Publications

Nazeen S, Wang X, Morrow AR, …, Khurana V, Sunyaev SR. NERINE reveals rare variant associations in gene networks in multiple phenotypes and implicates an SNCA-PRL-LRRK2 subnetwork in Parkinson’s disease. Cell Genomics 2026, 6 (7). Featured on the journal cover.

Kar P, Moldovan M, Guez J, Nazeen S, Goodrich JK, Karani T, Samocha KE, Karczewski K, Koch E, Seplyarskiy V, Sunyaev SR. Inference of elevated mutation rates and variant effects using 700k exomes. bioRxiv 2026. Under review at Science.

Murdock DR, Guo D, Guan P, Bermudez F, DePaolo J, Cabot J, Nazeen S, Nasir H, Gupta RM, Jha A, Elefteriades J, McGivern B, Anderson SK, Jones C, Damrauer S, Chen H, Milewicz DM. Gene-based, Rare Variant Burden Analyses of Biobank Data Reveal Novel Genes Conferring a High Risk for Thoracic Aortic Disease. bioRxiv 2026. Under review at Circulation.

Mitchel J, Nazeen S, Wang X, …, Kharchenko PV, Sunyaev SR. A single-cell genetic colocalization test improves power and resolves disease-mediating cell types. bioRxiv 2025. Under review at Nature Genetics.

Noori A, Polonuer J, Meyer K, Budnik B, Morton S, Wang X, Nazeen S, He Y, Arango I, Vittor L, Woodworth M, Krolewski R, Li M, Liu N, Kamath T, Macosko E, Rodriques S, Dagan N, Das S, Church G, Tam J, Khurana V, Zitnik M. Graph AI generates neurological hypotheses validated in molecular, organoid, and clinical systems. arXiv 2025.

Nazeen S^†, Wang X^†, Zielinski D^†, Lam I, Hallacli E, Xu P, …, Sunyaev SR, Khurana V. Deep sequencing of proteotoxicity modifier genes uncovers a Presenilin-2/beta-amyloid-actin genetic risk module shared among alpha-synucleinopathies. bioRxiv 2024. [†: equal contributions]

Bendapudi P, Nazeen S, Ryu J, Söylemez O, …, Maas R, Sunyaev SR, Losman JA. Low-frequency inherited complement receptor variants are associated with purpura fulminans. Blood 2024, 143 (11): 1032–1044.

Connally N, Nazeen S, Lee D, Shi H, Stamatoyannopoulos J, Chun S, Cotsapas C, Cassa C, Sunyaev S. The missing link between genetic association and regulatory function. eLife 2023, 11: e74970.

Hallacli E, Kayatekin C, Nazeen S, Wang X, Sheinkopf Z, Sathyakumar S, Sarkar S, Jiang X, Dong X, DiMaio R, Wang W, Keeney M, Felsky D, Sandoe J, Vahdatshoar A, Udeshi N, Mani DR, Carr S, Lindquist S, Jager P, Myers C, Bartel D, Greenamyre T, Feany M, Sunyaev SR, Chung CY, Khurana V. The Parkinson’s disease protein alpha-synuclein is a direct modulator of RNA processing-bodies and mRNA stability. Cell 2022, 185(12): 2035–2056.e33.

Nazeen S, Yu YW, Berger B. Carnelian uncovers hidden functional patterns across diverse study populations from whole metagenome sequencing reads. Genome Biology 2020, 21(1): 47.

Nazeen S^†, Palmer NP^†, Berger B, Kohane IS. Integrative analysis of genetic datasets reveals a shared innate immune component in autism spectrum disorder and its co-morbidities. Genome Biology 2016, 17(1): 228. [†: equal contributions]

Moosa TM, Nazeen S^†, Rahman SM, Reaz R^†. Inferring Strings from Cover Arrays. Discrete Mathematics, Algorithms and Applications 2013, 5(02): 1360005. Author names are in alphabetical order. [†: equal contributions]

Nazeen S^†, Rahman MS, Reaz R^†. Indeterminate String Inference Algorithms. Journal of Discrete Algorithms 2012, 10: 23–34. Author names are in alphabetical order. [†: equal contributions]

Uncovering novel disease mechanisms through network-aware rare variant testing with NERINE. Poster presentation at ASHG 2025: American Society of Human Genetics annual meeting (Statistical Genetics and Genetic Epidemiology track), Boston, MA, USA.

Latent structure modeling of genetic heterogeneity in complex diseases. Poster presentation at the Gordon Research Conference: Human Genetics and Genomics, University of Southern Maine, ME, USA.

NERINE: Network-based association test for rare variants in complex traits and diseases. Selected abstract for full-length talk at ESHG 2024: European Human Genetics Conference (Machine Learning and Statistics session), Berlin, Germany.

Carnelian: enhanced functional profiling of metagenomic reads. Selected abstract for full-length talk at the 17th European Conference on Computational Biology (ECCB 2018), Applications Track, Athens, Greece.

LAPRAS: An integrative model incorporating heterogeneous datasets to discover genetic etiology of autism spectrum disorder. Selected abstract for short oral presentation and poster presentation at the 23rd Annual International Conference on Intelligent Systems for Molecular Biology and 14th European Conference on Computational Biology (ISMB/ECCB 2015), Dublin, Ireland.

Integrative Analysis of Multiple Gene Expression Studies Reveals Genes and Pathways involved in Alteration of Steroidogenesis in Polycystic Ovary Syndrome (PCOS). Poster presentation at the 13th European Conference on Computational Biology (ECCB 2014), Strasbourg, France.

Moosa TM, Nazeen S^†, Rahman MS, Reaz R^†. Linear Time Inference of Strings from Cover Arrays using a Binary Alphabet. In Md. S. Rahman and S.-i. Nakano (eds.), Proceedings of WALCOM 2012. LNCS 7157: 160–172. Springer, Heidelberg. Peer-reviewed; author names are in alphabetical order. [†: equal contributions]

Linear Time Inference of Strings from Cover Arrays using a Binary Alphabet. Selected abstract for full-length talk at the 6th International Workshop on Algorithm and Computation (WALCOM 2012), Dhaka, Bangladesh.

Nazeen S. Computational methods for functional interpretation of diverse omics data. Ph.D. Thesis. Massachusetts Institute of Technology.

Nazeen S. Integrative analysis of heterogeneous genomic datasets to discover genetic etiology of autism spectrum disorders. S.M. Thesis. Massachusetts Institute of Technology.

Nazeen S, Reaz R. Indeterminate string inference algorithms. B.Sc. Engg. Thesis. Bangladesh University of Engineering and Technology.