José N. Onuchic

17 papers Journal 17
YearRankTypeTitle / Venue / Authors
2025 J jnl
Epigenetics is all you need: A transformer to decode chromatin structural compartments from the epigenome.
PLoS Comput. Biol.
Esteban Dodero-Rojas, Angel Mendieta, Yao Fehlis, Nicholas Mayala, Vinícius G. Contessoto, José N. Onuchic
2023 J jnl
An associative memory Hamiltonian model for DNA and nucleosomes.
PLoS Comput. Biol.
Weiqi Lu, José N. Onuchic, Michele Di Pierro
2022 J jnl
Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway.
PLoS Comput. Biol.
Madeline Galbraith, Federico Bocci, José N. Onuchic
2021 J jnl
Gene Circuit Explorer (GeneEx): an interactive web-app for visualizing, simulating and analyzing gene regulatory circuits.
Bioinform.
Vivek Kohar, Danya Gordin, Ataur Katebi, Herbert Levine, José N. Onuchic, Mingyang Lu
2021 J jnl
Rapid assessment of T-cell receptor specificity of the immune repertoire.
Nat. Comput. Sci.
Xingcheng Lin, Jason T. George, Nicholas P. Schafer, Kevin Ng Chau, Michael E. Birnbaum, Cecilia Clementi, José N. Onuchic, Herbert Levine
2021 J jnl
The Nucleome Data Bank: web-based resources to simulate and analyze the three-dimensional genome.
Nucleic Acids Res.
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
2018 J jnl
RACIPE: a computational tool for modeling gene regulatory circuits using randomization.
BMC Syst. Biol.
Bin Huang, Dongya Jia, Jingchen Feng, Herbert Levine, José N. Onuchic, Mingyang Lu
2017 J jnl
A magnesium-induced triplex pre-organizes the SAM-II riboswitch.
PLoS Comput. Biol.
Susmita Roy, Heiko Lammert, Ryan L. Hayes, Bin Chen, Regan LeBlanc, T. Kwaku Dayie, José N. Onuchic, Karissa Y. Sanbonmatsu
2017 J jnl
Interrogating the topological robustness of gene regulatory circuits by randomization.
PLoS Comput. Biol.
Bin Huang, Mingyang Lu, Dongya Jia, Eshel Ben-Jacob, Herbert Levine, José N. Onuchic
2016 J jnl
SMOG 2: A Versatile Software Package for Generating Structure-Based Models.
PLoS Comput. Biol.
Jeffrey K. Noel, Mariana Levi, Mohit Raghunathan, Heiko Lammert, Ryan L. Hayes, José N. Onuchic, Paul C. Whitford
2016 J jnl
Strain Mediated Adaptation Is Key for Myosin Mechanochemistry: Discovering General Rules for Motor Activity.
PLoS Comput. Biol.
Biman Jana, José N. Onuchic
2014 J jnl
Pierced Lasso Bundles Are a New Class of Knot-like Motifs.
PLoS Comput. Biol.
Ellinor Haglund, Joanna I. Sulkowska, Jeffrey K. Noel, Heiko Lammert, José N. Onuchic, Patricia A. Jennings
2012 J jnl
Substrate-Specific Reorganization of the Conformational Ensemble of CSK Implicates Novel Modes of Kinase Function.
PLoS Comput. Biol.
Michael A. Jamros, Leandro C. Oliveira, Paul C. Whitford, José N. Onuchic, Joseph A. Adams, Patricia A. Jennings
2012 J jnl
The Dominant Folding Route Minimizes Backbone Distortion in SH3.
PLoS Comput. Biol.
Heiko Lammert, Jeffrey K. Noel, José N. Onuchic
2012 J jnl
The Origin of Minus-end Directionality and Mechanochemistry of Ncd Motors.
PLoS Comput. Biol.
Biman Jana, Changbong Hyeon, José N. Onuchic
2010 J jnl
A Stevedore's Protein Knot.
PLoS Comput. Biol.
Daniel Bölinger, Joanna I. Sulkowska, Hsiao-Ping Hsu, Leonid A. Mirny, Mehran Kardar, José N. Onuchic, Peter Virnau
2010 J jnl
SMOG@ctbp: simplified deployment of structure-based models in GROMACS.
Nucleic Acids Res.
Jeffrey K. Noel, Paul C. Whitford, Karissa Y. Sanbonmatsu, José N. Onuchic