Suresh Kumar Poovathingal

A subtype-specific gene regulatory program controls differential circuit integration of deep CA3 pyramidal neurons

The paper identifies ST18 as a regulator of deep CA3 pyramidal neuron identity, showing its role in restricting a superficial-like program and shaping circuit integration through molecular and electrophysiological changes.

Multimodal profiling and intersectional genetics reveal CA1 border inhibitory neuron diversity and postnatal emergence of retrosplenial connectivity

The paper identifies molecular and developmental diversity in CA1 border inhibitory neurons and shows their postnatal emergence of retrosplenial connectivity.

SWI/SNF-Dependent Chromatin Remodelling Establishes Gene Regulatory Programs in Early Human Embryos and Blastoids

This study shows that SWI/SNF chromatin remodellers are critical for lineage specification in human embryos and blastoids by regulating enhancer accessibility and transcription factor binding.

Unique transcriptional profiles of adult human immature neurons in healthy aging, Alzheimer's disease, and cognitive resilience

The paper identifies unique transcriptional profiles of immature neurons in aged human hippocampus across healthy, Alzheimer's disease, and resilient conditions, linking them to homeostasis and cognitive resilience.

Human Myelin Spheres for In Vitro Oligodendrocyte Maturation, Myelination and Neurological Disease Modeling

This paper introduces human myelin spheres (MyS) as a model for studying myelination and demyelination, showing their ability to form myelinated neurons and mimic in vivo oligodendrocyte development.

HyDrop v2: Scalable atlas construction for training sequence-to-function models

The paper introduces HyDrop v2, a microfluidic system for generating large scATAC-seq atlases, and shows its data is comparable to commercial platforms for training sequence-to-function models.

A dynamic gene regulatory code drives synaptic development of hippocampal granule cells

The paper identifies a dynamic gene regulatory code in hippocampal granule cells that orchestrates synapse development through sequential regulation of transcription factors and target genes.

Synaptic deregulation of cholinergic projection neurons causes olfactory dysfunction across 5 fly Parkinsonism models

The paper identifies synaptic dysfunction in cholinergic projection neurons as an early indicator of Parkinsonism across multiple fly models and links it to olfactory dysfunction and dopaminergic decline.

Enhancer-driven cell type comparison reveals similarities between the mammalian and bird pallium

The paper compares enhancer codes of cell types between mammalian neocortex and avian pallium using deep learning, finding higher divergence in excitatory neurons than other cell types.

Nova-ST: Nano-Patterned Ultra-Dense platform for spatial transcriptomics

Nova-ST is a cost-effective, high-resolution spatial transcriptomics platform that outperforms existing methods in sensitivity for mouse brain sections.

Traumatic brain injury modifies adult hippocampal neural stem cell fate to promote neurogenesis at the cost of astrogliogenesis.

This study shows that traumatic brain injury shifts adult hippocampal neural stem cell fate toward neurogenesis and away from astrogliogenesis, using single-cell RNA sequencing and spatial transcriptomics.

A multi-pronged human microglia response to Alzheimer's disease Aβ pathology

This study identifies distinct microglial responses to amyloid-beta in AD using single-cell data, highlighting HLA-related and cytokine responses and their genetic modulation.

Unravelling cell type specific response to Parkinson's Disease at single cell resolution

The paper analyzes single-cell transcriptomics data from Parkinson's Disease patients and controls to identify cell type-specific molecular responses and pathways involved in neurodegeneration.

The microcephaly gene ASPM is required for the timely generation of human outer-radial glia progenitors by controlling mitotic spindle orientation

This study shows ASPM mutations disrupt mitotic spindle orientation in human cortical progenitors, leading to premature oRGC generation and reduced cortical progenitor numbers.

SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

SCENIC+ infers enhancer-driven gene regulatory networks from single-cell multi-omics data, improving TF identification and enabling analysis of regulatory dynamics and perturbations.

Molecular and cognitive signatures of ageing partially restored through synthetic delivery of IL2 to the brain

This study shows that delivering IL2 to the brain in aging mice partially restores molecular signatures of aging and improves spatial learning.

Neuronal identity defines a-synuclein and tau toxicity

The paper identifies molecular signatures of neuronal vulnerability to α-synuclein and tau toxicity, showing differential susceptibility independent of expression levels.

Single-nucleus co-expression networks of dopaminergic neurons support iron accumulation as a plausible explanation to their vulnerability in Parkinson's disease

The paper introduces scCoExpNets and CovCoExpNets to analyze cell-type specific gene co-expression networks from single-cell RNA-seq data, identifying iron accumulation as a factor in dopaminergic neuron vulnerability in Parkinson's disease.

Enhancer grammar of liver cell types and hepatocyte zonation states

The paper maps enhancer gene regulatory networks (GRNs) in liver cell types and identifies TFs governing hepatocyte zonation states using multiomics and deep learning.

Cell type diversity in a developing octopus brain

The paper profiles cell diversity in the paralarval octopus brain to create a cell type atlas and identifies molecular similarities between octopus and fly glial cells.

Hexanucleotide repeat expansions in C9orf72 alter microglial responses and prevent a coordinated glial reaction in ALS

This study shows that C9orf72 hexanucleotide repeat expansions impair microglial function and disrupt glial communication in ALS, contributing to disease risk.

HyDrop: droplet-based scATAC-seq and scRNA-seq using dissolvable hydrogel beads

HyDrop is a droplet microfluidic platform for scATAC-seq and scRNA-seq that improves throughput and sensitivity while reducing cost.

Comparative analysis of antibody- and lipid-based multiplexing methods for single-cell RNA-seq

This study compares antibody- and lipid-based hashing methods for single-cell RNA-seq, finding antibody-based hashing more efficient and cost-effective for clinical samples.

Species-specific mitochondria dynamics and metabolism regulate the timing of neuronal development

This study shows that slower mitochondrial development and lower metabolic activity in human cortical neurons compared to mice delay neuronal maturation, and stimulating mitochondria accelerates this process.

Melanin Concentrating Hormone- and sleep-dependent synaptic downscaling is impaired in Alzheimer's Disease

This study identifies impaired MCH-system function in AD models and patients, disrupting synaptic downscaling and neuronal activity stability.

Identification of genomic enhancers through spatial integration of single-cell transcriptomics and epigenomics

The paper spatially integrates single-cell transcriptomics and epigenomics data to identify enhancers and gene regulatory relationships in Drosophila eye-antennal disc.

Xenotransplanted human cortical neurons reveal species-specific development and functional integration into mouse visual circuits.

This study transplants human cortical neurons into mice to study their development and integration into mouse visual circuits, finding prolonged juvenile features and functional synaptic integration.

Stem cell derived human microglia transplanted in mouse brain to study genetic risk of Alzheimer's Disease

The paper demonstrates that human microglia derived from embryonic stem cells can engraft mouse brains and express Alzheimer's risk genes when exposed to Aβ, offering a new model to study genetic risk in AD.

Single-cell gene regulatory network analysis reveals new melanoma cell states and transition trajectories during phenotype switching

The paper identifies an intermediate cell state in melanoma through single-cell RNA-seq and ATAC-seq, revealing a gene regulatory network that governs phenotype switching and potential therapeutic targets.

A single-cell catalogue of regulatory states in the ageing Drosophila brain

This study creates a single-cell transcriptome catalogue of the Drosophila brain across its lifespan, revealing regulatory erosion and identifying novel neuronal states linked to ageing.