José N. Onuchic

About

José N. Onuchic is the Harry C. and Olga K. Wiess Chair of Physics and a Professor of Chemistry and BioSciences at Rice University. His research has led the biological physics community to develop an integrated understanding of various biochemical and biological systems, spanning from molecular interactions to cellular and multi-cellular structures. His work has expanded into medical applications, particularly focusing on cancer. In the field of protein folding, he introduced the concept of protein folding funnels, which describe how convergent kinetic pathways guide folding to a unique, stable, native conformation. His theoretical framework, based on energy landscape theory and the funnel concept, addresses questions related to protein folding and function mechanisms. Additionally, he works on the theory of chemical reactions in condensed matter with an emphasis on biological electron transfer. His research interests also include stochastic effects in gene networks, with connections to bacterial decision-making and cancer, and his group is currently focusing on chromatin folding and function. Dr. Onuchic holds a BS in Electrical Engineering, a BS in Physics, and an MS in Applied Physics from Universidade de Sao Paulo, and a PhD in Chemistry from the California Institute of Technology.

Research topics

• Biology
• Computer Science
• Genetics
• Cell biology
• Computer Security
• Biochemistry
• Chemistry
• Biophysics
• Virology
• Computational biology

Selected publications

• 3D genomics across the tree of life reveals condensin II as a determinant of architecture type

  Science · 2021 · 297 citations

  We investigated genome folding across the eukaryotic tree of life. We find two types of three-dimensional (3D) genome architectures at the chromosome scale. Each type appears and disappears repeatedly during eukaryotic evolution. The type of genome architecture that an organism exhibits correlates with the absence of condensin II subunits. Moreover, condensin II depletion converts the architecture of the human genome to a state resembling that seen in organisms such as fungi or mosquitoes. In th…

  PublisherOA PDFDOI

• Enhancing intracellular accumulation and target engagement of PROTACs with reversible covalent chemistry

  Nature Communications · 2020 · 201 citations

  Current efforts in the proteolysis targeting chimera (PROTAC) field mostly focus on choosing an appropriate E3 ligase for the target protein, improving the binding affinities towards the target protein and the E3 ligase, and optimizing the PROTAC linker. However, due to the large molecular weights of PROTACs, their cellular uptake remains an issue. Through comparing how different warhead chemistry, reversible noncovalent (RNC), reversible covalent (RC), and irreversible covalent (IRC) binders, a…

  DOI

• Design and proof of concept for targeted phage-based COVID-19 vaccination strategies with a streamlined cold-free supply chain

  Proceedings of the National Academy of Sciences · 2021 · 65 citations

  Development of effective vaccines against coronavirus disease 2019 (COVID-19) is a global imperative. Rapid immunization of the entire human population against a widespread, continually evolving, and highly pathogenic virus is an unprecedented challenge, and different vaccine approaches are being pursued. Engineered filamentous bacteriophage (phage) particles have unique potential in vaccine development due to their inherent immunogenicity, genetic plasticity, stability, cost-effectiveness for l…

  DOI

• Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion

  eLife · 2021 · 64 citations

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is highly contagious, and transmission involves a series of processes that may be targeted by vaccines and therapeutics. During transmission, host cell invasion is controlled by a large-scale (200-300 Å) conformational change of the Spike protein. This conformational rearrangement leads to membrane fusion, which creates transmembrane pores through which the viral genome is passed to the host. During Spike-protein-mediated fusion, the f…

  DOI

• The need to implement FAIR principles in biomolecular simulations

  Nature Methods · 2025-04-01 · 53 citations

  articleOpen access
  PublisherOA PDFDOI

Recent grants

• The energy landscape for folding and function of biomolecules: integrating physical models, genetic information and experiments

  NSF · $1.4M · 2016–2023

• Collaborative Research: International Physics of Living Systems Graduate Research Network

  NSF · $3.4M · 2021–2026

• Collaborative Research: PoLS Student Research Network

  NSF · $3.0M · 2015–2022

Frequent coauthors

• Herbert Levine

  Northeastern University

  313 shared

• Vinícius G. Contessoto

  169 shared

• Peter G. Wolynes

  Rice University

  162 shared

• Mohit Kumar Jolly

  Indian Institute of Science Bangalore

  157 shared

• Eshel Ben‐Jacob

  132 shared

• Federico Bocci

  University of California, Irvine

  131 shared

• Dongya Jia

  123 shared

• Mingyang Lu

  Nanchang University

  120 shared

Similar researchers at Rice University

• Frank Geurtsh-157
• Karl Ecklundh-142
• Pengcheng Daih-95