PUBLICATIONS & PRESENTATIONS

The success of students in PRIME is clearly demonstrated in the academic publications that have been generated through its research activities.

2012

  • Lo YH, Chitters R, Peachey T, Abramson D, Michailova A, “Sensitivity of rabbit ventricular action potential and Ca2+ dynamics to small variations in membrane currents and ion diffusion coefficients,” General Physiology and Biophysics Journal, Submitted October 25, 2012. [Yuan Hung Lo PRIME 2012 student, Ramya Chitters PRIME 2009 student, both at Monash University, Australia.]
  • Wong, JI, David Baddeley, Eric Bushong, Mark Ellisman, Masahiko Hoshijima, Christian Soeller, “3D Imaging of Nanoscopic Membrane Systems Regulating Cardiac E-C Coupling: Multi-Color Optical Super Resolution and Serial Block-Face Scanning Electron Microscopy,” 56th Annual Biophysical Society Meeting: Excitation-Contraction Coupling Platform Presentation, February 25-29, 2012. [Joseph Wong was a PRIME 2011 student at the University of Auckland, New Zealand.]

2011

  • Lu, Sheng-Shan, Michael Perry, Michael Nekrasov, Tony Fountain, Peter Arzberger, Yu-Huang Wang, Chau-Chin Lin, “Automatic analysis of Camera Image Data: an Example of Honey Bee (Apis cerana) Images from Shanping Wireless Sensor Network,” Taiwan Journal of Forest Science, Research Notes, In press (4 May 2011). [Michael Perry was a PRIME 2010 student at the Taiwan Forest Research Institute, Taipei, Taiwan; Michael Nekrasov was a PRIME 2009 student at the National Museum of Marine Biology and Aquarium, Kenting Taiwan.]
  • Mullica Jaroensutasinee, Krisanadej Jaroensutasinee, Tony Fountain, Michael Nekrasov, Sirilak Chumkiew, Premrudee Noonsang, Uthai Kuhapong, Scott Bainbridge, “Coral sensor network at Racha Island, Thailand,” Environmental Information Management, submitted 2011. [Michael Nekrasov was a PRIME 2009 student at the National Museum of Marine Biology and Aquarium, Kenting Taiwan.]

2010

  • Hoshijima M, Hayashi T, Jeon YE, Fu Z, Gu Y, Dalton N, Ellisman MH, Xia X, Powell FL, Ross J, Jr., “Delta-sarcoglycan gene therapy halts progression of cardiac dysfunction, improves respiratory failure and prolongs life in myopathic hamsters,” Circulation: Heart Failure. 4(1):89-97, October 29, 2010. [Young Jeon was a PRIME 2007 student at Osaka University, Japan.]
  • Yim WW, Chien S, Kusumoto Y, Date S, and Haga J, “Grid Heterogeneity in In-silico Experiments: An Exploration of Drug Screening Using DOCK on Cloud Environments,” HealthGrid 2010, June 28-30, 2010. [Wen-wai Yim was a PRIME 2009 student at Osaka University, Japan.]
  • Lau CD, Levesque MJ, Chien S, Date S, Haga JH, “ViewDock TDW: high-throughput visualization of virtual screening results,” Bioinformatics, June 15, 2010, 1;26(15): 1915-7. [Chris Lau was a PRIME 2009 student; Marshall Levesque was a PRIME 2006 student, both at Osaka University, Japan.]
  • Abramson D, Bethwaite B, Enticott C, Garic S, Peachey T, Michailova A, Amirriazi S, “Embedding Optimization Computational Science Workflows,” Journal of Computational Science, 1:41-47, May 2010. (invited paper). Previously appeared in ICCS 2010. [Saleh Amirriazi was a PRIME 2007 Student at Monash University, Australia.]
  • Abramson, D., Bethwaite, B., Enticott, C. Garic, S., Peachey, T., Michailova, A, and Amirriazi, S, “Automatic Design Optimization using Parallel Workflows”, Proceedings of the International Conference on Computational Science, Amsterdam, May 31-June 2, 2010. Reprinted in the Journal of Computational Science (see above). [Saleh Amirriazi was a PRIME 2007 student at Monash University, Australia.]

2009

  • Abramson D, Bethwaite B, Enticott C, Garic S, Peachey T, Michailova A, Amirriazi S, Chitters R, “Robust Workflows for Science and Engineering,” 2nd ACM Workshop on Many-Task Computing on Grids and Supercomputers, November 2009, co- located with International Conference for High Performance, Networking, Storage and Analysis (ACM/IEEE SC09), Portland, OR, Nov 16, 2009. [Saleh Amirriazi was a PRIME 2007 Student; R Chitters was a PRIME 2009 student; both in Monash University, Australia.]
  • Newhouse EI, Xu D, Markwick PRL, Amaro RE, Pao HC, Wu KJ, Alam M, McCammon AJ, Li WW, "Mechanism of Glycan Receptor Recognition and Specificity Switch for Avian, Swine and Human Adapted Influenza Virus Hemagglutinins: A Molecular Dynamics Perspective," J Am Chem Soc, November 5, 2009. [Hsing Pao was a PRIME2007 student; Kevin Wu was a PRIME 2008 student, both at the Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.]
  • Jeon Y, Hayashi T, Xiao X, Ross J, Hoshijima M, “Restoration of Sarcoglycan Complex Halted Disease Progression in BIO14.6 Hamsters With Established Heart Failure,” Circulation 120 (18): S593, Abstract, November 3, 2009. [Young Jeon was a PRIME 2007 student at Osaka University, Japan.]
  • Xu D, Newhouse EI, Amaro RE, Pao HC, Cheng LS, Markwick PRL, McCammon JA, Li WW, Arzberger PW, “Distinct Glycan Topology for Avian and Human Sialo-Pentasaccharide Receptor Analogues upon Binding Different Hemagglutinins: A Molecular Dynamics Perspective,” J. Mol Bio, March 27, 2009 387(2):465-91. Epub 2009 Feb 5. [Hsing Pao was a PRIME 2007 student, Lily Cheng was a PRIME 2006 student, both at the Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.]

2008

  • Chu, R., D. Tenedorio, J. Schulze, S. Date, S.Kuwabara, A. Nakazawa, H. Takemura, F-P Lin, “Optimized Rendering for a 3D Videoconferencing System,” 4th IEEE Intl Conf., e-science, PRAGMA Workshop, December 7, 2008. (Proceedings of co-located PRAGMA Workshop on e-Science Indianapolis, IN, December 8-12, 2008). [Rachel Chu was a PRIME 2008 Students Chu at Osaka University, Japan; and Daniel Tenedorio was a PRIME 2008 student at the National Center for High-performance Computing in Hsinchu Taiwan.]
  • Pham, P., M. Levesque, K. Ichikawa, S. Date, J. H. Haga, “Identification of a Specific Inhibitor for the Dual-Specificity Enzyme SSH-2 via Docking Experiments on the Grid,” 4th IEEE Intl Conf., e-science, PRAGMA Workshop, Indianapolis, IN, December 7, 2008. [Phillip Pham was a PRIME 2008 student, Marshall Levesque was a PRIME 2006 student, both at Osaka University, Japan.]
  • Han, S. X., M. Levesque, K. Ichikawa, S. Date, J. Haga, “Virtual Screening for SHP-2 Specific Inhibitors Using Grid Computing,” 4th IEEE Intl Conf., e-science, PRAGMA Workshop, Indianapolis, IN, December 7, 2008). [Xian Han was a PRIME 2008 student, Marshall Levesque was a PRIME 2006 student, both at Osaka University, Japan.]
  • Peachey TC, Diamond NT, Abramson DA, Sudholt W, Michailova A, Amirriazi S, “Fractional Factorial Design for Parameter Sweep Experiments using Nimrod/E,” Journal of Scientific Programming, 16(2,3):217-230, November 2008. [Saleh Amirriazi was a PRIME 2007 student in 2007 at Monash University, Australia.]
  • Levesque M.J., K. Ichikawa, S. Date, J. H. Haga, “Bringing Flexibility to Virtual Screening for Enzymatic Inhibitors on the Grid,” Grid2008, Tsukuba Japan 29 Sep-1 Oct, 2008. [Marshall Levesque was a PRIME 2006 student at Osaka University, Japan.]
  • Levesque M.J., K. Ichikawa, S. Date, J. H. Haga, “Design of a Grid Service-based Platform for In Silico Protein-Ligand Screening,” Computer Methods and Programs in Biomedicine, September 3, 2008, www.ncbi.nlm.nih.gov/pubmed/18771812. [Marshall Levesque was a PRIME 2006 student at Osaka University, Japan.]
  • Cheng, L.S., R.E. Amaro, D. Xu, W. W. Li, P.W. Arzberger, J. A. McCammon, “Ensemble based Virtual Screening Reveals Novel Antiviral Compounds for Avian Influenza Neuraminidase,” J Med Chem (51) 13, 3878-3894, July 2008, DOI: 10.1021/jm8001197. [Lily Cheng was a PRIME 2006 Student at the Computer Network Information Center, Chinese Academy of Sciences, Beijing, China. To read more about this research, read a profile of Cheng’s work on the Calit2 website at www.calit2.net/newsroom/release.php?id=1324.]
  • Hashemi, M, M. Buibas, G.A. Silva, “Automated detection of intercellular signaling in astrocyte networks using the converging squares algorithm,” Journal of Neuroscience Methods, May 30, 2008. 170(2): 294-299. [Mahboubeh Hashemi was a PRIME 2006 student at the National Center for High-performance Computing, Hsinchu, Taiwan.]

2007

  • Amaro, R.E., D. D. L. Minh, L. S. Cheng, W. M. Lindstrom Jr., A. J. Olson, J. H. Lin, W. W. Li, J. A. McCammon, “Remarkable Loop Flexibility in Avian Influenza N1 and Its Implications for Antiviral Drug Design,” J Am Chem Soc, 2007 (129) 7764-7765. [Lily Cheng was a PRIME 2006 student at the Computer Network Information Center, Chinese Academy of Sciences, Beijing, China.]

2006

  • Abramson D, Amoreira C, Baldridge K, Berstis L, Kondrick C, Peachey TC, “A Flexible Framework for Protein-Ligand Docking,” 2nd IEEE International Conference on e-Science and Grid Computing. Dec. 4- 6, 2006, Amsterdam, IEEE Computer Society, Los Alamitos USA, pp. 1-8. [Laura Berstis was a PRIME 2005 student, Chris Kondrick was a PRIME 2004 student, both at Monash University, Australia.]

2005

  • Sudholt W, Baldridge K, Abramson D, Enticott C, Garic S, Kondrick C, Nguyen D., “Application of Grid Computing to Parameter Sweeps and Optimizations in Molecular Modeling,” Future Generation Computer Systems,” (Invited paper), January 1, 2005. 21, 27-35. [Chris Kondrick and Duy Nguyen were PRIME 2004 students at Monash University, Australia.]