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551. Baldridge, Kim, Bourne, Philip E., (2002), "The new biology and the Grid": pg: 907--922
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552. Aksoylu, Burak, Holst, Michael, (2002), "An odyssey into local refinement and multilevel preconditioning I: Optimality of the BPX preconditioner", SIAM J. Numer. Anal: pg: 1--20
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553. Young, Alistair A., Dokos, Socrates, Powell, Kimerly A., Sturm, Bernhard, McCulloch, Andrew D., Starling, Randall C., McCarthy, Patrick M., White, Richard D., (2001), "Regional heterogeneity of function in nonischemic dilated cardiomyopathy.", Cardiovascular research, 49, 2: pg: 308--18, 1164937359 0008-6363, (DOI: 10.1016/S0008-6363(00)00248-0).
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554. Vetter, F. J., McCulloch, A. D., (2001), "Mechanoelectric feedback in a model of the passively inflated left ventricle", Annals of Biomedical Engineering, 29, 5: pg: 414--426, 00906964, (DOI: 10.1114/1.1366670).
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555. Usyk, T. P., Omens, J. H., McCulloch, A. D., (2001), "Regional septal dysfunction in a three-dimensional computational model of focal myofiber disarray.", American journal of physiology. Heart and circulatory physiology, 281, 2: pg: H506--14, 0363-6135, (DOI: 10.1016/j.jacc.2006.08.036).
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556. Tai, Kaishu, Shen, Tongye, Brjesson, Ulf, Philippopoulos, Marios, McCammon, J. Andrew, (2001), "Analysis of a 10-ns molecular dynamics simulation of mouse acetylcholinesterase.", Biophysical journal, 81, 2: pg: 715--24, 0006-3495 (Print)$\backslash$r0006-3495 (Linking) (DOI: 10.1016/S0006-3495(01)75736-0).
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557. Sung, D., and Mills, R., McCulloch, A. D., (2001), "Phase shifting prior to spatial filtering enhances optical recordings of cardiac action potential propagation.", Annals of biomedical engineering, 29, 10: pg: 854--61, 0090-6964, (DOI: 10.1114/1.1408927).
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558. Shindyalov, I. N., Bourne, P. E., (2001), "A database and tools for 3-D protein structure comparison and alignment using the Combinatorial Extension (CE) algorithm.", Nucleic acids research, 29, 1: pg: 228--9, 1362-4962 (Electronic)$\backslash$r0305-1048 (Link, (DOI: 10.1093/nar/29.1.228).
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559. Shoop, R. D., Chang, K. T., Ellisman, M. H., Berg, D. K., (2001), "Synaptically driven calcium transients via nicotinic receptors on somatic spines.", The Journal of neuroscience : the official journal of the Society for Neuroscience, 21, 3: pg: 771--81, 1529-2401 (Electronic) 1529-2401
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560. Sept, D., McCammon, J. A., (2001), "Thermodynamics and kinetics of actin filament nucleation.", Biophysical journal, 81, 2: pg: 667--74, 0006-3495 (Print) 0006-3495, (DOI: 10.1016/S0006-3495(01)75731-1).
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561. Reiter, L. T., (2001), "A Systematic Analysis of Human Disease-Associated Gene Sequences In Drosophila melanogaster", Genome Research, 11, 6: pg: 1114--1125, 10889051, (DOI: 10.1101/gr.169101).
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562. Ramakrishna, R., Edwards, J. S., McCulloch, A., Palsson, B. O., (2001), "Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints.", American journal of physiology. Regulatory, integrative and comparative physiology, 280, 3: pg: R695--704, 0363-6119 (Print) 0363-6119
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563. Paternostro, Giovanni, Vignola, Carlo, Bartsch, D. U., Omens, Jeff H., McCulloch, A. D., Reed, John C., (2001), "Age-Associated Cardiac Dysfunction in Drosophila melanogaster", Circulation Research, 88, 10: pg: 1053--1058, 0009-7330, (DOI: 10.1161/hh1001.090857).
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564. Nolen, Brad, Yun, Chi Y., Wong, Chung F., McCammon, J. A., Fu, X. D., Ghosh, G., (2001), "The structure of Sky1p reveals a novel mechanism for constitutive activity.", Nature structural biology, 8, 2: pg: 176--83, 1072-8368 (Print)$\backslash$r1072-8368 (Linking) (DOI: 10.1038/84178).
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565. Mser, P., Thomine, S., Schroeder, Julian I., Ward, John M., Hirschi, Kendal, Sze, Heven, Talke, Ina N., Amtmann, Anna, Maathuis, F. J., Sanders, Dale, Harper, Jeff F., Tchieu, Jason, Gribskov, Michael, Persans, Michael W., Salt, David E., Kim, Sun A., Guerinot, Mary Lou, (2001), "Phylogenetic relationships within cation transporter families of Arabidopsis.", Plant physiology, 126, 4: pg: 1646--67, 0032-0889 (Print) 0032-0889, (DOI: 10.1104/pp.126.4.1646).
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566. Michailova, A., McCulloch, A., (2001), "Model study of ATP and ADP buffering, transport of Ca(2+) and Mg(2+), and regulation of ion pumps in ventricular myocyte.", Biophysical journal, 81, 2: pg: 614--29, 0006-3495, (DOI: 10.1016/S0006-3495(01)75727-X).
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567. Masys, D. R., Welsh, J. B. and, (2001), "Use of keyword hierarchies to interpret gene expression patterns.", Bioinformatics (Oxford, England), 17, 4: pg: 319--26, 1367-4803, (DOI: 10.1093/bioinformatics/17.4.319).
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568. Harmon, Alice C., Gribskov, Michael, Gubrium, Erika, Harper, Jeffrey F., (2001), "The CDPK superfamily of protein kinases", New Phytologist, 151, 1: pg: 175--183, 1469-8137 0028646X, (DOI: 10.1046/j.1469-8137.2001.00171.x).
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569. Guda, C., Scheeff, E. D., Bourne, P. E., Shindyalov, I. N., (2001), "A new algorithm for the alignment of multiple protein structures using Monte Carlo optimization", Pac.Symp.Biocomput., 286: pg: 275
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570. Gribskov, M., Fana, F., Harper, J., Hope, D. a, Harmon, a C., Smith, D. W., Tax, F. E., Zhang, G., (2001), "PlantsP: a functional genomics database for plant phosphorylation.", Nucleic acids research, 29, 1: pg: 111--3, 1362-4962 (Electronic)$\backslash$r0305-1048 (Link, (DOI: 10.1093/nar/29.1.111).
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571. Ghassemian, Majid, Waner, David, Tchieu, Jason, Gribskov, Michael, Schroeder, Julian I., (2001), "An integrated Arabidopsis annotation database for Affymetrix Genechip data analysis, and tools for regulatory motif searches.", Trends in plant science, 6, 10: pg: 448--9, 1360-1385, (DOI: 10.1016/S1360-1385(01)02092-1).
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572. Elcock, A. H., McCammon, J. A., (2001), "Calculation of weak protein-protein interactions: the pH dependence of the second virial coefficient.", Biophysical journal, 80, 2: pg: 613--25, 0006-3495, (DOI: 10.1016/S0006-3495(01)76042-0).
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573. Elcock, a H., McCammon, J. a, (2001), "Identification of protein oligomerization states by analysis of interface conservation.", Proceedings of the National Academy of Sciences of the United States of America, 98, 6: pg: 2990--4, 0027-8424 (Print)$\backslash$r0027-8424 (Linking) (DOI: 10.1073/pnas.061411798).
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574. Baldridge, K. K., Siegel, J. S., (2001), "Quantum mechanical designs toward planar delocalized cyclooctatetraene: a new target for synthesis.", Journal of the American Chemical Society, 123, 8: pg: 1755--9, 0002-7863, (DOI: 10.1021/ja003383+).
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575. Baker, N. A., Sept, D., Joseph, S., Holst, M. J., McCammon, J. A., (2001), "Electrostatics of nanosystems: application to microtubules and the ribosome.", Proceedings of the National Academy of Sciences of the United States of America, 98, 18: pg: 10037--41, 0027-8424 (Print)$\backslash$r0027-8424 (Linking) (DOI: 10.1073/pnas.181342398).
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576. Baker, N. A., Sept, D., Holst, M. J., McCammon, J. A., (2001), "The adaptive multilevel finite element solution of the Poisson-Boltzmann equation on massively parallel computers", IBM Journal of Research and Development, 45, 3-4: pg: 1--27, 00188646
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577. Arts, T., Costa, K. D., Covell, J. W., McCulloch, A. D., (2001), "Relating myocardial laminar architecture to shear strain and muscle fiber orientation.", American journal of physiology. Heart and circulatory physiology, 280, 5: pg: H2222--9, 0363-6135 (Print) 0363-6135
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578. Andrianantoandro, E., Blanchoin, L., Sept, D., McCammon, J. a, Pollard, T. D., (2001), "Kinetic mechanism of end-to-end annealing of actin filaments.", Journal of molecular biology, 312, 4: pg: 721--30, 0022-2836 (Print)$\backslash$r0022-2836 (Linking) (DOI: 10.1006/jmbi.2001.5005).
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579. Wiseman, Paul W., Squier, J. A., Ellisman, M. H., Wilson, K. R., (2000), "Two-photon image correlation spectroscopy and image cross-correlation spectroscopy.", Journal of microscopy, 200, Pt 1: pg: 14--25, 0022-2720
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580. Westbrook, John D., Bourne, Philip E., (2000), "STAR/mmCIF: an ontology for macromolecular structure.", Bioinformatics (Oxford, England), 16, 2: pg: 159--68, 1367-4803
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581. Vetter, F. J., McCulloch, a D., (2000), "Three-dimensional stress and strain in passive rabbit left ventricle: a model study.", Annals of biomedical engineering, 28, 7: pg: 781--92, 0090-6964 (Print) 0090-6964, (DOI: 10.1114/1.1289469).
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582. Tsigelny, I., Shindyalov, I. N., Bourne, P. E., Sdhof, T. C., Taylor, P., (2000), "Common EF-hand motifs in cholinesterases and neuroligins suggest a role for Ca2+ binding in cell surface associations.", Protein science : a publication of the Protein Society, 9, 1: pg: 180--5, 0961-8368, (DOI: 10.1110/ps.9.1.180).
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583. Smallen, S., Crine, W., Frey, J., Berman, F., Wolski, Su, M. H., Kesselman, Young, S., Ellisman, M. H., (2000), "Combining workstations and supercomputers to support Grid applications: The parallel tomography experience", Proceedings 9th Heterogeneous Computing Workshop HCW 2000 Cat NoPR00556: pg: 241--252, 0769505562
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584. Mazhari, Reza, Omens, Jeffrey H., Covell, James W., McCulloch, Andrew D., (2000), "Structural basis of regional dysfunction in acutely ischemic myocardium.", Cardiovascular research, 47, 2: pg: 284--93, 0008-6363, (DOI: 10.1016/S0008-6363(00)00089-4).
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585. Gross, Larry A., Baird, Geoffrey S., Hoffman, Ross C., Baldridge, Kim K., Tsien, Roger Y., (2000), "The structure of the chromophore within DsRed, a red fluorescent protein from coral.", Proceedings of the National Academy of Sciences of the United States of America, 97, 22: pg: 11990--5, 0027-8424 (Print)$\backslash$r0027-8424 (Linking) (DOI: 10.1073/pnas.97.22.11990).
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586. Gad, H., Ringstad, N., Lw, P., Kjaerulff, O., Gustafsson, J., Wenk, M. and, (2000), "Fission and uncoating of synaptic clathrin-coated vesicles are perturbed by disruption of interactions with the SH3 domain of endophilin.", Neuron, 27, 2: pg: 301--12, 0896-6273 (Print) 0896-6273, (DOI: 10.1016/S0896-6273(00)00038-6).
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587. Fan, G. Y., Ellisman, M. H., (2000), "Digital imaging in transmission electron microscopy.", Journal of microscopy, 200, Pt 1: pg: 1--13, 0022-2720, (DOI: 10.1046/j.1365-2818.2000.00737.x).
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588. Bourne, Philip E., (2000), "Bioinformatics meets data mining: time to dance?", Trends in biotechnology, 18, 6: pg: 228--30, 0167-7799, (DOI: 10.1016/S0167-7799(00)01430-X).
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589. Bolding, Barry, Baldridge, Kim, (2000), "Multithreaded shared memory parallel implementation of the electronic structure code GAMESS", Computer Physics Communications, 128, 1-2: pg: 55--66, 00104655, (DOI: 10.1016/S0010-4655(00)00067-9).
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590. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N., Bourne, P. E., (2000), "The Protein Data Bank.", Nucleic acids research, 28, 1: pg: 235--42, 0305-1048, (DOI: 10.1093/nar/28.1.235).
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591. Baldridge, Kim K., Uzan, Olivier, Martin, Jan M. L., (2000), "The Silabenzenes: Structure, Properties, and Aromaticity", Organometallics, 19, 8: pg: 1477--1487, 0276-7333, (DOI: 10.1021/om9903745).
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592. Bailey, Timothy L., Gribskov, Michael, (2000), "Concerning the accuracy of MAST E-values.", Bioinformatics (Oxford, England), 16, 5: pg: 488--9, 1367-4803
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593. Weissig, H., Bourne, P. E., (1999), "An analysis of the Protein Data Bank in search of temporal and global trends.", Bioinformatics (Oxford, England), 15, 10: pg: 807--31, 1367-4803
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594. Sanner, Michel F., (1999), "Python: a programming language for software integration and development.", Journal of molecular graphics \& modelling, 17, 1: pg: 57--61, 1093-3263
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595. Rosin, C. D., Belew, R. K., Morris, G. M., Olson, a J., Goodsell, D. S., (1999), "Coevolutionary analysis of resistance-evading peptidomimetic inhibitors of HIV-1 protease.", Proceedings of the National Academy of Sciences of the United States of America, 96, 4: pg: 1369--74, 0027-8424 (Print)$\backslash$r0027-8424 (Linking) (DOI: 10.1073/pnas.96.4.1369).
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596. Quinn, Gregory B., Taylor, Ashton, Wang, Hsi Ping, Bourne, Philip E., (1999), "Development of Internet-based multimedia applications.", Trends in biochemical sciences, 24, 8: pg: 321--4, 0968-0004, (DOI: 10.1016/S0968-0004(99)01434-6).
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597. Baldridge, Kim K., O'Connor, Joseph M., Chen, Ming-Chou, Siegel, Jay S., (1999), "Envelope-Flip Dynamics in CpCo(Diene) Complexes: an ab Initio Quantum Mechanical Study", The Journal of Physical Chemistry A, 103, 49: pg: 10126--10131, 1089-5639, (DOI: 10.1021/jp992322z).
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598. Shindyalov, I. N., Bourne, P. E., (1998), "Protein structure alignment by incremental combinatorial extension (CE) of the optimal path.", Protein engineering, 11, 9: pg: 739--47, 0269-2139 (Print) 0269-2139, (DOI: 10.1093/protein/11.9.739).
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599. Morris, Garrett M., Goodsell, David S., Halliday, Robert S., Huey, Ruth, Hart, William E., Belew, Richard K., Olson, Arthur J., (1998), "Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function", Journal of Computational Chemistry, 19, 14: pg: 1639--1662, 0192-8651, (DOI: 10.1002/(SICI)1096-987X(19981115)19:14<1639::AID-JCC10>3.0.CO;2-B).
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600. Mazhari, R., Omens, J. H., Waldman, L. K., McCulloch, A. D., (1998), "Regional myocardial perfusion and mechanics: a model-based method of analysis.", Annals of biomedical engineering, 26, 5: pg: 743--55, 0090-6964 (Print) 0090-6964
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