José N. Onuchic

Career Trajectory

Research Cluster Map

Direct collaborators. Node size = influence, colour = community, dashed = past collaboration.

• Exploring functional transitions of the 2’-dG riboswitch aptamer

  Proceedings of the National Academy of Sciences · 2026-04-13

• Exploring the energy landscape of bacterial chromosome segregation

  Proceedings of the National Academy of Sciences · 2026-03-17 · 1 citations

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

  bioRxiv (Cold Spring Harbor Laboratory) · 2026-02-05

• A data-driven chromatin model reveals spatial and dynamic features of genome organization

  Proceedings of the National Academy of Sciences · 2026-01-23 · 1 citations

• Quantum simulation of charge and exciton transfer in multi-mode models using engineered reservoirs

  Nature Communications · 2025-12-05 · 1 citations

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

  PLoS Computational Biology · 2025-12-03 · 1 citations

• Sequence-based calculation of local energetic frustration in proteins

  Structural Dynamics · 2025-11-01

• Mapping the energy landscape of a fold‐switching protein <scp>MAD2</scp>

  Protein Science · 2025-10-11 · 1 citations

• Critical Role of Mg²⁺ Ions in RNA Folding Transitions: Anchoring the A-Minor Twist in the SAM-II Riboswitch

  The Journal of Physical Chemistry B · 2025-09-02 · 6 citations

• Quantum Simulation of Charge and Exciton Transfer in Multi-mode Models with Engineered ReservoirsPreprint

  Research Square · 2025-07-31 · 1 citations

• Conformational ligand-directed targeting of calcium-dependent receptors in acute trauma

  Med · 2025-07-01 · 1 citations

• Quantum Simulation of Charge and Exciton Transfer in Multi-mode Models using Engineered ReservoirsPreprint

  ArXiv.org · 2025-05-28

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

  npj Systems Biology and Applications · 2025-05-10 · 5 citations

• Simulating biomolecules for physiological timescales

  Current Opinion in Structural Biology · 2025-04-10 · 9 citations

• The need to implement FAIR principles in biomolecular simulations

  Nature Methods · 2025-04-01 · 56 citations

• Energy landscape analysis of the development of the chromosome structure across the cell cycle

  Proceedings of the National Academy of Sciences · 2025-03-20 · 6 citations

• The synergy between compartmentalization and motorization in chromatin architecture

  The Journal of Chemical Physics · 2025-03-19 · 3 citations

• Conformational heterogeneity in the dGsw purine riboswitch: role of Mg²⁺ and 2’-dG in aptamer folding

  RNA · 2025-02-28 · 2 citations

• Evolving concepts of the protein universe

  iScience · 2025-02-13 · 12 citations

• Biguanides antithetically regulate tumor properties by the dose-dependent mitochondrial reprogramming-driven c-Src pathway

  Cell Reports Medicine · 2025-02-01 · 11 citations