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 001 (ISMB (Supplement of Bioinformatics), 2006)

F-Seq: a feature density estimator for high-throughput sequence tags. - Alan P. Boyle; Justin Guinney; Gregory E. Crawford; Terrence S. Furey (Bioinform., 2008)

Modeling Cancer Progression via Pathway Dependencies. - Elena J. Edelman; Justin Guinney; Jen-Tsan A. Chi; Phillip G. Febbo; Sayan Mukherjee 001 (PLoS Comput. Biol., 2008)

The Geometry of Cancer. - Justin Guinney (2009)

Learning Gradients: Predictive Models that Infer Geometry and Statistical Dependence. - Qiang Wu 003; Justin Guinney; Mauro Maggioni; Sayan Mukherjee 001 (J. Mach. Learn. Res., 2010)

Estimating variable structure and dependence in multitask learning via gradients. - Justin Guinney; Qiang Wu 003; Sayan Mukherjee 001 (Mach. Learn., 2011)

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)

GSVA: gene set variation analysis for microarray and RNA-Seq data. - Sonja Hänzelmann; Robert Castelo; Justin Guinney (BMC Bioinform., 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 002; Benjamin A. Sauerwine; Yishai Shimoni; Hans Kristian Moen Vollan; Brigham H. Mecham; Oscar M. Rueda; Jorg Tost; et al. (PLoS Comput. Biol., 2013)

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 (Pacific Symposium on Biocomputing, 2014)

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 (Pacific Symposium on Biocomputing, 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; et al. (J. Am. Medical Informatics Assoc., 2015)

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 (PSB, 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)

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)

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 (AMIA, 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)

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 003; Alfred Anzalone; Timothym Bergquist; Sarah Cutrona; Ben S. Gerber; et al. (AMIA, 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 (AMIA, 2021)

Establishing the reliability of algorithms. - Lara M. Mangravite; Sean D. Mooney; Iddo Friedberg; Justin Guinney (PSB, 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; et al. (J. Am. Medical Informatics Assoc., 2021)

Preview of "Interpretable systems biomarkers predict response to immune-checkpoint inhibitors". - Justin Guinney (Patterns, 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; et al. (PLoS Comput. Biol., 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., 2021)

Assessing Machine Learning Based Generators for Synthetic Electronic Health Records: A Benchmarking. - Chao Yan 004; Yao Yan; Ziqi Zhang 005; Zhiyu Wan; Justin Guinney; Sean D. Mooney; Bradley A. Malin (AMIA, 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 002; Connor Boyle; George Koslowski; Jiaxin Zheng; Nicholas J. Dobbins; Clement Essien; Hongfang Liu; Larsson Omberg; Meliha Yestigen; et al. (CoRR, 2022)

A Multifaceted Benchmarking of Synthetic Electronic Health Record Generation Models. - Chao Yan 004; Yao Yan; Zhiyu Wan; Ziqi Zhang 005; Larsson Omberg; Justin Guinney; Sean D. Mooney; Bradley A. Malin (CoRR, 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; et al. (J. Am. Medical Informatics Assoc., 2022)

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 002; Lukasz Charzewski; Zofia Nawalany; Ivan Brugere; Renata Retkute; Alidivinas Prusokas; et al. (J. Am. Medical Informatics Assoc., 2023)

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)

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; et al. (J. Am. Medical Informatics Assoc., 2025)