A categorization of spatial transcriptomics methods for cell–cell communication analysis
Comparing machine learning methods predicting transcriptome from epigenome with applications to association studies
Abstract Understanding how epigenome variation contributes to gene expression in disease and development is a fundamental challenge. Regulatory regions show cell type-specific …
fatemeh-behjati-ardakani
Improved RNA-DNA interaction calling suggests RNA-based gene regulation of phenotypic transitions
Chromatin-localized RNAs play diverse roles in gene regulation and nuclear architecture. Mapping genome-wide RNA-DNA interactions is possible using a variety of molecular methods, …
Simonida Zehr
Quantifying Components in a Model Vaccine with Machine-Learning-Augmented Raman Spectroscopy
Vaccination is a highly efficient strategy in controlling infections. Aluminum-containing adjuvants have long been used to enhance immunogenicity, but quantification of adsorbed …
jana-hahn
Probing transcription factor subsets in gene regulatory networks
Transcription factors (TFs) are essential players in the regulation of gene expression and thus have been the subject of interest in the context of diseases and the manipulation of …
lukas-geis
Predicting gene-specific regulation with transcriptomic and epigenetic single-cell data
MOTIVATION: Analysis of single cell ATAC-seq and RNA-seq data has allowed to gain unprecedented insights into gene regulation by allowing to define cell type-specific regulatory …
Enhancing KLF15 activity in cardiomyocytes: a novel approach to prevent pathological reprogramming and fibrosis via nuclease-deficient dCas9VPR
Transcriptional activity perturbation holds promise for selectively modulating harmful transcriptional networks, but its therapeutic potential remains largely unexplored. We …
eric-schoger
Cell type-specific epigenetic regulatory circuitry of coronary artery disease loci
Coronary artery disease is the leading cause of death worldwide. Recently, hundreds of genomic loci have been shown to increase risk for the disease, however, the molecular …
Comparative cross-methodological analysis of the IDH-wildtype glioblastoma tumor microenvironment
PURPOSE: Glioblastoma, IDH-wildtype is a highly aggressive and often recurrent brain malignancy characterized by a profoundly immunosuppressive and heterogeneous tumor …
pinar-cakmak
Cystine import and oxidative catabolism fuel vascular growth and repair via nutrient-responsive histone acetylation
Endothelial metabolism underpins tissue regeneration, health, and longevity. We uncover a nuclear oxidative catabolic pathway linking cystine to gene regulation. Cells preparing to …
maria-kyriaki-drekolia