Cyclin-dependent kinase 9 (CDK9) inhibition represents a promising therapeutic strategy in cancers that disrupts RNA polymerase II pause release and collapses oncogenic transcripts. Here, we show that...

A new study co-led by professor Valeriya Malysheva, group leader at the VIB-UAntwerp Center for Molecular Neurology, published in Nature Genetics, uncovers how the three-dimensional organization of DNA in rare immune cells can help explain genetic risk for Crohn's disease and other autoimmune conditions.

Palikyras and colleagues investigate chromatin reorganization upon senescence induction, reporting that components of nuclear speckles coordinate chromatin rewiring and a senescence-associated splicin...

Abstract. Clonal hematopoiesis (CH) — the expansion of genetic variants in blood — is a prime example of somatic evolution. Although it often precedes malignant transformation, many aspects of this pr...

Lung development generates a complex tree-like architecture through proximal-distal patterning and branching morphogenesis. However, the gene regulatory programs governing embryonic lung development remain poorly understood. Here, we present a comprehensive single-cell multi-omics atlas of mouse embryonic lungs, integrating gene expression and chromatin accessibility profiles. Through systematic analysis, we identify 13 distinct cell types and map cis-regulatory elements, peak-to-gene linkages, and transcription factors underlying lung development. Leveraging this multi-modal dataset, we uncover lineage-determining transcription factors driving cell differentiation, including the Activated Protein-1 complex. We further delineate gene regulatory networks involving diverse transcription regulators, including CCCTC-binding factor (CTCF). Using the Ctcf conditional knockout mouse, coupled with histological and multi-omics analyses, we demonstrate that CTCF orchestrates lung progenitor main

Histone modifications play crucial roles in genome function. However, how chromatin integrates physiological and metabolic responses at the molecular …

Nature Genetics - This study introduces a system called TArgeted Cohesin Loader (TACL) that recruits cohesin complexes at defined genomic regions and induces loop extrusion events in living cells,...

Single-cell transcriptomics (scRNA-seq) has facilitated the characterization of cell state heterogeneity and recapitulation of differentiation trajectories. However, the exclusive use of mRNA measurem...

Single-cell omics data analyses are complicated to design and difficult to distribute or reproduce. We present a web platform that enables no-code analysis pipeline design, computing, and the sharing ...

The discovery that DNA methylation of different CpG sites can serve as digital barcodes of clonal identity led to the development of EPI-Clone, an algorithm that enables single-cell lineage tracing th...

Leukemia - Is the bone marrow microenvironment the hidden catalyst in malignant haematopoiesis?

CEBPA is frequently mutated in acute myeloid leukemia (AML), but the transcriptional impact of the AML-associated isoform remains unclear. Here, the authors show that CEBPA-mutant cells have reduced i...

We are pleased to introduce the Sven Furberg Seminars in Bioinformatics and Statistical Genomics, an arena for learning, exchanging ideas, promoting scientific excellence, and triggering collaboration...

We often assume that single-cell sequencing gives us a complete picture of cellular diversity, but actually, we already saw in previous publications, like here and here, that one protocol is not reall...

It has been reported that human cancer cell lines present significant diversity across laboratories and become heterogeneous during long-term culture. Here, the authors show that oligo-mutated pediatr...

The representation of driver mutations in preleukemic HSCs provides a window into the somatic evolution that precedes AML. Here, Poon et al. isolate pHSCs from the bone marrow of 16 patients with AML ...

Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction and clustering-free ...