Publications by authors named "Jonathan Chen"

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Predicting treatment retention in medication for opioid use disorder: a machine learning approach using NLP and LLM-derived clinical features.
Fateme Nateghi Haredasht, Ivan Lopez, Steven Tate, Pooya Ashtari, Min Min Chan, Chwen-Yuen Angie Chen, Jonathan H Chen

J Am Med Inform Assoc· December 2025

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Comparison of integrated biological effectiveness of eye plaques with I and Pd photon sources using equivalent uniform RBE-weighted dose.
Yulun He, Kent Wallner, Jonathan J Chen, Ramesh Rengan, Andrew W Stacey

Med Phys· December 2025

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A typology of physician input approaches to using AI chatbots for clinical decision-making.
Rachel Siden, Hannah Kerman, Robert J Gallo, Joséphine A Cool, Jason Hom, Jonathan H Chen

NPJ Digit Med· December 2025

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Structure-function modulation of protein-rich pumpkin seed flour via microfluidization processing for plant-based applications.
Jonathan Chen, Oguz Kaan Ozturk

Food Chem· December 2025

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Spatially defined multicellular functional units in colorectal cancer revealed from single cell and spatial transcriptomics.
Inbal Avraham-Davidi, Simon Mages, Johanna Klughammer, Noa Moriel, Shinya Imada, Jonathan Chen, Fei Chen

Elife· December 2025

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Monitoring Deployed AI Systems in Health Care.
Timothy Keyes, Alison Callahan, Abby S Pandya, Nerissa Ambers, Juan M Banda, Jonathan H Chen

ArXiv· December 2025

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Activation and exhaustion of CD8 T cells in patients with chronic lymphocytic leukemia treated with ibrutinib and pembrolizumab.
Rui Mu, Katherine M Hornick, Neelam Redekar, Jonathan Chen, Pia Nierman

J Immunol· November 2025

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Potential application of MALDI-TOF MS to identify Streptococcus parapneumoniae, an emerging pathogen previously misidentified as Streptococcus pneumoniae.
Yan Zhao, Yuanchao Ma, Hwei Huih Lee, Wing Ho Li, Antonio Hung-Yee Ngan, Jonathan Hon-Kwan Chen, Vincent Chi-Chung Cheng

Int J Infect Dis· November 2025

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The carbapenem inoculum effect provides insights into the molecular mechanisms underlying carbapenem resistance in the Enterobacterales.
Alexis Jaramillo Cartagena, Kyra L Taylor, Leslie C Lopez, Jennifer Su, Joshua T Smith, Jonathan D Chen

mBio· November 2025

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A hybrid IGRT workflow using SGRT and CBCT for prostate SBRT: Feasibility, efficiency, and safety.
Juergen Meyer, Angelia Tran, Ting Martin Ma, Bing-Hao Chiang, Tamara Egan, Jonathan J Chen

J Appl Clin Med Phys· November 2025

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Deconver: A Deconvolutional Network for Medical Image Segmentation.
Pooya Ashtari, Shahryar Noei, Fateme Nateghi Haredasht, Jonathan H Chen, Giuseppe Jurman

IEEE J Biomed Health Inform· November 2025

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Implementing ocular treatment with pencil beam scanning: the FHCC experience.
Jatinder Saini, Andrew Stacey, Alexander Egan, Rajesh Regmi, Charles Bloch, Jonathan Chen

Radiat Oncol· 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, Jonathan C Chen

Cell· October 2025

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Simulation of Repair on Dynamic Patient-Specific Left Atrioventricular Valve Models.
Stephen Ching, Christopher Zelonis, Christian Herz, Patricia Sabin, Matthew Daemer, Jonathan M Chen, Elvis Chen

ArXiv· October 2025

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Pseudomonas aeruginosa senses exopolysaccharide trails using type IV pili and adhesins during biofilm formation.
William C Schmidt, Calvin K Lee, Xuhui Zheng, Jonathan W Chen, Kirsten L Fetah

Nat Microbiol· October 2025

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Indication, technical considerations, and outcome of remote central cannulation for repeat extracorporeal membrane oxygenation in congenital diaphragmatic hernia: a case report.
Enrico Danzer, Sabrina J Flohr, Holly L Hedrick, Geoffrey L Bird, Jonathan M Chen

J Extra Corpor Technol· September 2025

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Fine-Tuning Methods for Large Language Models in Clinical Medicine by Supervised Fine-Tuning and Direct Preference Optimization: Comparative Evaluation.
Thomas Savage, Stephen P Ma, Abdessalem Boukil, Ekanath Rangan, Vishwesh Patel, Jonathan Chen

J Med Internet Res· September 2025

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Optimizing large language models for detecting symptoms of depression/anxiety in chronic diseases patient communications.
Jiyeong Kim, Stephen P Ma, Michael L Chen, Isaac R Galatzer-Levy, John Torous, Jonathan H Chen

NPJ Digit Med· September 2025

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Operationalizing machine-assisted translation in healthcare.
Ivan Lopez, David E Velasquez, Jonathan H Chen, Jorge A Rodriguez

NPJ Digit Med· September 2025

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Laboratory Validation of a Fully Automated Point-of-Care Device for High-Order Multiplexing Real-Time PCR Detection of Respiratory Pathogens.
Libby C W Li, Deborah M S Tai, Anita Yee, Nancy B Y Tsui, Parker Y L Tsang, Jonathan H K Chen

Diagnostics (Basel)· September 2025

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Stewardship of Intravenous Fluids During Shortage and Beyond.
Andrew R Moore, Alexandra June Gordon, James T Marvel, Manoj V Maddali, Jonathan H Chen

J Emerg Med· September 2025

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Contrast-induced acute kidney injury and nephrogenic systemic fibrosis in children.
Alice Ming-Jie Chuah, Jonathan Chen, Alison Lap-Tak Ma, Kin Fen Kevin Fung, Eugene Yu-Hin Chan

Pediatr Nephrol· August 2025

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Real time machine learning prediction of next generation sequencing test results in live clinical settings.
Grace Y E Kim, Matthew Schwede, Conor K Corbin, Sajjad Fouladvand, Rondeep Brar, Jonathan H Chen

NPJ Digit Med· August 2025

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A typology of physician input approaches to using AI chatbots for clinical decision-making: a mixed methods study.
Rachel Siden, Hannah Kerman, Robert J Gallo, Joséphine A Cool, Jason Hom, Jonathan H Chen

medRxiv· July 2025

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Opportunistic Screening of Chronic Liver Disease with Deep-Learning-Enhanced Echocardiography.
Yuki Sahashi, Milos Vukadinovic, Fatemeh Amrollahi, Hirsh Trivedi, Justin Rhee, Jonathan Chen, Susan Cheng

NEJM AI· March 2025

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