Ayshwarya Subramanian

Dr. Subramanian is an assistant professor at the Department of Molecular Biology and Genetics in the College of Arts and Sciences, Cornell University.  She is a member of the Englander Institute for Precision Medicine (EIPM) and The Jill Roberts Institute for Research in Inflammatory Bowel Disease at Weill-Cornell Medicine. Dr. Subramanian received her undergraduate degree from the Birla Institute of Technology and Science (BITS-Pilani), India and Ph.D from Carnegie Mellon University. After completing her postdoctoral studies at the Broad Institute and the Harvard Chan School of Public Health, she joined Cornell University as faculty in 2024.

Research focus: Dr. Subramanian’s research focuses on understanding the principles governing cellular heterogeneity, crosstalk, and evolution in the context of human tissues and disease. Her interdisciplinary research program operates at the nexus of high-throughput data measurements, development and application of computational methods, and experimental design, with key collaborations for clinical samples, and mechanistic validations in vivo and in situ.

Selected Publications:

1. Kimura K†, Subramanian A†, Yin Z†, …, Butovsky O*, Kuchroo V.* Immune checkpoint TIM‑3 regulates microglia and Alzheimer’s disease. Nature. 2025.

2. Mangani D, Subramanian A‡, Huang L‡, …, Kuchroo V, Anderson A. Transcription factor TCF1 binds to RORγt and orchestrates a regulatory network that determines the homeostatic Th17 cell state. Immunity. 2024.

3. Subramanian A†,*, Vernon K†, Zhou Y† et al. Protective role for kidney TREM2high macrophages in obesity- and diabetes-induced kidney injury. Cell Reports. 2024 June 25.
4. Wilder A†, Supple M†, Subramanian A et al. Historical processes shape contemporary extinction risk in placental mammals. Science. 2023 Apr 28.
5. Subramanian A†,*, Alperovich M†,^, Yang Y and Li Bo. Biology-inspired data-driven quality control for scientific discovery in single-cell transcriptomics. Genome Biology. 2022 Dec 27.
6. Eraslan G† , Drokhlyansky E†, Anand S‡, Fiskin E‡, Subramanian A‡, et al. Single-nucleus cross-tissue molecular reference maps to decipher disease gene function. Science 2022 May 13.
7. Tang R, Acharya N, Subramanian A, et al. Tim-3 adapter protein Bat3 acts as an endogenous regulator of tolerogenic dendritic cell function. Science Immunology. 2022 Mar 11.
8. Delorey TM†, Ziegler CGK†, Heimberg G†, Normand R†, Yang Y†, Segerstolpe A†, Abbondanza D†, Fleming SJ†, Subramanian A†, et al. COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets. Nature. 2021 Apr 29.
9. Muus C†, Luecken MD†, Eraslan G†, Sikkema L†, Waghray A†, Heimberg G†, Kobayashi Y†, Vaishnav ED†, Subramanian A†, et al. Single-cell meta-analysis of SARS-CoV-2 entry genes across tissues and demographics. Nature Medicine. 2021 Mar.
10. Subramanian A†, Sidhom EH†, Emani M†, et al. Single cell census of human kidney organoids shows reproducibility and diminished off-target cells after transplantation. Nature Comm. 2019.
11. Subramanian A and Schwartz R. Reference-free inference of tumor phylogenies from single-cell sequencing data. BMC Genomics. 2015;16 Suppl 11:S7.
12. Subramanian A, Shackney S, Schwartz R. Novel multi-sample scheme for inferring phylogenetic markers from whole genome tumor profiles. IEEE/ACM Trans Comput Biol Bioinform. 2013.
13. Subramanian A, Shackney S, Schwartz R. Inference of tumor phylogenies from genomic assays on heterogeneous samples. J Biomed Biotechnol. 2012.