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1.
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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.
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2.
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An integrated encyclopedia of DNA elements in the human genome. Nature. 2012 Sep 6; 489(7414):57-74.
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3.
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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.
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4.
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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.
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5.
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A user's guide to the encyclopedia of DNA elements (ENCODE). PLoS Biol. 2011 Apr; 9(4):e1001046.
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6.
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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.
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7.
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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.
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8.
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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.
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9.
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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.
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10.
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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.
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11.
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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.
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12.
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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 Mar 7; 124(9):94503.
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13.
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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 Mar 2; 110(8):3624-37.
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14.
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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.
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15.
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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.
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16.
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Whitfield TW, Straub JE. Gravitational smoothing as a global optimization strategy. J Comput Chem. 2002 Aug; 23(11):1100-3.
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17.
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Whitfield TW, Bu L, Straub JE. Generalized parallel sampling. Physica A. 2002; 305(1-2):157-171.
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18.
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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.
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19.
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Whitfield TW, Straub JE . Uncertainty of path integral averages at low temperature. J Chem Phys. 2001; 115(15):6834-6840.
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