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    Jose Onuchic

    TitleEmeritus Professor
    SchoolUniversity of California, San Diego
    Address9500 Gilman Drive #0374
    CA La Jolla 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.
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      1. Karmi O, Holt SH, Song L, Tamir S, Luo Y, Bai F, Adenwalla A, Darash-Yahana M, Sohn YS, Jennings PA, Azad RK, Onuchic J, Morcos F, Nechushtai R, Mittler R. Interactions between mitoNEET and NAF-1 in cells. PLoS One. 2017; 12(4):e0175796. PMID: 28426722.
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      2. Huang B, Lu M, Jia D, Ben-Jacob E, Levine H, Onuchic J. Interrogating the topological robustness of gene regulatory circuits by randomization. PLoS Comput Biol. 2017 Mar; 13(3):e1005456. PMID: 28362798.
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      3. Inupakutika MA, Sengupta S, Nechushtai R, Jennings PA, Onuchic J, Azad RK, Padilla P, Mittler R. Phylogenetic analysis of eukaryotic NEET proteins uncovers a link between a key gene duplication event and the evolution of vertebrates. Sci Rep. 2017 Feb 16; 7:42571. PMID: 28205535.
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      4. Cheng RR, Nordesjö O, Hayes RL, Levine H, Flores SC, Onuchic J, Morcos F. Connecting the Sequence-Space of Bacterial Signaling Proteins to Phenotypes Using Coevolutionary Landscapes. Mol Biol Evol. 2016 Dec; 33(12):3054-3064. PMID: 27604223.
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      5. Boareto M, Jolly MK, Goldman A, Pietilä M, Mani SA, Sengupta S, Ben-Jacob E, Levine H, Onuchic J. Notch-Jagged signalling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype. J R Soc Interface. 2016 May; 13(118). PMID: 27170649; PMCID: PMC4892257.
      6. Noel JK, Morcos F, Onuchic J. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics. F1000Res. 2016; 5. PMID: 26918164; PMCID: PMC4755392.
      7. Huang B, Jolly MK, Lu M, Tsarfaty I, Ben-Jacob E, Onuchic J. Modeling the Transitions between Collective and Solitary Migration Phenotypes in Cancer Metastasis. Sci Rep. 2015 Dec 02; 5:17379. PMID: 26627083; PMCID: PMC4667179.
      8. Kirmizialtin S, Hennelly SP, Schug A, Onuchic J, Sanbonmatsu KY. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT. Methods Enzymol. 2015; 553:215-34. PMID: 25726467; PMCID: PMC4777697.
      9. Ben-Jacob E, Lu M, Schultz D, Onuchic J. The physics of bacterial decision making. Front Cell Infect Microbiol. 2014; 4:154. PMID: 25401094; PMCID: PMC4214203.
      10. 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 J, Jennings PA, Mittler R, Nechushtai R. 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. PMID: 25448035.
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      11. Lu M, Jolly MK, Onuchic J, Ben-Jacob E. Toward decoding the principles of cancer metastasis circuits. Cancer Res. 2014 Sep 01; 74(17):4574-87. PMID: 25183783.
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      12. Sulkowska JI, Noel JK, Onuchic J. Energy landscape of knotted protein folding. Proc Natl Acad Sci U S A. 2012 Oct 30; 109(44):17783-8. PMID: 22891304; PMCID: PMC3497829.
      13. Sulkowska JI, Rawdon EJ, Millett KC, Onuchic J, Stasiak A. Conservation of complex knotting and slipknotting patterns in proteins. Proc Natl Acad Sci U S A. 2012 Jun 26; 109(26):E1715-23. PMID: 22685208; PMCID: PMC3387036.
      14. Schug A, Weigt M, Hoch JA, Onuchic J, Hwa T, Szurmant H. Computational modeling of phosphotransfer complexes in two-component signaling. Methods Enzymol. 2010; 471:43-58. PMID: 20946841.
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      15. Mills JE, Whitford PC, Shaffer J, Onuchic J, Adams JA, Jennings PA. 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. PMID: 17137590; PMCID: PMC2741090.
      16. Onuchic J, Kobayashi C, Miyashita O, Jennings P, Baldridge KK. Exploring biomolecular machines: energy landscape control of biological reactions. Philos Trans R Soc Lond B Biol Sci. 2006 Aug 29; 361(1472):1439-43. PMID: 16873130; PMCID: PMC1647308.
      17. Okazaki K, Koga N, Takada S, Onuchic J, Wolynes PG. 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. PMID: 16877541; PMCID: PMC1567665.
      18. Hornos JE, Schultz D, Innocentini GC, Wang J, Walczak AM, Onuchic J, Wolynes PG. Self-regulating gene: an exact solution. Phys Rev E Stat Nonlin Soft Matter Phys. 2005 Nov; 72(5 Pt 1):051907. PMID: 16383645.
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      19. Levy Y, Caflisch A, Onuchic J, Wolynes PG. 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. PMID: 15184023.
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      20. Onuchic J, Wolynes PG. Theory of protein folding. Curr Opin Struct Biol. 2004 Feb; 14(1):70-5. PMID: 15102452.
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      21. Miyashita O, Onuchic J, Wolynes PG. 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. PMID: 14566052; PMCID: PMC240658.
      22. Sung NS, Gordon JI, Rose GD, Getzoff ED, Kron SJ, Mumford D, Onuchic J, Scherer NF, Sumners DL, Kopell NJ. Science education. Educating future scientists. Science. 2003 Sep 12; 301(5639):1485. PMID: 12970550.
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      23. Shea JE, Onuchic J, Brooks CL. 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. PMID: 12446834; PMCID: PMC138565.
      24. Miyashita O, Axelrod HL, Onuchic J. Different scenarios for inter-protein electron tunneling: the effect of water-mediated pathways. J Biol Phys. 2002 Sep; 28(3):383-94. PMID: 23345783; PMCID: PMC3456736.
      25. Clementi C, Jennings PA, Onuchic J. Prediction of folding mechanism for circular-permuted proteins. J Mol Biol. 2001 Aug 24; 311(4):879-90. PMID: 11518537.
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      26. Brooks CL, Onuchic J, Wales DJ. Statistical thermodynamics. Taking a walk on a landscape. Science. 2001 Jul 27; 293(5530):612-3. PMID: 11474087.
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      27. Balabin IA, Onuchic J. Dynamically controlled protein tunneling paths in photosynthetic reaction centers. Science. 2000 Oct 06; 290(5489):114-7. PMID: 11021791.
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      28. Plotkin SS, Onuchic J. 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. PMID: 10841554; PMCID: PMC18640.
      29. Clementi C, Jennings PA, Onuchic J. 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. PMID: 10811910; PMCID: PMC18526.
      30. Clementi C, Nymeyer H, Onuchic J. 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. PMID: 10801360.
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      31. Nymeyer H, Socci ND, Onuchic J. 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. PMID: 10639131; PMCID: PMC15382.
      32. Onuchic J, Nymeyer H, García AE, Chahine J, Socci ND. The energy landscape theory of protein folding: insights into folding mechanisms and scenarios. Adv Protein Chem. 2000; 53:87-152. PMID: 10751944.
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      33. Hillson N, Onuchic J, García AE. Pressure-induced protein-folding/unfolding kinetics. Proc Natl Acad Sci U S A. 1999 Dec 21; 96(26):14848-53. PMID: 10611301; PMCID: PMC24736.
      34. Shea JE, Onuchic J, Brooks CL. 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. PMID: 10535953; PMCID: PMC22965.
      35. Socci ND, Onuchic J, Wolynes PG. Stretching lattice models of protein folding. Proc Natl Acad Sci U S A. 1999 Mar 02; 96(5):2031-5. PMID: 10051589; PMCID: PMC26731.
      36. Brooks CL, Gruebele M, Onuchic J, Wolynes PG. Chemical physics of protein folding. Proc Natl Acad Sci U S A. 1998 Sep 15; 95(19):11037-8. PMID: 9736683; PMCID: PMC33893.
      37. Nelson ED, Onuchic J. Proposed mechanism for stability of proteins to evolutionary mutations. Proc Natl Acad Sci U S A. 1998 Sep 01; 95(18):10682-6. PMID: 9724764; PMCID: PMC27955.
      38. Socci ND, Onuchic J, Wolynes PG. Protein folding mechanisms and the multidimensional folding funnel. Proteins. 1998 Aug 01; 32(2):136-58. PMID: 9714155.
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      39. Nymeyer H, García AE, Onuchic J. Folding funnels and frustration in off-lattice minimalist protein landscapes. Proc Natl Acad Sci U S A. 1998 May 26; 95(11):5921-8. PMID: 9600893; PMCID: PMC34496.
      40. Onuchic J. Contacting the protein folding funnel with NMR. Proc Natl Acad Sci U S A. 1997 Jul 08; 94(14):7129-31. PMID: 9207055; PMCID: PMC34098.
      41. Onuchic J, Luthey-Schulten Z, Wolynes PG. Theory of protein folding: the energy landscape perspective. Annu Rev Phys Chem. 1997; 48:545-600. PMID: 9348663.
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      42. Wolynes P, Luthey-Schulten Z, Onuchic J. Fast-folding experiments and the topography of protein folding energy landscapes. Chem Biol. 1996 Jun; 3(6):425-32. PMID: 8807873.
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      43. Onuchic J, Socci ND, Luthey-Schulten Z, Wolynes PG. Protein folding funnels: the nature of the transition state ensemble. Fold Des. 1996; 1(6):441-50. PMID: 9080190.
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      44. Regan JJ, Di Bilio AJ, Langen R, Skov LK, Winkler JR, Gray HB, Onuchic J. Electron tunneling in azurin: the coupling across a beta-sheet. Chem Biol. 1995 Jul; 2(7):489-96. PMID: 9383451.
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      45. Wolynes PG, Onuchic J, Thirumalai D. Response. Science. 1995 May 19; 268(5213):960-1. PMID: 17774212.
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      46. Onuchic J, Wolynes PG, Luthey-Schulten Z, Socci ND. 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. PMID: 7724609; PMCID: PMC42220.
      47. Wolynes PG, Onuchic J, Thirumalai D. Navigating the folding routes. Science. 1995 Mar 17; 267(5204):1619-20. PMID: 7886447.
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      48. Bryngelson JD, Onuchic J, Socci ND, Wolynes PG. Funnels, pathways, and the energy landscape of protein folding: a synthesis. Proteins. 1995 Mar; 21(3):167-95. PMID: 7784423.
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      49. Leopold PE, Montal M, Onuchic J. 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. PMID: 1528885; PMCID: PMC49992.
      50. Onuchic J, Beratan DN, Winkler JR, Gray HB. Pathway analysis of protein electron-transfer reactions. Annu Rev Biophys Biomol Struct. 1992; 21:349-77. PMID: 1326356.
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      51. Beratan DN, Betts JN, Onuchic J. Protein electron transfer rates set by the bridging secondary and tertiary structure. Science. 1991 May 31; 252(5010):1285-8. PMID: 1656523.
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