Jose Onuchic

Title(s)Emeritus Professor, Physics
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help. to make corrections and additions.
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    1. Magnesium ions mitigate metastable states in the regulatory landscape of mRNA elements. RNA. 2024 Jul 16; 30(8):992-1010. Ding E, Chaudhury SN, Prajapati JD, Onuchic JN, Sanbonmatsu KY. PMID: 38777381; PMCID: PMC11251524.
      View in: PubMed   Mentions:    Fields:    Translation:Cells
    2. Theoretical and computational tools to model multistable gene regulatory networks. ArXiv. 2023 Jun 26. Bocci F, Jia D, Nie Q, Jolly MK, Onuchic J. PMID: 36824430; PMCID: PMC9949162.
      View in: PubMed   Mentions:
    3. Key aspects of the past 30 years of protein design. Rep Prog Phys. 2022 07 06; 85(8). Magi Meconi G, Sasselli IR, Bianco V, Onuchic JN, Coluzza I. PMID: 35704983.
      View in: PubMed   Mentions: 2     Fields:    Translation:Cells
    4. Intrinsically disordered proteins: Ensembles at the limits of Anfinsen's dogma. Biophys Rev (Melville). 2022 Mar; 3(1):011306. Kulkarni P, Leite VBP, Roy S, Bhattacharyya S, Mohanty A, Achuthan S, Singh D, Appadurai R, Rangarajan G, Weninger K, Orban J, Srivastava A, Jolly MK, Onuchic JN, Uversky VN, Salgia R. PMID: 38505224; PMCID: PMC10903413.
      View in: PubMed   Mentions: 10  
    5. BAP1 forms a trimer with HMGB1 and HDAC1 that modulates gene × environment interaction with asbestos. Proc Natl Acad Sci U S A. 2021 11 30; 118(48). Novelli F, Bononi A, Wang Q, Bai F, Patergnani S, Kricek F, Haglund E, Suarez JS, Tanji M, Xu R, Takanishi Y, Minaai M, Pastorino S, Morris P, Sakamoto G, Pass HI, Barbour H, Gaudino G, Giorgi C, Pinton P, Onuchic JN, Yang H, Carbone M. PMID: 34815344; PMCID: PMC8640737.
      View in: PubMed   Mentions: 13     Fields:    Translation:AnimalsCells
    6. SMOG 2 and OpenSMOG: Extending the limits of structure-based models. Protein Sci. 2022 01; 31(1):158-172. de Oliveira AB, Contessoto VG, Hassan A, Byju S, Wang A, Wang Y, Dodero-Rojas E, Mohanty U, Noel JK, Onuchic JN, Whitford PC. PMID: 34655449; PMCID: PMC8740843.
      View in: PubMed   Mentions: 3     Fields:    Translation:HumansAnimalsCells
    7. Sterically confined rearrangements of SARS-CoV-2 Spike protein control cell invasion. Elife. 2021 08 31; 10. Dodero-Rojas E, Onuchic JN, Whitford PC. PMID: 34463614; PMCID: PMC8456623.
      View in: PubMed   Mentions: 20     Fields:    Translation:HumansCells
    8. Exploring chromosomal structural heterogeneity across multiple cell lines. Elife. 2020 10 13; 9. Cheng RR, Contessoto VG, Lieberman Aiden E, Wolynes PG, Di Pierro M, Onuchic JN. PMID: 33047670; PMCID: PMC7593087.
      View in: PubMed   Mentions: 17     Fields:    Translation:HumansCells
    9. Decoding the mechanisms underlying cell-fate decision-making during stem cell differentiation by random circuit perturbation. J R Soc Interface. 2020 08; 17(169):20200500. Huang B, Lu M, Galbraith M, Levine H, Onuchic JN, Jia D. PMID: 32781932; PMCID: PMC7482558.
      View in: PubMed   Mentions: 10     Fields:    Translation:AnimalsCells
    10. Consensus report of the 8 and 9th Weinman Symposia on Gene x Environment Interaction in carcinogenesis: novel opportunities for precision medicine. Cell Death Differ. 2018 11; 25(11):1885-1904. Carbone M, Amelio I, Affar EB, Brugarolas J, Cannon-Albright LA, Cantley LC, Cavenee WK, Chen Z, Croce CM, Andrea A, Gandara D, Giorgi C, Jia W, Lan Q, Mak TW, Manley JL, Mikoshiba K, Onuchic JN, Pass HI, Pinton P, Prives C, Rothman N, Sebti SM, Turkson J, Wu X, Yang H, Yu H, Melino G. PMID: 30323273; PMCID: PMC6219489.
      View in: PubMed   Mentions: 15     Fields:    Translation:Humans
    11. Phylogenetic analysis of the CDGSH iron-sulfur binding domain reveals its ancient origin. Sci Rep. 2018 03 19; 8(1):4840. Sengupta S, Nechushtai R, Jennings PA, Onuchic JN, Padilla PA, Azad RK, Mittler R. PMID: 29556009; PMCID: PMC5859297.
      View in: PubMed   Mentions: 11     Fields:    Translation:HumansCells
    12. The unique fold and lability of the [2Fe-2S] clusters of NEET proteins mediate their key functions in health and disease. J Biol Inorg Chem. 2018 06; 23(4):599-612. Karmi O, Marjault HB, Pesce L, Carloni P, Onuchic JN, Jennings PA, Mittler R, Nechushtai R. PMID: 29435647; PMCID: PMC6006223.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansCells
    13. Interactions between mitoNEET and NAF-1 in cells. PLoS One. 2017; 12(4):e0175796. Karmi O, Holt SH, Song L, Tamir S, Luo Y, Bai F, Adenwalla A, Darash-Yahana M, Sohn YS, Jennings PA, Azad RK, Onuchic JN, Morcos F, Nechushtai R, Mittler R. PMID: 28426722; PMCID: PMC5398536.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansCells
    14. Interrogating the topological robustness of gene regulatory circuits by randomization. PLoS Comput Biol. 2017 03; 13(3):e1005456. Huang B, Lu M, Jia D, Ben-Jacob E, Levine H, Onuchic JN. PMID: 28362798; PMCID: PMC5391964.
      View in: PubMed   Mentions: 90     Fields:    Translation:Humans
    15. Phylogenetic analysis of eukaryotic NEET proteins uncovers a link between a key gene duplication event and the evolution of vertebrates. Sci Rep. 2017 02 16; 7:42571. Inupakutika MA, Sengupta S, Nechushtai R, Jennings PA, Onuchic JN, Azad RK, Padilla P, Mittler R. PMID: 28205535; PMCID: PMC5311916.
      View in: PubMed   Mentions: 24     Fields:    Translation:HumansAnimalsCells
    16. Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes. Mol Biol Evol. 2016 12; 33(12):3054-3064. Cheng RR, Nordesjö O, Hayes RL, Levine H, Flores SC, Onuchic JN, Morcos F. PMID: 27604223; PMCID: PMC5100047.
      View in: PubMed   Mentions: 35     Fields:    Translation:Cells
    17. Notch-Jagged signalling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype. J R Soc Interface. 2016 05; 13(118). Boareto M, Jolly MK, Goldman A, Pietilä M, Mani SA, Sengupta S, Ben-Jacob E, Levine H, Onuchic JN. PMID: 27170649; PMCID: PMC4892257.
      View in: PubMed   Mentions: 65     Fields:    Translation:HumansCells
    18. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics. F1000Res. 2016; 5. Noel JK, Morcos F, Onuchic JN. PMID: 26918164; PMCID: PMC4755392.
      View in: PubMed   Mentions: 9     Fields:    
    19. Modeling the Transitions between Collective and Solitary Migration Phenotypes in Cancer Metastasis. Sci Rep. 2015 Dec 02; 5:17379. Huang B, Jolly MK, Lu M, Tsarfaty I, Ben-Jacob E, Onuchic JN. PMID: 26627083; PMCID: PMC4667179.
      View in: PubMed   Mentions: 29     Fields:    Translation:HumansAnimals
    20. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT. Methods Enzymol. 2015; 553:215-34. Kirmizialtin S, Hennelly SP, Schug A, Onuchic JN, Sanbonmatsu KY. PMID: 25726467; PMCID: PMC4777697.
      View in: PubMed   Mentions: 10     Fields:    Translation:Cells
    21. The physics of bacterial decision making. Front Cell Infect Microbiol. 2014; 4:154. Ben-Jacob E, Lu M, Schultz D, Onuchic JN. PMID: 25401094; PMCID: PMC4214203.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    22. Structure-function analysis of NEET proteins uncovers their role as key regulators of iron and ROS homeostasis in health and disease. Biochim Biophys Acta. 2015 Jun; 1853(6):1294-315. Tamir S, Paddock ML, Darash-Yahana-Baram M, Holt SH, Sohn YS, Agranat L, Michaeli D, Stofleth JT, Lipper CH, Morcos F, Cabantchik IZ, Onuchic JN, Jennings PA, Mittler R, Nechushtai R. PMID: 25448035.
      View in: PubMed   Mentions: 90     Fields:    Translation:HumansCells
    23. Toward decoding the principles of cancer metastasis circuits. Cancer Res. 2014 Sep 01; 74(17):4574-87. Lu M, Jolly MK, Onuchic J, Ben-Jacob E. PMID: 25183783.
      View in: PubMed   Mentions: 29     Fields:    Translation:Humans
    24. Allosteric control in a metalloprotein dramatically alters function. Proc Natl Acad Sci U S A. 2013 Jan 15; 110(3):948-53. Baxter EL, Zuris JA, Wang C, Vo PL, Axelrod HL, Cohen AE, Paddock ML, Nechushtai R, Onuchic JN, Jennings PA. PMID: 23271805; PMCID: PMC3549116.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    25. Energy landscape of knotted protein folding. Proc Natl Acad Sci U S A. 2012 Oct 30; 109(44):17783-8. Sulkowska JI, Noel JK, Onuchic JN. PMID: 22891304; PMCID: PMC3497829.
      View in: PubMed   Mentions: 38     Fields:    Translation:Cells
    26. Conservation of complex knotting and slipknotting patterns in proteins. Proc Natl Acad Sci U S A. 2012 Jun 26; 109(26):E1715-23. Sulkowska JI, Rawdon EJ, Millett KC, Onuchic JN, Stasiak A. PMID: 22685208; PMCID: PMC3387036.
      View in: PubMed   Mentions: 88     Fields:    Translation:Cells
    27. Computational modeling of phosphotransfer complexes in two-component signaling. Methods Enzymol. 2010; 471:43-58. Schug A, Weigt M, Hoch JA, Onuchic JN, Hwa T, Szurmant H. PMID: 20946841.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    28. A novel disulfide bond in the SH2 Domain of the C-terminal Src kinase controls catalytic activity. J Mol Biol. 2007 Feb 02; 365(5):1460-8. Mills JE, Whitford PC, Shaffer J, Onuchic JN, Adams JA, Jennings PA. PMID: 17137590; PMCID: PMC2741090.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansCells
    29. Exploring biomolecular machines: energy landscape control of biological reactions. Philos Trans R Soc Lond B Biol Sci. 2006 Aug 29; 361(1472):1439-43. Onuchic JN, Kobayashi C, Miyashita O, Jennings P, Baldridge KK. PMID: 16873130; PMCID: PMC1647308.
      View in: PubMed   Mentions: 9     Fields:    Translation:Cells
    30. Multiple-basin energy landscapes for large-amplitude conformational motions of proteins: Structure-based molecular dynamics simulations. Proc Natl Acad Sci U S A. 2006 Aug 08; 103(32):11844-9. Okazaki K, Koga N, Takada S, Onuchic JN, Wolynes PG. PMID: 16877541; PMCID: PMC1567665.
      View in: PubMed   Mentions: 124     Fields:    Translation:HumansCells
    31. Self-regulating gene: an exact solution. Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Nov; 72(5 Pt 1):051907. Hornos JE, Schultz D, Innocentini GC, Wang J, Walczak AM, Onuchic JN, Wolynes PG. PMID: 16383645.
      View in: PubMed   Mentions: 75     Fields:    Translation:HumansAnimalsCells
    32. The folding and dimerization of HIV-1 protease: evidence for a stable monomer from simulations. J Mol Biol. 2004 Jun 25; 340(1):67-79. Levy Y, Caflisch A, Onuchic JN, Wolynes PG. PMID: 15184023.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    33. Theory of protein folding. Curr Opin Struct Biol. 2004 Feb; 14(1):70-5. Onuchic JN, Wolynes PG. PMID: 15102452.
      View in: PubMed   Mentions: 406     Fields:    Translation:Cells
    34. Nonlinear elasticity, proteinquakes, and the energy landscapes of functional transitions in proteins. Proc Natl Acad Sci U S A. 2003 Oct 28; 100(22):12570-5. Miyashita O, Onuchic JN, Wolynes PG. PMID: 14566052; PMCID: PMC240658.
      View in: PubMed   Mentions: 204     Fields:    Translation:Cells
    35. Science education. Educating future scientists. Science. 2003 Sep 12; 301(5639):1485. Sung NS, Gordon JI, Rose GD, Getzoff ED, Kron SJ, Mumford D, Onuchic JN, Scherer NF, Sumners DL, Kopell NJ. PMID: 12970550.
      View in: PubMed   Mentions: 7     Fields:    Translation:Humans
    36. Probing the folding free energy landscape of the Src-SH3 protein domain. Proc Natl Acad Sci U S A. 2002 Dec 10; 99(25):16064-8. Shea JE, Onuchic JN, Brooks CL. PMID: 12446834; PMCID: PMC138565.
      View in: PubMed   Mentions: 44     Fields:    Translation:AnimalsCells
    37. Different scenarios for inter-protein electron tunneling: the effect of water-mediated pathways. J Biol Phys. 2002 Sep; 28(3):383-94. Miyashita O, Axelrod HL, Onuchic JN. PMID: 23345783; PMCID: PMC3456736.
      View in: PubMed   Mentions: 1     Fields:    
    38. Prediction of folding mechanism for circular-permuted proteins. J Mol Biol. 2001 Aug 24; 311(4):879-90. Clementi C, Jennings PA, Onuchic JN. PMID: 11518537.
      View in: PubMed   Mentions: 28     Fields:    Translation:Cells
    39. Statistical thermodynamics. Taking a walk on a landscape. Science. 2001 Jul 27; 293(5530):612-3. Brooks CL, Onuchic JN, Wales DJ. PMID: 11474087.
      View in: PubMed   Mentions: 44     Fields:    Translation:Cells
    40. Dynamically controlled protein tunneling paths in photosynthetic reaction centers. Science. 2000 Oct 06; 290(5489):114-7. Balabin IA, Onuchic JN. PMID: 11021791.
      View in: PubMed   Mentions: 63     Fields:    Translation:Cells
    41. Investigation of routes and funnels in protein folding by free energy functional methods. Proc Natl Acad Sci U S A. 2000 Jun 06; 97(12):6509-14. Plotkin SS, Onuchic JN. PMID: 10841554; PMCID: PMC18640.
      View in: PubMed   Mentions: 29     Fields:    Translation:Cells
    42. How native-state topology affects the folding of dihydrofolate reductase and interleukin-1beta. Proc Natl Acad Sci U S A. 2000 May 23; 97(11):5871-6. Clementi C, Jennings PA, Onuchic JN. PMID: 10811910; PMCID: PMC18526.
      View in: PubMed   Mentions: 71     Fields:    Translation:Cells
    43. Topological and energetic factors: what determines the structural details of the transition state ensemble and "en-route" intermediates for protein folding? An investigation for small globular proteins. J Mol Biol. 2000 May 19; 298(5):937-53. Clementi C, Nymeyer H, Onuchic JN. PMID: 10801360.
      View in: PubMed   Mentions: 403     Fields:    Translation:Cells
    44. Landscape approaches for determining the ensemble of folding transition states: success and failure hinge on the degree of frustration. Proc Natl Acad Sci U S A. 2000 Jan 18; 97(2):634-9. Nymeyer H, Socci ND, Onuchic JN. PMID: 10639131; PMCID: PMC15382.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    45. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. Adv Protein Chem. 2000; 53:87-152. Onuchic JN, Nymeyer H, García AE, Chahine J, Socci ND. PMID: 10751944.
      View in: PubMed   Mentions: 61     Fields:    Translation:HumansAnimalsCells
    46. Pressure-induced protein-folding/unfolding kinetics. Proc Natl Acad Sci U S A. 1999 Dec 21; 96(26):14848-53. Hillson N, Onuchic JN, García AE. PMID: 10611301; PMCID: PMC24736.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    47. Exploring the origins of topological frustration: design of a minimally frustrated model of fragment B of protein A. Proc Natl Acad Sci U S A. 1999 Oct 26; 96(22):12512-7. Shea JE, Onuchic JN, Brooks CL. PMID: 10535953; PMCID: PMC22965.
      View in: PubMed   Mentions: 79     Fields:    Translation:Cells
    48. Stretching lattice models of protein folding. Proc Natl Acad Sci U S A. 1999 Mar 02; 96(5):2031-5. Socci ND, Onuchic JN, Wolynes PG. PMID: 10051589; PMCID: PMC26731.
      View in: PubMed   Mentions: 18     Fields:    Translation:Cells
    49. Chemical physics of protein folding. Proc Natl Acad Sci U S A. 1998 Sep 15; 95(19):11037-8. Brooks CL, Gruebele M, Onuchic JN, Wolynes PG. PMID: 9736683; PMCID: PMC33893.
      View in: PubMed   Mentions: 39     Fields:    Translation:Cells
    50. Proposed mechanism for stability of proteins to evolutionary mutations. Proc Natl Acad Sci U S A. 1998 Sep 01; 95(18):10682-6. Nelson ED, Onuchic JN. PMID: 9724764; PMCID: PMC27955.
      View in: PubMed   Mentions: 11     Fields:    Translation:Cells
    51. Protein folding mechanisms and the multidimensional folding funnel. Proteins. 1998 Aug 01; 32(2):136-58. Socci ND, Onuchic JN, Wolynes PG. PMID: 9714155.
      View in: PubMed   Mentions: 45     Fields:    Translation:Cells
    52. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc Natl Acad Sci U S A. 1998 May 26; 95(11):5921-8. Nymeyer H, García AE, Onuchic JN. PMID: 9600893; PMCID: PMC34496.
      View in: PubMed   Mentions: 92     Fields:    Translation:HumansAnimalsCells
    53. Contacting the protein folding funnel with NMR. Proc Natl Acad Sci U S A. 1997 Jul 08; 94(14):7129-31. Onuchic JN. PMID: 9207055; PMCID: PMC34098.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    54. Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem. 1997; 48:545-600. Onuchic JN, Luthey-Schulten Z, Wolynes PG. PMID: 9348663.
      View in: PubMed   Mentions: 581     Fields:    Translation:Cells
    55. Fast-folding experiments and the topography of protein folding energy landscapes. Chem Biol. 1996 Jun; 3(6):425-32. Wolynes P, Luthey-Schulten Z, Onuchic J. PMID: 8807873.
      View in: PubMed   Mentions: 22     Fields:    Translation:Cells
    56. Protein folding funnels: the nature of the transition state ensemble. Fold Des. 1996; 1(6):441-50. Onuchic JN, Socci ND, Luthey-Schulten Z, Wolynes PG. PMID: 9080190.
      View in: PubMed   Mentions: 93     Fields:    Translation:HumansAnimalsCells
    57. Electron tunneling in azurin: the coupling across a beta-sheet. Chem Biol. 1995 Jul; 2(7):489-96. Regan JJ, Di Bilio AJ, Langen R, Skov LK, Winkler JR, Gray HB, Onuchic JN. PMID: 9383451.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    58. Response. Science. 1995 May 19; 268(5213):960-1. Wolynes PG, Onuchic JN, Thirumalai D. PMID: 17774212.
      View in: PubMed   Mentions: 1     Fields:    
    59. Toward an outline of the topography of a realistic protein-folding funnel. Proc Natl Acad Sci U S A. 1995 Apr 11; 92(8):3626-30. Onuchic JN, Wolynes PG, Luthey-Schulten Z, Socci ND. PMID: 7724609; PMCID: PMC42220.
      View in: PubMed   Mentions: 134     Fields:    Translation:Cells
    60. Navigating the folding routes. Science. 1995 Mar 17; 267(5204):1619-20. Wolynes PG, Onuchic JN, Thirumalai D. PMID: 7886447.
      View in: PubMed   Mentions: 280     Fields:    Translation:Cells
    61. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins. 1995 Mar; 21(3):167-95. Bryngelson JD, Onuchic JN, Socci ND, Wolynes PG. PMID: 7784423.
      View in: PubMed   Mentions: 732     Fields:    Translation:Cells
    62. Protein folding funnels: a kinetic approach to the sequence-structure relationship. Proc Natl Acad Sci U S A. 1992 Sep 15; 89(18):8721-5. Leopold PE, Montal M, Onuchic JN. PMID: 1528885; PMCID: PMC49992.
      View in: PubMed   Mentions: 253     Fields:    Translation:Cells
    63. Pathway analysis of protein electron-transfer reactions. Annu Rev Biophys Biomol Struct. 1992; 21:349-77. Onuchic JN, Beratan DN, Winkler JR, Gray HB. PMID: 1326356.
      View in: PubMed   Mentions: 58     Fields:    Translation:AnimalsCells
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