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301. Perkins, Guy a, Sosinsky, Gina E., Ghassemzadeh, Sassan, Perez, Alex, Jones, Ying, Ellisman, Mark H., (2008), "Electron tomographic analysis of cytoskeletal cross-bridges in the paranodal region of the node of Ranvier in peripheral nerves.", Journal of structural biology, 161, 3: pg: 469--80, 1095-8657, (DOI: 10.1016/j.jsb.2007.10.005).
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302. Peachey, T. C., Diamond, N. T., Abramson, D. A., Sudholt, W., Michailova, A., Amirriazi, S., (2008), "Fractional factorial design for parameter sweep experiments using Nimrod E", Scientific Programming, 16: pg: 217--230, (DOI: 10.3233/SPR-2008-0250).
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303. Mura, Cameron, McCammon, J. Andrew, (2008), "Molecular dynamics of a kappaB DNA element: base flipping via cross-strand intercalative stacking in a microsecond-scale simulation.", Nucleic acids research, 36, 15: pg: 4941--55, 03051048 (ISSN) 1362-4962, (DOI: 10.1093/nar/gkn473).
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304. Morikis, Dimitrios, Elcock, Adrian H., Jennings, Patricia A., McCammon, J. Andrew, (2008), "Proton transfer dynamics of GART: The pH-dependent catalytic mechanism examined by electrostatic calculations", Protein Science, 10, 11: pg: 2379--2392, 09618368, (DOI: 10.1110/ps.17301).
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305. Mills, R. W., Narayan, S. M., McCulloch, A. D., (2008), "Mechanisms of conduction slowing during myocardial stretch by ventricular volume loading in the rabbit", Am J Physiol Heart Circ Physiol, 295, 3: pg: H1270--H1278, 0363-6135 (Print)$\backslash$r0363-6135 (Linking) (DOI: 10.1152/ajpheart.00350.2008).
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306. Mills, Robert W., Narayan, Sanjiv M., McCulloch, Andrew D., (2008), "Mechanisms of conduction slowing during myocardial stretch by ventricular volume loading in the rabbit.", American journal of physiology. Heart and circulatory physiology, 295, 3: pg: H1270--H1278, 0363-6135 (Print)$\backslash$r0363-6135 (Linking) (DOI: 10.1152/ajpheart.00350.2008).
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307. Michailova, Anushka, McCulloch, Andrew D., (2008), "Effects of Mg2+, pH and PCr on cardiac excitation-metabolic coupling.", Magnesium research, 21, 1: pg: 16--28, 0953-1424
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308. Michailova, Anushka, McCulloch, Andrew D., (2008), "Effects of Mg2+, pH and PCr on cardiac excitation-metabolic coupling.", Magnesium research, 21, 1: pg: 16--28, 0953-1424, (DOI: 10.1684/mrh.2008.0126).
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309. Martone, Maryann E., Tran, Joshua, Wong, Willy W., Sargis, Joy, Fong, Lisa, Larson, Stephen, Lamont, Stephan P., Gupta, Amarnath, Ellisman, Mark H., (2008), "The cell centered database project: an update on building community resources for managing and sharing 3D imaging data.", Journal of structural biology, 161, 3: pg: 220--31, 1095-8657, (DOI: 10.1016/j.jsb.2007.10.003).
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310. Lu, Benzhuo, McCammon, J. Andrew, (2008), "Molecular surface-free continuum model for electrodiffusion processes.", Chemical physics letters, 451, 4-6: pg: 282--286, 00092614 0009-2614, (DOI: 10.1016/j.cplett.2007.11.101).
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311. Lopreore, Courtney L., Bartol, Thomas M., Coggan, Jay S., Keller, Daniel X., Sosinsky, Gina E., Ellisman, Mark H., Sejnowski, Terrence J., (2008), "Computational modeling of three-dimensional electrodiffusion in biological systems: application to the node of Ranvier.", Biophysical journal, 95, 6: pg: 2624--35, 1542-0086 (Electronic)$\backslash$n0006-3495 (Link, (DOI: 10.1529/biophysj.108.132167).
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312. Lim, Byung-kwan, Xiong, Dingding, Dorner, Andrea, Youn, Tae-jin, Yung, Aaron, Liu, Taylor I., Gu, Yusu, Dalton, Nancy D., Wright, Adam T., Evans, Sylvia M., Chen, Ju, Peterson, Kirk L., McCulloch, Andrew D., Yajima, Toshitaka, Knowlton, Kirk U., (2008), "Coxsackievirus and adenovirus receptor (CAR) mediates atrioventricular-node function and connexin 45 localization in the murine heart.", The Journal of clinical investigation, 118, 8: pg: 2758--70, 0021-9738, (DOI: 10.1172/JCI34777).
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313. Li, Weihui, Gurev, Viatcheslav, McCulloch, Andrew D., Trayanova, Natalia A., (2008), "The role of mechanoelectric feedback in vulnerability to electric shock.", Progress in biophysics and molecular biology, 97, 2-3: pg: 461--78, 8585348585 0079-6107, (DOI: 10.1016/j.pbiomolbio.2008.02.020).
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314. Li, Weihui, Gurev, Viatcheslav, McCulloch, Andrew D., Trayanova, Natalia A., (2008), "The role of mechanoelectric feedback in vulnerability to electric shock.", Progress in biophysics and molecular biology, 97, 2-3: pg: 461--78, 8585348585 0079-6107, (DOI: 10.1016/j.pbiomolbio.2008.02.020).
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315. Lee, Sun-Joo, Song, Yuhua, Baker, Nathan a, (2008), "Molecular dynamics simulations of asymmetric NaCl and KCl solutions separated by phosphatidylcholine bilayers: potential drops and structural changes induced by strong Na+-lipid interactions and finite size effects.", Biophysical journal, 94, 9: pg: 3565--76, 3143622040 1542-0086, (DOI: 10.1529/biophysj.107.116335).
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316. Lanman, Jason, Crum, John, Deerinck, Thomas J., Gaietta, Guido M., Schneemann, Anette, Sosinsky, Gina E., Ellisman, Mark H., Johnson, John E., (2008), "Visualizing flock house virus infection in Drosophila cells with correlated fluorescence and electron microscopy.", Journal of structural biology, 161, 3: pg: 439--46, 1095-8657, (DOI: 10.1016/j.jsb.2007.09.009).
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317. Landon, Melissa R., Amaro, Rommie E., Baron, Riccardo, Ngan, Chi Ho, Ozonoff, David, McCammon, J. Andrew, Vajda, Sandor, (2008), "Novel druggable hot spots in avian influenza neuraminidase H5N1 revealed by computational solvent mapping of a reduced and representative receptor ensemble.", Chemical biology \& drug design, 71, 2: pg: 106--16, 1747-0277 1747-0285, (DOI: 10.1111/j.1747-0285.2007.00614.x).
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318. Khavrutskii, Ilja V., Dzubiella, Joachim, McCammon, J. Andrew, (2008), "Computing accurate potentials of mean force in electrolyte solutions with the generalized gradient-augmented harmonic Fourier beads method.", The Journal of chemical physics, 128, 4: pg: 044106, 0021-9606, (DOI: 10.1063/1.2825620).
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319. Kerckhoffs, Roy C. P., Narayan, Sanjiv M., Omens, Jeffrey H., Mulligan, Lawrence J., McCulloch, Andrew D., (2008), "Computational modeling for bedside application.", Heart failure clinics, 4, 3: pg: 371--8, 8585348585 1551-7136, (DOI: 10.1016/j.hfc.2008.02.009).
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320. Kerckhoffs, R. C. P., Lumens, J., Vernooy, K., Omens, J. H., Mulligan, L. J., Delhaas, T., Arts, T., McCulloch, A. D., Prinzen, F. W., (2008), "Cardiac resynchronization: insight from experimental and computational models.", Progress in biophysics and molecular biology, 97, 2-3: pg: 543--61, 0079-6107, (DOI: 10.1016/j.pbiomolbio.2008.02.024).
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321. Keator, David B., Grethe, J. S., Marcus, D., Ozyurt, B., Gadde, S., Murphy, Sean, Pieper, S., Greve, D., Notestine, R., Bockholt, H. J., Papadopoulos, P., and, Coordinating, Birn, (2008), "A national human neuroimaging collaboratory enabled by the Biomedical Informatics Research Network (BIRN).", IEEE transactions on information technology in biomedicine : a publication of the IEEE Engineering in Medicine and Biology Society, 12, 2: pg: 162--72, 2122633255 1089-7771, (DOI: 10.1109/TITB.2008.917893).
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322. Jin, Liang, Milazzo, Anna-Clare, Kleinfelder, Stuart, Li, Shengdong, Leblanc, Philippe, Duttweiler, Fred, Bouwer, James C., Peltier, Steven T., Ellisman, Mark H., Xuong, Nguyen-Huu, (2008), "Applications of direct detection device in transmission electron microscopy.", Journal of structural biology, 161, 3: pg: 352--8, 8585348585 1095-8657, (DOI: 10.1016/j.jsb.2007.10.007).
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323. Jacot, Jeffrey G., McCulloch, Andrew D., Omens, Jeffrey H., (2008), "Substrate stiffness affects the functional maturation of neonatal rat ventricular myocytes.", Biophysical journal, 95, 7: pg: 3479--87, 0006-3495 1542-0086, (DOI: 10.1529/biophysj.107.124545).
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324. Gorfe, Alemayehu A., McCammon, J. Andrew, (2008), "Similar membrane affinity of mono- and Di-S-acylated ras membrane anchors: a new twist in the role of protein lipidation.", Journal of the American Chemical Society, 130, 38: pg: 12624--5, 1520-5126 (Electronic) 1520-5126, (DOI: 10.1021/ja805110q).
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325. Gorfe, Alemayehu A., Grant, Barry J., McCammon, J. Andrew, (2008), "Mapping the nucleotide and isoform-dependent structural and dynamical features of Ras proteins.", Structure (London, England : 1993), 16, 6: pg: 885--96, 0969-2126 (Print) 0969-2126, (DOI: 10.1016/j.str.2008.03.009).
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326. Gorfe, Alemayehu A., Baron, Riccardo, McCammon, J. Andrew, (2008), "Water-membrane partition thermodynamics of an amphiphilic lipopeptide: an enthalpy-driven hydrophobic effect.", Biophysical journal, 95, 7: pg: 3269--77, 0006-3495 1542-0086, (DOI: 10.1529/biophysj.108.136481).
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327. Garduo, Edgar, Wong-Barnum, Mona, Volkmann, Niels, Ellisman, Mark H., (2008), "Segmentation of electron tomographic data sets using fuzzy set theory principles.", Journal of structural biology, 162, 3: pg: 368--79, 8585348585 1095-8657, (DOI: 10.1016/j.jsb.2008.01.017).
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328. Fajer, Mikolai, Hamelberg, Donald, McCammon, J. Andrew, (2008), "Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration.", Journal of chemical theory and computation, 4, 10: pg: 1565--1569, 1549-9618 1549-9626, (DOI: 10.1021/ct800250m).
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329. Dong, Feng, Olsen, Brett, Baker, Nathan A., (2008), "Computational methods for biomolecular electrostatics.", Methods in cell biology, 84, 8: pg: 843--70, 8585348585 0091-679X, (DOI: 10.1016/S0091-679X(07)84026-X).
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330. de Oliveira, Csar Augusto F., Hamelberg, Donald, McCammon, J. Andrew, (2008), "Coupling Accelerated Molecular Dynamics Methods with Thermodynamic Integration Simulations.", Journal of chemical theory and computation, 4, 9: pg: 1516--1525, 1549-9626, (DOI: 10.1021/ct800160q).
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331. Davalos, Dimitrios, Lee, Jae K., Smith, W. Bryan, Brinkman, Brendan, Ellisman, Mark H., Zheng, Binhai, Akassoglou, Katerina, (2008), "Stable in vivo imaging of densely populated glia, axons and blood vessels in the mouse spinal cord using two-photon microscopy.", Journal of neuroscience methods, 169, 1: pg: 1--7, 8585348585 0165-0270, (DOI: 10.1016/j.jneumeth.2007.11.011).
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332. Cosconati, Sandro, Hong, Jiyoung A., Novellino, Ettore, Carroll, Kate S., Goodsell, David S., Olson, Arthur J., (2008), "Structure-based virtual screening and biological evaluation of Mycobacterium tuberculosis adenosine 5'-phosphosulfate reductase inhibitors.", Journal of medicinal chemistry, 51, 21: pg: 6627--30, 1520-4804, (DOI: 10.1021/jm800571m).
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333. Coquin, Laurence, Feala, Jacob D., McCulloch, Andrew D., Paternostro, Giovanni, (2008), "Metabolomic and flux-balance analysis of age-related decline of hypoxia tolerance in Drosophila muscle tissue.", Molecular systems biology, 4, 233: pg: 233, 1744-4292 (Electronic) 1744-4292, (DOI: 10.1038/msb.2008.71).
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334. Chang, Max W., Belew, Richard K., Carroll, Kate S., Olson, Arthur J., Goodsell, David S., (2008), "Empirical entropic contributions in computational docking: evaluation in APS reductase complexes.", Journal of computational chemistry, 29, 11: pg: 1753--61, 1096-987X, (DOI: 10.1002/jcc.20936).
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335. Chang, Chia-En A., McLaughlin, William A., Baron, Riccardo, Wang, Wei, McCammon, J. Andrew, (2008), "Entropic contributions and the influence of the hydrophobic environment in promiscuous protein-protein association.", Proceedings of the National Academy of Sciences of the United States of America, 105, 21: pg: 7456--61, 1091-6490 (Electronic) 1091-6490, (DOI: 10.1073/pnas.0800452105).
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336. Canales, Jos, Fernndez, Ascensin, Ribeiro, Joo Meireles, Cabezas, Alicia, Rodrigues, Joaquim Rui, Cameselle, Jos Carlos, Costas, Mara Jess, (2008), "Mn2+-dependent ADP-ribose/CDP-alcohol pyrophosphatase: a novel metallophosphoesterase family preferentially expressed in rodent immune cells.", The Biochemical journal, 413, 1: pg: 103--13, 1470-8728 (Electronic)$\backslash$r0264-6021 (Link, (DOI: 10.1042/BJ20071471).
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337. Campbell, Stuart G., Flaim, Sarah N., Leem, Chae H., McCulloch, Andrew D., (2008), "Mechanisms of transmurally varying myocyte electromechanics in an integrated computational model.", Philosophical transactions. Series A, Mathematical, physical, and engineering sciences, 366, 1879: pg: 3361--80, 1364-503X (Print)$\backslash$r1364-503X (Linking) (DOI: 10.1098/rsta.2008.0088).
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338. Campbell, Patrick H., Hunt, Darlene L., Jones, Ying, Harwood, Fred, Amiel, David, Omens, Jeffrey H., McCulloch, Andrew D., (2008), "Effects of biglycan deficiency on myocardial infarct structure and mechanics.", Molecular \& cellular biomechanics : MCB, 5, 1: pg: 27--35, 1556-5297
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339. Calzolari, Diego, Bruschi, Stefania, Coquin, Laurence, Schofield, Jennifer, Feala, Jacob D., Reed, John C., McCulloch, Andrew D., Paternostro, Giovanni, (2008), "Search algorithms as a framework for the optimization of drug combinations.", PLoS computational biology, 4, 12: pg: e1000249, 1553-7358 (Electronic)$\backslash$r1553-734X (Link, (DOI: 10.1371/journal.pcbi.1000249).
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340. Bradley, Michael J., Chivers, Peter T., Baker, Nathan A., (2008), "Molecular dynamics simulation of the Escherichia coli NikR protein: equilibrium conformational fluctuations reveal interdomain allosteric communication pathways.", Journal of molecular biology, 378, 5: pg: 1155--73, 8585348585 1089-8638, (DOI: 10.1016/j.jmb.2008.03.010).
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341. Baron, Riccardo, Wong, Sergio E., de Oliveira, Cesar A. F., McCammon, J. Andrew, (2008), "E9-Im9 colicin DNase-immunity protein biomolecular association in water: a multiple-copy and accelerated molecular dynamics simulation study.", The journal of physical chemistry. B, 112, 51: pg: 16802--14, 1858534291 1520-6106, (DOI: 10.1021/jp8061543).
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342. Baron, Riccardo, McCammon, J. Andrew, (2008), "(Thermo)dynamic role of receptor flexibility, entropy, and motional correlation in protein-ligand binding.", Chemphyschem : a European journal of chemical physics and physical chemistry, 9, 7: pg: 983--8, 1439-7641 (Electronic) 1439-7641, (DOI: 10.1002/cphc.200700857).
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343. Barglow, Katherine T., Saikatendu, Kumar S., Bracey, Michael H., Huey, Ruth, Morris, Garrett M., Olson, Arthur J., Stevens, Raymond C., Cravatt, Benjamin F., (2008), "Functional proteomic and structural insights into molecular recognition in the nitrilase family enzymes.", Biochemistry, 47, 51: pg: 13514--23, 1520-4995, (DOI: 10.1021/bi801786y).
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344. Babakhani, Arneh, Gorfe, Alemayehu A., Kim, Judy E., McCammon, J. Andrew, (2008), "Thermodynamics of peptide insertion and aggregation in a lipid bilayer.", The journal of physical chemistry. B, 112, 34: pg: 10528--34, 1520-6106, (DOI: 10.1021/jp804710v).
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345. Amaro, Rommie E., Schnaufer, Achim, Interthal, Heidrun, Hol, Wim, Stuart, Kenneth D., McCammon, J. Andrew, (2008), "Discovery of drug-like inhibitors of an essential RNA-editing ligase in Trypanosoma brucei.", Proceedings of the National Academy of Sciences of the United States of America, 105, 45: pg: 17278--83, 0027-8424 1091-6490, (DOI: 10.1073/pnas.0805820105).
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346. Amaro, Rommie E., Baron, Riccardo, McCammon, J. Andrew, (2008), "An improved relaxed complex scheme for receptor flexibility in computer-aided drug design.", Journal of computer-aided molecular design, 22, 9: pg: 693--705, 0920-654X, (DOI: 10.1007/s10822-007-9159-2).
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347. Zhang, Yibing, Sekar, Rajesh B., McCulloch, Andrew D., Tung, Leslie, (2008), "Cell cultures as models of cardiac mechanoelectric feedback.", Progress in biophysics and molecular biology, 97, 2-3: pg: 367--82, 8585348585 0079-6107, (DOI: 10.1016/j.pbiomolbio.2008.02.017).
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348. Zhao, Yong, Sanner, Michel F., (2008), "Protein-ligand docking with multiple flexible side chains.", Journal of computer-aided molecular design, 22, 9: pg: 673--9, 0000000000000 0920-654X, (DOI: 10.1007/s10822-007-9148-5).
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349. Zhou, Y. C., Holst, Michael, McCammon, J. Andrew, (2008), "A Nonlinear Elasticity Model of Macromolecular Conformational Change Induced by Electrostatic Forces.", Journal of mathematical analysis and applications, 340, 1: pg: 135--164, 0022247X 0022-247X, (DOI: 10.1016/j.jmaa.2007.07.084).
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350. Zhou, Y. C., Lu, Benzhuo, Huber, Gary A., Holst, Michael J., McCammon, J. Andrew, (2008), "Continuum simulations of acetylcholine consumption by acetylcholinesterase: a Poisson-Nernst-Planck approach.", The journal of physical chemistry. B, 112, 2: pg: 270--5, 1520-6106, (DOI: 10.1021/jp074900e).
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