous evolution at scale. bioRxiv. 2026.
  3. Golas SM, Gill B, Wardlow K, Baydush A, Linzbach J, Chory EJ. A purpose-built open source liquid handler for industry-class automated experiments. bioRxiv. 2026.
  4. Holmes AZ, Shyti I, Hoffman AL, Duncker KE, Ma HR, Zhou Z, Lee D, Maddamsetti R, Kim K, Şimşek E, Hamrick GS, Son H, Villalobos CA, Lu J, Ha Y, Shende AR, Yao Z, Liu S, Shapiro DM, Kholina K, Davis H, Baig Y, Wu F, Wang S, Wang X, Chatterjee P, Lynch M, Lopatkin AJ, David L, Chory E, You L. A foundation model for microbial growth dynamics. bioRxiv. 2025.

Reviews

  1. Golas S, Chory EJ. Proximity labeling of endogenous protein interactions enabled by directed evolution. Trends in Biotechnology. 2023. 36710130
  2. Garzon-Porras AM, Chory E, Gryder BE. Dynamic opposition of histone modifications. 2022. 35297606
  3. Stanton BZ*, Chory EJ*, Crabtree GR. Chemically induced proximity in biology and medicine. Science. 2018. PMC6417506

Postdoctoral publications

Preprints

  1. Gretton D, Wang B, Edison R, Foner L, Berlips J, Vogel T, Kysel M, Chen W, Sage-Ling F, Van Hauwe L, Wooster S, Weinstein-Raun B, DeBenedictis E A, Liu A B, Chory EJ, Cui H, Li X, Dong J, Fabrega A, Dennison C, Don O, Ye C, Uberoy K, Rivest R L, Gao M, Yu Y, Baum C, Damgard I, Yao A C, Esvelt K M. Random adversarial threshold search enables automated DNA screening. bioRxiv. 2024.

Peer-reviewed publications

  1. Buchthal J, Chory EJ, Hill Z, Zhou Y, Bondage D, DeAmelio S, Freeman J, Jaenisch R, Markoulaki S, Marasco W A, Telford S, Esvelt K M. Heritable Immunization Establishes a New Model for Pathogen Control. Nature Communications. 2026.
  2. Buchthal J*, Chory EJ*, Hill Z, Dennison C, Tu B, Wierenga R P, Çevrim Ç, Golas S, Meier G, Lan T C T, Chung H, Boucher M, Telford S R, McKinley K L, Markoulaki S, Jaenisch R, Esvelt K M. Non-invasive ovulation tracking enables genetic engineering in wild rodents. Cell Reports Methods. 2026.
  3. Chory EJ*, Wang M*, Ceribelli M, Michalowska AM, Golas S, Beck E, Klumpp-Thomas C, Chen L, McKnight C, Itkin Z, Wilson KM, Holland D, Divakaran S, Bradner J, Khan J, Gryder BE, Thomas CJ, Stanton BZ. High-throughput approaches to uncover synergistic drug combinations in leukemia. SLAS Discovery. 2023. PMC10449086
  4. DeBenedictis EA*, Chory EJ*, Gretton DW, Wang B, Golas S, Esvelt KM. Systematic molecular evolution enables robust biomolecule discovery. Nature Methods. 2022. PMC11655129
  5. Zhao EM, Mao AS, Puig HD, Zhang K, Tippens ND, Tan X, Ran FA, Han I, Nguyen PQ, Chory EJ, Hua TY, Ramesh P, Thompson DB, Oh CY, Zigon ES, English MA, Collins JJ. RNA-responsive elements for eukaryotic translational control. Nature biotechnology. 2022. 34711989
  6. Chory EJ*, Gretton DW*, DeBenedictis EA, Esvelt KM. Enabling high‐throughput biology with flexible open‐source automation. Molecular systems biology. 2021. PMC7993322
  7. Stokes JM, Yang K, Swanson K, Jin W, Cubillos-Ruiz A, Donghia NM, MacNair CR, French S, Carfrae LA, Bloom-Ackermann Z, Tran VM, Chiappino-Pepe A, Badran AH, Andrews IW, Chory EJ, Church GM, Brown ED, Jaakkola TS, Barzilay R, Collins JJ. A deep learning approach to antibiotic discovery. Cell. 2020. PMC8349178

Patents

  1. Chory EJ, Esvelt K, Mukkamala V. System for the directed evolution of biomolecules in multi-body complexes. USPTO. 2024.
  2. Collins JJ, Xiao T, Fei R, Mao AS, Guixe HDP, CHORY EJ. Riboswitch modules and methods for controlling eukaryotic protein translation. USPTO. 2023.
  3. Chory EJ, Crabtree GR, Dykhuizen EC. BAF complex modulating compounds and methods of using the same. USPTO. 2022.
  4. Avila M, Esvelt KM, Strait EA, Chory EJ. Methods of multiplexing CRISPR. USPTO. 2021.

Pre-doctoral publications

Peer-reviewed publications

  1. Chory EJ, Kirkland JG, Chang C, D’Andrea VD, Gourisankar S, Dykhuizen EC, Crabtree GR. Chemical Inhibitors of a Selective SWI/SNF Function Synergize with ATR Inhibition in Cancer Cell Killing. ACS Chemical Biology. 2020. PMC8273930
  2. Chory EJ, Calarco JP, Hathaway NA, Bell O, Neel DS, Crabtree GR. Nucleosome turnover regulates histone methylation patterns over the genome. Molecular cell. 2019. PMC6510544
  3. Braun SM, Kirkland JG, Chory EJ, Husmann D, Calarco JP, Crabtree GR. Rapid and reversible epigenome editing by endogenous chromatin regulators. Nature communications. 2017. PMC5601922
  4. Kadoch C, Williams RT, Calarco JP, Miller EL, Weber CM, Braun SM, Pulice JL, Chory EJ, Crabtree GR. Dynamics of BAF–Polycomb complex opposition on heterochromatin in normal and oncogenic states. Nature genetics. 2017. PMC5285326
  5. Yi JS, Federation AJ, Qi J, Dhe-Paganon S, Hadler M, Xu X, Pierre RS, Varca AC, Wu L, Marineau JJ, Smith WB, Souza A, Chory EJ, Armstrong SA, Bradner JE. Structure-guided DOT1L probe optimization by label-free ligand displacement. ACS chemical biology. 2015. PMC4504433
  6. Vickers DA, Chory EJ, Harless MC, Murthy SK. P38 signaling and receptor recycling events in a microfluidic endothelial cell adhesion assay. Plos one. 2013. PMC3676332
  7. Vickers DA, Chory EJ, Murthy SK. Separation of two phenotypically similar cell types via a single common marker in microfluidic channels. Lab on a Chip. 2012. 22782544
  8. Yu W, Chory EJ, Wernimont AK, Tempel W, Scopton A, Federation A, Marineau JJ, Qi J, Barsyte-Lovejoy D, Yi J, Marcellus R, Iacob RE, Engen JR, Griffin C, Aman A, Wienholds E, Li F, Pineda J, Estiu G, Shatseva T, Hajian T, Al-Awar R, Dick JE, Vedadi M, Brown PJ, Arrowsmith CH, Bradner JE, Schapira M. Catalytic site remodelling of the DOT1L methyltransferase by selective inhibitors. Nature communications. 2012. 23250418