Justin Guinney

According to our database, Justin Guinney authored at least 31 papers between 2006 and 2025.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2025

National COVID Cohort Collaborative data enhancements: a path for expanding common data models.

Kellie M. Walters, Marshall Clark, Sofia Dard, Stephanie S. Hong, Elizabeth Kelly, Kristin Kostka, Adam M. Lee, Robert T. Miller, Michele Morris, Matvey B. Palchuk, Emily R. Pfaff, Adam B. Wilcox, Alexis Graves, Alfred (jerrod) Anzalone, Amin Manna, Amit Saha, Amy Olex, Andrea Zhou, Andrew E. Williams, Andrew Southerland, Andrew T. Girvin, Anita Walden, Anjali A Sharathkumar, Benjamin Amor, Benjamin Bates, Brian Hendricks, Brijesh Patel, Caleb Alexander, Carolyn T. Bramante, Cavin Ward-Caviness, Charisse Madlock-Brown, Christine Suver, Christopher Chute, Christopher Dillon, Chunlei Wu, Clare Schmitt, Cliff Takemoto, Dan Housman, Davera Gabriel, David A Eichmann, Diego Mazzotti, Don Brown, Eilis Boudreau, Elaine Hill, Elizabeth Zampino, Emily Carlson Marti, Evan French, Farrukh M. Koraishy, Federico Mariona, Fred Prior, George Sokos, Greg Martin, Harold Lehmann, Heidi Spratt, Hemalkumar Mehta, Hongfang Liu, Hythem Sidky, J. W. Awori Hayanga, Jami Pincavitch, Jaylyn Clark, Jeremy Richard Harper, Jessica Islam, Jin Ge, Joel Gagnier, Joel H. Saltz, Joel Saltz, Johanna Loomba, John Buse, Jomol Mathew, Joni L. Rutter, Julie A McMurry, Justin Guinney, Justin Starren, Karen Crowley, Katie Rebecca Bradwell, Ken Wilkins, Kenneth R. Gersing, Kenrick Dwain Cato, Kimberly Murray, Lavance Northington, Lee Allan Pyles, Leonie Misquitta, Lesley Cottrell, Lili Portilla, Mariam Deacy, Mark M. Bissell, Mary Emmett, Mary Morrison Saltz, Melissa A Haendel, Meredith Adams, Meredith Temple-O'Connor, Michael G. Kurilla, Nabeel Qureshi, Nasia Safdar, Nicole Garbarini, Noha Sharafeldin, Ofer Sadan, Patricia A Francis, Penny Wung Burgoon, Peter Robinson, Philip R. O. Payne, Rafael Fuentes, Randeep Jawa, Rebecca Erwin-Cohen, Rena Patel, Richard A Moffitt, Richard L. Zhu, Rishi Kamaleswaran, Robert Hurley, Saiju Pyarajan, Sam G. Michael, Samuel Bozzette, Sandeep Mallipattu, Satyanarayana Vedula, Scott Chapman, Shawn T. O'Neil, Soko Setoguchi, Steve Johnson, Tellen D. Bennett, Tiffany Callahan, Umit Topaloglu, Usman Sheikh, Valery Gordon, Vignesh Subbian, Warren A Kibbe, Wenndy Hernandez, Will Beasley, Will Cooper, William Hillegass, Xiaohan Tanner Zhang

J. Am. Medical Informatics Assoc., 2025

2024

AI Competitions and Benchmarks, Practical issues: Proposals, grant money, sponsors, prizes, dissemination, publicity.

Magali Richard, Yuna Blum, Justin Guinney, Gustavo Stolovitzky, Adrien Pavão

CoRR, 2024

2023

Evaluation of crowdsourced mortality prediction models as a framework for assessing artificial intelligence in medicine.

Timothy Bergquist, Thomas Schaffter, Yao Yan, Thomas Yu, Justin Prosser, Jifan Gao, Guanhua Chen, Lukasz Charzewski, Zofia Nawalany, Ivan Brugere, Renata Retkute, Alidivinas Prusokas, Augustinas Prusokas, Yonghwa Choi, Sanghoon Lee, Junseok Choe, Inggeol Lee, Sunkyu Kim, Jaewoo Kang, Sean D. Mooney, Justin Guinney

J. Am. Medical Informatics Assoc., December, 2023

2022

Demonstrating an approach for evaluating synthetic geospatial and temporal epidemiologic data utility: results from analyzing >1.8 million SARS-CoV-2 tests in the United States National COVID Cohort Collaborative (N3C).

Jason A. Thomas, Randi E. Foraker, Noa Zamstein, Jon D. Morrow, Philip R. O. Payne, Adam B. Wilcox, Melissa A. Haendel, Christopher G. Chute, Kenneth R. Gersing, Anita Walden, Tellen D. Bennett, David A. Eichmann, Justin Guinney, Warren A. Kibbe, Hongfang Liu, Emily R. Pfaff, Peter N. Robinson, Joel H. Saltz, Heidi Spratt, Justin Starren, Christine Suver, Chunlei Wu, Davera Gabriel, Stephanie S. Hong, Kristin Kostka, Harold P. Lehmann, Richard A. Moffitt, Michele Morris, Matvey B. Palchuk, Xiaohan Tanner Zhang, Richard L. Zhu, Benjamin R. C. Amor, Mark M. Bissell, Marshall Clark, Andrew T. Girvin, Adam M. Lee, Robert T. Miller, Kellie M. Walters, Yooree Chae, Connor Cook, Alexandra Dest, Racquel R. Dietz, Thomas Dillon, Patricia A. Francis, Rafael Fuentes, Alexis Graves, Andrew J. Neumann, Shawn T. O'Neil, Usman Sheikh, Andréa M. Volz, Elizabeth Zampino, Christopher P. Austin, Samuel Bozzette, Mariam Deacy, Nicole Garbarini, Michael G. Kurilla, Sam G. Michael, Joni L. Rutter, Meredith Temple-O'Connor, Katie Rebecca Bradwell, Amin Manna, Nabeel Qureshi, Mary Morrison Saltz, Julie A. McMurry, Carolyn T. Bramante, Jeremy Richard Harper, Wenndy Hernandez, Farrukh M. Koraishy, Federico Mariona, Saidulu Mattapally, Amit Saha, Satyanarayana Vedula, Yujuan Fu, Nisha Mathews, Ofer Mendelevitch

J. Am. Medical Informatics Assoc., 2022

A Multifaceted Benchmarking of Synthetic Electronic Health Record Generation Models.

Chao Yan, Yao Yan, Zhiyu Wan, Ziqi Zhang, Larsson Omberg, Justin Guinney, Sean D. Mooney, Bradley A. Malin

CoRR, 2022

The NLP Sandbox: an efficient model-to-data system to enable federated and unbiased evaluation of clinical NLP models.

Yao Yan, Thomas Yu, Kathleen Muenzen, Sijia Liu, Connor Boyle, George Koslowski, Jiaxin Zheng, Nicholas J. Dobbins, Clement Essien, Hongfang Liu, Larsson Omberg, Meliha Yestigen, Bradley Taylor, James A. Eddy, Justin Guinney, Sean D. Mooney, Thomas Schaffter

CoRR, 2022

Assessing Machine Learning Based Generators for Synthetic Electronic Health Records: A Benchmarking.

Chao Yan, Yao Yan, Ziqi Zhang, Zhiyu Wan, Justin Guinney, Sean D. Mooney, Bradley A. Malin

Proceedings of the AMIA 2022, 2022

2021

Knowledge-based classification of fine-grained immune cell types in single-cell RNA-Seq data.

Xuan Liu, Sara J. C. Gosline, Lance T. Pflieger, Pierre Wallet, Archana Iyer, Justin Guinney, Andrea H. Bild, Jeffrey T. Chang

Briefings Bioinform., September, 2021

Crowdsourced identification of multi-target kinase inhibitors for RET- and TAU- based disease: The Multi-Targeting Drug DREAM Challenge.

Zhaoping Xiong, Minji Jeon, Robert J. Allaway, Jaewoo Kang, Donghyeon Park, Jinhyuk Lee, Hwisang Jeon, Miyoung Ko, Hualiang Jiang, Mingyue Zheng, Aik Choon Tan, Xindi Guo, Multi-Targeting Drug DREAM Challenge Community, Kristen K. Dang, Alex Tropsha, Chana Hecht, Tirtha K. Das, Heather A. Carlson, Ruben Abagyan, Justin Guinney, Avner Schlessinger, Ross L. Cagan

PLoS Comput. Biol., 2021

Preview of "Interpretable systems biomarkers predict response to immune-checkpoint inhibitors".

Justin Guinney

Patterns, 2021

The National COVID Cohort Collaborative (N3C): Rationale, design, infrastructure, and deployment.

Melissa A. Haendel, Christopher G. Chute, Tellen D. Bennett, David A. Eichmann, Justin Guinney, Warren A. Kibbe, Philip R. O. Payne, Emily R. Pfaff, Peter N. Robinson, Joel H. Saltz, Heidi Spratt, Christine Suver, John Wilbanks, Adam B. Wilcox, Andrew E. Williams, Chunlei Wu, Clair Blacketer, Robert L. Bradford, James J. Cimino, Marshall Clark, Evan W. Colmenares, Patricia A. Francis, Davera Gabriel, Alexis Graves, Raju Hemadri, Stephanie S. Hong, George Hripcsak, Dazhi Jiao, Jeffrey G. Klann, Kristin Kostka, Adam M. Lee, Harold P. Lehmann, Lora Lingrey, Robert T. Miller, Michele Morris, Shawn N. Murphy, Karthik Natarajan, Matvey B. Palchuk, Usman Sheikh, Harold Solbrig, Shyam Visweswaran, Anita Walden, Kellie M. Walters, Griffin M. Weber, Xiaohan Tanner Zhang, Richard L. Zhu, Benjamin R. C. Amor, Andrew T. Girvin, Amin Manna, Nabeel Qureshi, Michael G. Kurilla, Sam G. Michael, Lili M. Portilla, Joni L. Rutter, Christopher P. Austin, Ken R. Gersing

J. Am. Medical Informatics Assoc., 2021

Establishing the reliability of algorithms.

Lara M. Mangravite, Sean D. Mooney, Iddo Friedberg, Justin Guinney

Proceedings of the Biocomputing 2021: Proceedings of the Pacific Symposium, 2021

A Continuous Crowd-sourced Challenge for Benchmarking COVID-19 Health Outcome Prediction.

Yao Yan, Thomas Schaffter, Timothy Bergquist, Thomas Yu, Justin Prosser, Sean D. Mooney, Justin Guinney

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

COVID-19 Mortality Prediction among Patients with Cancer Using a Large National Cohort.

Feifan Liu, Noha Sharafeldin, Vithal Madhira, Katie R. Bradwell, Qianqian Song, Benjamin Bates, Yu R. Shao, Jing Su, Alfred Anzalone, Timothym Bergquist, Sarah Cutrona, Ben S. Gerber, Peter N. Robinson, Justin Guinney, Umit Topaloglu

Proceedings of the AMIA 2021, American Medical Informatics Association Annual Symposium, San Diego, CA, USA, October 30, 2021, 2021

2020

Piloting a model-to-data approach to enable predictive analytics in health care through patient mortality prediction.

Timothy Bergquist, Yao Yan, Thomas Schaffter, Thomas Yu, Vikas Pejaver, Noah Hammarlund, Justin Prosser, Justin Guinney, Sean D. Mooney

J. Am. Medical Informatics Assoc., 2020

Global research consortia and data harmonization projects drive the clinical interpretation of cancers.

Justin Guinney, Subha Madhavan, Melissa A. Haendel, Alex H. Wagner, Ratna R. Thangudu

Proceedings of the AMIA 2020, 2020

2018

Probing the chemical-biological relationship space with the Drug Target Explorer.

Robert J. Allaway, Salvatore La Rosa, Justin Guinney, Sara J. C. Gosline

J. Cheminformatics, 2018

2016

rCGH: a comprehensive array-based genomic profile platform for precision medicine.

Frederic Commo, Justin Guinney, Charles Ferté, Brian M. Bot, Celine Lefebvre, Jean-Charles Soria, Fabrice André

Bioinform., 2016

Personalized Hypothesis Tests for Detecting Medication Response in Parkinson Disease Patients Using iPhone Sensor Data.

Elias Chaibub Neto, Brian M. Bot, Thanneer M. Perumal, Larsson Omberg, Justin Guinney, Mike Kellen, Arno Klein, Stephen H. Friend, Andrew D. Trister

Proceedings of the Biocomputing 2016: Proceedings of the Pacific Symposium, 2016

2015

The NIH BD2K center for big data in translational genomics.

Benedict Paten, Mark Diekhans, Brian J. Druker, Stephen H. Friend, Justin Guinney, Nadine Gassner, Mitchell Guttman, W. James Kent, Patrick Mantey, Adam A. Margolin, Matt Massie, Adam M. Novak, Frank A. Nothaft, Lior Pachter, David A. Patterson, Maciej Smuga-Otto, Joshua M. Stuart, Laura J. van't Veer, Barbara J. Wold, David Haussler

J. Am. Medical Informatics Assoc., 2015

Stepwise Group Sparse Regression (SGSR): Gene-Set-Based Pharmacogenomic Predictive Models with Stepwise Selection of Functional Priors.

In Sock Jang, Rodrigo Dienstmann, Adam A. Margolin, Justin Guinney

Proceedings of the Biocomputing 2015: Proceedings of the Pacific Symposium, 2015

2014

Systematic Assessment of Analytical Methods for Drug Sensitivity Prediction from Cancer Cell Line Data.

In Sock Jang, Elias Chaibub Neto, Justin Guinney, Stephen H. Friend, Adam A. Margolin

Proceedings of the Biocomputing 2014: Proceedings of the Pacific Symposium, 2014

2013

Improving Breast Cancer Survival Analysis through Competition-Based Multidimensional Modeling.

Erhan Bilal, Janusz Dutkowski, Justin Guinney, In Sock Jang, Benjamin A. Logsdon, Gaurav Pandey, Benjamin A. Sauerwine, Yishai Shimoni, Hans Kristian Moen Vollan, Brigham H. Mecham, Oscar M. Rueda, Jorg Tost, Christina Curtis, Mariano J. Alvarez, Vessela N. Kristensen, Samuel Aparicio, Anne-Lise Børresen-Dale, Carlos Caldas, Andrea Califano, Stephen H. Friend, Trey Ideker, Eric E. Schadt, Gustavo A. Stolovitzky, Adam A. Margolin

PLoS Comput. Biol., 2013

GSVA: gene set variation analysis for microarray and RNA-Seq data.

Sonja Hänzelmann, Robert Castelo, Justin Guinney

BMC Bioinform., 2013

2012

Correlation set analysis: detecting active regulators in disease populations using prior causal knowledge.

Chia-Ling Huang, John Lamb, Leonid Chindelevitch, Jarek Kostrowicki, Justin Guinney, Charles DeLisi, Daniel Ziemek

BMC Bioinform., 2012

2011

Estimating variable structure and dependence in multitask learning via gradients.

Justin Guinney, Qiang Wu, Sayan Mukherjee

Mach. Learn., 2011

2010

Learning Gradients: Predictive Models that Infer Geometry and Statistical Dependence.

Qiang Wu, Justin Guinney, Mauro Maggioni, Sayan Mukherjee

J. Mach. Learn. Res., 2010

2009

The Geometry of Cancer.

Justin Guinney

PhD thesis, 2009

2008

Modeling Cancer Progression via Pathway Dependencies.

Elena J. Edelman, Justin Guinney, Jen-Tsan A. Chi, Phillip G. Febbo, Sayan Mukherjee

PLoS Comput. Biol., 2008

F-Seq: a feature density estimator for high-throughput sequence tags.

Alan P. Boyle, Justin Guinney, Gregory E. Crawford, Terrence S. Furey

Bioinform., 2008

2006

Analysis of sample set enrichment scores: assaying the enrichment of sets of genes for individual samples in genome-wide expression profiles.

Elena J. Edelman, Alessandro Porrello, Justin Guinney, Bala Balakumaran, Andrea Bild, Phillip G. Febbo, Sayan Mukherjee

Proceedings of the Proceedings 14th International Conference on Intelligent Systems for Molecular Biology 2006, 2006