Efthymios Motakis

Single-cell decoding of human islet cell type-specific alterations in type 2 diabetes reveals converging genetic- and state-driven β-cell gene expression defects

The paper analyzes single-cell transcriptomes of human islet cells across glycemic states to identify gene expression defects in beta cells associated with type 2 diabetes.

TEAL-seq: Targeted Expression Analysis Sequencing

TEAL-seq enables sensitive, species-specific gene expression analysis in complex microbial communities using highly multiplexed probes and isothermal amplification.

Gene neighbourhood integrity disrupted by CTCF loss in vivo

This study shows that loss of CTCF in mouse cardiomyocytes disrupts gene neighbourhoods, leading to ectopic enhancer-promoter interactions and heart failure.

C1 CAGE detects transcription start sites and enhancer activity at single-cell resolution

C1 CAGE detects transcription start sites and enhancer activity in lung cancer cells, revealing subpopulations with distinct responses to TGF-β and enhancer RNA dynamics.

CONFESS: Fluorescence-based single-cell ordering in R

CONFESS is a method for analyzing fluorescence images from the Fluidigm C1 system to infer cell cycle progression, integrating with RNA-seq data for deeper biological insights.

Single-cell transcriptomes of fluorescent, ubiquitination-based cell cycle indicator cells

The paper generates a single-cell RNA-seq dataset of HeLa cells labeled with Fucci reporters and provides an open workflow for data processing and quality control.