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ORCIDJosé N. Onuchic
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- affiliation: Rice University, Houston, TX, USA
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Journal Articles
- 2023
[j16]Weiqi Lu
, José N. Onuchic, Michele Di Pierro:
An associative memory Hamiltonian model for DNA and nucleosomes. PLoS Comput. Biol. 19(3) (2023)- 2022
- [j15]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) - 2021
- [j14]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): 1327-1329 (2021) - [j13]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): D172-D182 (2021) - [j12]Xingcheng Lin, Jason T. George, Nicholas P. Schafer, Kevin Ng Chau, Michael E. Birnbaum, Cecilia Clementi, José N. Onuchic, Herbert Levine:
Rapid assessment of T-cell receptor specificity of the immune repertoire. Nat. Comput. Sci. 1(5): 362-373 (2021) - 2018
- [j11]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): 74:1-74:12 (2018) - 2017
- [j10]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) - [j9]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) - 2016
- [j8]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) - [j7]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) - 2014
- [j6]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) - 2012
- [j5]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) - [j4]Biman Jana, Changbong Hyeon, José N. Onuchic:
The Origin of Minus-end Directionality and Mechanochemistry of Ncd Motors. PLoS Comput. Biol. 8(11) (2012) - [j3]Heiko Lammert, Jeffrey K. Noel, José N. Onuchic:
The Dominant Folding Route Minimizes Backbone Distortion in SH3. PLoS Comput. Biol. 8(11) (2012) - 2010
- [j2]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): 657-661 (2010) - [j1]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)
Coauthor Index
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