José N. Onuchic

According to our database, José N. Onuchic authored at least 17 papers between 2010 and 2025.

Collaborative distances:

• Dijkstra number of five.
• Erdős number of four.

2025

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

Esteban Dodero-Rojas, Angel Mendieta, Yao Fehlis, Nicholas Mayala, Vinícius G. Contessoto, José N. Onuchic

PLoS Comput. Biol., 2025

2023

An associative memory Hamiltonian model for DNA and nucleosomes.

Weiqi Lu, José N. Onuchic, Michele Di Pierro

PLoS Comput. Biol., March, 2023

2022

Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway.

Madeline Galbraith, Federico Bocci, José N. Onuchic

PLoS Comput. Biol., 2022

2021

Rapid assessment of T-cell receptor specificity of the immune repertoire.

Xingcheng Lin, Jason T. George, Nicholas P. Schafer, Kevin Ng Chau, Michael E. Birnbaum, Cecilia Clementi, José N. Onuchic, Herbert Levine

Nat. Comput. Sci., 2021

The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome.

Vinícius G. Contessoto, Ryan R. Cheng, Arya Hajitaheri, Esteban Dodero-Rojas, Matheus F. Mello, Erez Lieberman Aiden, Peter G. Wolynes, Michele Di Pierro, José N. Onuchic

Nucleic Acids Res., 2021

Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits.

Vivek Kohar, Danya Gordin, Ataur Katebi, Herbert Levine, José N. Onuchic, Mingyang Lu

Bioinform., 2021

2018

RACIPE: a computational tool for modeling gene regulatory circuits using randomization.

Bin Huang, Dongya Jia, Jingchen Feng, Herbert Levine, José N. Onuchic, Mingyang Lu

BMC Syst. Biol., 2018

2017

A magnesium-induced triplex pre-organizes the SAM-II riboswitch.

Susmita Roy, Heiko Lammert, Ryan L. Hayes, Bin Chen, Regan LeBlanc, T. Kwaku Dayie, José N. Onuchic, Karissa Y. Sanbonmatsu

PLoS Comput. Biol., 2017

Interrogating the topological robustness of gene regulatory circuits by randomization.

Bin Huang, Mingyang Lu, Dongya Jia, Eshel Ben-Jacob, Herbert Levine, José N. Onuchic

PLoS Comput. Biol., 2017

2016

SMOG 2: A Versatile Software Package for Generating Structure-Based Models.

Jeffrey K. Noel, Mariana Levi, Mohit Raghunathan, Heiko Lammert, Ryan L. Hayes, José N. Onuchic, Paul C. Whitford

PLoS Comput. Biol., 2016

Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity.

Biman Jana, José N. Onuchic

PLoS Comput. Biol., 2016

2014

Pierced Lasso Bundles Are a New Class of Knot-like Motifs.

Ellinor Haglund, Joanna I. Sulkowska, Jeffrey K. Noel, Heiko Lammert, José N. Onuchic, Patricia A. Jennings

PLoS Comput. Biol., 2014

2012

The Dominant Folding Route Minimizes Backbone Distortion in SH3.

Heiko Lammert, Jeffrey K. Noel, José N. Onuchic

PLoS Comput. Biol., 2012

The Origin of Minus-end Directionality and Mechanochemistry of Ncd Motors.

Biman Jana, Changbong Hyeon, José N. Onuchic

PLoS Comput. Biol., 2012

Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function.

Michael A. Jamros, Leandro C. Oliveira, Paul C. Whitford, José N. Onuchic, Joseph A. Adams, Patricia A. Jennings

PLoS Comput. Biol., 2012

2010

A Stevedore's Protein Knot.

Daniel Bölinger, Joanna I. Sulkowska, Hsiao-Ping Hsu, Leonid A. Mirny, Mehran Kardar, José N. Onuchic, Peter Virnau

PLoS Comput. Biol., 2010

SMOG@ctbp: simplified deployment of structure-based models in GROMACS.

Jeffrey K. Noel, Paul C. Whitford, Karissa Y. Sanbonmatsu, José N. Onuchic

Nucleic Acids Res., 2010