D. Jost

Kinetic properties of optogenetic site-specific DNA recombination by LiCre-loxP

This paper characterizes the kinetic properties of the optogenetic LiCre-loxP system using in vitro and in vivo experiments, revealing temperature-dependent efficiency and a model for recombination synapse formation.

DNA replication and polymer chain duplication reshape the genome in space and time

The paper develops a computational framework to model DNA replication dynamics and their impact on chromosome organization, showing replication-dependent loop extrusion and sister chromatid interactions in yeast.

Transcription regulates the spatio-temporal dynamics of genes through micro-compartmentalization

The paper uses Micro-C data from mouse embryonic stem cells to show that transcriptional activity influences 3D gene folding through Pol II-mediated micro-compartmentalization.

Topological constraints and finite-size effects in quantitative polymer models of chromatin organization

This paper investigates the minimal chromosome length needed for accurate polymer simulations of chromatin organization, showing how topological constraints and finite-size effects influence sub-chromosomal structure and dynamics.

Biophysical ordering transitions underlie genome 3D re-organization during cricket spermiogenesis.

This study identifies a biophysical mechanism underlying genome 3D reorganization during cricket spermiogenesis, revealing a liquid crystal-like chromatin structure formed by SNBP-mediated compaction.

HP1-driven phase separation recapitulates the thermodynamics and kinetics of heterochromatin condensate formation

This paper investigates how HP1-driven phase separation forms PCH condensates in vivo, showing that HP1-chromatin interactions and genomic H3K9me2/3 distribution govern their thermodynamics and kinetics.

3DPolyS-LE: an accessible simulation framework to model the interplay between chromatin and loop extrusion

3DPolyS-LE simulates chromatin loop extrusion and its impact on 3D chromosome structure, enabling comparison with Hi-C data.

Painters in chromatin: a unified quantitative framework to systematically characterize epigenome regulation and memory

The paper introduces a unified modeling framework to analyze epigenome regulation and memory, showing how chromatin organization and enzyme dynamics affect domain stability and gene expression.

Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin

The paper investigates how chromosome organization and topologically-associating domains (TADs) influence chromatin motion, showing that TAD compaction drives transitions between liquid-like and gel-like dynamical states.

RNA polymerase backtracking results in the accumulation of fission yeast condensin at active genes

This study shows that RNA polymerase backtracking at gene ends causes condensin accumulation, and relocating backtracked RNAP redistributes condensin evenly across transcription units.

Polymer modelling unveils the roles of heterochromatin andnucleolar organizing regions in shaping 3D genome organization inArabidopsis thaliana

The paper uses polymer modeling to show that nucleolar organizing regions and heterochromatin drive 3D genome organization in Arabidopsis thaliana.

How epigenome drives chromatin folding and dynamics, insights from efficient coarse-grained models of chromosomes

The paper develops efficient coarse-grained models to simulate chromosome dynamics and shows they reproduce experimental data and predict dynamic chromatin motion during the cell cycle.