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Chirag Lakhani

Research Scientist
New York Genome Center
clakhani (at) nygenome.org


About Me

I am a Senior Research Scientist in the Knowles Lab at the New York Genome Center where I am broadly interested in utilizing genomic deep learning models to better understand Alzheimer’s disease genetics. I am an active member of the Artificial Intelligence/Machine Learning working group within the NIH Alzheimer’s Disease Sequencing Project Consortium, where I work with the broader community to elucidate the functional mechanism of common and rare AD risk variants.

Research Interests

Publications

  1. Mosaic chromosomal alterations in blood are associated with an increased risk of Alzheimer's disease
    Tatsuhiko Naito, Kosei Hirata, Beomjin Jang, Chirag M. Lakhani, Alice Buonfiglioli, Wan-Ping Lee, Otto Valladares, Li-San Wang, Yukinori Okada, Hong-Hee Won, et al.
    medRxiv, 2025
    Link

  2. Integration of Deep Learning Annotations with Functional Genomics Improves Identification of Causal Alzheimer's Disease Variants
    Chirag M. Lakhani, Jui-Shan T. Lin, Anjali Das, Tatsuhiko Naito, Towfique Raj, David A. Knowles
    medRxiv, 2025
    Link

  3. Leveraging functional annotations to map rare variants associated with Alzheimer's disease with gruyere
    Anjali Das, Chirag Lakhani, Chloé Terwagne, Jui-Shan T. Lin, Tatsuhiko Naito, Towfique Raj, David A. Knowles
    medRxiv, 2025
    Link

  4. LDmat: efficiently queryable compression of linkage disequilibrium matrices
    Rockwell J. Weiner, Chirag Lakhani, David A. Knowles, Gamze Gürsoy
    Bioinformatics, vol. 39, no. 2, pp. btad092, 2023
    Link Code Project Page

  5. Association and interaction of genetics and area-level socioeconomic factors on the prevalence of type 2 diabetes and obesity
    Sara J. Cromer, Chirag M. Lakhani, Josep M. Mercader, Timothy D. Majarian, Philip Schroeder, Joanne B. Cole, Jose C. Florez, Chirag J. Patel, Alisa K. Manning, Sherri-Ann M. Burnett-Bowie, et al.
    Diabetes Care, vol. 46, no. 5, pp. 944-952, 2023
    Link

  6. A new method for estimating the probability of causal relationships from observational data: Application to the study of the short-term effects of air pollution on cardiovascular and respiratory disease
    Bryan Andrews, Chirayu Wongchokprasitti, Shyam Visweswaran, Chirag M. Lakhani, Chirag J. Patel, Gregory F. Cooper
    Artificial intelligence in medicine, vol. 139, pp. 102546, 2023
    Link

  7. The impact of socioeconomic status on subsequent neurological outcomes in multiple sclerosis
    Devi Sai Sri Kavya Boorgu, Shruthi Venkatesh, Chirag M. Lakhani, Elizabeth Walker, Ines M. Aguerre, Claire Riley, Chirag J. Patel, Philip L. De Jager, Zongqi Xia
    Multiple sclerosis and related disorders, vol. 65, pp. 103994, 2022
    Link

  8. Identifying communities at risk for COVID-19--related burden across 500 US cities and within New York City: unsupervised learning of the coprevalence of health indicators
    Andrew Deonarine, Genevieve Lyons, Chirag Lakhani, Walter De Brouwer
    JMIR Public Health and Surveillance, vol. 7, no. 8, pp. e26604, 2021
    Link

  9. Comparisons of polyexposure, polygenic, and clinical risk scores in risk prediction of type 2 diabetes
    Yixuan He, Chirag M. Lakhani, Danielle Rasooly, Arjun K. Manrai, Ioanna Tzoulaki, Chirag J. Patel
    Diabetes Care, vol. 44, no. 4, pp. 935-943, 2021
    Link

  10. Geospatial analysis of individual and community-level socioeconomic factors impacting SARS-CoV-2 prevalence and outcomes
    Sara J. Cromer, Chirag M. Lakhani, Deborah J. Wexler, Sherri-Ann M. Burnett-Bowie, Miriam Udler, Chirag J. Patel
    MedRxiv, 2020
    Link

  11. Repurposing large health insurance claims data to estimate genetic and environmental contributions in 560 phenotypes
    Chirag M. Lakhani, Braden T. Tierney, Arjun K. Manrai, Jian Yang, Peter M. Visscher, Chirag J. Patel
    Nature genetics, vol. 51, no. 2, pp. 327-334, 2019
    Link Code Project Page Press Coverage: Washington Post | The Verge | CNN | Axios | Harvard Magazine | NIEHS Environmental Factor

  12. The GIT compactification of quintic threefolds
    Chirag Lakhani
    arXiv preprint arXiv:1010.3803, 2010
    Link


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