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)

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)

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)

The Origin of Minus-end Directionality and Mechanochemistry of Ncd Motors. - Biman Jana; Changbong Hyeon; José N. Onuchic (PLoS Comput. Biol., 2012)

The Dominant Folding Route Minimizes Backbone Distortion in SH3. - Heiko Lammert; Jeffrey K. Noel; José N. Onuchic (PLoS Comput. Biol., 2012)

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)

Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity. - Biman Jana; José N. Onuchic (PLoS Comput. Biol., 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)

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)

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)

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)

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)

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)

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)

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)

An associative memory Hamiltonian model for DNA and nucleosomes. - Weiqi Lu; José N. Onuchic; Michele Di Pierro (PLoS Comput. Biol., 2023)