G. V. Shivashankar

Partially Shared Multi-Modal Embedding Learns Holistic Representation of Cell State

APOLLO learns shared and modality-specific information from multi-modal single-cell data to improve understanding of cell state and regulatory mechanisms.

Identifying regulators of aged fibroblast activation in 3D tissue models

This study identifies three master regulators of aged fibroblast activation using 3D tissue models and pharmacological inhibitors.

Acute chromatin decompaction stiffens the nucleus as revealed by nanopillar-induced nuclear deformation in cells

The paper shows that acute chromatin decompaction increases nuclear stiffness in some cells but not others, depending on their ability to recompact chromatin.

Compressive forces induce epigenetic activation of aged human dermal fibroblasts through ERK signalling pathway

This study shows compressive forces rejuvenate aged human dermal fibroblasts via ERK signaling, inducing epigenetic changes and increased collagen I.

Multi-Domain Translation between Single-Cell Imaging and Sequencing Data using Autoencoders

This paper introduces an autoencoder-based method to integrate single-cell imaging and sequencing data, identifying sub-populations of human naive CD4+ T-cells.

Autoencoder and Optimal Transport to Infer Single-Cell Trajectories of Biological Processes

This paper introduces ImageAEOT, a method combining autoencoders and optimal transport to infer single-cell trajectories from imaging data, validated on chromatin images of cancer cells and tissues.