Nandini Manickam

Genetic integration with cell-specific nucleosome positioning resolves causal relationships underlying chromatin accessibility profiles

The paper maps cell type-specific genetic effects on nucleosome-free regions and nucleosome occupancy using snATAC-seq data from human muscle biopsies, showing causal relationships between these elements and GWAS traits.

Single-nucleus multi-omics reveals reversible molecular signatures in skeletal muscle of patients with heart failure with preserved ejection fraction

The paper uses single-nucleus multi-omics to study skeletal muscle changes in HFpEF patients and shows some molecular changes are reversible with lifestyle interventions.

Erosion of regenerative regulation: age-associated shifts in the skeletal muscle fiber epigenome and transcriptome

The paper identifies age-associated changes in the skeletal muscle epigenome and transcriptome, revealing shifts in chromatin accessibility and gene expression linked to metabolic and senescence pathways.

Integrated Analysis of Skeletal Muscle Transcriptional Networks Characterizes Dysregulation in Pathways and Trait-Associated Regulatory Regions in Type 2 Diabetes

The paper identifies dysregulated pathways and candidate driver genes in skeletal muscle from individuals with type 2 diabetes using co-expression networks and single-nucleus RNA-seq data.

Genetic demultiplexing and transcript start site identification from nanopore sequencing of 10x Genomics multiome libraries

This study demonstrates nanopore sequencing of 10x Genomics multiome libraries to capture full-length transcripts and identify TSS, showing concordance with short-read methods despite higher error rates.

Inverse directions of association of higher physical activity and higher insulin resistance with human skeletal muscle cell type abundance and fiber type-level gene expression

The paper examines how physical activity and insulin resistance relate to skeletal muscle cell type abundance and gene expression in humans, finding inverse associations with specific cell types and gene expression patterns.

Skeletal muscle enhancer programming of intrinsic cardiorespiratory fitness

The paper identifies enhancer architecture differences in skeletal muscle between high and low cardiorespiratory fitness rats, linking them to gene expression and metabolic traits.

Population-scale skeletal muscle single-nucleus multi-omic profiling reveals extensive context specific genetic regulation

The paper performs population-scale single-nucleus multi-omic profiling of skeletal muscle to identify genetic regulation across cell types and traits.

Single-cell gene expression and chromatin accessibility profiling of human pancreatic islets at basal and stimulatory conditions nominates mechanisms of type 1 diabetes genetic risk

This study integrates single-cell gene expression and chromatin accessibility data from human pancreatic islets to identify T1D risk mechanisms involving multiple cell types and genetic variants.

Human and rat skeletal muscle single-nuclei multi-omic integrative analyses nominate causal cell types, regulatory elements, and SNPs for complex traits

The paper integrates snATAC-seq and snRNA-seq data from human and rat skeletal muscle to identify cell types, regulatory elements, and SNPs associated with complex traits.