James Y Zou (James Zou)

Publication Activity (10 Years)

Years Active: 2018-2024
Publications (10 Years): 69

Top Topics

Top Venues

Nature communications

Bioinformatics (Oxford, England)

NPJ digital medicine

This page only lists publications with an associated author ORCID identifier.

Publications

John Weston Hughes, Sulaiman Somani, Pierre A Elias, James Tooley, Albert J Rogers, Timothy Poterucha, Christopher M Haggerty, Michael Salerno, David Ouyang, Euan Ashley, James Y Zou, Marco V Perez
Simple models vs. deep learning in detecting low ejection fraction from the electrocardiogram. European heart journal. Digital health 5 (4) (2024)
Kyle Swanson, Parker Walther, Jeremy Leitz, Souhrid Mukherjee, Joseph C Wu, Rabindra V Shivnaraine, James Y Zou
ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries. Bioinformatics (Oxford, England) 40 (7) (2024)
Kyle Swanson, Parker Walther, Jeremy Leitz, Souhrid Mukherjee, Joseph C Wu, Rabindra V Shivnaraine, James Y Zou
ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries. Bioinformatics (Oxford, England) 40 (7) (2024)
Kyle Swanson, Parker Walther, Jeremy Leitz, Souhrid Mukherjee, Joseph C Wu, Rabindra V Shivnaraine, James Y Zou
ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries. Bioinformatics (Oxford, England) 40 (7) (2024)
Kevin E Wu, Kevin K Yang, Rianne van den Berg, Sarah Alamdari, James Y Zou, Alex X Lu, Ava P Soleimany
Protein structure generation via folding diffusion. Nature communications 15 (1) (2024)
Eric D Sun, Rong Ma, Paloma Navarro Negredo, Anne Brunet, James Y Zou
TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses. Nature methods 21 (3) (2024)
John Weston Hughes, Sulaiman Somani, Pierre A Elias, James Tooley, Albert J Rogers, Timothy Poterucha, Christopher M Haggerty, Michael Salerno, David Ouyang, Euan Ashley, James Y Zou, Marco V Perez
Simple models vs. deep learning in detecting low ejection fraction from the electrocardiogram. European heart journal. Digital health 5 (4) (2024)
Kevin E Wu, Kevin K Yang, Rianne van den Berg, Sarah Alamdari, James Y Zou, Alex X Lu, Ava P Soleimany
Protein structure generation via folding diffusion. Nature communications 15 (1) (2024)
Elana Simon, Kyle Swanson, James Y Zou
Language models for biological research: a primer. Nature methods 21 (8) (2024)
Minji Kang, Jose Juan Almagro Armenteros, Gunsagar Singh Gulati, Rachel Gleyzer, Susanna Avagyan, Erin L Brown, Wubing Zhang, Abul Usmani, Noah J Earland, Zhenqin Wu, James Y Zou, Ryan C Fields, David Y Chen, Aadel A Chaudhuri, Aaron M Newman
Mapping single-cell developmental potential in health and disease with interpretable deep learning. bioRxiv : the preprint server for biology (2024)
Kevin E Wu, Kevin K Yang, Rianne van den Berg, Sarah Alamdari, James Y Zou, Alex X Lu, Ava P Soleimany
Protein structure generation via folding diffusion. Nature communications 15 (1) (2024)
Eric D Sun, Rong Ma, James Y Zou
SPRITE: improving spatial gene expression imputation with gene and cell networks. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Eric D Sun, Rong Ma, Paloma Navarro Negredo, Anne Brunet, James Y Zou
TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses. Nature methods 21 (3) (2024)
Eric D Sun, Rong Ma, James Y Zou
SPRITE: improving spatial gene expression imputation with gene and cell networks. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Eric D Sun, Rong Ma, Paloma Navarro Negredo, Anne Brunet, James Y Zou
TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses. Nature methods 21 (3) (2024)
Eric D Sun, Rong Ma, Paloma Navarro Negredo, Anne Brunet, James Y Zou
TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses. Nature methods (2024)
Kyle Swanson, Parker Walther, Jeremy Leitz, Souhrid Mukherjee, Joseph C Wu, Rabindra V Shivnaraine, James Y Zou
ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries. Bioinformatics (Oxford, England) 40 (7) (2024)
Kai Zhang, Rong Zhou, Eashan Adhikarla, Zhiling Yan, Yixin Liu, Jun Yu, Zhengliang Liu, Xun Chen, Brian D Davison, Hui Ren, Jing Huang, Chen Chen, Yuyin Zhou, Sunyang Fu, Wei Liu, Tianming Liu, Xiang Li, Yong Chen, Lifang He, James Y Zou, Quanzheng Li, Hongfang Liu, Lichao Sun
A generalist vision-language foundation model for diverse biomedical tasks. Nature medicine (2024)
Elana Simon, Kyle Swanson, James Y Zou
Language models for biological research: a primer. Nature methods 21 (8) (2024)
Eric D Sun, Rong Ma, Paloma Navarro Negredo, Anne Brunet, James Y Zou
TISSUE: uncertainty-calibrated prediction of single-cell spatial transcriptomics improves downstream analyses. Nature methods (2024)
Lea Lemaitre, Nia Adeniji, Akanksha Suresh, Reshma Reguram, Josephine Zhang, Jangho Park, Amit Reddy, Alexandro E Trevino, Aaron T Mayer, Anja Deutzmann, Aida S Hansen, Ling Tong, Vinodhini Arjunan, Neeraja Kambham, Brendan C Visser, Monica M Dua, C Andrew Bonham, Nishita Kothary, H Blaize D'Angio, Ryan Preska, Yanay Rosen, James Y Zou, Vivek Charu, Dean W Felsher, Renumathy Dhanasekaran
Spatial analysis reveals targetable macrophage-mediated mechanisms of immune evasion in hepatocellular carcinoma minimal residual disease. Nature cancer (2024)
Zhi Huang, Eric Yang, Jeanne Shen, Dita A Gratzinger, Frederick Eyerer, Brooke Liang, Jeffrey J Nirschl, David Bingham, Alex M Dussaq, Christian A Kunder, Rebecca Rojansky, Aubre Gilbert, Alexandra L Chang-Graham, Brooke E Howitt, Ying Liu, Emily E Ryan, Troy B Tenney, Xiaoming Zhang, Ann Folkins, Edward J Fox, Kathleen S Montine, Thomas J Montine, James Y Zou
A pathologist-AI collaboration framework for enhancing diagnostic accuracies and efficiencies. Nature biomedical engineering (2024)
Eric D Sun, Rong Ma, James Y Zou
SPRITE: improving spatial gene expression imputation with gene and cell networks. Bioinformatics (Oxford, England) 40 (Supplement_1) (2024)
Kevin E Wu, Kevin K Yang, Rianne van den Berg, Sarah Alamdari, James Y Zou, Alex X Lu, Ava P Soleimany
Protein structure generation via folding diffusion. Nature communications 15 (1) (2024)
Andre Esteva, Jean Feng, Douwe van der Wal, Shih-Cheng Huang, Jeffry P Simko, Sandy DeVries, Emmalyn Chen, Edward M Schaeffer, Todd M Morgan, Yilun Sun, Amirata Ghorbani, Nikhil Naik, Dhruv Nathawani, Richard Socher, Jeff M Michalski, Mack Roach, Thomas M Pisansky, Jedidiah M Monson, Farah Naz, James Wallace, Michelle J Ferguson, Jean-Paul Bahary, James Y Zou, Matthew Lungren, Serena Yeung, Ashley E Ross, null null, Howard M Sandler, Phuoc T Tran, Daniel E Spratt, Stephanie Pugh, Felix Y Feng, Osama Mohamad
Author Correction: Prostate cancer therapy personalization via multi-modal deep learning on randomized phase III clinical trials. NPJ digital medicine 6 (1) (2023)
Md Tauhidul Islam, Zixia Zhou, Hongyi Ren, Masoud Badiei Khuzani, Daniel Kapp, James Y Zou, Lu Tian, Joseph C Liao, Lei Xing
Revealing hidden patterns in deep neural network feature space continuum via manifold learning. Nature communications 14 (1) (2023)
Zhi Huang, Gennifer E Merrihew, Eric B Larson, Jea Park, Deanna L Plubell, Edward J Fox, Kathleen S Montine, Caitlin S Latimer, C Dirk Keene, James Y Zou, Michael J MacCoss, Thomas J Montine
Brain proteomic analysis implicates actin filament processes and injury response in resilience to Alzheimer's disease. Nature communications 14 (1) (2023)
Md Tauhidul Islam, Zixia Zhou, Hongyi Ren, Masoud Badiei Khuzani, Daniel Kapp, James Y Zou, Lu Tian, Joseph C Liao, Lei Xing
Revealing hidden patterns in deep neural network feature space continuum via manifold learning. Nature communications 14 (1) (2023)
Md Tauhidul Islam, Zixia Zhou, Hongyi Ren, Masoud Badiei Khuzani, Daniel Kapp, James Y Zou, Lu Tian, Joseph C Liao, Lei Xing
Revealing hidden patterns in deep neural network feature space continuum via manifold learning. Nature communications 14 (1) (2023)
Zhi Huang, Federico Bianchi, Mert Yuksekgonul, Thomas J Montine, James Y Zou
A visual-language foundation model for pathology image analysis using medical Twitter. Nature medicine (2023)
Anoop Manjunath, Nathan Kahrobai, Jaya Manjunath, Angelina Seffens, Arya Gowda, Rohaan Umbarkar, Esha Umbarkar, James Y Zou, Ishan Kumar
Who counts as an inventor? Seniority and gender in 430,000 biomedical inventor-researcher teams. Nature biotechnology 41 (5) (2023)
Girmaw Abebe Tadesse, Celia Cintas, Kush R Varshney, Peter Staar, Chinyere Agunwa, Skyler Speakman, Justin Jia, Elizabeth E Bailey, Ademide Adelekun, Jules B Lipoff, Ginikanwa Onyekaba, Jenna C Lester, Veronica M Rotemberg, James Y Zou, Roxana Daneshjou
Skin Tone Analysis for Representation in Educational Materials (STAR-ED) using machine learning. NPJ digital medicine 6 (1) (2023)
Eric Wu, Alexandro E Trevino, Zhenqin Wu, Kyle Swanson, Honesty J Kim, H Blaize D'Angio, Ryan Preska, Aaron E Chiou, Gregory W Charville, Piero Dalerba, Umamaheswar Duvvuri, Alexander D Colevas, Jelena Levi, Nikita Bedi, Serena Chang, John B Sunwoo, Ann Marie Egloff, Ravindra Uppaluri, Aaron T Mayer, James Y Zou
7-UP: Generating in silico CODEX from a small set of immunofluorescence markers. PNAS nexus 2 (6) (2023)
Andre Esteva, Jean Feng, Douwe van der Wal, Shih-Cheng Huang, Jeffry P Simko, Sandy DeVries, Emmalyn Chen, Edward M Schaeffer, Todd M Morgan, Yilun Sun, Amirata Ghorbani, Nikhil Naik, Dhruv Nathawani, Richard Socher, Jeff M Michalski, Mack Roach, Thomas M Pisansky, Jedidiah M Monson, Farah Naz, James Wallace, Michelle J Ferguson, Jean-Paul Bahary, James Y Zou, Matthew Lungren, Serena Yeung, Ashley E Ross, null null, Howard M Sandler, Phuoc T Tran, Daniel E Spratt, Stephanie Pugh, Felix Y Feng, Osama Mohamad
Author Correction: Prostate cancer therapy personalization via multi-modal deep learning on randomized phase III clinical trials. NPJ digital medicine 6 (1) (2023)
Prashnna K Gyawali, Yann Le Guen, Xiaoxia Liu, Michael E Belloy, Hua Tang, James Y Zou, Zihuai He
Improving genetic risk prediction across diverse population by disentangling ancestry representations. Communications biology 6 (1) (2023)
Md Tauhidul Islam, Zixia Zhou, Hongyi Ren, Masoud Badiei Khuzani, Daniel Kapp, James Y Zou, Lu Tian, Joseph C Liao, Lei Xing
Revealing hidden patterns in deep neural network feature space continuum via manifold learning. Nature communications 14 (1) (2023)
Kyle Swanson, Parker Walther, Jeremy Leitz, Souhrid Mukherjee, Joseph C Wu, Rabindra V Shivnaraine, James Y Zou
ADMET-AI: A machine learning ADMET platform for evaluation of large-scale chemical libraries. bioRxiv : the preprint server for biology (2023)
Zhi Huang, Gennifer E Merrihew, Eric B Larson, Jea Park, Deanna L Plubell, Edward J Fox, Kathleen S Montine, Caitlin S Latimer, C Dirk Keene, James Y Zou, Michael J MacCoss, Thomas J Montine
Brain proteomic analysis implicates actin filament processes and injury response in resilience to Alzheimer's disease. Nature communications 14 (1) (2023)
Md Tauhidul Islam, Zixia Zhou, Hongyi Ren, Masoud Badiei Khuzani, Daniel Kapp, James Y Zou, Lu Tian, Joseph C Liao, Lei Xing
Revealing hidden patterns in deep neural network feature space continuum via manifold learning. Nature communications 14 (1) (2023)
Md Tauhidul Islam, Zixia Zhou, Hongyi Ren, Masoud Badiei Khuzani, Daniel Kapp, James Y Zou, Lu Tian, Joseph C Liao, Lei Xing
Revealing hidden patterns in deep neural network feature space continuum via manifold learning. Nature communications 14 (1) (2023)
Rong Ma, Eric D Sun, James Y Zou
A spectral method for assessing and combining multiple data visualizations. Nature communications 14 (1) (2023)
Bryan He, Alan C Kwan, Jae Hyung Cho, Neal Yuan, Charles Pollick, Takahiro Shiota, Joseph Ebinger, Natalie A Bello, Janet Wei, Kiranbir Josan, Grant Duffy, Melvin Jujjavarapu, Robert Siegel, Susan C Cheng, James Y Zou, David Ouyang
Blinded, randomized trial of sonographer versus AI cardiac function assessment. Nature (2023)
Kyle Swanson, Parker Walther, Jeremy Leitz, Souhrid Mukherjee, Joseph C Wu, Rabindra V Shivnaraine, James Y Zou
ADMET-AI: A machine learning ADMET platform for evaluation of large-scale chemical libraries. bioRxiv : the preprint server for biology (2023)
Rong Ma, Eric D Sun, James Y Zou
A spectral method for assessing and combining multiple data visualizations. Nature communications 14 (1) (2023)
Md Tauhidul Islam, Zixia Zhou, Hongyi Ren, Masoud Badiei Khuzani, Daniel Kapp, James Y Zou, Lu Tian, Joseph C Liao, Lei Xing
Revealing hidden patterns in deep neural network feature space continuum via manifold learning. Nature communications 14 (1) (2023)
Lauri Holmstrom, Matthew Christensen, Neal Yuan, J Weston Hughes, John Theurer, Melvin Jujjavarapu, Pedram Fatehi, Alan C Kwan, Roopinder K Sandhu, Joseph Ebinger, Susan Cheng, James Y Zou, Sumeet S Chugh, David Ouyang
Deep learning-based electrocardiographic screening for chronic kidney disease. Communications medicine 3 (1) (2023)
Md Tauhidul Islam, Zixia Zhou, Hongyi Ren, Masoud Badiei Khuzani, Daniel Kapp, James Y Zou, Lu Tian, Joseph C Liao, Lei Xing
Revealing hidden patterns in deep neural network feature space continuum via manifold learning. Nature communications 14 (1) (2023)
Rong Ma, Eric D Sun, James Y Zou
A spectral method for assessing and combining multiple data visualizations. Nature communications 14 (1) (2023)
Kevin E Wu, James Y Zou, Howard Chang
Machine learning modeling of RNA structures: methods, challenges and future perspectives. Briefings in bioinformatics (2023)
Eric D Sun, Rong Ma, James Y Zou
Dynamic visualization of high-dimensional data. Nature computational science 3 (1) (2022)
Angela Zhang, Lei Xing, James Y Zou, Joseph C Wu
Shifting machine learning for healthcare from development to deployment and from models to data. Nature biomedical engineering (2022)
Eric D Sun, Rong Ma, James Y Zou
Dynamic visualization of high-dimensional data. Nature computational science 3 (1) (2022)
Ruishan Liu, Shemra Rizzo, Sarah Waliany, Marius Rene Garmhausen, Navdeep Pal, Zhi Huang, Nayan Chaudhary, Lisa Wang, Chris Harbron, Joel Neal, Ryan Copping, James Y Zou
Systematic pan-cancer analysis of mutation-treatment interactions using large real-world clinicogenomics data. Nature medicine 28 (8) (2022)
Eric D Sun, Rong Ma, James Y Zou
Dynamic visualization of high-dimensional data. Nature computational science 3 (1) (2022)
Zhenqin Wu, Alexandro E Trevino, Eric Wu, Kyle Swanson, Honesty J Kim, H Blaize D'Angio, Ryan Preska, Gregory W Charville, Piero D Dalerba, Ann Marie Egloff, Ravindra Uppaluri, Umamaheswar Duvvuri, Aaron T Mayer, James Y Zou
Graph deep learning for the characterization of tumour microenvironments from spatial protein profiles in tissue specimens. Nature biomedical engineering (2022)
Andre Esteva, Jean Feng, Douwe van der Wal, Shih-Cheng Huang, Jeffry P Simko, Sandy DeVries, Emmalyn Chen, Edward M Schaeffer, Todd M Morgan, Yilun Sun, Amirata Ghorbani, Nikhil Naik, Dhruv Nathawani, Richard Socher, Jeff M Michalski, Mack Roach, Thomas M Pisansky, Jedidiah M Monson, Farah Naz, James Wallace, Michelle J Ferguson, Jean-Paul Bahary, James Y Zou, Matthew Lungren, Serena Yeung, Ashley E Ross, null null, Howard M Sandler, Phuoc T Tran, Daniel E Spratt, Stephanie Pugh, Felix Y Feng, Osama Mohamad
Prostate cancer therapy personalization via multi-modal deep learning on randomized phase III clinical trials. NPJ digital medicine 5 (1) (2022)
Ruishan Liu, Shemra Rizzo, Samuel Whipple, Navdeep Pal, Arturo Lopez Pineda, Michael Lu, Brandon Arnieri, Ying Lu, William Capra, Ryan Copping, James Y Zou
Evaluating eligibility criteria of oncology trials using real-world data and AI. Nature 592 (7855) (2021)
Anoop Manjunath, Hongyu Li, Shuchen Song, Zhixing Zhang, Shu Liu, Nathan Kahrobai, Arya Gowda, Angelina Seffens, James Y Zou, Ishan Kumar
Comprehensive analysis of 2.4 million patent-to-research citations maps the biomedical innovation and translation landscape. Nature biotechnology 39 (6) (2021)
Martin Jinye Zhang, Angela Oliveira Pisco, Spyros Darmanis, James Y Zou
Mouse aging cell atlas analysis reveals global and cell type-specific aging signatures. eLife 10 (2021)
Eric Wu, Kevin Wu, Roxana Daneshjou, David Ouyang, Daniel E Ho, James Y Zou
How medical AI devices are evaluated: limitations and recommendations from an analysis of FDA approvals. Nature medicine 27 (4) (2021)
Ludvig Bergenstråhle, Bryan He, Joseph Bergenstråhle, Xesús M Abalo, Reza Mirzazadeh, Kim Thrane, Andrew L Ji, Alma Andersson, Ludvig Larsson, Nathalie Stakenborg, Guy Boeckxstaens, Paul A Khavari, James Y Zou, Joakim Lundeberg, Jonas Maaskola
Super-resolved spatial transcriptomics by deep data fusion. Nature biotechnology (2021)
Amirata Ghorbani, David Ouyang, Abubakar Abid, Bryan He, Jonathan H Chen, Robert A Harrington, David H Liang, Euan A Ashley, James Y Zou
Deep learning interpretation of echocardiograms. NPJ digital medicine 3 (2020)
Bryan He, Ludvig Bergenstråhle, Linnea Stenbeck, Abubakar Abid, Alma Andersson, Åke Borg, Jonas Maaskola, Joakim Lundeberg, James Y Zou
Integrating spatial gene expression and breast tumour morphology via deep learning. Nature biomedical engineering 4 (8) (2020)
David Ouyang, Bryan He, Amirata Ghorbani, Neal Yuan, Joseph E Ebinger, Curtis P Langlotz, Paul A Heidenreich, Robert A Harrington, David H Liang, Euan A Ashley, James Y Zou
Video-based AI for beat-to-beat assessment of cardiac function. Nature 580 (7802) (2020)
Dimitre R Simeonov, Alexander J Brandt, Alice Y Chan, Jessica T Cortez, Zhongmei Li, Jonathan M Woo, Youjin Lee, Claudia M B Carvalho, Alyssa C Indart, Theodore L Roth, James Y Zou, Andrew P May, James R Lupski, Mark S Anderson, F William Buaas, Daniel S Rokhsar, Alexander Marson
A large CRISPR-induced bystander mutation causes immune dysregulation. Communications biology 2 (2019)
Ryan T Leenay, Amirali Aghazadeh, Joseph Hiatt, David Tse, Theodore L Roth, Ryan Apathy, Eric Shifrut, Judd F Hultquist, Nevan Krogan, Zhenqin Wu, Giana Cirolia, Hera Canaj, Manuel D Leonetti, Alexander Marson, Andrew P May, James Y Zou
Large dataset enables prediction of repair after CRISPR-Cas9 editing in primary T cells. Nature biotechnology 37 (9) (2019)
Yuhui Zhang, Allen Nie, Ashley Zehnder, Rodney L Page, James Y Zou
VetTag: improving automated veterinary diagnosis coding via large-scale language modeling. NPJ digital medicine 2 (2019)
Martin Jinye Zhang, Fei Xia, James Y Zou
Fast and covariate-adaptive method amplifies detection power in large-scale multiple hypothesis testing. Nature communications 10 (1) (2019)
James Y Zou, Mikael Huss, Abubakar Abid, Pejman Mohammadi, Ali Torkamani, Amalio Telenti
A primer on deep learning in genomics. Nature genetics 51 (1) (2018)