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251. Wong, Sergio, Amaro, Rommie E., McCammon, J. Andrew, (2009), "MM-PBSA Captures Key Role of Intercalating Water Molecules at a Protein-Protein Interface.", Journal of chemical theory and computation, 5, 2: pg: 422--429, 1549-9618 (Print)$\backslash$r1549-9618 (Linking) (DOI: 10.1021/ct8003707).
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252. Williams, Sarah L. and, (2009), "Conformational dynamics of the flexible catalytic loop in Mycobacterium tuberculosis 1-deoxy-D-xylulose 5-phosphate reductoisomerase.", Chemical biology \& drug design, 73, 1: pg: 26--38, 1747-0285, (DOI: 10.1111/j.1747-0285.2008.00749.x).
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253. Williams, Sarah L. and, (2009), "Conformational dynamics of the flexible catalytic loop in Mycobacterium tuberculosis 1-deoxy-D-xylulose 5-phosphate reductoisomerase.", Chemical biology \& drug design, 73, 1: pg: 26--38, 1747-0285, (DOI: 10.1111/j.1747-0285.2008.00749.x).
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254. Swift, Robert V., Durrant, Jacob, Amaro, Rommie E., McCammon, J. Andrew, (2009), "Toward understanding the conformational dynamics of RNA ligation.", Biochemistry, 48, 4: pg: 709--19, 1520-4995 (Electronic)$\backslash$r0006-2960 (Link, (DOI: 10.1021/bi8018114).
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255. Swift, Robert V., Durrant, Jacob, Amaro, Rommie E., McCammon, J. Andrew, (2009), "Toward understanding the conformational dynamics of RNA ligation.", Biochemistry, 48, 4: pg: 709--19, 1520-4995, (DOI: 10.1021/bi8018114).
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256. Shawkey, Matthew D., Saranathan, Vinodkumar, Plsdttir, Hildur, Crum, John, Ellisman, Mark H., Auer, Manfred, Prum, Richard O., (2009), "Electron tomography, three-dimensional Fourier analysis and colour prediction of a three-dimensional amorphous biophotonic nanostructure", Journal of the Royal Society, Interface / the Royal Society, 6 Suppl 2, January: pg: S213--20, 1742-5689 (Print)$\backslash$r1742-5662 (Linking) (DOI: 10.1098/rsif.2008.0374.focus).
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257. Shawkey, Matthew D., Saranathan, Vinodkumar, Plsdttir, Hildur, Crum, John, Ellisman, Mark H., Auer, Manfred, Prum, Richard O., (2009), "Electron tomography, three-dimensional Fourier analysis and colour prediction of a three-dimensional amorphous biophotonic nanostructure.", Journal of the Royal Society, Interface / the Royal Society, 6 Suppl 2, Suppl \_ 2: pg: S213--20, 1742-5689 (Print)$\backslash$r1742-5662 (Linking) (DOI: 10.1098/rsif.2008.0374.focus).
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258. Lawrence, Albert F., Phan, Sebastien, Moussavi, Farshid, (2009), "3D reconstruction from electron microscope images with TxBR": pg: 1131--1134, 978-1-4244-3931-7, (DOI: 10.1109/ISBI.2009.5193256).
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259. Lawrence, Albert, Phan, Sbastien, Singh, Rajvikram, (2009), "Parallel Processing and Large-Field Electron Microscope Tomography", 3, July: pg: 339--343, 978-0-7695-3507-4, (DOI: 10.1109/CSIE.2009.859).
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260. Krishnan, Sriram, Clementi, Luca, Ren, Jingyuan, Papadopoulos, Philip, Li, Wilfred, (2009), "Design and Evaluation of Opal2: A Toolkit for Scientific Software as a Service": pg: 709--716, 978-0-7695-3708-5, (DOI: 10.1109/SERVICES-I.2009.52).
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261. Krishnan, Sriram, Clementi, Luca, Ren, Jingyuan, Papadopoulos, Philip, Li, Wilfred, (2009), "Design and Evaluation of Opal2: A Toolkit for Scientific Software as a Service": pg: 709--716, 978-0-7695-3708-5, (DOI: 10.1109/SERVICES-I.2009.52).
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262. Krishnan, Sriram, Bhatia, Karan, (2009), "SOAs for Scientific Applications: Experiences and Challenges.", Future generations computer systems : FGCS, 25, 4: pg: 466--473, 8585348585 0167-739X, (DOI: 10.1016/j.future.2008.09.001).
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263. Khavrutskii, Ilja V., Gorfe, Alemayehu A., Lu, Benzhuo, McCammon, J. Andrew, (2009), "Free energy for the permeation of Na(+) and Cl(-) ions and their ion-pair through a zwitterionic dimyristoyl phosphatidylcholine lipid bilayer by umbrella integration with harmonic fourier beads.", Journal of the American Chemical Society, 131, 5: pg: 1706--16, 1520-5126 (Electronic)$\backslash$r0002-7863 (Link, (DOI: 10.1021/ja8081704).
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264. Khavrutskii, Ilja V., Gorfe, Alemayehu A., Lu, Benzhuo, McCammon, J. Andrew, (2009), "Free energy for the permeation of Na(+) and Cl(-) ions and their ion-pair through a zwitterionic dimyristoyl phosphatidylcholine lipid bilayer by umbrella integration with harmonic fourier beads.", Journal of the American Chemical Society, 131, 5: pg: 1706--16, 1520-5126 (Electronic)$\backslash$r0002-7863 (Link, (DOI: 10.1021/ja8081704).
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265. Kerckhoffs, Roy C. P., McCulloch, Andrew D., Omens, Jeffrey H., Mulligan, Lawrence J., (2009), "Effects of biventricular pacing and scar size in a computational model of the failing heart with left bundle branch block.", Medical image analysis, 13, 2: pg: 362--9, 8585348585 1361-8423, (DOI: 10.1016/j.media.2008.06.013).
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266. Ju, Won-Kyu, Kim, Keun-Young, Lindsey, James D., Angert, Mila, Patel, Ankur, Scott, Ray T., Liu, Quan, Crowston, Jonathan G., Ellisman, Mark H., Perkins, Guy a, Weinreb, Robert N., (2009), "Elevated hydrostatic pressure triggers release of OPA1 and cytochrome C, and induces apoptotic cell death in differentiated RGC-5 cells.", Molecular vision, 15, December 2007: pg: 120--34, 1090-0535 (Electronic)$\backslash$r1090-0535 (Link
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267. Ju, Won-Kyu, Kim, Keun-Young, Lindsey, James D., Angert, Mila, Patel, Ankur, Scott, Ray T., Liu, Quan, Crowston, Jonathan G., Ellisman, Mark H., Perkins, Guy a, Weinreb, Robert N., (2009), "Elevated hydrostatic pressure triggers release of OPA1 and cytochrome C, and induces apoptotic cell death in differentiated RGC-5 cells.", Molecular vision, 15, December 2007: pg: 120--34, 1090-0535 (Electronic)$\backslash$r1090-0535 (Link
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268. Ju, Won-Kyu, Kim, Keun-Young, Angert, Mila, Duong-Polk, Karen X., Lindsey, James D., Ellisman, Mark H., Weinreb, Robert N., (2009), "Memantine blocks mitochondrial OPA1 and cytochrome c release and subsequent apoptotic cell death in glaucomatous retina.", Investigative ophthalmology \& visual science, 50, 2: pg: 707--16, 6176321972 1552-5783, (DOI: 10.1167/iovs.08-2499).
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269. Ju, Won-Kyu, Kim, Keun-Young, Angert, Mila, Duong-Polk, Karen X., Lindsey, James D., Ellisman, Mark H., Weinreb, Robert N., (2009), "Memantine blocks mitochondrial OPA1 and cytochrome c release and subsequent apoptotic cell death in glaucomatous retina.", Investigative ophthalmology \& visual science, 50, 2: pg: 707--16, 6176321972 1552-5783, (DOI: 10.1167/iovs.08-2499).
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270. Hayashi, Takeharu, Martone, Maryann E., Yu, Zeyun, Thor, Andrea, Doi, Masahiro, Holst, Michael J., Ellisman, Mark H., Hoshijima, Masahiko, (2009), "Three-dimensional electron microscopy reveals new details of membrane systems for Ca2+ signaling in the heart.", Journal of cell science, 122, Pt 7: pg: 1005--13, 0021-9533, (DOI: 10.1242/jcs.028175).
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271. Hayashi, Takeharu, Martone, Maryann E., Yu, Zeyun, Thor, Andrea, Doi, Masahiro, Holst, Michael J., Ellisman, Mark H., Hoshijima, Masahiko, (2009), "Three-dimensional electron microscopy reveals new details of membrane systems for Ca2+ signaling in the heart.", Journal of cell science, 122, Pt 7: pg: 1005--13, 0021-9533, (DOI: 10.1242/jcs.028175).
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272. Hamelberg, Donald, McCammon, J. Andrew, (2009), "Mechanistic insight into the role of transition-state stabilization in cyclophilin A.", Journal of the American Chemical Society, 131, 1: pg: 147--52, 1520-5126, (DOI: 10.1021/ja806146g).
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273. Hamelberg, Donald, McCammon, J. Andrew, (2009), "Mechanistic insight into the role of transition-state stabilization in cyclophilin A.", Journal of the American Chemical Society, 131, 1: pg: 147--52, 1520-5126, (DOI: 10.1021/ja806146g).
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274. Durrant, Jacob D., Amaro, Rommie E., McCammon, J. Andrew, (2009), "AutoGrow: a novel algorithm for protein inhibitor design.", Chemical biology \& drug design, 73, 2: pg: 168--78, 1747-0285, (DOI: 10.1111/j.1747-0285.2008.00761.x).
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275. Durrant, Jacob D., Amaro, Rommie E., McCammon, J. Andrew, (2009), "AutoGrow: a novel algorithm for protein inhibitor design.", Chemical biology \& drug design, 73, 2: pg: 168--78, 1747-0285, (DOI: 10.1111/j.1747-0285.2008.00761.x).
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276. Chen, Long, Holst, Michael, Xu, Jinchao, (2009), "Convergence and optimality of adaptive mixed finite element methods", Mathematics of Computation, 78, 265: pg: 35--35, 0470846992 0025-5718, (DOI: 10.1090/S0025-5718-08-02155-8).
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277. Chen, Long, Holst, Michael, Xu, Jinchao, (2009), "Convergence and optimality of adaptive mixed finite element methods", Mathematics of Computation, 78, 265: pg: 35--35, 0470846992 0025-5718, (DOI: 10.1090/S0025-5718-08-02155-8).
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278. Chen, Long, Holst, Michael, Xu, Jinchao, (2009), "Convergence and optimality of adaptive mixed finite element methods", Mathematics of Computation, 78, 265: pg: 35--35, 0470846992 0025-5718, (DOI: 10.1090/S0025-5718-08-02155-8).
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279. Campbell, Stuart G., Howard, Elliot, Aguado-Sierra, Jazmin, Coppola, Benjamin A., Omens, Jeffrey H., Mulligan, Lawrence J., McCulloch, Andrew D., Kerckhoffs, Roy C. P., (2009), "Effect of transmurally heterogeneous myocyte excitation-contraction coupling on canine left ventricular electromechanics.", Experimental physiology, 94, 5: pg: 541--52, 0000000000000 1469-445X, (DOI: 10.1113/expphysiol.2008.044057).
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280. Campbell, Stuart G., Howard, Elliot, Aguado-Sierra, Jazmin, Coppola, Benjamin A., Omens, Jeffrey H., Mulligan, Lawrence J., McCulloch, Andrew D., Kerckhoffs, Roy C. P., (2009), "Effect of transmurally heterogeneous myocyte excitation-contraction coupling on canine left ventricular electromechanics.", Experimental physiology, 94, 5: pg: 541--52, 0000000000000 1469-445X, (DOI: 10.1113/expphysiol.2008.044057).
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281. Bumbarger, Daniel J., Wijeratne, Sitara, Carter, Cale, Crum, John, Ellisman, Mark H., Baldwin, James G., (2009), "Three-dimensional reconstruction of the amphid sensilla in the microbial feeding nematode, Acrobeles complexus (Nematoda: Rhabditida).", The Journal of comparative neurology, 512, 2: pg: 271--81, 8585348585 1096-9861, (DOI: 10.1002/cne.21882).
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282. Bumbarger, Daniel J., Wijeratne, Sitara, Carter, Cale, Crum, John, Ellisman, Mark H., Baldwin, James G., (2009), "Three-dimensional reconstruction of the amphid sensilla in the microbial feeding nematode, Acrobeles complexus (Nematoda: Rhabditida).", The Journal of comparative neurology, 512, 2: pg: 271--81, 8585348585 1096-9861, (DOI: 10.1002/cne.21882).
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283. Bailey, Timothy L., Boden, Mikael, Buske, Fabian A., Frith, Martin, Grant, Charles E., Clementi, Luca, Ren, Jingyuan, Li, Wilfred W., Noble, William S., (2009), "MEME SUITE: tools for motif discovery and searching.", Nucleic acids research, 37, Web Server issue: pg: W202--8, 1362-4962; 0305-1048 1362-4962, (DOI: 10.1093/nar/gkp335).
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284. Bailey, Timothy L., Boden, Mikael, Buske, Fabian A., Frith, Martin, Grant, Charles E., Clementi, Luca, Ren, Jingyuan, Li, Wilfred W., Noble, William S., (2009), "MEME Suite: Tools for motif discovery and searching", Nucleic Acids Research, 37, SUPPL. 2: pg: 202--208, 1362-4962; 0305-1048 03051048, (DOI: 10.1093/nar/gkp335).
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285. Babakhani, Arneh, Talley, Todd T., Taylor, Palmer, McCammon, J. A., (2009), "A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach.", Computational biology and chemistry, 33, 2: pg: 160--70, 8585348585 1476-928X, (DOI: 10.1016/j.compbiolchem.2008.12.002).
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286. Babakhani, Arneh, Talley, Todd T., Taylor, Palmer, McCammon, J. A., (2009), "A virtual screening study of the acetylcholine binding protein using a relaxed-complex approach.", Computational biology and chemistry, 33, 2: pg: 160--70, 8585348585 1476-928X, (DOI: 10.1016/j.compbiolchem.2008.12.002).
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287. Yu, Zeyun, Holst, Michael J. and, (2008), "High-fidelity geometric modeling for biomedical applications", Finite Elements in Analysis and Design, 44, 11: pg: 715--723, 0168874X, (DOI: 10.1016/j.finel.2008.03.004).
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288. Yu, Zeyun, Holst, Michael J., Hayashi, Takeharu, Bajaj, Chandrajit L., Ellisman, Mark H., McCammon, J. Andrew, Hoshijima, Masahiko, (2008), "Three-dimensional geometric modeling of membrane-bound organelles in ventricular myocytes: bridging the gap between microscopic imaging and mathematical simulation.", Journal of structural biology, 164, 3: pg: 304--13, 1095-8657, (DOI: 10.1016/j.jsb.2008.09.004).
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289. Yamaguchi, Ryuji, Lartigue, Lydia, Perkins, Guy, Scott, Ray T., Dixit, Amruta, Kushnareva, Yulia, Kuwana, Tomomi, Ellisman, Mark H., Newmeyer, Donald D., (2008), "Opa1-mediated cristae opening is Bax/Bak and BH3 dependent, required for apoptosis, and independent of Bak oligomerization.", Molecular cell, 31, 4: pg: 557--69, 0000000000000 1097-4164, (DOI: 10.1016/j.molcel.2008.07.010).
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290. Wong, Sergio E., Baron, Riccardo, McCammon, J. Andrew, (2008), "Hot-spot residues at the E9/Im9 interface help binding via different mechanisms.", Biopolymers, 89, 11: pg: 916--20, 0006-3525, (DOI: 10.1002/bip.21035).
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291. Wei, Xiaohui, Li, Wilfred Wenfeng, (2008), "VJM-A Deadlock Free Resource Co-allocation Model for Cross Domain Parallel Jobs":
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292. Tsai, Jeng-Wei, Kratz, Timothy K., Hanson, Paul C., Wu, Jiunn-Tzong, Chang, William Y. B., Arzberger, Peter W., Lin, Bing-Shih, Lin, Fang-Pang, Chou, Hsiu-Mei, Chiu, Chih-Yu, (2008), "Seasonal dynamics, typhoons and the regulation of lake metabolism in a subtropical humic lake", Freshwater Biology, 53, 10: pg: 1929--1941, 1365-2427 00465070, (DOI: 10.1111/j.1365-2427.2008.02017.x).
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293. Sosinsky, Gina E., Crum, John, Jones, Ying Z., Lanman, Jason, Smarr, Benjamin, Terada, Masako, Martone, Maryann E., Deerinck, Thomas J., Johnson, John E., Ellisman, Mark H., (2008), "The combination of chemical fixation procedures with high pressure freezing and freeze substitution preserves highly labile tissue ultrastructure for electron tomography applications.", Journal of structural biology, 161, 3: pg: 359--71, 1095-8657, (DOI: 10.1016/j.jsb.2007.09.002).
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294. Sheikh, Farah, Raskin, Anna, Chu, Pao-hsien, Lange, Stephan, Domenighetti, Andrea A., Zheng, Ming, Liang, Xingqun, Zhang, Tong, Yajima, Toshitaka, Gu, Yusu, Dalton, Nancy D., Mahata, Sushil K., Dorn, Gerald W., Brown, Joan Heller, Heller-Brown, Joan, Peterson, Kirk L., Omens, Jeffrey H., McCulloch, Andrew D., Chen, Ju, (2008), "An FHL1-containing complex within the cardiomyocyte sarcomere mediates hypertrophic biomechanical stress responses in mice.", The Journal of clinical investigation, 118, 12: pg: 3870--80, 0021-9738, (DOI: 10.1172/JCI34472).
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295. Sen, Debasish, Deerinck, Thomas J., Ellisman, Mark H., Parker, Ian, Cahalan, Michael D., (2008), "Quantum dots for tracking dendritic cells and priming an immune response in vitro and in vivo.", PloS one, 3, 9: pg: e3290, 1932-6203, (DOI: 10.1371/journal.pone.0003290).
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296. Saini, Vaibhav, Martyshkin, Dmitri V., Mirov, Sergei B., Perez, Alex, Perkins, Guy, Ellisman, Mark H., Towner, Victoria D., Wu, Hongju, Pereboeva, Larisa, Borovjagin, Anton, Curiel, David T., Everts, Maaike, (2008), "An adenoviral platform for selective self-assembly and targeted delivery of nanoparticles.", Small (Weinheim an der Bergstrasse, Germany), 4, 2: pg: 262--9, 1613-6829 (Electronic) 1613-6829, (DOI: 10.1002/smll.200700403).
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297. Rudy, Yoram, Ackerman, Michael J., Bers, Donald M., Clancy, Colleen E., Houser, Steven R., London, Barry, McCulloch, Andrew D., Przywara, Dennis A., Rasmusson, Randall L., Solaro, R. John, Trayanova, Natalia A. and, (2008), "Systems approach to understanding electromechanical activity in the human heart: a national heart, lung, and blood institute workshop summary.", Circulation, 118, 11: pg: 1202--11, 6176321972 1524-4539, (DOI: 10.1161/CIRCULATIONAHA.108.772715).
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298. Ragsdale, Erik J., Crum, John, Ellisman, Mark H., Baldwin, James G., (2008), "Three-dimensional reconstruction of the stomatostylet and anterior epidermis in the nematode Aphelenchus avenae (Nematoda: Aphelenchidae) with implications for the evolution of plant parasitism.", Journal of morphology, 269, 10: pg: 1181--96, 8585348585 1097-4687, (DOI: 10.1002/jmor.10651).
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299. 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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300. 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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