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    Last Name

    Troy W Whitfield PhD

    TitleResearch Assistant Professor
    InstitutionUniversity of Massachusetts Medical School
    AddressUniversity of Massachusetts Medical School
    364 Plantation Street, LRB
    Worcester MA 01605
      Other Positions
      InstitutionUMMS - School of Medicine
      DepartmentCell and Developmental Biology

      InstitutionUMMS - Programs, Centers and Institutes
      DepartmentBioinformatics and Integrative Biology

        selected publications
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        1. Tavella D, Deveau LM, Whitfield TW, Massi F. Structural Basis of the Disorder in the Tandem Zinc Finger Domain of the RNA-Binding Protein Tristetraprolin. J Chem Theory Comput. 2016 Oct 11; 12(10):4717-4725.
          View in: PubMed
        2. Grandy RA, Whitfield TW, Wu H, Fitzgerald MP, VanOudenhove JJ, Zaidi SK, Montecino MA, Lian JB, van Wijnen AJ, Stein JL, Stein GS. Genome-Wide Studies Reveal that H3K4me3 Modification in Bivalent Genes Is Dynamically Regulated during the Pluripotent Cell Cycle and Stabilized upon Differentiation. Mol Cell Biol. 2016 Feb; 36(4):615-27.
          View in: PubMed
        3. Trombly DJ, Whitfield TW, Padmanabhan S, Gordon JA, Lian JB, van Wijnen AJ, Zaidi SK, Stein JL, Stein GS. Genome-wide co-occupancy of AML1-ETO and N-CoR defines the t(8;21) AML signature in leukemic cells. BMC Genomics. 2015; 16:309.
          View in: PubMed
        4. Barutcu AR, Tai PW, Wu H, Gordon JA, Whitfield TW, Dobson JR, Imbalzano AN, Lian JB, van Wijnen AJ, Stein JL, Stein GS. The bone-specific Runx2-P1 promoter displays conserved three-dimensional chromatin structure with the syntenic Supt3h promoter. Nucleic Acids Res. 2014; 42(16):10360-72.
          View in: PubMed
        5. Tai PW, Wu H, Gordon JA, Whitfield TW, Barutcu AR, van Wijnen AJ, Lian JB, Stein GS, Stein JL. Epigenetic landscape during osteoblastogenesis defines a differentiation-dependent Runx2 promoter region. Gene. 2014 Oct 15; 550(1):1-9.
          View in: PubMed
        6. Wu H, Whitfield TW, Gordon JA, Dobson JR, Tai PW, van Wijnen AJ, Stein JL, Stein GS, Lian JB. Genomic occupancy of Runx2 with global expression profiling identifies a novel dimension to control of osteoblastogenesis. Genome Biol. 2014; 15(3):R52.
          View in: PubMed
        7. Jones AP, Crain J, Sokhan VP, Whitfield TW, Martyna GJ. Quantum Drude oscillator model of atoms and molecules: Many-body polarization and dispersion interactions for atomistic simulation. Phys. Rev. B. 2013; 87(14):144103.
        8. Whitfield TW, Wang J, Collins PJ, Partridge EC, Aldred SF, Trinklein ND, Myers RM, Weng Z. Functional analysis of transcription factor binding sites in human promoters. Genome Biol. 2012; 13(9):R50.
          View in: PubMed
        9. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6; 489(7414):57-74.
          View in: PubMed
        10. Wang J, Zhuang J, Iyer S, Lin X, Whitfield TW, Greven MC, Pierce BG, Dong X, Kundaje A, Cheng Y, Rando OJ, Birney E, Myers RM, Noble WS, Snyder M, Weng Z. Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Res. 2012 Sep; 22(9):1798-812.
          View in: PubMed
        11. Hwang H, Vreven T, Whitfield TW, Wiehe K, Weng Z. A machine learning approach for the prediction of protein surface loop flexibility. Proteins. 2011 Aug; 79(8):2467-74.
          View in: PubMed
        12. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046.
          View in: PubMed
        13. Yu H, Mazzanti CL, Whitfield TW, Koeppe RE, Andersen OS, Roux B. A combined experimental and theoretical study of ion solvation in liquid N-methylacetamide. J Am Chem Soc. 2010 Aug 11; 132(31):10847-56.
          View in: PubMed
        14. Hung JH, Whitfield TW, Yang TH, Hu Z, Weng Z, DeLisi C. Identification of functional modules that correlate with phenotypic difference: the influence of network topology. Genome Biol. 2010; 11(2):R23.
          View in: PubMed
        15. Yu H, Whitfield TW, Harder E, Lamoureux G, Vorobyov I, Anisimov VM, Mackerell AD, Roux B. Simulating Monovalent and Divalent Ions in Aqueous Solution Using a Drude Polarizable Force Field. J Chem Theory Comput. 2010; 6(3):774-786.
          View in: PubMed
        16. Harder E, Anisimov VM, Whitfield T, MacKerell AD, Roux B. Understanding the dielectric properties of liquid amides from a polarizable force field. J Phys Chem B. 2008 Mar 20; 112(11):3509-21.
          View in: PubMed
        17. Whitfield TW, Martyna GJ. Low variance energy estimators for systems of quantum Drude oscillators: treating harmonic path integrals with large separations of time scales. J Chem Phys. 2007 Feb 21; 126(7):074104.
          View in: PubMed
        18. Whitfield TW, Varma S, Harder E, Lamoureux G, Rempe SB, Roux B. A theoretical study of aqueous solvation of K comparing ab initio, polarizable, and fixed-charge models. J Chem Theory Comput. 2007; 3(6):2068-2082.
          View in: PubMed
        19. Whitfield TW, Crain J, Martyna GJ. Structural properties of liquid N-methylacetamide via ab initio, path integral, and classical molecular dynamics. J. Chem. Phys. 2006; 9(124):094503.
        20. Whitfield TW, Martyna GJ, Allison S, Bates SP, Vass H, Crain J. Structure and hydrogen bonding in neat N-methylacetamide: Classical molecular dynamics and Raman spectroscopy studies of a liquid of peptidic fragments. J. Phys. Chem. B. 2006; 110(8):3624-3637.
        21. Whitfield TW, Martyna GJ. A unified formalism for many-body polarization and dispersion: The quantum Drude model applied to fluid xenon. Chem Phys Lett. 2006; 424(4-6):409-413.
        22. Whitfield TW, Martyna GJ, Allison S, Bates SP, Crain J. Liquid NMA: A surprisingly realistic model for hydrogen bonding motifs in proteins. Chem Phys Lett. 2005; 414(1-3):210-214.
        23. Whitfield TW, Straub JE. Gravitational smoothing as a global optimization strategy. J Comput Chem. 2002 Aug; 23(11):1100-3.
          View in: PubMed
        24. Whitfield TW, Bu L, Straub JE. Generalized parallel sampling. Physica A. 2002; 305(1-2):157-171.
        25. Whitfield TW, Straub JE. Enhanced sampling in numerical path integration: an approximation for the quantum statistical density matrix based on the nonextensive thermostatistics. Phys Rev E Stat Nonlin Soft Matter Phys. 2001 Dec; 64(6 Pt 2):066115.
          View in: PubMed
        26. Whitfield TW, Straub JE . Uncertainty of path integral averages at low temperature. J Chem Phys. 2001; 115(15):6834-6840.
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