Daniel Jost

Understanding the role of chromatin accessibility and compaction on loop extrusion dynamics

This paper develops a biophysical model of loop extrusion that links motor dynamics to chromatin accessibility and compaction, revealing how nucleosome spacing affects extrusion speed.

Rad55-Rad57 and Srs2 regulate homology search onset, coordination, reach and inactivation

This study investigates how Rad55-Rad57 and Srs2 regulate homology search in yeast by controlling Rad51-ssDNA filament stability and coordination.

Loss of SUMOylation drives aberrant PRC1 clustering and 3D genome rewiring independent of H3K27me3

This study shows that SUMOylation loss in Drosophila disrupts PRC1 condensates, causing 3D genome rewiring and gene misregulation without affecting H3K27me3 levels.

Modeling the spatial organization of replicated chromosomes in yeast reveals a loose asymmetric cohesion between sister chromatids

The paper models the spatial organization of replicated chromosomes in yeast, finding that cohesion between sister chromatids is asymmetric and loosely aligned.

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.

Condensin loop extrusion properties, roadblocks, and role in homology search in S. cerevisiae

The paper identifies condensin-dependent loop extrusion and roadblocks in S. cerevisiae, showing their role in homology search during DNA repair.

Genome-wide modeling of DNA replication in space and time confirms the emergence of replication specific patterns in vivo in eukaryotes

The paper models DNA replication in yeast to show replication-dependent spatial patterns and chromatin dynamics in the nucleus.

Cohesin forms fountains at active enhancers in C. elegans

The paper identifies cohesin-dependent 3D chromatin structures called fountains around active enhancers in C. elegans, showing their role in repressing enhancer activity and linking genome architecture to behavior.

Loop extrusion provides mechanical robustness to chromatin

This study develops a force-dependent model of chromatin loop extrusion and shows it alters DNA force-extension behavior non-monotonically, providing mechanical robustness to chromatin.

Transient histone deacetylase inhibition induces cellular memory of gene expression and three-dimensional genome folding

The paper shows that transient histone deacetylase inhibition in mESCs induces cellular memory of gene expression and 3D genome folding, with genome architecture maintaining perturbed conformations.

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.

Mechanism of homology search expansion during recombinational DNA break repair

This paper investigates the mechanism of homology search expansion during DNA break repair, revealing how chromatin structure, NPF stiffening, and resection drive genome-wide search.

Dynamical modeling of the H3K27 epigenetic landscape in mouse embryonic stem cells

The paper develops a mathematical model to predict H3K27 modification distributions in mouse embryonic stem cells, showing quantitative agreement with experimental data on acetylation and methylation.

Context-dependent transcriptional remodeling of TADs during differentiation

The paper investigates TAD remodeling during mouse thymocyte differentiation using Capture Hi-C, finding transcription can directly alter chromatin structure.

Live imaging and biophysical modeling support a button-based mechanism of somatic homolog pairing in Drosophila

Guidelines for cell-type heterogeneity quantification based on a comparative analysis of reference-free DNA methylation deconvolution software

This study evaluates DNA methylation deconvolution methods for cell-type proportion inference, identifies critical steps for accuracy, and develops a benchmark pipeline.

In vivo, chromatin is a fluctuating polymer chain at equilibrium constrained by internal friction

The paper models chromatin fiber dynamics in vivo, finding that transcription affects chromatin fluctuations through internal friction and transient contacts.

Assigning Function To Natural Allelic Variation Via Dynamic Modeling Of Gene Network Induction

The paper uses dynamic modeling of gene networks to interpret natural DNA variants by personalizing model parameters based on genotype, revealing how variants affect molecular regulation in yeast.

Exploiting single-cell quantitative data to map genetic variants having probabilistic effects

This paper introduces a method to detect genetic variants with probabilistic effects on cellular traits using single-cell data, showing improved detection of linkages missed by classical genetic mapping.