JO
Jose' N. Onuchic
Protein FoldingModels, MolecularbiophysicsMolecular Dynamics SimulationModels, ChemicalProtein ConformationModels, BiologicalComputer SimulationGene Regulatory NetworksModels, Genetic
On Valency
published · living versionsW_zkn5w8bg·v1 · currentpublished
How native state topology affects the folding of Dihydrofolate Reductase and Interleukin-1beta
with Cecilia Clementi, Patricia A. Jennings
1 version
Preprints & journals
348 papers in the corpus · 1988–2026Asynchronous structural rearrangements govern constriction of the human nuclear pore complex.42619942 · Ding, Erdong, Mello, Matheus F, Contessoto, Vinícius G et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
Structural Topology-based Electrostatic Model (STEM) Reveals Ion-Coordination Exchange as a Driver of RNA Folding Dynamics.42427654 · Mainan, Avijit, Jaiswar, Akhilesh, Onuchic, José N et al.2026 · 1 citationbioRxiv : the preprint server for biology. 2026
Exploring functional transitions of the 2'-dG riboswitch aptamer.41973925 · Ding, Erdong, Chaudhury, Susmit Narayan, Sanbonmatsu, Karissa Y et al.2026 · 1 citationProceedings of the National Academy of Sciences of the United States of America. 2026;123(16):e2528806123
Exploring the energy landscape of bacterial chromosome segregation.41843667 · Brahmachari, Sumitabha, Oliveira, Antonio B, Mello, Matheus F et al.2026 · 4 citationsProceedings of the National Academy of Sciences of the United States of America. 2026;123(12):e2535321123
A biophysical framework for accurately identifying antigen single-amino acid escape variants and corresponding variant-specific compensatory TCR sequences10.64898/2026.02.02.703411v2 · Ghoreyshi, Z. S., Levine, H., Lin, X. et al.2026 · 1 citationbioRxiv
A data-driven chromatin model reveals spatial and dynamic features of genome organization.41576073 · Oliveira Junior, Antonio B, Mello, Matheus F, Oliveira, Ronaldo J et al.2026 · 2 citationsProceedings of the National Academy of Sciences of the United States of America. 2026;123(4):e2530583123
Quantum simulation of charge and exciton transfer in multi-mode models using engineered reservoirs.41350538 · So, Visal, Duraisamy Suganthi, Midhuna, Zhu, Mingjian et al.2026 · 5 citationsNature communications. 2025;17(1):438
Epigenetics is all you need: A transformer to decode chromatin structural compartments from the epigenome.41337156 · Dodero-Rojas, Esteban, Mendieta, Angel, Fehlis, Yao et al.2025 · 3 citationsPLoS computational biology. 2025;21(12):e1012326
Sequence-based calculation of local energetic frustration in proteins.41312536 · Kuhn, Adam M, Contessoto, Vinícius G, Onuchic, José N et al.2025 · 1 citationStructural dynamics (Melville, N.Y.). 2025;12(6):064101
Mapping the energy landscape of a fold-switching protein MAD2.41074798 · Pereira, Ander F, Contessoto, Vinícius G, Martínez, Leandro et al.2025 · 2 citationsProtein science : a publication of the Protein Society. 2025;34(11):e70329
Critical Role of Mg2+ Ions in RNA Folding Transitions: Anchoring the A-Minor Twist in the SAM-II Riboswitch.40892043 · Viegas, Rafael G, Sinha, Anushree, Mainan, Avijit et al.2025 · 8 citationsThe journal of physical chemistry. B. 2025;129(36):9058-9067
Conformational ligand-directed targeting of calcium-dependent receptors in acute trauma.40609540 · Pasqualini, Renata, Markosian, Christopher, Staquicini, Daniela I et al.2025 · 1 citationMed (New York, N.Y.). 2025;6(7):100638
Computational modeling of cancer cell metabolism along the catabolic-anabolic axes.40348758 · Villela-Castrejon, Javier, Levine, Herbert, Kaipparettu, Benny A et al.2025 · 10 citationsNPJ systems biology and applications. 2025;11(1):46
High-throughput prediction of peptide structural conformations with AlphaFold2.39677766 · Ille, Alexander M, Markosian, Christopher, Burley, Stephen K et al.2025 · 3 citationsbioRxiv : the preprint server for biology. 2025
Simulating biomolecules for physiological timescales.40215701 · Whitford, Paul C, Onuchic, José N2025 · 9 citationsCurrent opinion in structural biology. 2025;92:103039
The need to implement FAIR principles in biomolecular simulations.40175561 · Amaro, Rommie E, Åqvist, Johan, Bahar, Ivet et al.2026 · 76 citationsNature methods. 2025;22(4):641-645
The synergy between compartmentalization and motorization in chromatin architecture.40105139 · Oliveira, Ronaldo J, Oliveira Junior, Antonio B, Contessoto, Vinícius G et al.2025 · 4 citationsThe Journal of chemical physics. 2025;162(11)
Energy landscape analysis of the development of the chromosome structure across the cell cycle.40112110 · Contessoto, Vinícius G, Oliveira, Antonio B, Brahmachari, Sumitabha et al.2025 · 7 citationsProceedings of the National Academy of Sciences of the United States of America. 2025;122(12):e2425225122
Conformational heterogeneity in the dGsw purine riboswitch: role of Mg2+ and 2'-dG in aptamer folding.40021341 · Chaudhury, Susmit Narayan, Ding, Erdong, Jespersen, Nathan E et al.2025 · 2 citationsRNA (New York, N.Y.). 2025;31(5):724-733
Evolving concepts of the protein universe.40124498 · Kulkarni, Prakash, Porter, Lauren, Chou, Tsui-Fen et al.2026 · 15 citationsiScience. 2025;28(3):112012
Biguanides antithetically regulate tumor properties by the dose-dependent mitochondrial reprogramming-driven c-Src pathway.39933530 · Park, Jun Hyoung, Jung, Kwang Hwa, Jia, Dongya et al.2025 · 12 citationsCell reports. Medicine. 2025;6(2):101941
Trapped-ion quantum simulation of electron transfer models with tunable dissipation.39705352 · So, Visal, Duraisamy Suganthi, Midhuna, Menon, Abhishek et al.2026 · 29 citationsScience advances. 2024;10(51):eads8011
Designing proteins: Mimicking natural protein sequence heterogeneity.39546369 · Lequerica-Mateos, Marcos, Martin, Jonathan, Onuchic, José N et al.2024 · 1 citationThe Journal of chemical physics. 2024;161(19)
Structure and inhibition of SARS-CoV-2 spike refolding in membranes.39146425 · Grunst, Michael W, Qin, Zhuan, Dodero-Rojas, Esteban et al.2024 · 55 citationsScience (New York, N.Y.). 2024;385(6710):757-765
Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements.38777381 · Ding, Erdong, Chaudhury, Susmit Narayan, Prajapati, Jigneshkumar Dahyabhai et al.2024 · 14 citationsRNA (New York, N.Y.). 2024;30(8):992-1010
Germline BARD1 variants predispose to mesothelioma by impairing DNA repair and calcium signaling.38990952 · Novelli, Flavia, Yoshikawa, Yoshie, Vitto, Veronica Angela Maria et al.2024 · 14 citationsProceedings of the National Academy of Sciences of the United States of America. 2024;121(29):e2405231121
Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample.38996487 · Sandoval-Velasco, Marcela, Dudchenko, Olga, Rodríguez, Juan Antonio et al.2024 · 51 citationsCell. 2024;187(14):3541-3562.e51
Nucleosomes play a dual role in regulating transcription dynamics.38968124 · Brahmachari, Sumitabha, Tripathi, Shubham, Onuchic, José N et al.2024 · 10 citationsProceedings of the National Academy of Sciences of the United States of America. 2024;121(28):e2319772121
Machine learning in biological physics: From biomolecular prediction to design.38913893 · Martin, Jonathan, Lequerica Mateos, Marcos, Onuchic, José N et al.2024 · 13 citationsProceedings of the National Academy of Sciences of the United States of America. 2024;121(27):e2311807121
CISD3/MiNT is required for complex I function, mitochondrial integrity, and skeletal muscle maintenance.38781208 · Nechushtai, Rachel, Rowland, Linda, Karmi, Ola et al.2024 · 15 citationsProceedings of the National Academy of Sciences of the United States of America. 2024;121(22):e2405123121
RACER-m leverages structural features for sparse T cell specificity prediction.38748791 · Wang, Ailun, Lin, Xingcheng, Chau, Kevin Ng et al.2024 · 21 citationsScience advances. 2024;10(20):eadl0161
Spatial-temporal order-disorder transition in angiogenic NOTCH signaling controls cell fate specification.38376371 · Kang, Tae-Yun, Bocci, Federico, Nie, Qing et al.2024 · 9 citationseLife. 2024;12
Residue coevolution and mutational landscape for OmpR and NarL response regulator subfamilies.38291753 · Shibata, Mayu, Lin, Xingcheng, Onuchic, José N et al.2024 · 1 citationBiophysical journal. 2024;123(6):681-692
Regulation of chromatin transcription dynamics by DNA supercoiling10.1101/2023.11.06.565891v1 · Brahmachari, S., Tripathi, S., Onuchic, J. N. et al.2023 · 2 citationsbioRxiv
Theoretical and computational tools to model multistable gene regulatory networks.36824430 · Bocci, Federico, Jia, Dongya, Nie, Qing et al.2023 · 13 citationsArXiv. 2023
PyMEGABASE: Predicting Cell-Type-Specific Structural Annotations of Chromosomes Using the Epigenome.37302549 · Dodero-Rojas, Esteban, Mello, Matheus F, Brahmachari, Sumitabha et al.2023 · 9 citationsJournal of molecular biology. 2023;435(15):168180
Temporally correlated active forces drive segregation and enhanced dynamics in chromosome polymers10.1101/2023.04.23.528410v2 · Brahmachari, S., Markovich, T., MacKintosh, F. C. et al.2023 · 29 citationsbioRxiv
An associative memory Hamiltonian model for DNA and nucleosomes.36972316 · Lu, Weiqi, Onuchic, José N, Di Pierro, Michele2023 · 5 citationsPLoS computational biology. 2023;19(3):e1011013
Structural reorganization and relaxation dynamics of axially stressed chromosomes.36960531 · Ruben, Benjamin S, Brahmachari, Sumitabha, Contessoto, Vinícius G et al.2023 · 16 citationsBiophysical journal. 2023;122(9):1633-1645
BAP1 is a novel regulator of HIF-1α.36656861 · Bononi, Angela, Wang, Qian, Zolondick, Alicia A et al.2023 · 31 citationsProceedings of the National Academy of Sciences of the United States of America. 2023;120(4):e2217840120
Interphase chromosomes of the Aedes aegypti mosquito are liquid crystalline and can sense mechanical cues.36658127 · Contessoto, Vinícius G, Dudchenko, Olga, Aiden, Erez Lieberman et al.2023 · 28 citationsNature communications. 2023;14(1):326
Road-blocker HSP disease mutation disrupts pre-organization for ATP hydrolysis in kinesin through a second sphere control.36574689 · Manna, Rabindra Nath, Onuchic, José N, Jana, Biman2022 · 6 citationsProceedings of the National Academy of Sciences of the United States of America. 2023;120(1):e2215170120
Decoding the coupled decision-making of the epithelial-mesenchymal transition and metabolic reprogramming in cancer.36582834 · Galbraith, Madeline, Levine, Herbert, Onuchic, José N et al.2023 · 9 citationsiScience. 2023;26(1):105719
Exploring the Energy Landscape of Riboswitches Using Collective Variables Based on Tertiary Contacts.35963460 · Prajapati, Jigneshkumar Dahyabhai, Onuchic, José N, Sanbonmatsu, Karissa Y2022 · 11 citationsJournal of molecular biology. 2022;434(18):167788
Erratum: "Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes" [J. Chem. Phys. 156, 195101 (2022)].35922346 · Freitas, Frederico Campos, Maldonado, Michelli, Oliveira Junior, Antonio Bento et al.2022 · 0 citationsThe Journal of chemical physics. 2022;157(4):049901
Stochastic fluctuations promote ordered pattern formation of cells in the Notch-Delta signaling pathway.35862460 · Galbraith, Madeline, Bocci, Federico, Onuchic, José N2022 · 16 citationsPLoS computational biology. 2022;18(7):e1010306
Uncovering the statistical physics of 3D chromosomal organization using data-driven modeling.35839701 · Contessoto, Vinícius G, Cheng, Ryan R, Onuchic, José N2022 · 25 citationsCurrent opinion in structural biology. 2022;75:102418
Key aspects of the past 30 years of protein design.35704983 · Magi Meconi, Giulia, Sasselli, Ivan R, Bianco, Valentino et al.2022 · 8 citationsReports on progress in physics. Physical Society (Great Britain). 2022;85(8)
Contact map dependence of a T-cell receptor binding repertoire.35974642 · Ng Chau, Kevin, George, Jason T, Onuchic, José N et al.2022 · 8 citationsPhysical review. E. 2022;106(1-1):014406
Biotin-painted proteins have thermodynamic stability switched by kinetic folding routes.35597640 · Freitas, Frederico Campos, Maldonado, Michelli, Oliveira Junior, Antonio Bento et al.2022 · 6 citationsThe Journal of chemical physics. 2022;156(19):195101
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