Chromatin profiling methods, such as ChIP-seq (chromatin immunoprecipitation followed by sequencing), are used to characterize the genomic localization of DNA-associated proteins. While ChIP and ChIP-...

Deep learning for single-cell Gene Regulatory Networks - aertslab/deepSCENIC

The Dorrity group at EMBL Heidelberg is seeking a motivated and skilled molecular biologist to join as a Laboratory Officer. Our group uses cutting-edge single-cell genomic techniques to study how cel...

The genomic regions regulating gene expression are often themselves transcribed into a variety of noncoding RNAs (ncRNAs). However, the regulatory roles of this noncoding transcription remain largely ...

This Review discusses how rare-disease-causing variants in the noncoding genome impact gene regulation, why these examples are so few and how new approaches could accelerate discovery of noncoding var...

Registration for the 2026 Virtual Cell Challenge is open at virtualcellchallenge.org. This year the task is zero-shot: we are not releasing a training set, and the evaluation dataset is far more expan...

This study uses single-molecule footprinting to quantify chromatin accessibility at enhancers and promoters in mouse embryonic stem cells and to dissect the contributions of transcription factor bindi...

Results from a panel of assays that analyse different aspects of DNA sequence specificity reveal more than 100 new motifs to aid the characterization of putative human transcription factors.

We show that, in a genomic locus with minimal complexity, the distance between promoter and enhancer modulates the frequency of clustered transcriptional bursts. Thus, besides the nucleotide sequence,...

Alzheimer’s disease (AD) disrupts brain function through cell type–specific transcriptomic and epigenomic alterations, yet the contribution of three-dimensional (3D) genome organization to AD remains ...

RNAs adopt complex structures that regulate key biological processes, making accurate structure prediction essential. Chemical probing coupled with Nanopore direct RNA sequencing (DRS) offers a route ...

Comparison of single-cell RNA Velocity methods in developmental contexts - czbiohub-sf/comparison-RNAVelo

Folddisco enables protein structural motif search in million scale databases.

Mallory et al. develop plasmid Fiber-seq to map chromatin architecture along individual transfected plasmids at near-nucleotide resolution, which reveals that plasmids adopt heterogeneous chromatin pa...

An analytical pipeline called Iteratively Defined Lengths of Inaccessibility (IDLI) maps the genome-wide occupancy of a range of nucleosome types and shows that most nucleosomes exhibit programmed ‘di...

Gene regulatory networks (GRNs) define the regulatory relationships among molecules such as transcription factors, chromatin remodelers, and target genes. GRNs play a critical role in diverse biologic...

A new genetic roadmap reveals hundreds of hidden players in HIV infection, including two proteins that stop HIV in its tracks.