Rosana Collepardo‐Guevara

This study shows RNA synthesis and degradation dynamically regulate transcriptional condensates through non-equilibrium feedback, affecting their composition and stability.

This study introduces OpenCGChromatin, a model that simulates chromatin structure and phase separation, revealing how linker-DNA length and histone modifications affect chromatin organization.

This study reveals a dimer-seeded nucleation mechanism for ProTα-H1 biomolecular condensates using simulations and shows how electrostatic screening and protein supersaturation control nucleation and condensate properties.

PepSpace designs specific peptides using physics-driven directed evolution, achieving stronger predicted interactions and better binding specificity than machine learning models.

This study identifies how RNA-regulated fusion dynamics of hnRNPK-based nucleolar condensates prevent coalescence and maintain size control.

This study shows how RNA and protein interactions influence the aging of FUS condensates through molecular mechanisms involving LARKS and cross-β-sheet structures.

The paper quantifies force-induced nucleosome unwrapping using a coarse-grained model, showing DNA flexibility and histone chemistry determine nucleosome stability and plasticity.

This paper maps the free-energy landscapes of chromatin structures and shows how linker DNA geometry and sequence modulate their topologies, influencing phase separation and structural polymorphism.

This study shows that cross-β-sheet nucleation, linked to ageing, preferentially occurs at biomolecular condensate interfaces due to a general physical mechanism, not specific protein sequences.

The paper introduces LASSI, a method to measure nucleosome spacing in chromatin interactions, revealing fiber homotypy as a structural pattern influenced by genomic features and cohesin dynamics.

RNA2PS predicts RNA structure and phase separation behavior from sequence, showing sequence-dependent duplex stability and condensation differences in trinucleotide repeat RNAs.

This study shows that linker histone H1 acts as a liquid-like glue in chromatin domains, enabling dynamic interactions that support DNA transactions in human cells.

The paper identifies condensate-driven transcriptional programs in esophageal and gastric cancers, showing their role in tumor viability and suggesting therapeutic targets.

This study shows that electrostatic attraction compacts fragmented DNA during apoptosis, preventing its release, and demonstrates a synthetic approach to probe physical forces in genome organization.

This study uses all-atom simulations to analyze nucleotide-nucleotide and nucleotide-amino acid interactions, revealing key binding modes and their role in biomolecular condensate formation.

The paper investigates the structure of chromatin condensates across scales and shows how nucleosome arrangement and histone interactions influence their physical properties.

This study uses molecular dynamics simulations to reveal how misfolded α1-antitrypsin forms liquid-like droplets that harden into solid clusters, explaining the pathogenesis of α1-antitrypsin deficiency.

This study shows Oct4 promotes DNA accessibility by forming clusters that deform chromatin and expose DNA through liquid-like states, enhancing gene activation during reprogramming.

This paper introduces two thermodynamic integration schemes to accurately calculate saturation concentrations of phase-separating proteins in simulations, enabling comparison with experimental data.

This study identifies electrostatic repulsion as the mechanism driving centromere positioning at the chromatin surface, independent of condensin or microtubules.

The paper designs a computational pipeline to identify small peptides that slow condensate ageing in TDP-43 and FUS by reducing condensate density through electrostatic interactions.

The paper shows that nucleosome spacing affects chromatin phase separation stability and dynamics through inter- and intramolecular stacking trade-offs.

The paper shows cold-induced changes in nucleosome dynamics at the FLC locus in Arabidopsis, leading to transcriptional repression through chromatin structure transitions.

This study uses simulations to show how charged mutations in FUS affect condensate ageing kinetics by altering β-sheet accumulation and aggregate formation.

The paper identifies sequence determinants of long-range chromatin contacts across cell types, showing AT-rich sequences and heterochromatin association.

This study uses Molecular Dynamics simulations to show how different biomolecules affect the ageing kinetics of TDP-43 condensates, with arginine-rich peptides accelerating and poly-Uridine RNA slowing the formation of harmful cross-β-sheet structures.

The paper introduces Mpipi-Recharged, a coarse-grained model that improves electrostatic force description in charge-rich biomolecular condensates by incorporating asymmetric potentials from atomistic simulations.

This study benchmarks six residue-resolution coarse-grained models to evaluate their accuracy in simulating the phase behavior and material properties of hnRNPA1 LCD condensates.

This study designs a synthetic biomolecular condensate platform using CTPR proteins and intrinsically-disordered domains to tune condensate properties and recruit target proteins.

This study evaluates five coarse-grained protein models for predicting phase diagrams of hnRNPA1 LCD mutants, finding that only three accurately reproduce experimental data, highlighting the need to balance single-molecule and collective properties.