Spatial Omics and Bioinformatics Lab Department of Biotechnology, IIT Madras
Centre for Integrative Biology and Systems Medicine (IBSE), IIT Madras

Publications

Our published journal/conference papers, book chapters and granted patents are tabulated below.

Highlighted

High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer
High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer
Michelli Faria de Oliveira, Juan Pablo Romero, Meii Chung, Stephen R. Williams, Andrew D. Gottscho, …, Juan Pablo Romero, Stephen R. Williams, David M. Patterson, Sarah E. B. Taylor, Sarah E. B. Taylor
Nature Genetics  ·  01 Jun 2025  ·  doi:10.1038/s41588-025-02193-3
Mapping the transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq
Mapping the transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq
Anushka Gupta, Vissarion Efthymiou, Sean D. Kodani, Farnaz Shamsi, Mary Elizabeth Patti, Yu-Hua Tseng, Aaron Streets
Molecular Metabolism  ·  01 Aug 2023  ·  doi:10.1016/j.molmet.2023.101746
Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
Anushka Gupta, Farnaz Shamsi, Nicolas Altemose, Gabriel F. Dorlhiac, Aaron M. Cypess, Andrew P. White, Nir Yosef, Mary Elizabeth Patti, Yu-Hua Tseng, Aaron Streets
Genome Research  ·  18 Jan 2022  ·  doi:10.1101/gr.275509.121

Preprints

Single-Nucleus Analysis of Human White Adipose Tissue Reveals Adipocyte Subsets with Distinct Metabolic Profiles
Single-Nucleus Analysis of Human White Adipose Tissue Reveals Adipocyte Subsets with Distinct Metabolic Profiles
Vissarion Efthymiou, Adhideb Ghosh, Sean D. Kodani, Xavier Caubit, Laurent Fasano, …, Farnaz Shamsi, Ashley Vernon, Aaron Streets, Yu-Hua Tseng, Mary Elizabeth Patti
openRxiv  ·  16 Sep 2025  ·  doi:10.1101/2025.09.14.673351

All

2025

Single-Nucleus Analysis of Human White Adipose Tissue Reveals Adipocyte Subsets with Distinct Metabolic Profiles
Single-Nucleus Analysis of Human White Adipose Tissue Reveals Adipocyte Subsets with Distinct Metabolic Profiles
Vissarion Efthymiou, Adhideb Ghosh, Sean D. Kodani, Xavier Caubit, Laurent Fasano, …, Farnaz Shamsi, Ashley Vernon, Aaron Streets, Yu-Hua Tseng, Mary Elizabeth Patti
openRxiv  ·  16 Sep 2025  ·  doi:10.1101/2025.09.14.673351
High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer
High-definition spatial transcriptomic profiling of immune cell populations in colorectal cancer
Michelli Faria de Oliveira, Juan Pablo Romero, Meii Chung, Stephen R. Williams, Andrew D. Gottscho, …, Juan Pablo Romero, Stephen R. Williams, David M. Patterson, Sarah E. B. Taylor, Sarah E. B. Taylor
Nature Genetics  ·  01 Jun 2025  ·  doi:10.1038/s41588-025-02193-3

2024

Ceria-Based Nanocrystalline Oxide Catalysts: Synthesis, Characterization, and Applications
Ceria-Based Nanocrystalline Oxide Catalysts: Synthesis, Characterization, and Applications
Nanomaterials  ·  01 Dec 2024  ·  [no id info]

2023

Mapping the transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq
Mapping the transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq
Anushka Gupta, Vissarion Efthymiou, Sean D. Kodani, Farnaz Shamsi, Mary Elizabeth Patti, Yu-Hua Tseng, Aaron Streets
Molecular Metabolism  ·  01 Aug 2023  ·  doi:10.1016/j.molmet.2023.101746

2022

Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
Characterization of transcript enrichment and detection bias in single-nucleus RNA-seq for mapping of distinct human adipocyte lineages
Anushka Gupta, Farnaz Shamsi, Nicolas Altemose, Gabriel F. Dorlhiac, Aaron M. Cypess, Andrew P. White, Nir Yosef, Mary Elizabeth Patti, Yu-Hua Tseng, Aaron Streets
Genome Research  ·  18 Jan 2022  ·  doi:10.1101/gr.275509.121

2021

Vascular smooth muscle-derived Trpv1 progenitors are a source of cold-induced thermogenic adipocytes
Vascular smooth muscle-derived Trpv1+ progenitors are a source of cold-induced thermogenic adipocytes
Farnaz Shamsi, Mary Piper, Li-Lun Ho, Tian Lian Huang, Anushka Gupta, Aaron Streets, Matthew D. Lynes, Yu-Hua Tseng
Nature Metabolism  ·  12 Apr 2021  ·  doi:10.1038/s42255-021-00373-z

2020

μCB-seq: microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells
μCB-seq: microfluidic cell barcoding and sequencing for high-resolution imaging and sequencing of single cells
Tyler N. Chen, Anushka Gupta, Mansi D. Zalavadia, Aaron Streets
Lab on a Chip  ·  01 Jan 2020  ·  doi:10.1039/D0LC00169D

2019

Quantitative imaging of lipid droplets in single cells
Quantitative imaging of lipid droplets in single cells
Anushka Gupta, Gabriel F. Dorlhiac, Aaron M. Streets
The Analyst  ·  01 Jan 2019  ·  doi:10.1039/C8AN01525B

2016

Digital microfluidic platform for dielectrophoretic patterning of cells encapsulated in hydrogel droplets
Digital microfluidic platform for dielectrophoretic patterning of cells encapsulated in hydrogel droplets
B. A. Nestor, E. Samiei, R. Samanipour, A. Gupta, A. Van den Berg, M. Diaz de Leon Derby, Z. Wang, H. Rezaei Nejad, K. Kim, M. Hoorfar
RSC Advances  ·  01 Jan 2016  ·  doi:10.1039/c6ra10412f