Jose Onuchic

TitleEmeritus Professor
InstitutionUniversity of California San Diego
Address9500 Gilman Drive #0374
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.
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    1. Sengupta S, Nechushtai R, Jennings PA, Onuchic JN, Padilla PA, Azad RK, Mittler R. Phylogenetic analysis of the CDGSH iron-sulfur binding domain reveals its ancient origin. Sci Rep. 2018 Mar 19; 8(1):4840. PMID: 29556009.
      View in: PubMed
    2. Karmi O, Marjault HB, Pesce L, Carloni P, Onuchic JN, Jennings PA, Mittler R, Nechushtai R. 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 Feb 12. PMID: 29435647.
      View in: PubMed
    3. 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. Interactions between mitoNEET and NAF-1 in cells. PLoS One. 2017; 12(4):e0175796. PMID: 28426722.
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    4. Huang B, Lu M, Jia D, Ben-Jacob E, Levine H, Onuchic JN. Interrogating the topological robustness of gene regulatory circuits by randomization. PLoS Comput Biol. 2017 Mar; 13(3):e1005456. PMID: 28362798.
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    5. Inupakutika MA, Sengupta S, Nechushtai R, Jennings PA, Onuchic JN, 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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    6. Boareto M, Jolly MK, Goldman A, Pietilä M, Mani SA, Sengupta S, Ben-Jacob E, Levine H, Onuchic JN. Notch-Jagged signalling can give rise to clusters of cells exhibiting a hybrid epithelial/mesenchymal phenotype. J R Soc Interface. 2016 05; 13(118). PMID: 27170649; PMCID: PMC4892257.
    7. Noel JK, Morcos F, Onuchic JN. Sequence co-evolutionary information is a natural partner to minimally-frustrated models of biomolecular dynamics. F1000Res. 2016; 5. PMID: 26918164; PMCID: PMC4755392.
    8. Huang B, Jolly MK, Lu M, Tsarfaty I, Ben-Jacob E, Onuchic JN. Modeling the Transitions between Collective and Solitary Migration Phenotypes in Cancer Metastasis. Sci Rep. 2015 Dec 02; 5:17379. PMID: 26627083; PMCID: PMC4667179.
    9. Kirmizialtin S, Hennelly SP, Schug A, Onuchic JN, Sanbonmatsu KY. Integrating molecular dynamics simulations with chemical probing experiments using SHAPE-FIT. Methods Enzymol. 2015; 553:215-34. PMID: 25726467; PMCID: PMC4777697.
    10. Ben-Jacob E, Lu M, Schultz D, Onuchic JN. The physics of bacterial decision making. Front Cell Infect Microbiol. 2014; 4:154. PMID: 25401094; PMCID: PMC4214203.
    11. 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. 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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    12. 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.
      View in: PubMed
    13. Baxter EL, Zuris JA, Wang C, Vo PL, Axelrod HL, Cohen AE, Paddock ML, Nechushtai R, Onuchic JN, Jennings PA. Allosteric control in a metalloprotein dramatically alters function. Proc Natl Acad Sci U S A. 2013 Jan 15; 110(3):948-53. PMID: 23271805; PMCID: PMC3549116.
    14. Sulkowska JI, Noel JK, Onuchic JN. Energy landscape of knotted protein folding. Proc Natl Acad Sci U S A. 2012 Oct 30; 109(44):17783-8. PMID: 22891304; PMCID: PMC3497829.
    15. Sulkowska JI, Rawdon EJ, Millett KC, Onuchic JN, 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.
    16. Schug A, Weigt M, Hoch JA, Onuchic JN, 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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    17. Mills JE, Whitford PC, Shaffer J, Onuchic JN, 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.
    18. Onuchic JN, 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.
    19. Okazaki K, Koga N, Takada S, Onuchic JN, 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.
    20. Levy Y, Caflisch A, Onuchic JN, 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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    21. Onuchic JN, Wolynes PG. Theory of protein folding. Curr Opin Struct Biol. 2004 Feb; 14(1):70-5. PMID: 15102452.
      View in: PubMed
    22. Sung NS, Gordon JI, Rose GD, Getzoff ED, Kron SJ, Mumford D, Onuchic JN, 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 JN, 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.