For a comprehensive listing see Google Scholar and Harvard Profiles.

Selected Publications (reverse chronological order)

Association of 152 biomarker reference intervals with all-cause mortality in participants of a general United States survey from 1999 to 2010.
Clinical Chemistry
December 2020
Nam Pho, Arjun K Manrai, John T Leppert, Glenn M Chertow, John PA Ioannidis, Chirag J Patel

A systematic machine learning and data type comparison yields metagenomic predictors of infant age, sex, breastfeeding, antibiotic usage, country of origin, and delivery type.
PLoS Computational Biology
May 2020
Alan Le Goallec, Braden T Tierney, Jacob Luber, Evan Cofer, Aleksander Kostic, Chirag J Patel

Characteristics of undiagnosed diabetes in men and women under the age of 50 years in the Indian subcontinent: the National Family Health Survey (NFHS-4)/Demographic Health Survey 2015–2016.
BMJ Open Diabetes Research and Care
February 2020
Kajal T Claypool, Ming-Kei Chung, Andrew Deonarine, Edward W Gregg, Chirag J Patel

Signals Among Signals: Prioritizing Nongenetic Associations in Massive Data Sets.
American Journal of Epidemiology
May 2019
Arjun K Manrai, John P A Ioannidis, Chirag J Patel

Family History–Wide Association Study to Identify Clinical and Environmental Risk Factors for Common Chronic Diseases.
American Journal of Epidemiology
August 2019
Danielle Rasooly, John P A Ioannidis, Muin J Khoury, Chirag J Patel

Landscape of genetic content in the Human Microbiome.
Cell Host and Microbe
August 2019
Braden T.Tierney, Zhen Yang, Jacob M.Luber, Marc Beaudin, Marsha C.Wibowo, Christina Baek, Eleanor Mehlenbacher, Chirag J.Patel*, Aleksandar D.Kostic*
see also: GitHub | Microbial Genes Web App

Repurposing large health insurance claims data to estimate genetic and environmental contributions in 560 phenotypes.
Nature Genetics
January 2019
Chirag M Lakhani, Braden T Tierney, Arjun K Manrai, Jian Yang, Peter M Visscher, Chirag J Patel
see also: GitHub | CaTCH Web Application

Toward Capturing the Exposome: Exposure Biomarker Variability and Coexposure Patterns in the Shared Environment .
Environmental Science and Technology
August, 2018
Ming Kei (Jake) Chung, Kurunthachalam Kannan, Germaine M. Louis, and Chirag J. Patel
see also:GitHub

In the Era of Precision Medicine and Big Data, Who Is Normal? .
May, 2018
Arjun K Manrai, Chirag J Patel, John PA Ioannidis

Systematic identification of correlates of HIV infection: an X-wide association study.
April, 2018
Chirag J Patel, Jay Bhattacharya, John PA Ioannidis, Eran Bendavid

Aether: Leveraging Linear Programming For Optimal Cloud Computing In Genomics.
December, 2017
Jacob Luber*, Braden T Tierney*, Evan Cofer, Chirag J Patel*, and Aleksander D Kostic*
see also: Aether

Opportunities and challenges for environmental exposure assessment in population-based studies.
Cancer Epidemiology, Biomarkers, and Prevention
September, 2017
Chirag J Patel, Jacqueline Kerr, Duncan C. Thomas, Bhramar Mukherjee, Beate Ritz, Nilanjan Chatterjee, Marta Jankowska, Juliette Madan, Margaret R. Karagas, Kimberly A. McAllister, Leah E. Mechanic, M. Daniele Fallin, Christine Ladd-Acosta, Ian A. Blair, Susan L. Teitelbaum and Christopher I. Amos

Leveraging population-based clinical quantitative phenotyping for drug repositioning.
CPT: Pharmacometrics and Systems Pharmacology
September, 2017
Adam S Brown, Danielle Rasooly, Chirag J Patel

RepoDB: A Standard Database for Drug Repositioning.
Nature Scientific Data
March, 2017
Adam S Brown and Chirag J Patel
see also: RepoDB

Informatics and Data Analytics to Support Exposome-Based Discovery for Public Health.
Annual Review of Public Health
March, 2017
Arjun K Manrai, Yuxia Cui, Pierre R Bushel, Molly Hall, Spyros Karakitsios, Carolyn Mattingly, Marylyn Ritchie, Charles Schmitt, Denis A Sarigiannis, Duncan C Thomas, David Wishart, David M Balshaw, Chirag J Patel

A review of validation strategies for computational drug repositioning.
Briefings in Bioinformatics
November, 2016
Adam S Brown, Chirag J Patel

A data-driven search for semen-related phenotypes in conception delay.
October, 2016
Chirag J Patel, Sundaram Rajeshwari, Germaine Buck Louis

A database of human exposomes and phenomes from the US National Health and Nutrition Examination Survey.
Scientific Data
October, 2016
Chirag J Patel, Nam Pho, Michael McDuffie, Jeremy Easton-Marks, Cartik Kothari, Isaac S Kohane, Paul Avillach

MeSHDD: Literature-based drug-drug similarity for drug repositioning.
Journal of the American Medical Informatics Association
September, 2016
Adam S Brown, Chirag J Patel

Systematic assessment of pharmaceutical prescriptions in association with cancer risk: a method to conduct a population-wide medication-wide longitudinal study.
Scientific Reports
August, 2016
Chirag J Patel, Ji J, Jan Sundquist, John PA Ioannidis, Kristina Sundquist

Environment-Wide Association Study of Blood Pressure in the National Health and Nutrition Examination Survey (1999–2012).
Scientific Reports
July, 2016
Denise McGinnis, JS Brownstein, Chirag J Patel

Systematic correlation of environmental exposure and physiological and self-reported behaviour factors with leukocyte telomere length.
International Journal of Epidemiology
April, 2016
Chirag J Patel, Arjun K Manrai, Erik Corona, Isaac S Kohane

Analytical Complexity in Detection of Gene Variant-by-Environment Exposure Interactions in High-Throughput Genomic and Exposomic Research.
Current Environmental Health Reports
March, 2016
Chirag J Patel

ksRepo: a generalized platform for computational drug repositioning.
BMC Bioinformatics
January, 2016
Adam S Borwn, Sek Won Kong, Isaac S Kohane, Chirag J Patel
Fork the software here.

Assessment of vibration of effects due to model specification can demonstrate the instability of observational associations.
Clinical Journal of Epidemiology
June, 2015
Chirag J Patel, Burford B, John PA Ioanndis
Check out our code and figures here.

Systematic Assessment of the Correlations of Household Income With Infectious, Biochemical, Physiological, and Environmental Factors.
American Journal of Epidemiology
January, 2015
Chirag J Patel, Mark R Cullen, John PA Ioannidis JPAI, David Rehkopf
Featured by the American Journal of Epidemiology as an editor's choice paper!

Development of Exposome Globes to Map Out Environment-Wide Associations.
Pacific Symposium on Biocomputing
January, 2015
Chirag J Patel, Arjun K Manrai

Placing epidemiological results in the context of multiplicity and typical correlations of exposures. Journal of Epidemiology and Community Health
June 12, 2014
Chirag J Patel, John PA Ioannidis

Studying the elusive environment in large scale.
June 4, 2014
Chirag J Patel, John PA Ioannidis

Investigation of maternal environmental exposures in association with self-reported preterm birth.
Reproductive Toxicology
June 4, 2014
Chirag J Patel, Yang T, Hu Z, Wen Q, Sung J, El-Sayed YY, Cohen H, Gould J, Stevenson DK, Shaw GM, Ling XB, Butte AJ

Systematic evaluation of environmental and behavioural factors associated with all-cause mortality.
International Journal of Epidemiology
December, 2013
Chirag J Patel, Rehkopf DH, Leppert JT, Bortz WM, Cullen MR, Chertow GM, John PA Ioannidis

Whole genome sequencing in support of wellness and health maintenance.
Genome Medicine
June 27, 2013
Chirag J Patel, Sivadas A, Tabassum R, Preeprem T, Zhao J, Arafat D, Chen R, Morgan AA, Martin GS, Brigham KL, Butte AJ, Gibson G
Featured in GenomeWeb (6/17/2013) and accompanied by an editorial in Genome Medicine, Genetic parts to a preventive medicine whole by Nicholas J Schork.

Systematic identification of interaction effects between genome- and environment-wide associations in type 2 diabetes mellitus.
Human Genetics
May 27, 2013
Chirag J Patel, Chen R, Kodama K, Ioannidis JP, Butte AJ
Featured in Everyday Health (1/2013) and (1/2013)

A nutrient-wide association study on blood pressure.
Nov 20, 2012
Ioanna Tzoulaki*, Chirag J Patel*, Okamura T, Chan Q, Brown IJ, Miura K, Ueshima H, Zhao L, Van Horn L, Daviglus ML, Stamler J, Butte AJ, Ioannidis JP, Elliott P
Featured in an editorial in Circulation

Data-driven integration of epidemiological and toxicological data to select candidate interacting genes and environmental factors in association with disease.
June 15, 2012
Chirag J Patel, Rong Chen, Atul J Butte
Winner of best paper in translational bioinformatics during International Society of Molecular Biology (ISMB) 2012.

Systematic evaluation of environmental factors: persistent pollutants and nutrients correlated with serum lipid levels.
International Journal of Epidemiology
June 15, 2012
Chirag J Patel, Mark R Cullen, John PA Ioannidis, Atul J Butte
Featured in GenomeWeb (3/2012).

An Environment-Wide Association Study (EWAS) on type 2 diabetes mellitus.
May 20, 2010
Chirag J Patel, Jay Bhattacharya, Atul J Butte
Cited >150 times as of 11/2014.
Featured in MIT Technology Review (5/2010), Scientific American (5/2010), ABC News (5/2010), San Jose Mercury News (5/2010), Nature Biotechnology (1/2011), Nature (2/2011), and Nature (5/2012).

Predicting environmental chemical factors associated with disease-related gene expression data.
BMC Medical Genomics
May 6, 2010
Chirag J Patel, Atul J Butte

ChMP: A collaborative medical history portal.
AMIA Annual Symposium Proceedings
Noah H Zimmerman*, Chirag J Patel*, and David P Chen*.