James J. Collins - Publications, H-index & Citations

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James J. Collins

Broad Institute of MIT and Harvard

162H-index

589Paper Count

11.2WCitation Count

Published Papers 201

Publication Date

Deep learning–enabled discovery of antibiotics effective against Neisseria gonorrhoeae

Science Translational Medicine

IF14.6

2026-06-17

PREAI

Melis N. Anahtar; Jacqueline A. Valeri; Seyed Majed Modaresi; Aarti Krishnan; Nina M. Donghia; Samantha G. Palace; Erica J. Zheng; Aakanksha Gulati; Alicia Jorgenson; Abidemi Junaid; Parijat Bandyopadhyay; Andreas Luttens; Krishna Suresh; Paige Edwards; Felix Wong; Yu Zhang; Danilo Ritz; Margaux Gaborieau; Edmund Loh; Massimiliano Gaetani; Marie-Stephanie Aschtgen; Amir Ata Saei; Yonatan H. Grad; Donald E. Ingber; James J. Collins

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Generative AI for synthetic biology: Designing biological parts, circuits, and genomes

Cell Systems

IF7.7

2026-02-18

PREAI

Nayoung Kim; Giuliano De Carluccio; Kehan Zhang; James J. Collins

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A field‑deployable CRISPR-based biosensing platform for monitoring marine ecosystems

Nature Sustainability

IF27.1

2026-01-27

PREAI

Nayoung Kim; Daniel S. Collins; Nina M. Donghia; Benjamin S. Miller; Hani M. Sallum; Silvi R. Lybbert; Elena Perini; James B. Niemi; James J. Collins; Peter Q. Nguyen

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Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes

Science

IF45.8

2025-10-23

PREAI

Benjamin DeMeo; Charlotte Nesbitt; Samuel A. Miller; Daniel B. Burkhardt; Inna Lipchina; Doris Fu; Peter Holderrieth; David Kim; Sergey Kolchenko; Artur Szalata; Ishan Gupta; Christine Kerr; Thomas Pfefer; Raziel Rojas-Rodriguez; Sunil Kuppassani; Laurens Kruidenier; Parul B. Doshi; Mahdi Zamanighomi; James J. Collins; Alex K. Shalek; Fabian J. Theis; Mauricio Cortes

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Convergence of nanotechnology and CRISPR-based diagnostics

Nature Nanotechnology

IF34.9

2025-10-02

PREAI

Midori Johnston; Schan Dissanayake-Perera; James J. Collins; Molly M. Stevens; Can Dincer

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The Bionic Interface: Considering the Material Mediated Electrical Stimulation of Stem Cells

ADVANCED MATERIALS

IF26.8

2025-09-01

OAAI

Zhang, Kaiwen; De Maria, Daniel; Jebakumar, Mercyjayapriya; Collins, James; Fox, Kate E.; Sherrell, Peter C.; Gelmi, Amy

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Optogenetics-enabled discovery of integrated stress response modulators

Cell

IF42.5

2025-07-11

PREAI

Felix Wong; Alicia Li; Satotaka Omori; Ryan S. Lach; Jose Nunez; Yunke Ren; Sean P. Brown; Vipul Singhal; Brent R. Lyda; Taivan Batjargal; Ethan Dickson; Jose Roberto Rodrigues Reyes; Juan Manual Uruena Vargas; Shalaka Wahane; Hahn Kim; James J. Collins; Maxwell Z. Wilson

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An explainable deep learning platform for molecular discovery

NATURE PROTOCOLS

IF16

2024-12-09

PREAI

Wong, Felix; Omori, Satotaka; Li, Alicia; Krishnan, Aarti; Lach, Ryan S.; Rufo, Joseph; Wilson, Maxwell Z.; Collins, James J.

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Accurate RNA 3D structure prediction using a language model-based deep learning approach

NATURE METHODS

IF32.1

2024-11-21

OAAI

Shen, Tao; Hu, Zhihang; Sun, Siqi; Liu, Di; Wong, Felix; Wang, Jiuming; Chen, Jiayang; Wang, Yixuan; Hong, Liang; Xiao, Jin; Zheng, Liangzhen; Krishnamoorthi, Tejas; King, Irwin; Wang, Sheng; Yin, Peng; Collins, James J.; Li, Yu

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Deep generative design of RNA aptamers using structural predictions

NATURE COMPUTATIONAL SCIENCE

IF18.3

2024-11-06

PREAI

Wong, Felix; He, Dongchen; Krishnan, Aarti; Hong, Liang; Wang, Alexander Z.; Wang, Jiuming; Hu, Zhihang; Omori, Satotaka; Li, Alicia; Rao, Jiahua; Yu, Qinze; Jin, Wengong; Zhang, Tianqing; Ilia, Katherine; Chen, Jack X.; Zheng, Shuangjia; King, Irwin; Li, Yu; Collins, James J.

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Customizable gene sensing and response without altering endogenous coding sequences

NATURE CHEMICAL BIOLOGY

IF13.7

2024-09-12

PREAI

Caliendo, Fabio; Vitu, Elvira; Wang, Junmin; Kuo, Shuo-Hsiu; Sandt, Hayden; Enghuus, Casper Norskov; Tordoff, Jesse; Estrada, Neslly; Collins, James J.; Weiss, Ron

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Rapid discovery and evolution of nanosensors containing fluorogenic amino acids

NATURE COMMUNICATIONS

IF15.7

2024-09-05

OAAI

Kuru, Erkin; Rittichier, Jonathan; de Puig, Helena; Flores, Allison; Rout, Subhrajit; Han, Isaac; Reese, Abigail E.; Bartlett, Thomas M.; De Moliner, Fabio; Bernier, Sylvie G.; Galpin, Jason D.; Marchand, Jorge; Bedell, William; Robinson-McCarthy, Lindsey; Ahern, Christopher A.; Bernhardt, Thomas G.; Rudner, David Z.; Collins, James J.; Vendrell, Marc; Church, George M.

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Rapid, multiplexed, and enzyme-free nucleic acid detection using programmable aptamer-based RNA switches

CHEM

IF19.6

2024-07-01

PREAI

Yan, Zhaoqing; Eshed, Amit; Tang, Anli A.; Arevalos, Nery R.; Ticktin, Zachary M.; Chaudhary, Soma; Ma, Duo; Mccutcheon, Griffin; Li, Yudan; Wu, Kaiyue; Saha, Sanchari; Alcantar-Fernandez, Jonathan; Moreno-Camacho, Jose L.; Campos-Romero, Abraham; Collins, James J.; Yin, Peng; Green, Alexander A.

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Designing microbial consortia with defined social interactions (vol 14, pg 821, 2018)

NATURE CHEMICAL BIOLOGY

IF13.7

2024-04-22

OAAI

Kong, Wentao; Collins, James J.; Lu, Ting

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Discovery of antibiotics that selectively kill metabolically dormant bacteria

CELL CHEMICAL BIOLOGY

IF7.2

2024-04-01

PREAI

Zheng, Erica J.; Valeri, Jacqueline A.; Andrews, Ian W.; Krishnan, Aarti; Bandyopadhyay, Parijat; Anahtar, Melis N.; Herneisen, Alice; Schulte, Fabian; Linnehan, Brooke; Wong, Felix; Stokes, Jonathan M.; Renner, Lars D.; Lourido, Sebastian; Collins, James J.

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Next Generation Chemiluminescent Probes for Antimalarial Drug Discovery

ACS INFECTIOUS DISEASES

IF3.8

2024-04-01

OAAI

Hellingman, Angela; Sifoniou, Kleopatra; Buser, Tamara; Thommen, Basil T.; Walz, Annabelle; Passecker, Armin; Collins, James; Hupfeld, Mario; Wittlin, Sergio; Witmer, Kathrin; Brancucci, Nicolas M. B.

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Synthetic genetic circuits to uncover the OCT4 trajectories of successful reprogramming of human fibroblasts

SCIENCE ADVANCES

IF12.5

2023-12-01

OAAI

Ilia, Katherine; Shakiba, Nika; Bingham, Trevor; Jones, Ross D.; Kaminski, Michael M.; Aravera, Eliezer; Bruno, Simone; Palacios, Sebastian; Weiss, Ron; Collins, James J.; Del Vecchio, Domitilla; Schlaeger, Thorsten M.

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Engineering microbial division of labor for plastic upcycling

NATURE COMMUNICATIONS

IF15.7

2023-09-26

OAAI

Bao, Teng; Qian, Yuanchao; Xin, Yongping; Collins, James J.; Lu, Ting

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Harnessing synthetic biology to enhance ocean health

TRENDS IN BIOTECHNOLOGY

IF14.9

2023-07-01

OAAI

Nguyen, Peter Q.; Huang, Xiaoning; Collins, Daniel S.; Collins, James J.; Lu, Ting

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BioAutoMATED: An end-to-end automated machine learning tool for explanation and design of biological sequences

CELL SYSTEMS

IF7.7

2023-06-01

OAAI

Valeri, Jacqueline A.; Soenksen, Luis R.; Collins, Katherine M.; Ramesh, Pradeep; Cai, George; Powers, Rani; Angenent-Mari, Nicolaas M.; Camacho, Diogo M.; Wong, Felix; Lu, Timothy K.; Collins, James J.

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Research Directions