José N. Onuchic

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.

A biophysical framework for accurately identifying antigen single-amino acid escape variants and corresponding variant-specific compensatory TCR sequences

This paper develops a biophysical computational framework to identify antigen escape variants and compensatory TCR sequences by integrating mutagenesis data and structural modeling.

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.

Structural Topology-based Electrostatic Model (STEM) Reveals Ion-Coordination Exchange as a Driver of RNA Folding Dynamics

The paper introduces STEM, a model that captures ion-coordination dynamics in RNA folding, showing how Mg2+ coordination drives conformational transitions and folding pathways.

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.

Computational modeling of cancer cell metabolism along the catabolic-anabolic axes

This paper develops a computational model of cancer metabolism integrating catabolic and anabolic pathways, identifying four metabolic phenotypes and their association with patient survival.

High-throughput prediction of peptide structural conformations with AlphaFold2

This study evaluates AlphaFold2's ability to predict peptide structural conformations using NMR data, finding varying accuracy with RMSD under 2.5 Å and RMSF under 1.5 Å.

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.

Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification

The paper investigates spatial and temporal patterns of Tip/Stalk specification during angiogenesis using a controlled model and mathematical analysis, revealing an order-disorder transition in NOTCH signaling.

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.

Drug-tolerant idling melanoma cells exhibit theory-predicted metabolic low-low phenotype

The paper identifies a drug-tolerant metabolic state in melanoma cells that reduces both glycolysis and oxidative phosphorylation, supporting survival but limiting growth.

Pericytes enable effective angiogenesis in the presence of pro inflammatory signals

The paper shows that pericytes enhance angiogenesis under high TNF doses, with a mathematical model explaining the switch from pro- to anti-angiogenic effects of TNF.

Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

The paper uses super-resolution imaging and integrative modeling to achieve 10 kb resolution of chromosome folding.

Testing the Gene Expression Classification of the EMT Spectrum

The paper uses computational methods to classify gene expression profiles into epithelial, hybrid E/M, and mesenchymal categories based on EMT dynamics and scoring metrics.

Towards Decoding the Metabolic Plasticity in Cancer: Coupling of Gene Regulation and Metabolic Pathways

The paper models the coupling of gene regulation and metabolic pathways in cancer, showing AMPK and HIF-1 activity correlates with metabolic pathway activities in tumor samples.

RACIPE: A computational tool for Modeling Gene Regulatory Circuits using Randomization

RACIPE is a computational tool that models gene regulatory circuits by randomizing parameters to identify robust dynamical features without requiring detailed kinetic data.

Guiding the design of bacterial signaling interactions using a coevolutionary landscape

This study uses a co-evolutionary landscape to select mutations in bacterial signaling proteins, showing improved efficiency in enhancing phosphotransfer activity compared to random mutagenesis.

Interrogating the Topological Robustness of Gene Regulatory Circuits

The paper introduces RACIPE, a computational method to assess the robustness of gene regulatory circuits by analyzing their dynamical behavior under parameter perturbations, showing topology dominates over kinetic parameters.

A Transferable Model For Chromosome Architecture

The paper introduces a theoretical model that explains and accurately reproduces the three-dimensional structure of interphase chromosomes using experimental data.

Connecting the sequence-space of bacterial signaling proteins to phenotypes using coevolutionary landscapes

The paper constructs a Potts model to predict how mutations affect TCS protein interactions and validates it against experimental data on PhoQ kinase variants.