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Troy W Whitfield PhD

TitleAssistant Professor
InstitutionUniversity of Massachusetts Medical School
DepartmentMedicine
AddressUniversity of Massachusetts Medical School
364 Plantation Street, LRB
Worcester MA 01605
Phone508-856-2272
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    Other Positions
    InstitutionUMMS - School of Medicine
    DepartmentMedicine

    InstitutionUMMS - School of Medicine
    DepartmentRadiology

    InstitutionUMMS - Programs, Centers and Institutes
    DepartmentBioinformatics and Integrative Biology


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    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Faculty can login to make corrections and additions.
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    PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Whitfield TW, Ragland DA, Zeldovich KB, Schiffer CA. Characterizing protein-ligand binding using atomistic simulation and machine learning: Application to drug resistance in HIV-1 protease. J Chem Theory Comput. 2019 Dec 26. PMID: 31877249.
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    2. Henes M, Kosovrasti K, Lockbaum GJ, Leidner F, Nachum GS, Nalivaika EA, Bolon DNA, Kurt Yilmaz N, Schiffer CA, Whitfield TW. Molecular determinants of epistasis in HIV-1 protease: Elucidating the interdependence of L89V and L90M mutations in resistance. Biochemistry. 2019 Aug 06. PMID: 31386353.
      Citations:    
    3. Boucher JI, Whitfield TW, Dauphin A, Nachum G, Hollins C, Zeldovich KB, Swanstrom R, Schiffer CA, Luban J, Bolon DNA. Constrained mutational sampling of amino acids in HIV-1 protease evolution. Mol Biol Evol. 2019 Feb 04. PMID: 30721995.
      Citations:    
    4. Canale AS, Venev SV, Whitfield TW, Caffrey DR, Marasco WA, Schiffer CA, Kowalik TF, Jensen JD, Finberg RW, Zeldovich KB, Wang JP, Bolon DNA. Synonymous mutations at the beginning of the influenza A virus hemagglutinin gene impact experimental fitness. J Mol Biol. 2018 Feb 18. PMID: 29466705.
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    5. Ragland DA, Whitfield TW, Lee SK, Swanstrom R, Zeldovich KB, Kurt-Yilmaz N, Schiffer CA. Elucidating the Interdependence of Drug Resistance from Combinations of Mutations. J Chem Theory Comput. 2017 Oct 09. PMID: 28915040.
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    6. Hall LL, Byron M, Carone DM, Whitfield TW, Pouliot GP, Fischer A, Jones P, Lawrence JB. Demethylated HSATII DNA and HSATII RNA Foci Sequester PRC1 and MeCP2 into Cancer-Specific Nuclear Bodies. Cell Rep. 2017 Mar 21; 18(12):2943-2956. PMID: 28329686.
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    7. Wu H, Gordon JA, Whitfield TW, Tai PW, van Wijnen AJ, Stein JL, Stein GS, Lian JB. Chromatin Dynamics Regulate Mesenchymal Stem Cell Lineage Specification and Differentiation to Osteogenesis. Biochim Biophys Acta. 2017 Jan 08. PMID: 28077316.
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    8. 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. PMID: 27487322.
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    9. 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. 2015 Dec 07; 36(4):615-27. PMID: 26644406.
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    10. 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 Apr 17; 16:309. PMID: 25928846.
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    11. 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. PMID: 25120271.
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    12. 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. PMID: 24881813.
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    13. 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 Mar 21; 15(3):R52. PMID: 24655370.
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    14. 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.
    15. 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 Sep 26; 13(9):R50. PMID: 22951020.
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    16. An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 06; 489(7414):57-74. PMID: 22955616.
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    17. 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. PMID: 22955990.
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    18. 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. PMID: 21633973.
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    19. A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046. PMID: 21526222.
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    20. 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. PMID: 20681718.
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    21. 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. PMID: 20187943.
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    22. 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. PMID: 20300554.
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    23. 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. PMID: 18302362.
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    24. 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. PMID: 17328590.
      Citations:    
    25. 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. PMID: 21785577.
      Citations:    
    26. 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. View Publication.
    27. 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.
    28. 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.
    29. 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.
    30. Whitfield TW, Straub JE. Gravitational smoothing as a global optimization strategy. J Comput Chem. 2002 Aug; 23(11):1100-3. PMID: 12116396.
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    31. Whitfield TW, Bu L, Straub JE. Generalized parallel sampling. Physica A. 2002; 305(1-2):157-171.
    32. 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. PMID: 11736244.
      Citations:    
    33. Whitfield TW, Straub JE . Uncertainty of path integral averages at low temperature. J Chem Phys. 2001; 115(15):6834-6840.
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