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    Terence Hwa

    SchoolUniversity of California, San Diego
    DepartmentMolecular Biology
    Address9500 Gilman Drive #0374
    CA La Jolla 92093
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      Collapse Research 
      Collapse Research Activities and Funding
      Quantitative studies of metabolic switches in enteric bacteria
      NIH/NIGMS R01GM109069Feb 17, 2014 - Jan 31, 2018
      Role: Principal Investigator
      Quantitative Studies of Bacterial Growth Physiology
      NIH/NIGMS R01GM095903Aug 1, 2011 - Aug 31, 2019
      Role: Principal Investigator
      Quantitative Characterization &Modeling of sRNA-Mediated Gene Regulation
      NIH/NIGMS R01GM077298May 1, 2007 - Apr 30, 2012
      Role: Principal Investigator
      Combinational Transcription Control in Bacteria
      NIH/NIGMS R21GM070915Apr 1, 2004 - Sep 30, 2007
      Role: Principal Investigator

      Collapse Bibliographic 
      Collapse Publications
      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.
      List All   |   Timeline
      1. Cremer J, Arnoldini M, Hwa T. Effect of water flow and chemical environment on microbiota growth and composition in the human colon. Proc Natl Acad Sci U S A. 2017 Jun 20; 114(25):6438-6443. PMID: 28588144.
        View in: PubMed
      2. Basan M, Zhu M, Dai X, Warren M, Sévin D, Wang YP, Hwa T. Inflating bacterial cells by increased protein synthesis. Mol Syst Biol. 2015 Oct 30; 11(10):836. PMID: 26519362; PMCID: PMC4631207.
      3. Hermsen R, Okano H, You C, Werner N, Hwa T. A growth-rate composition formula for the growth of E.coli on co-utilized carbon substrates. Mol Syst Biol. 2015 Apr 09; 11(4):801. PMID: 25862745; PMCID: PMC4422558.
      4. Hui S, Silverman JM, Chen SS, Erickson DW, Basan M, Wang J, Hwa T, Williamson JR. Quantitative proteomic analysis reveals a simple strategy of global resource allocation in bacteria. Mol Syst Biol. 2015 Feb 12; 11(1):784. PMID: 25678603; PMCID: PMC4358657.
      5. Deris JB, Kim M, Zhang Z, Okano H, Hermsen R, Groisman A, Hwa T. The innate growth bistability and fitness landscapes of antibiotic-resistant bacteria. Science. 2013 Nov 29; 342(6162):1237435. PMID: 24288338; PMCID: PMC4059556.
      6. You C, Okano H, Hui S, Zhang Z, Kim M, Gunderson CW, Wang YP, Lenz P, Yan D, Hwa T. Coordination of bacterial proteome with metabolism by cyclic AMP signalling. Nature. 2013 Aug 15; 500(7462):301-6. PMID: 23925119; PMCID: PMC4038431.
      7. Hermsen R, Deris JB, Hwa T. On the rapidity of antibiotic resistance evolution facilitated by a concentration gradient. Proc Natl Acad Sci U S A. 2012 Jul 03; 109(27):10775-80. PMID: 22711808; PMCID: PMC3390829.
      8. Sulkowska JI, Morcos F, Weigt M, Hwa T, Onuchic JN. Genomics-aided structure prediction. Proc Natl Acad Sci U S A. 2012 Jun 26; 109(26):10340-5. PMID: 22691493; PMCID: PMC3387073.
      9. Kim M, Zhang Z, Okano H, Yan D, Groisman A, Hwa T. Need-based activation of ammonium uptake in Escherichia coli. Mol Syst Biol. 2012; 8:616. PMID: 23010999; PMCID: PMC3472687.
      10. Morcos F, Pagnani A, Lunt B, Bertolino A, Marks DS, Sander C, Zecchina R, Onuchic JN, Hwa T, Weigt M. Direct-coupling analysis of residue coevolution captures native contacts across many protein families. Proc Natl Acad Sci U S A. 2011 Dec 06; 108(49):E1293-301. PMID: 22106262; PMCID: PMC3241805.
      11. Hermsen R, Erickson DW, Hwa T. Speed, sensitivity, and bistability in auto-activating signaling circuits. PLoS Comput Biol. 2011 Nov; 7(11):e1002265. PMID: 22125482; PMCID: PMC3219618.
      12. McHale P, Mizutani CM, Kosman D, MacKay DL, Belu M, Hermann A, McGinnis W, Bier E, Hwa T. Gene length may contribute to graded transcriptional responses in the Drosophila embryo. Dev Biol. 2011 Dec 01; 360(1):230-40. PMID: 21920356; PMCID: PMC3661008.
      13. Hermsen R, Hwa T. Sources and sinks: a stochastic model of evolution in heterogeneous environments. Phys Rev Lett. 2010 Dec 10; 105(24):248104. PMID: 21231560; PMCID: PMC4038430.
      14. Scott M, Gunderson CW, Mateescu EM, Zhang Z, Hwa T. Interdependence of cell growth and gene expression: origins and consequences. Science. 2010 Nov 19; 330(6007):1099-102. PMID: 21097934.
        View in: PubMed
      15. 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.
        View in: PubMed
      16. Klumpp S, Zhang Z, Hwa T. Growth rate-dependent global effects on gene expression in bacteria. Cell. 2009 Dec 24; 139(7):1366-75. PMID: 20064380; PMCID: PMC2818994.
      17. Schug A, Weigt M, Onuchic JN, Hwa T, Szurmant H. High-resolution protein complexes from integrating genomic information with molecular simulation. Proc Natl Acad Sci U S A. 2009 Dec 29; 106(52):22124-9. PMID: 20018738; PMCID: PMC2799721.
      18. Klumpp S, Hwa T. Traffic patrol in the transcription of ribosomal RNA. RNA Biol. 2009 Sep-Oct; 6(4):392-4. PMID: 19502817; PMCID: PMC2859892.
      19. Weigt M, White RA, Szurmant H, Hoch JA, Hwa T. Identification of direct residue contacts in protein-protein interaction by message passing. Proc Natl Acad Sci U S A. 2009 Jan 06; 106(1):67-72. PMID: 19116270; PMCID: PMC2629192.
      20. Klumpp S, Hwa T. Growth-rate-dependent partitioning of RNA polymerases in bacteria. Proc Natl Acad Sci U S A. 2008 Dec 23; 105(51):20245-50. PMID: 19073937; PMCID: PMC2629260.
      21. Klumpp S, Hwa T. Stochasticity and traffic jams in the transcription of ribosomal RNA: Intriguing role of termination and antitermination. Proc Natl Acad Sci U S A. 2008 Nov 25; 105(47):18159-64. PMID: 19017803; PMCID: PMC2587539.
      22. Levine E, Hwa T. Small RNAs establish gene expression thresholds. Curr Opin Microbiol. 2008 Dec; 11(6):574-9. PMID: 18935980; PMCID: PMC2613760.
      23. Liu J, Desai A, Onuchic JN, Hwa T. An integrated mechanobiochemical feedback mechanism describes chromosome motility from prometaphase to anaphase in mitosis. Proc Natl Acad Sci U S A. 2008 Sep 16; 105(37):13752-7. PMID: 18780795; PMCID: PMC2544526.
      24. Liu J, Desai A, Onuchic JN, Hwa T. A mechanobiochemical mechanism for monooriented chromosome oscillation in mitosis. Proc Natl Acad Sci U S A. 2007 Oct 09; 104(41):16104-9. PMID: 17911248; PMCID: PMC2042169.
      25. Levine E, Zhang Z, Kuhlman T, Hwa T. Quantitative characteristics of gene regulation by small RNA. PLoS Biol. 2007 Sep; 5(9):e229. PMID: 17713988; PMCID: PMC1994261.
      26. Levine E, Hwa T. Stochastic fluctuations in metabolic pathways. Proc Natl Acad Sci U S A. 2007 May 29; 104(22):9224-9. PMID: 17517669; PMCID: PMC1890476.
      27. Scott M, Hwa T, Ingalls B. Deterministic characterization of stochastic genetic circuits. Proc Natl Acad Sci U S A. 2007 May 01; 104(18):7402-7. PMID: 17446275; PMCID: PMC1863463.
      28. Kuhlman T, Zhang Z, Saier MH, Hwa T. Combinatorial transcriptional control of the lactose operon of Escherichia coli. Proc Natl Acad Sci U S A. 2007 Apr 03; 104(14):6043-8. PMID: 17376875; PMCID: PMC1851613.
      29. Gerland U, Bundschuh R, Hwa T. Translocation of structured polynucleotides through nanopores. Phys Biol. 2004 Jun; 1(1-2):19-26. PMID: 16204818.
        View in: PubMed
      30. Peng W, Levine H, Hwa T, Kessler DA. Analytical study of the effect of recombination on evolution via DNA shuffling. Phys Rev E Stat Nonlin Soft Matter Phys. 2004 May; 69(5 Pt 1):051911. PMID: 15244851.
        View in: PubMed
      31. Arndt PF, Petrov DA, Hwa T. Distinct changes of genomic biases in nucleotide substitution at the time of Mammalian radiation. Mol Biol Evol. 2003 Nov; 20(11):1887-96. PMID: 12885958.
        View in: PubMed
      32. Gerland U, Bundschuh R, Hwa T. Mechanically probing the folding pathway of single RNA molecules. Biophys J. 2003 May; 84(5):2831-40. PMID: 12719217; PMCID: PMC1302848.
      33. Buchler NE, Gerland U, Hwa T. On schemes of combinatorial transcription logic. Proc Natl Acad Sci U S A. 2003 Apr 29; 100(9):5136-41. PMID: 12702751; PMCID: PMC404558.
      34. Hwa T, Marinari E, Sneppen K, Tang LH. Localization of denaturation bubbles in random DNA sequences. Proc Natl Acad Sci U S A. 2003 Apr 15; 100(8):4411-6. PMID: 12672955; PMCID: PMC404689.
      35. Peng W, Gerland U, Hwa T, Levine H. Dynamics of competitive evolution on a smooth landscape. Phys Rev Lett. 2003 Feb 28; 90(8):088103. PMID: 12633464.
        View in: PubMed
      36. Arndt PF, Burge CB, Hwa T. DNA sequence evolution with neighbor-dependent mutation. J Comput Biol. 2003; 10(3-4):313-22. PMID: 12935330.
        View in: PubMed
      37. Gerland U, Hwa T. On the selection and evolution of regulatory DNA motifs. J Mol Evol. 2002 Oct; 55(4):386-400. PMID: 12355260.
        View in: PubMed
      38. Gerland U, Moroz JD, Hwa T. Physical constraints and functional characteristics of transcription factor-DNA interaction. Proc Natl Acad Sci U S A. 2002 Sep 17; 99(19):12015-20. PMID: 12218191; PMCID: PMC129390.
      39. Bundschuh R, Hwa T. Statistical mechanics of secondary structures formed by random RNA sequences. Phys Rev E Stat Nonlin Soft Matter Phys. 2002 Mar; 65(3 Pt 1):031903. PMID: 11909105.
        View in: PubMed
      40. Sásik R, Iranfar N, Hwa T, Loomis WF. Extracting transcriptional events from temporal gene expression patterns during Dictyostelium development. Bioinformatics. 2002 Jan; 18(1):61-6. PMID: 11836212.
        View in: PubMed
      41. Gerland U, Bundschuh R, Hwa T. Force-induced denaturation of RNA. Biophys J. 2001 Sep; 81(3):1324-32. PMID: 11509348; PMCID: PMC1301613.
      42. Iranfar N, Fuller D, Sasik R, Hwa T, Laub M, Loomis WF. Expression patterns of cell-type-specific genes in Dictyostelium. Mol Biol Cell. 2001 Sep; 12(9):2590-600. PMID: 11553701; PMCID: PMC59697.
      43. Sásik R, Hwa T, Iranfar N, Loomis WF. Percolation clustering: a novel approach to the clustering of gene expression patterns in Dictyostelium development. Pac Symp Biocomput. 2001; 335-47. PMID: 11262953.
        View in: PubMed
      44. Olsen R, Bundschuh R, Hwa T. Rapid assessment of extremal statistics for gapped local alignment. Proc Int Conf Intell Syst Mol Biol. 1999; 211-22. PMID: 10786304.
        View in: PubMed
      45. Olsen R, Hwa T, Lässig M. Optimizing Smith-Waterman alignments. Pac Symp Biocomput. 1999; 302-13. PMID: 10380206.
        View in: PubMed