Vinícius G. Contessoto

Learning from Hi-C reveals nuclear dynamical reorganization in budding yeast across the cell cycle

This paper uses Hi-C data to infer 3D genome structure and chromatin dynamics in budding yeast without prior assumptions about nuclear organization.

The compartmental polarization of interphase human chromosomes within the nucleus: A mechanism for transcriptional regulation of large chromosomes

The paper uses simulations and imaging data to show that lamina-associated chromosomes have polarized compartmentalization and enhanced euchromatin contacts, potentially improving transcription for large chromosomes.

Asynchronous structural rearrangements govern constriction of the human nuclear pore complex

The paper uses a structure-based model to study the asynchronous structural rearrangements during nuclear pore complex constriction and their energetic contributions.

Exploring the energy landscape of bacterial chromosome segregation

The paper develops an energy-landscape framework to study bacterial chromosome segregation, showing SMC complexes enable a mid-replication transition crucial for faithful segregation.

Epigenetics is all you need: A Transformer to decode chromatin structural compartments from the epigenome

This paper introduces TECSAS, a Transformer model that predicts chromatin subcompartment annotations from epigenomic data, revealing the impact of long-range epigenomic context on chromatin organization.

Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

This paper reports the 3D genome architecture of a 52,000-year-old woolly mammoth using a novel method, revealing conserved epigenetic features across elephantids.

Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues

The paper uses physical simulations to study the 3D genome architecture of Aedes aegypti, revealing liquid crystalline structures and sensitivity to nuclear deformation.

The Nucleome Data Bank: Web-based Resources to Simulate and Analyze the Three-Dimensional Genome

The paper introduces the Nucleome Data Bank, a web-based platform for simulating and analyzing the 3D genome using epigenetic data, and provides tools for visualization and data analysis.

TKSA-MC: A Web Server for rational mutation through the optimization of protein charge interactions

TKSA-MC calculates protein charge-charge interactions to identify residues for mutation to enhance thermal stability.

Non-native Interactions Explain the Folding Rate Differences in α-Spectrin Domains and the Origin of Internal Friction Effects

The paper investigates internal friction in protein folding by simulating α-spectrin domains with non-native interactions, showing that cooperativity among these interactions explains folding rate differences and internal friction effects.