Davide Marenduzzo

This study models how 3D confinement affects RNA folding and circularization in the Zika virus genome, showing increased circularization under confinement.

The paper compares two scRNA-seq platforms to quantify transcriptional noise and identifies gene length and CpG-island promoters as factors influencing noise levels.

The paper shows that nucleosome positioning determines chromatin's physical state, with irregular positioning enabling accessibility for transcription while maintaining genome protection.

The paper shows CpG islands act as topological sinks for transcription-induced DNA supercoiling by focusing torsional stress and promoting DNA melting.

The paper introduces a database format called strion to capture chromosome structure and function by encoding transcription unit activity and interactions across cells and time.

This paper shows that RNA and SAF-A form a microgel network in the nucleus near the sol-gel transition, exhibiting viscoelastic properties and reconciling solid-like and fluid-like behaviors.

The paper shows that membrane affinity differences between MinD monomer and dimer are not crucial for MinD gradient formation in Bacillus subtilis, instead diffusion rate differences are important.

The paper identifies ultra-long-range chromatin interactions between active regulatory elements in vertebrate and invertebrate genomes, showing they are driven by three distinct mechanisms independent of RNA polymerase II and some cofactors.

The paper uses simulations to link 3D gene structure with transcription noise in human chromosomes, showing structural heterogeneity drives gene expression variability.

The paper shows RNA polymerase II is necessary for spatial chromatin reorganization after mitosis, as demonstrated by Hi-C and in silico modeling.

The paper introduces capC-MAP, a software package for analyzing Capture-C data, and benchmarks it against another package for similar data.

The paper develops a polymer model to predict 3-D chromatin folding using epigenetic and structural data, validated on gene loci across cell types.

This paper uses magnetic polymer models to study how epigenetic marks and 3D genome organization interact, showing that epigenetic switches stabilize micro-phase separated compartments in the nucleus.

The paper uses simulations to show that dynamic protein-DNA interactions drive the formation of nuclear bodies and chromatin domains through non-equilibrium processes.

This paper introduces a mesoscopic model for simulating double-stranded DNA at single-nucleotide resolution, capable of handling large DNA molecules and comparing results with experimental data.