Publications by authors named "JJ Collins"

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Unusual inheritance of a functional homolog in the human pathogen .
George R Wendt, James J Collins

Sci Adv· December 2025

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Loss of vitamin C biosynthesis protects from the pathology of a parasitic infection.
Gongwen Chen, Ji Hyung Jun, Tobias Wijshake, Edward O Kwarteng, Yunyang Li, James J Collins

Proc Natl Acad Sci U S A· December 2025

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Active learning framework leveraging transcriptomics identifies modulators of disease phenotypes.
Benjamin DeMeo, Charlotte Nesbitt, Samuel A Miller, Daniel B Burkhardt, Inna Lipchina, James J Collins

Science· November 2025

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Reversing transgene silencing via targeted chromatin editing.
Sebastian Palacios, Elia Salibi, Eric Lu, Ron Weiss, Thorsten M Schlaeger, James J Collins

bioRxiv· November 2025

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A generative deep learning approach to de novo antibiotic design.
Aarti Krishnan, Melis N Anahtar, Jacqueline A Valeri, Wengong Jin, Nina M Donghia, James J Collins

Cell· October 2025

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The impact of hyperoxia and antibiotics on lung mesenchymal cells in experimental bronchopulmonary dysplasia.
Cathy van Horik, Joël Meyboom, Anne Boerema-de Munck, Marjon Buscop-van Kempen, Evelien Eenjes, Jennifer J P Collins

Am J Physiol Lung Cell Mol Physiol· October 2025

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Convergence of nanotechnology and CRISPR-based diagnostics.
Midori Johnston, Schan Dissanayake-Perera, James J Collins, Molly M Stevens, Can Dincer

Nat Nanotechnol· October 2025

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The physical demands of Major League Soccer match-play with specific reference to high-intensity activity by position, venue and opposition quality.
James J Collins, Javier Fernandez Navarro, Allistair P McRobert, Holly Silvers-Granelli, Shane Malone, Kieran D Collins

PLoS One· October 2025

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Optogenetics-enabled discovery of integrated stress response modulators.
Felix Wong, Alicia Li, Satotaka Omori, Ryan S Lach, Jose Nunez, James J Collins

Cell· September 2025

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Using geographic information system (GIS) technology to evaluate a hospital-based mobile blood donation program.
Kristen N Ruby, Walter H Dzik, Julia J Collins, Hongying Tang, Shawn Ela

Transfusion· September 2025

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A genome-scale drug discovery pipeline uncovers therapeutic targets and a unique p97 allosteric binding site in .
Dylon R Stephens, Ho Yee Joyce Fung, Yan Han, Jue Liang, Zhe Chen, James J Collins

Proc Natl Acad Sci U S A· September 2025

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Mitigating antimicrobial resistance by innovative solutions in AI (MARISA): a modified James Lind Alliance analysis.
William J Waldock, Hannah Thould, Leonid Chindelevitch, Nicholas J Croucher, César de la Fuente, James J Collins

NPJ Antimicrob Resist· September 2025

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Essay: Using Machine Learning for Antibiotic Discovery.
Cesar de la Fuente-Nunez, James J Collins

Phys Rev Lett· July 2025

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Loss of vitamin C biosynthesis protects from a parasitic infection.
Gongwen Chen, Ji Hyung Jun, Tobias Wijshake, Yunyang Li, Minwei Yuan, James J Collins

bioRxiv· July 2025

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Induction of Multipotential Hematopoietic Progenitors from Human Pluripotent Stem Cells via Respecification of Lineage-Restricted Precursors.
Sergei Doulatov, Linda T Vo, Stephanie S Chou, Peter G Kim, Natasha Arora, James J Collins

Cell Stem Cell· June 2025

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An explainable deep learning platform for molecular discovery.
Felix Wong, Satotaka Omori, Alicia Li, Aarti Krishnan, Ryan S Lach, James J Collins

Nat Protoc· April 2025

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Machine learning for synthetic gene circuit engineering.
Sebastian Palacios, James J Collins, Domitilla Del Vecchio

Curr Opin Biotechnol· April 2025

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A genome-scale drug discovery pipeline uncovers new therapeutic targets and a unique p97 allosteric binding site in .
Dylon R Stephens, Ho Yee Joyce Fung, Yan Han, Jue Liang, Zhe Chen, James J Collins

bioRxiv· March 2025

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Accurate RNA 3D structure prediction using a language model-based deep learning approach.
Tao Shen, Zhihang Hu, Siqi Sun, Di Liu, Felix Wong, James J Collins

Nat Methods· December 2024

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A proof-of-concept multi-tiered Bayesian approach for the integration of physiochemical properties and toxicokinetic time-course data for Daphnia magna.
Jacob-Joe Collins, Joe Reynolds, Bruno Campos, Patrik Engi, Claudia Rivetti

Aquat Toxicol· November 2024

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Deep generative design of RNA aptamers using structural predictions.
Felix Wong, Dongchen He, Aarti Krishnan, Liang Hong, Alexander Z Wang, James J Collins

Nat Comput Sci· November 2024

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Catalase activity deficiency sensitizes multidrug-resistant Mycobacterium tuberculosis to the ATP synthase inhibitor bedaquiline.
Boatema Ofori-Anyinam, Meagan Hamblin, Miranda L Coldren, Barry Li, Gautam Mereddy, James J Collins

Nat Commun· November 2024

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UROPOT: study protocol for a randomized, double-blind phase I/II trial for metabolism-based potentiation of antimicrobial prophylaxis in the urological tract.
Kevin Stritt, Beat Roth, Audrey Masnada, Felix Hammann, Damien Jacot, James J Collins

Trials· October 2024

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Machine learning for antimicrobial peptide identification and design.
Fangping Wan, Felix Wong, James J Collins, Cesar de la Fuente-Nunez

Nat Rev Bioeng· May 2024

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