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351. 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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352. 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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353. 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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354. 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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355. Zemljic-Harpf, Alice E., Miller, Joel C., Henderson, Scott a, Wright, Adam T., Manso, Ana Maria, Elsherif, Laila, Dalton, Nancy D., Thor, Andrea K., Perkins, Guy a, McCulloch, Andrew D., Ross, Robert S., (2007), "Cardiac-myocyte-specific excision of the vinculin gene disrupts cellular junctions, causing sudden death or dilated cardiomyopathy.", Molecular and cellular biology, 27, 21: pg: 7522--37, 0270-7306, (DOI: 10.1128/MCB.00728-07).
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356. Ye, Chun, Eskin, Eleazar, (2007), "Discovering tightly regulated and differentially expressed gene sets in whole genome expression data.", Bioinformatics (Oxford, England), 23, 2: pg: e84--90, 1367-4811, (DOI: 10.1093/bioinformatics/btl315).
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357. Xuong, Nguyen-Huu, Jin, Liang, Kleinfelder, Stuart, Li, Shengdong, Leblanc, Philippe, Duttweiler, Fred, Bouwer, James C., Peltier, Steven T., Milazzo, Anna-Clare, Ellisman, Mark, (2007), "Future directions for camera systems in electron microscopy.", Methods in cell biology, 79, 06: pg: 721--39, 9780123706478 0091-679X, (DOI: 10.1016/S0091-679X(06)79028-8).
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358. Xu, Lan, Chong, Youhoon, Hwang, Inkyu, D'Onofrio, Anthony, Amore, Kristen, Beardsley, G. Peter, Li, Chenglong, Olson, Arthur J., Boger, Dale L., Wilson, Ian A., (2007), "Structure-based design, synthesis, evaluation, and crystal structures of transition state analogue inhibitors of inosine monophosphate cyclohydrolase.", The Journal of biological chemistry, 282, 17: pg: 13033--46, 0021-9258 (Print)$\backslash$r0021-9258 (Linking) (DOI: 10.1074/jbc.M607293200).
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359. Xie, Lei, Wang, Jian, Bourne, Philip E., (2007), "In silico elucidation of the molecular mechanism defining the adverse effect of selective estrogen receptor modulators.", PLoS computational biology, 3, 11: pg: e217, 1553-7358, (DOI: 10.1371/journal.pcbi.0030217).
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360. Ultanir, Sila K., Kim, Ji-Eun, Hall, Benjamin J., Deerinck, Thomas, Ellisman, Mark, Ghosh, Anirvan, (2007), "Regulation of spine morphology and spine density by NMDA receptor signaling in vivo.", Proceedings of the National Academy of Sciences of the United States of America, 104, 49: pg: 19553--8, 1091-6490 (Electronic)$\backslash$n0027-8424 (Link, (DOI: 10.1073/pnas.0704031104).
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361. Trylska, Joanna, Tozzini, Valentina, Chang, Chia-en A., McCammon, J. Andrew, (2007), "HIV-1 protease substrate binding and product release pathways explored with coarse-grained molecular dynamics.", Biophysical journal, 92, 12: pg: 4179--87, 0006-3495 (Print) 0006-3495, (DOI: 10.1529/biophysj.106.100560).
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362. Tozzini, Valentina, Trylska, Joanna, Chang, Chia-en, McCammon, J. Andrew, (2007), "Flap opening dynamics in HIV-1 protease explored with a coarse-grained model.", Journal of structural biology, 157, 3: pg: 606--15, 3905050943 1047-8477, (DOI: 10.1016/j.jsb.2006.08.005).
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363. Swanson, Jessica M. J., Wagoner, Jason A., Baker, Nathan A., McCammon, J. A., (2007), "Optimizing the Poisson Dielectric Boundary with Explicit Solvent Forces and Energies: Lessons Learned with Atom-Centered Dielectric Functions.", Journal of chemical theory and computation, 3, 1: pg: 170--83, 1549-9618, (DOI: 10.1021/ct600216k).
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364. Pezzoli, Keith, Tukey, Robert, Sarabia, Hiram, Zaslavsky, Ilya, Miranda, Marie Lynn, Suk, William A., Lin, Abel, Ellisman, Mark, (2007), "The NIEHS Environmental Health Sciences Data Resource Portal: placing advanced technologies in service to vulnerable communities.", Environmental health perspectives, 115, 4: pg: 564--71, 0091-6765 (Print) 0091-6765, (DOI: 10.1289/ehp.9817).
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365. Papadopoulos, Philip, Bruno, Greg, Katz, Mason J., (2007), "Beyound Beowulf Clusters", Acm Queue, April:
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366. Olson, Arthur J., Hu, Yunfeng H. E., Keinan, Ehud, (2007), "Chemical mimicry of viral capsid self-assembly.", Proceedings of the National Academy of Sciences of the United States of America, 104, 52: pg: 20731--6, 1091-6490 (Electronic)$\backslash$r0027-8424 (Link, (DOI: 10.1073/pnas.0709489104).
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367. Ngo, Jacky Chi Ki, Gullingsrud, Justin, Giang, Kayla, Yeh, Melinda Jean, Fu, Xiang-Dong, Adams, Joseph A., McCammon, J. Andrew, Ghosh, Gourisankar, (2007), "SR protein kinase 1 is resilient to inactivation.", Structure (London, England : 1993), 15, 1: pg: 123--33, 0969-2126 (Print)$\backslash$r0969-2126 (Linking) (DOI: 10.1016/j.str.2006.11.011).
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368. Minh, David D. L., Hamelberg, Donald, McCammon, J. Andrew, (2007), "Accelerated entropy estimates with accelerated dynamics.", The Journal of chemical physics, 127, 15: pg: 154105, 0021-9606, (DOI: 10.1063/1.2794754).
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369. Mongan, John, Simmerling, Carlos, McCammon, J. ANdrew, Case, David A., Onufriev, Alexey, (2007), "Generalized Born model with a simple, robust molecular volume correction.", Journal of chemical theory and computation, 3, 1: pg: 156--169, 1549-9618 (Print)$\backslash$r1549-9618 (Linking) (DOI: 10.1021/ct600085e).
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370. Michailova, Anushka, Lorentz, William, McCulloch, Andrew, (2007), "Modeling transmural heterogeneity of K(ATP) current in rabbit ventricular myocytes.", American journal of physiology. Cell physiology, 293, 2: pg: C542--57, 0363-6143, (DOI: 10.1152/ajpcell.00148.2006).
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371. Lu, Benzhuo, Zhou, Y. C., Huber, Gary A., Bond, Stephen D., Holst, Michael J., McCammon, J. Andrew, (2007), "Electrodiffusion: a continuum modeling framework for biomolecular systems with realistic spatiotemporal resolution.", The Journal of chemical physics, 127, 13: pg: 135102, 0021-9606, (DOI: 10.1063/1.2775933).
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372. Lu, Benzhuo, McCammon, J. Andrew, (2007), "Improved Boundary Element Methods for Poisson-Boltzmann Electrostatic Potential and Force Calculations.", Journal of chemical theory and computation, 3, 3: pg: 1134--42, 1549-9618, (DOI: 10.1021/ct700001x).
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373. Kerckhoffs, Roy C. P., Neal, Maxwell L., Gu, Quan, Bassingthwaighte, James B., Omens, Jeff H., McCulloch, Andrew D., (2007), "Coupling of a 3D finite element model of cardiac ventricular mechanics to lumped systems models of the systemic and pulmonic circulation.", Annals of biomedical engineering, 35, 1: pg: 1--18, 1043900692127 0090-6964, (DOI: 10.1007/s10439-006-9212-7).
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374. Kerckhoffs, Roy C. P., McCulloch, Andrew D., Omens, Jeffrey H., Mulligan, Lawrence J., (2007), "Effect of Pacing Site and Infarct Location on Regional Mechanics and Global Hemodynamics in a Model Based Study of Heart Failure": pg: 350--360, 978-3-540-72906-8 03029743, (DOI: 10.1007/978-3-540-72907-5_36).
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375. Ju, Won-Kyu, Liu, Quan, Kim, Keun-Young, Crowston, Jonathan G., Lindsey, James D., Agarwal, Neeraj, Ellisman, Mark H., Perkins, Guy A., Weinreb, Robert N., (2007), "Elevated hydrostatic pressure triggers mitochondrial fission and decreases cellular ATP in differentiated RGC-5 cells.", Investigative ophthalmology \& visual science, 48, 5: pg: 2145--51, 0146-0404 (Print) 0146-0404, (DOI: 10.1167/iovs.06-0573).
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376. Johnson, Jerry E., Perkins, Guy A., Giddabasappa, Anand, Chaney, Shawntay, Xiao, Weimin, White, Andrew D., Brown, Joshua M., Waggoner, Jenna, Ellisman, Mark H., Fox, Donald A., (2007), "Spatiotemporal regulation of ATP and Ca2+ dynamics in vertebrate rod and cone ribbon synapses.", Molecular vision, 13, February: pg: 887--919, 1090-0535 (Electronic)$\backslash$r1090-0535 (Link, (DOI: v13/a97 [pii]).
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377. Ivanov, Ivaylo, Tainer, John a, McCammon, J. Andrew, (2007), "Unraveling the three-metal-ion catalytic mechanism of the DNA repair enzyme endonuclease IV.", Proceedings of the National Academy of Sciences of the United States of America, 104, 5: pg: 1465--70, 0027-8424, (DOI: 10.1073/pnas.0603468104).
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378. Ingrassia, Christopher M., Usyk, Taras P., Kerckhoffs, Roy C. P., McCulloch, Andrew D., Costa, Kevin D., Holmes, Jeffrey W., (2007), "Model-based development of four-dimensional wall motion measures", Computer Methods in Applied Mechanics and Engineering, 196, 31-32: pg: 3061--3069, 00457825, (DOI: 10.1016/j.cma.2006.06.016).
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379. Huey, Ruth, Morris, Garrett M., Olson, Arthur J., Goodsell, David S., (2007), "A semiempirical free energy force field with charge-based desolvation.", Journal of computational chemistry, 28, 6: pg: 1145--52, 0192-8651, (DOI: 10.1002/jcc.20634).
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380. Hamelberg, Donald, Shen, Tongye, McCammon, J. Andrew, (2007), "A proposed signaling motif for nuclear import in mRNA processing via the formation of arginine claw.", Proceedings of the National Academy of Sciences of the United States of America, 104, 38: pg: 14947--51, 0027-8424, (DOI: 10.1073/pnas.0703151104).
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381. Hamelberg, Donald, de Oliveira, Csar Augusto F., McCammon, J. Andrew, (2007), "Sampling of slow diffusive conformational transitions with accelerated molecular dynamics.", The Journal of chemical physics, 127, 15: pg: 155102, 0021-9606 (Print) 0021-9606, (DOI: 10.1063/1.2789432).
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382. Gupta, Nitin, Tanner, Stephen, Jaitly, Navdeep, Adkins, Joshua N., Lipton, Mary, Edwards, Robert, Romine, Margaret, Osterman, Andrei, Bafna, Vineet, Smith, Richard D., Pevzner, Pavel a, (2007), "Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation.", Genome research, 17, 9: pg: 1362--77, 1088-9051, (DOI: 10.1101/gr.6427907).
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383. Grant, Barry J., McCammon, J. Andrew, Caves, Leo S. D., Cross, Robert A., (2007), "Multivariate analysis of conserved sequence-structure relationships in kinesins: coupling of the active site and a tubulin-binding sub-domain.", Journal of molecular biology, 368, 5: pg: 1231--48, 0022-2836, (DOI: 10.1016/j.jmb.2007.02.049).
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384. Feala, Jacob D., Coquin, Laurence, McCulloch, Andrew D., Paternostro, Giovanni, (2007), "Flexibility in energy metabolism supports hypoxia tolerance in Drosophila flight muscle: metabolomic and computational systems analysis.", Molecular systems biology, 3, 99: pg: 99, 17444292 1744-4292, (DOI: 10.1038/msb4100139).
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385. Evans, Michael J., Morris, Garrett M., Wu, Jane, Olson, Arthur J., Sorensen, Erik J., Cravatt, Benjamin F., (2007), "Mechanistic and structural requirements for active site labeling of phosphoglycerate mutase by spiroepoxides.", Molecular bioSystems, 3, 7: pg: 495--506, 1742-206X (Print)$\backslash$r1742-2051 (Linking) (DOI: 10.1039/b705113a).
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386. Ding, Zhaohui, Wei, Xiaohui, Tatebe, Osamu, Arzberger, Peter W., Papadopoulos, Philip, Li, Wilfred W., (2007), "Cyberinfrastructure for Biomedical Applications: Metascheduling as Essential Component for Pervasive Computing": pg: 59--92
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387. Dolinsky, Todd J., Czodrowski, Paul, Li, Hui, Nielsen, Jens E., Jensen, Jan H., Klebe, Gerhard, Baker, Nathan A., (2007), "PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations.", Nucleic acids research, 35, Web Server issue: pg: W522--5, 1362-4962 (Electronic) 1362-4962, (DOI: 10.1093/nar/gkm276).
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388. Ding, Zhaohui, Wei, Xiaohui, Luo, Yuan, Ma, Da, Arzberger, Peter W., Li, Wilfred W., (2007), "Customized Plug-in Modules in Metascheduler CSF4 for Life Sciences Applications", New Generation Computing, 25, 4: pg: 373--394, 0288-3635, (DOI: 10.1007/s00354-007-0024-6).
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389. de Oliveira, Cesar Augusto F., Zissen, Maurice, Mongon, John, McCammon, J. Andrew, (2007), "Molecular dynamics simulations of metalloproteinases types 2 and 3 reveal differences in the dynamic behavior of the S1' binding pocket.", Current pharmaceutical design, 13, 34: pg: 3471--5, 1381-6128 1873-4286, (DOI: 10.2174/138161207782794211).
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390. Costandi, Peter N., McCulloch, Andrew D., Omens, Jeffrey H., Frank, Lawrence R., (2007), "High-resolution longitudinal MRI of the transition to heart failure.", Magnetic resonance in medicine, 57, 4: pg: 714--20, 0000000000000 0740-3194, (DOI: 10.1002/mrm.21182).
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391. Coppola, Benjamin A., Covell, James W., McCulloch, Andrew D., Omens, Jeffrey H., (2007), "Asynchrony of ventricular activation affects magnitude and timing of fiber stretch in late-activated regions of the canine heart.", American journal of physiology. Heart and circulatory physiology, 293, 1: pg: H754--61, 8585348585 0363-6135, (DOI: 10.1152/ajpheart.01225.2006).
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392. Cickovski, Trevor, Sweet, Chris, Izaguirre, Jesus A., (2007), "MDL, A Domain-Specific Language for Molecular Dynamics": pg: 256--266, 0-7695-2814-7, (DOI: 10.1109/ANSS.2007.26).
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393. Clementi, Luca, Ding, Zhaohui, Krishnan, Sriram, Wei, Xiaohui, Arzberger, Peter, Li, Wilfred, (2007), "Providing Dynamic Virtualized Access to Grid Resources via the Web 2.0 Paradigm", 3:
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394. Chen, Long, Holst, Michael J., Xu, Jinchao, (2007), "The Finite Element Approximation of the Nonlinear Poisson–Boltzmann Equation", SIAM Journal on Numerical Analysis, 45, 6: pg: 2298--2320, 0036-1429, (DOI: 10.1137/060675514).
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395. Chang, Max W., Lindstrom, William, Olson, Arthur J., Belew, Richard K., (2007), "Analysis of HIV wild-type and mutant structures via in silico docking against diverse ligand libraries.", Journal of chemical information and modeling, 47, 3: pg: 1258--62, 1549-9596 (Print)$\backslash$r1549-9596 (Linking) (DOI: 10.1021/ci700044s).
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396. Chang, Chia-En A., Trylska, Joanna, Tozzini, Valentina and, (2007), "Binding Pathways of Ligands to HIV-1 Protease: Coarse-grained and Atomistic Simulations", Chemical Biology \& Drug Design, 69, 1: pg: 5--13, 1747-0277, (DOI: 10.1111/j.1747-0285.2007.00464.x).
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397. Cerutti, David S., Baker, Nathan A., McCammon, J. Andrew, (2007), "Solvent reaction field potential inside an uncharged globular protein: a bridge between implicit and explicit solvent models?", The Journal of chemical physics, 127, 15: pg: 155101, 8585348585 0021-9606, (DOI: 10.1063/1.2771171).
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398. Broderick, Kate E., Balasubramanian, Maheswari, Chan, Adriano, Potluri, Prasanth, Feala, Jake, Belke, Darrell D., McCulloch, Andrew, Sharma, Vijay S., Pilz, Renate B., Bigby, Timothy D., Boss, Gerry R., (2007), "The cobalamin precursor cobinamide detoxifies nitroprusside-generated cyanide.", Experimental biology and medicine (Maywood, N.J.), 232, 6: pg: 789--98, 1535-3702 (Print)$\backslash$r1535-3699 (Linking)
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399. Bielas, Stephanie L., Serneo, Finley F., Chechlacz, Magdalena, Deerinck, Thomas J., Perkins, Guy A., Allen, Patrick B., Ellisman, Mark H., Gleeson, Joseph G., (2007), "Spinophilin facilitates dephosphorylation of doublecortin by PP1 to mediate microtubule bundling at the axonal wrist.", Cell, 129, 3: pg: 579--91, 0000000000000 0092-8674, (DOI: 10.1016/j.cell.2007.03.023).
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400. Bencheikh-Latmani, Rizlan, Obraztsova, Anna, Mackey, Mason R., Ellisman, Mark H., Tebo, Bradley M., (2007), "Toxicity of Cr(III) to Shewanella sp. Strain MR-4 during Cr(VI) Reduction", Environmental Science \& Technology, 41, 1: pg: 214--220, 0013-936X (Print) 0013-936X, (DOI: 10.1021/es0622655).
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