Spatial Omics and Bioinformatics Lab Department of Biotechnology, IIT Madras

Publications

Highlighted

Open collaborative writing with Manubot
Open collaborative writing with Manubot
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
PLOS Computational Biology  ·  24 Jun 2019  ·  doi:10.1371/journal.pcbi.1007128

Preprints

All

2025

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]
Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling
Characterization of immune cell populations in the tumor microenvironment of colorectal cancer using high definition spatial profiling
Michelli F. Oliveira, Juan P. Romero, Meii Chung, Stephen Williams, Andrew D. Gottscho, …, Syrus Mohabbat, Nandhini Raman, David Sukovich, David Patterson, Sarah E. B. Taylor
openRxiv  ·  05 Jun 2024  ·  doi:10.1101/2024.06.04.597233

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

Mapping the temporal transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq
Mapping the temporal transcriptional landscape of human white and brown adipogenesis using single-nuclei RNA-seq
Anushka Gupta, Farnaz Shamsi, Mary Elizabeth Patti, Yu-Hua Tseng, Aaron Streets
openRxiv  ·  30 May 2022  ·  doi:10.1101/2022.05.30.494007
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
Characterization of transcript enrichment and detection bias in single-nuclei RNA-seq for mapping of distinct human adipocyte lineages
Characterization of transcript enrichment and detection bias in single-nuclei RNA-seq for mapping of distinct human adipocyte lineages
Anushka Gupta, Farnaz Shamsi, Nicolas Altemos, Gabriel F. Dorlhiac, Aaron M. Cypess, Andrew P. White, Mary Elizabeth Patti, Yu-Hua Tseng, Aaron Streets
openRxiv  ·  25 Mar 2021  ·  doi:10.1101/2021.03.24.435852

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

Open collaborative writing with Manubot
Open collaborative writing with Manubot
Daniel S. Himmelstein, Vincent Rubinetti, David R. Slochower, Dongbo Hu, Venkat S. Malladi, Casey S. Greene, Anthony Gitter
PLOS Computational Biology  ·  24 Jun 2019  ·  doi:10.1371/journal.pcbi.1007128
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