José N. Onuchic

Publication Activity (10 Years)

Years Active: 2010-2023
Publications (10 Years): 9

Top Topics

Associative Memory

Software Package

Gene Regulatory

Systems Biology

Top Venues

PLoS Comput. Biol.

Nucleic Acids Res.

BMC Syst. Biol.

Publications

Weiqi Lu, José N. Onuchic, Michele Di Pierro
An associative memory Hamiltonian model for DNA and nucleosomes. PLoS Comput. Biol. 19 (3) (2023)
Madeline Galbraith, Federico Bocci, José N. Onuchic
Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway. PLoS Comput. Biol. 18 (7) (2022)
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
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome. Nucleic Acids Res. 49 (Database-Issue) (2021)
Vivek Kohar, Danya Gordin, Ataur Katebi, Herbert Levine, José N. Onuchic, Mingyang Lu
Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits. Bioinform. 37 (9) (2021)
Bin Huang, Dongya Jia, Jingchen Feng, Herbert Levine, José N. Onuchic, Mingyang Lu
RACIPE: a computational tool for modeling gene regulatory circuits using randomization. BMC Syst. Biol. 12 (1) (2018)
Susmita Roy, Heiko Lammert, Ryan L. Hayes, Bin Chen, Regan LeBlanc, T. Kwaku Dayie, José N. Onuchic, Karissa Y. Sanbonmatsu
A magnesium-induced triplex pre-organizes the SAM-II riboswitch. PLoS Comput. Biol. 13 (3) (2017)
Bin Huang, Mingyang Lu, Dongya Jia, Eshel Ben-Jacob, Herbert Levine, José N. Onuchic
Interrogating the topological robustness of gene regulatory circuits by randomization. PLoS Comput. Biol. 13 (3) (2017)
Biman Jana, José N. Onuchic
Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity. PLoS Comput. Biol. 12 (8) (2016)
Jeffrey K. Noel, Mariana Levi, Mohit Raghunathan, Heiko Lammert, Ryan L. Hayes, José N. Onuchic, Paul C. Whitford
SMOG 2: A Versatile Software Package for Generating Structure-Based Models. PLoS Comput. Biol. 12 (3) (2016)
Ellinor Haglund, Joanna I. Sulkowska, Jeffrey K. Noel, Heiko Lammert, José N. Onuchic, Patricia A. Jennings
Pierced Lasso Bundles Are a New Class of Knot-like Motifs. PLoS Comput. Biol. 10 (6) (2014)
Heiko Lammert, Jeffrey K. Noel, José N. Onuchic
The Dominant Folding Route Minimizes Backbone Distortion in SH3. PLoS Comput. Biol. 8 (11) (2012)
Michael A. Jamros, Leandro C. Oliveira, Paul C. Whitford, José N. Onuchic, Joseph A. Adams, Patricia A. Jennings
Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function. PLoS Comput. Biol. 8 (9) (2012)
Biman Jana, Changbong Hyeon, José N. Onuchic
The Origin of Minus-end Directionality and Mechanochemistry of Ncd Motors. PLoS Comput. Biol. 8 (11) (2012)
Daniel Bölinger, Joanna I. Sulkowska, Hsiao-Ping Hsu, Leonid A. Mirny, Mehran Kardar, José N. Onuchic, Peter Virnau
A Stevedore's Protein Knot. PLoS Comput. Biol. 6 (4) (2010)
Jeffrey K. Noel, Paul C. Whitford, Karissa Y. Sanbonmatsu, José N. Onuchic
SMOG@ctbp: simplified deployment of structure-based models in GROMACS. Nucleic Acids Res. 38 (Web-Server-Issue) (2010)