Jose Onuchic

Title(s)Emeritus Professor, Physics
SchoolVc-academic Affairs
Address9500 Gilman Drive #
La Jolla CA 92093
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    1. 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:
    2. 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: 1     Fields:    Translation:Cells
    3. 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: 1  
    4. 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: 8     Fields:    Translation:AnimalsCells
    5. 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: 2     Fields:    
    6. 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: 15     Fields:    Translation:HumansCells
    7. 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: 16     Fields:    Translation:HumansCells
    8. 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: 9     Fields:    Translation:AnimalsCells
    9. 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
    10. 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: 7     Fields:    Translation:HumansCells
    11. 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: 27     Fields:    Translation:HumansCells
    12. 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: 25     Fields:    Translation:HumansCells
    13. 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: 81     Fields:    Translation:Humans
    14. 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: 21     Fields:    Translation:HumansAnimalsCells
    15. 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: 32     Fields:    Translation:Cells
    16. 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: 57     Fields:    Translation:HumansCells
    17. 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:    
    18. 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
    19. 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: 9     Fields:    Translation:Cells
    20. 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: 10     Fields:    Translation:Cells
    21. 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: 78     Fields:    Translation:HumansCells
    22. 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
    23. 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
    24. 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
    25. 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: 84     Fields:    Translation:Cells
    26. 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
    27. 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
    28. 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: 10     Fields:    Translation:Cells
    29. 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: 123     Fields:    Translation:HumansCells
    30. 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: 79     Fields:    Translation:HumansAnimalsCells
    31. 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: 28     Fields:    Translation:Cells
    32. Theory of protein folding. Curr Opin Struct Biol. 2004 Feb; 14(1):70-5. Onuchic JN, Wolynes PG. PMID: 15102452.
      View in: PubMed   Mentions: 412     Fields:    Translation:Cells
    33. 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: 211     Fields:    Translation:Cells
    34. 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
    35. 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:    
    36. 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
    37. 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
    38. 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: 69     Fields:    Translation:Cells
    39. 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
    40. 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: 32     Fields:    Translation:Cells
    41. 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: 63     Fields:    Translation:HumansAnimalsCells
    42. 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
    43. 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: 83     Fields:    Translation:Cells
    44. 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: 19     Fields:    Translation:Cells
    45. 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: 40     Fields:    Translation:Cells
    46. 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: 10     Fields:    Translation:Cells
    47. 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: 49     Fields:    Translation:Cells
    48. 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: 96     Fields:    Translation:HumansAnimalsCells
    49. 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
    50. 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: 578     Fields:    Translation:Cells
    51. 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: 24     Fields:    Translation:Cells
    52. 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: 92     Fields:    Translation:HumansAnimalsCells
    53. 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: 27     Fields:    Translation:Cells
    54. Response. Science. 1995 May 19; 268(5213):960-1. Wolynes PG, Onuchic JN, Thirumalai D. PMID: 17774212.
      View in: PubMed   Mentions: 1     Fields:    
    55. 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
    56. Navigating the folding routes. Science. 1995 Mar 17; 267(5204):1619-20. Wolynes PG, Onuchic JN, Thirumalai D. PMID: 7886447.
      View in: PubMed   Mentions: 278     Fields:    Translation:Cells
    57. 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: 738     Fields:    Translation:Cells
    58. 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: 254     Fields:    Translation:Cells
    59. 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: 61     Fields:    Translation:AnimalsCells
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