Publications

Dutta, D., Ray, D., and Chatterjee, N. “Genetic association tests with multiple phenotypes: A review of current methods”. Sankhyā B (to appear), 2022.

Ray, D., Vergara, C., Taub, M.A., Wojcik, G., Ladd-Acosta, C., ^Beaty, T.H., and ^Duggal, P. “Benchmarking statistical methods for analyzing parent-child dyads in genetic association studies”, Genetic Epidemiology, 46:266-284, 2022. [link] [software] [tweetorial]

Ray, D., and Chatterjee, N. "A powerful method for pleiotropic analysis under composite null hypothesis identifies novel shared loci between type 2 diabetes and prostate cancer". PLoS Genetics, 16(12): e1009218, 2020. [link] [software] [tweetorial]

Ray, D., and Chatterjee, N. "Effect of Non-Normality and Low Count Variants on Cross-Phenotype Association Tests in GWAS". European Journal of Human Genetics, 28:300-312, 2019. [link] [supp] [software] [free readonly]

Ray, D., and Boehnke, M. "Meta-analysis of Multiple Traits using GWAS Summary Statistics". Genetic Epidemiology, 42:134-145, 2018. [link] [supp] [software]  

• One of Genetic Epidemiology journal's top 20 downloaded recent papers between July 2016 and June 2018.

• Among the top 5 most cited articles in Genetic Epidemiology as of 13 September 2021.

Ray, D., and Basu, S. "A Novel Association Test for Multiple Secondary Phenotypes from a Case-control GWAS". Genetic Epidemiology, 41:413-426, 2017. [link] [supp] [software]

Ray, D., Pankow, J.S., and Basu, S. "USAT: A Unified Score-based Association Test for Multiple Phenotype-Genotype Analysis". Genetic Epidemiology, 40(1):20-34, 2016. [link] [supp] [software]

Ray, D., Li, X., Pan, W., Pankow, J.S., and Basu, S. "A Bayesian Partitioning Model for Detection of Multilocus Effects in Case-Control Studies". Human Heredity, 79(2):69-79, 2015. [link] [supp] [Software available on request]

de Andrade, M., Ray, D., Pereira, A.C., and Soler, J.M.P. "Global Individual Ancestry using Principal Components for Family Data". Human Heredity, 80:1-11, 2015. [link] [supp]

Basu, S., Zhang, Y., Ray, D., Miller, M.B., Iacono, W.G., and McGue, M. "A Rapid Gene-Based Genome-Wide Association Test with Multivariate Traits". Human Heredity, 76(2):53-63, 2013. [pdf] [software]

*Venkataraghavan, S., Pankow, J.S., Boerwinkle, E., Fornage, M., Selvin, E., and Ray, D. “Epigenome-wide association study of incident type 2 diabetes in Black and White participants from the Atherosclerosis Risk in Communities Study”. medRxiv, 2023. [preprint]

• Manuscript resulting from the PhD thesis of advisee S. Venkataraghavan.

Ray, D., *Loomis, S.J., *Venkataraghavan, S., Tin, A., Yu, B., Chatterjee, N., Selvin, E., and Duggal, P. “Characterizing common and rare variations in nontraditional glycemic biomarkers using multivariate approaches on multi-ancestry ARIC study”. medRxiv, 2023. [preprint]

*Wang, J.R., Zafereo, M.E., Wang, W., †Joshu, C., and †Ray, D. "Association of polygenic score with tumor molecular subtypes in papillary thyroid carcinoma", The Journal of Clinical Endocrinology & Metabolism, 2023. [link]

Meng, W., Reel, P.S., Nangia, C., Rajendrakumar, A.L., Hebert, H.L., Adams, M.J., Zheng, H., Lu, Z.H., 23andMe Research Team, Ray, D., Colvin, L.A., Palmer, C., McIntosh, A., and Smith, B.H. “A meta-analysis of the genome-wide association studies on two genetically correlated phenotypes suggests four new risk loci for headaches”, Phenomics, 3:64-76, 2023. [link]

Awotoye, W., Mossey, P.A., Hetmanski, J.B., Gowans, L.J.J., Eshete, M.A., Adeyemo, W.L., Alade, A., Zeng, E., Adamson, O., Fashina, A., . . . , Ray, D., . . . , Butali, A. “Damaging mutations in AFDN contribute to risk of nonsyndromic cleft lip with or without cleft palate”. The Cleft Palate-Craniofacial Journal, 2022. [link]

^Qi, G., ^Dutta, D., Leroux, A., Ray, D., Muschelli, J., Crainiceanu, C., and Chatterjee, N. “Genome-wide association studies of 27 accelerometry-derived physical activity measurements identifies novel loci and genetic mechanisms”, Genetic Epidemiology, 46:122-138, 2022. [link] [preprint]

Jaworek, T., Xu, H., Gaynor, B.J., Cole, J.W., Rannikmäe, K., Stanne, T.M., Tomppo, L., [. . .] , Ray, D., [. . .] , de Leeuw, F.-E., Lindgren, A., Pare, G., Anderson, C., Markus, H., Jern, C., Malik, R., Dichgans, M., Mitchell, B.D., and Kittner, S.J. “Contribution of common genetic variants to risk of early-onset ischemic stroke”. Neurology, 99 (16):e1738-e1754, 2022. [link]

Qi, G., Chhetri, S.B., Ray, D., Dutta, D., Battle, A., Bhattacharjee, S., and Chatterjee, N. “Genome-wide large-scale multi-trait analysis characterizes global patterns of pleiotropy and unique trait-specific variants”, bioRxiv, 2022. [preprint]

†Ray, D., *Venkataraghavan, S., *Zhang, W., Leslie, E.J., Hetmanski, J.B., Weinberg, S.M., Marazita, M.L., Ruczinski, I., Taub, M.A., and †Beaty, T.H. "Pleiotropy method identifies genetic overlap between orofacial clefts at multiple loci from GWAS of multi-ethnic trios". PLoS Genetics, 7(7):e1009584, 2021. [link] [software] [tweetorial]

Chen, J., Spracklen, C.N., Marenne, G., Varshney, A., Corbin, L.J., Luan, J., [...] Ray, D., [...] Parker, S.C.J., Mohlke, K.L., Langenberg, C., Wheeler, E., Morris, A.P., Barroso, I. "The trans-ancestral genomic architecture of glycaemic traits". Nature Genetics, 53:840–860, 2021. [link]

*^Zhang, W., *^Venkataraghavan, S., Hetmanski, J.B., Leslie, E.J., Marazita, M.L., Feingold, E., Ruczinski, I., Taub, M.A., Scott, A.F., †Ray, D. and †Beaty, T.H. "Detecting gene-environment interaction for maternal exposures using case-parent trios ascertained through an orofacial cleft case." Frontiers in Cell and Developmental Biology, 9:621018, 2021. [link] [software]

^Duggal, P., ^Ladd-Acosta, C., ^Ray, D., and ^Beaty, T.H. "The evolving field of genetic epidemiology: From familial aggregation to genomic sequencing". American Journal of Epidemiology, 188:2069-2077, 2019. [link]

Locke, A.E., Steinberg, K.M., Chiang, C., Service, S., Havulinna, A., Stell, L., [...] Ray, D., [...]  Ripatti, S., Boehnke, M., and Freimer, N. "Exome sequencing identifies high impact trait-associated alleles enriched in Finns".  Nature, 572:323-328, 2019. [link] [supp] [tweetorial]

Misra, S., Wagner, R., Ozkan, B., Schön, M., Sevilla-Gonzalez, M., Prystupa, K., Wang, C.C., Kreienkamp, R.J., Cromer, S.J., Rooney, M.R., [. . .] Ray, D., Selvin, E., Florez, J.C., ADA/EASD PMDI, Meigs, J.B., and Udler, M.S. “Systematic review of precision subclassification of type 2 diabetes”. medRxiv, 2023. [preprint]

†Ray, D., Muñoz, A., Zhang, M., Li, X., Chatterjee, N., Jacobson, L.P., and †Lau, B. "Meta-analysis under imbalance in measurement of confounders in cohort studies using only summary-level data", BMC Medical Research Methodology, 22:143, 2022. [link] [supp] [software] [tweetorial]

Salvatore, M., Purkayastha, S., Ganapathi, L., Bhattacharyya, R., Kundu, R., Zimmermann, L., Ray, D., Hazra, A., Kleinsasser, M., Solomon, S., Subbaraman, R., and Mukherjee, B. "Lessons from SARS-CoV-2 in India: A data-driven framework for pandemic resilience", Science Advances, 8:eabp8621, 2022. [link] [supp] [code]

Purkayastha, S., Kundu, R., Bhaduri, R., Barker, D., Kleinsasser, M., Ray, D., and Mukherjee, B. “Estimating the wave 1 and wave 2 infection fatality rates from SARS-CoV-2 in India”. BMC Research Notes, 14:262, 2021. [link] [supp] [software]

Babu, G.R., Ray, D., Bhaduri, R., Halder, A., Kundu, R., Menon, G.I., and Mukherjee, B. "COVID-19 pandemic in India: through the lens of modeling''. Global Health: Science and Practice, 9(2), 2021. [link]

Salvatore, M., Bhattacharyya, R., Purkayastha, S., Zimmermann, L., Ray, D., Hazra, A., Kleinsasser, M., Mellan, T., Whittaker, C., Flaxman, S., Bhatt, S., Mishra, S., and Mukherjee, B. “Resurgence of SARS-CoV-2 in India: Potential role of the B.1.617.2 (Delta) variant and delayed interventions”, medRxiv, 2021. [link]

Purkayastha, S., Bhattacharyya, R., Bhaduri, R., Kundu, R., Gu, X., Salvatore, M., Ray, D., Mishra, S., and Mukherjee, B. "A comparison of five epidemiological models for transmission of SARS-CoV-2 in India''.  BMC Infectious Diseases, 21:533, 2021. [link] [supp] [code]

Bhattacharyya, R., Kundu, R., Bhaduri, R., Ray, D., Beesley, L.J., Salvatore, M., and Mukherjee, B. "Incorporating false negative tests in epidemiological models for SARS-CoV-2 transmission and reconciling with seroprevalence estimates''. Scientific Reports, 11:9748, 2021. [link] [supp] [software] [tweetorial]

Ray, D., Bhattacharyya, R., and Mukherjee, B. “Discussion on ‘The timing and effectiveness of implementing mild interventions of COVID-19 in large industrial regions via a synthetic control method’ by Tian et al”. Statistics and Its Interface, 14:25-28, 2021. [link]

^Ray, D., ^Salvatore, M., Bhattacharyya, R., Wang, L., Du, J., Mohammed, S., Purkayastha, S., Halder, A., Rix, A., Barker, D., Kleinsasser, M., Zhou, Y., Song, P., Bose, D., Banerjee, M., Baladandayuthapani, V., Ghosh, P., and Mukherjee, B. “Predictions, role of interventions and effects of a historic national lockdown in India’s response to the COVID-19 pandemic: data science call to arms”. Harvard Data Science Review, DOI 10.1162/99608f92.60e08ed5 [link] [RShiny app]

Salvatore, M., Basu, D., Ray, D., Kleinsasser, M., Purkayastha, S., Bhattacharyya, R., and Mukherjee, B. “Comprehensive public health evaluation of lockdown as a non-pharmaceutical intervention on COVID-19 spread in India: national trends masking state-level variations”. BMJ Open, 10:e041778, 2020. [pdf][RShiny app]

Shet, A., Ray, D., Malavige, N., Santosham, M., and Bar-Zeev, N. “BCG vaccine use within national immunization programs is associated with lower COVID-19-attributable mortality: an ecological analysis”.  medRxiv, 2020. [link] [tweetorial]

Ray, D., Bhattacharyya, R., Wang, L., Salvatore, M., Mohammed, S., Halder, A., Zhou, Y., Song, P., Purkayastha, S., Bose, D., Banerjee, M., Baladandayuthapani, V., Ghosh, P., and Mukherjee, B. "Predictions and role of interventions for COVID-19 outbreak in India". Medium (March 21, 2020). [link]

Salvatore, M., Wang, L., Bhattacharyya, R., Purkayastha, S., Mohammed, S., Halder, A., Barker, D., Kleinsasser, M., Rix, A., Banerjee, M., Baladandayuthapani, V., Ray, D., and Mukherjee, B. "Historic lockdown, prediction models to study lockdown effects and the role of data in the crisis of virus in India". Medium (April 3, 2020) [link]

Salvatore, M., Ray, D., Du, J., Wang, L., Kleinsasser, M., Rix, A., Barker, D., and Mukherjee, B. "Unlocking the 40-day national lockdown in India: There is no magic key". Medium (April 25, 2020) [link]