Francis S. Collins

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.

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.

Donor-matched iPSC model reveals context-dependent T2D genetic signals in fibro-adipogenic progenitors

The paper uses donor-matched iPSC-derived FAPs to show that T2D GWAS signals are enriched in adipogenic FAP subtypes under high-insulin exposure.

Scalable Hypothalamic Arcuate Neuron Differentiation from Human Pluripotent Stem Cells Suitable for Modeling Metabolic and Reproductive Disorders

This paper describes a scalable method to differentiate human pluripotent stem cells into hypothalamic arcuate neurons, which can model metabolic and reproductive disorders.

Genetics of growth rate in induced pluripotent stem cells

The paper identifies genetic factors influencing iPSC growth rates, finding rare variants in WDR54 and a polygenic background explaining most variance.

Associations of Combined Genetic and Lifestyle Risks with Incident Type 2 Diabetes in the UK Biobank

This study examines how genetic and lifestyle factors together influence the risk of developing type 2 diabetes in the UK Biobank population.

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.

Detecting Protein-DNA Binding in Single Molecules using Antibody Guided Methylation

The paper introduces a method to detect protein-DNA binding in single molecules using antibody-guided methylation, generating identifiable methylation patterns near binding sites.

Direct RNA nanopore sequencing reveals rapid RNA modification changes following glucose stimulation of human pancreatic beta-cell lines

The paper uses direct RNA nanopore sequencing to identify RNA modification changes in human pancreatic beta-cells after glucose stimulation, finding 1,697 differentially modified sites linked to type 2 diabetes genes.

Single-cell transcriptomic profiling of human pancreatic islets reveals genes responsive to glucose exposure over 24 hours

This study uses single-cell RNA sequencing to analyze gene expression changes in human pancreatic islets under different glucose conditions over 24 hours, identifying genes and modules associated with time, glucose exposure, and their interaction.

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.

Adipose tissue eQTL meta-analysis reveals the contribution of allelic heterogeneity to gene expression regulation and cardiometabolic traits

The paper identifies additional eQTL signals in adipose tissue and shows they contribute to cardiometabolic traits through gene dosage effects.

Functional interrogation of twenty type 2 diabetesassociated genes using isogenic hESC-derived β-like cells

This study functionally interrogates 20 T2D-associated genes using isogenic hESC-derived β-like cells, identifying variants and genes linked to insulin production and lipotoxicity sensitivity.

Modeling islet enhancers using deep learning identifies candidate causal variants at loci associated with T2D and glycemic traits.

Human pancreatic islet microRNAs implicated in diabetes and related traits by large-scale genetic analysis

This paper identifies miRNAs associated with type 2 diabetes and glycemic traits through genetic analysis of miRNA expression in human pancreatic islets.

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.

ACE2 expression in adipose tissue is associated with COVID-19 cardio-metabolic risk factors and cell type composition

The paper examines the association between adipose tissue ACE2 expression and cardio-metabolic risk factors, finding lower ACE2 levels linked to T2D, obesity, and inflammation-related cell type changes.

Genome-wide association study of 1,391 plasma metabolites in 6,136 Finnish men identifies 303 novel signals and provides biological insights into human diseases

This study identifies 303 novel genetic signals associated with plasma metabolites in Finnish men, revealing biological insights into disease mechanisms.

A transcription start site map in human pancreatic islets reveals functional regulatory signatures

The paper maps transcription start sites in human pancreatic islets and identifies functional regulatory elements linked to type 2 diabetes GWAS signals.

Influence of genetic variants on gene expression in human pancreatic islets - implications for type 2 diabetes

The paper investigates how genetic variants affect gene expression in human pancreatic islets and identifies candidate genes linked to type 2 diabetes.

Single cell ATAC-seq in human pancreatic islets and deep learning upscaling of rare cells reveals cell-specific type 2 diabetes regulatory signatures

The paper uses single-cell ATAC-seq and deep learning to analyze pancreatic islet cells, revealing cell-specific regulatory signatures linked to type 2 diabetes.

A Novel Type 2 Diabetes Locus in sub-Saharan Africans, ZRANB3, is Implicated in Beta Cell Proliferation

The paper identifies a novel type 2 diabetes locus, ZRANB3, in sub-Saharan Africans and shows its potential role in beta cell proliferation through zebrafish studies.

PROTEIN-CODING VARIANTS IMPLICATE NOVEL GENES RELATED TO LIPID HOMEOSTASIS CONTRIBUTING TO BODY FAT DISTRIBUTION

This study identifies 15 common and 9 low-frequency protein-coding variants associated with body fat distribution, implicating novel genes related to lipid homeostasis and type 2 diabetes.

EndoC-βH1 multi-genomic profiling defines gene regulatory programs governing human pancreatic β cell identity and function

The paper provides multi-genomic maps of the EndoC-βH1 cell model to define gene regulatory programs in human pancreatic β cells and identifies allelic effects on cis-regulatory elements.

Genetic discovery and translational decision support from exome sequencing of 20,791 type 2 diabetes cases and 24,440 controls from five ancestries

This study identifies rare genetic variants associated with type 2 diabetes using exome sequencing of 20,791 cases and 24,440 controls, and provides a Bayesian framework to improve variant prioritization.

BoostMe accurately predicts DNA methylation values in whole-genome bisulfite sequencing of multiple human tissues

BoostMe improves DNA methylation imputation in WGBS data, enhancing concordance with the MethylationEPIC array and identifying tissue-specific regulatory features.

Interactions between genetic variation and cellular environment in skeletal muscle gene expression

The paper identifies genetic-environment interactions in skeletal muscle gene expression using allele-specific expression and clinical traits as environmental proxies.

Narrow-sense heritability estimation of complex traits using identity-by-descent information.

This paper estimates narrow-sense heritability using identity-by-descent information in unrelated individuals and finds that IBD-based methods can capture rare variant contributions but are affected by stratification.

Fine-mapping of an expanded set of type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps

This study fine-maps type 2 diabetes loci to single-variant resolution using high-density imputation and islet-specific epigenome maps, identifying 73 variants with >80% posterior probability of association.