Publications
Peer-review papers:
Jun Ni: “Science and Engineering Online Solution Library for Education,” WebNet2000, pp. 972-973, Charles B. Owen (Eds.): Proceedings of WebNet 2000 - World Conference on the WWW and Internet, San Antonio, Texas, USA, October 30 - November 4, 2000. AACE 2000, ISBN 1-880094-40-1, 2000
Lili Huang, Ge Wang, S. Kao, and Jun Ni, “VoluMeasureTM: A Portable Java program for Stereological Volume Measurement, “Education Exhibition, Radiological Society of North American Scientific Assembly and Annual Meeting, Chicago, and December 1-6. 2002
Shaowen Wang, Boyd Knosp, Jun Ni, Alexi Mestvirishvili, Yasar Onel, Ahmet Sedat Ayan, Jonathan Olson, and Ugur Akgun, “Building Collaborative Environments for Grid-based Large Hadron Collider Analysis - Efforts at the University of Iowa,” in Workshop on Large Hadron Collider (LHC) Global Science – Developing Proposals and Plans for Building the Environment for a Global Collaborative Science Community, Lawrence Berkeley National Laboratory, Berkeley, CA, USA, November 12-13, 2002
Xiang Li, Jun Ni, Ge Wang, “Parallel Iterative CT Image Reconstruction on a Linux Cluster of Legacy Computers,” to High Performance Computing and Applications (HPCA2004), Shanghai, China, August 8-10, 2004, accepted and being published in Lecture Note in Computer Science (LNCS), Springer-Verlag Heidelberg, Germany, ISBN 3-540-25785-3, 2004
Xiang Li, Tao He, Jun Ni, Ge Wang, “P2P-enhanced Distributed Parallel Iterative Cone Beam CT Image Reconstruction,” Radiology Society of North America, the 90th Assembly and Annual Meeting (RSNA2004), Nov. 28 - Dec. 3, 2004, McCormick Place, Chicago, Illinois, USA
Jun Ni, Tao He, Xiang Li, Shaowen Wang, Ge Wang, “Internet-based Distributed Computing System for EM Medical Image Reconstruction,” the third International Grid and Cooperative Computing (GCC2004), Wuhan, China, Oct. 21-24, Lecture Note in Computer Science (LNCS), Vol. 3251, pp 495-501, Springer-Verlag Heidelberg, Germany, 2004
Xiang Li, Tao He, Shaowen Wang, Ge Wang, and Jun Ni, “P2P-enhanced Distributed Computing in Medical Image EM Reconstruction,” presented and published at the 2004 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'04), Las Vegas, Nevada, USA, June 21-24, 2004, Hamid R. Arabnia and Jun Ni (Eds.), pp. 822-828, Vol. II, ISBN: 1-932415-24-6, CSREA Press, 2004
Shaowen Wang, A. Padmanabham, Y. Liu, R. Briggs, Jun Ni, Tao He, Boyd Knosp, and Y. Onel, “A Multi-agent System Architecture for End-user Grid Monitoring Using Geographic information Systems (MAGGIS): Architecture and Implementation,” Lecture Note in Computer Science, Vol. 3032, pp. 536 – 543, ISBN: 3-540-21988-9, Springer-Verlag Heidelberg, 2004
Tao He, Jun Ni, Shaowen Wang, and Boyd Knosp, "Java Grid Computing Library --- A Distributed Programming Solution for Grid Computing," in the conference proceeding of 2nd International Workshop of Grid and Cooperative Computing (GCC2003), Shanghai, China, 2003, Lecture Note in Computer Science, Volume 3032, pp. 428 – 435, 2004, ISBN: 3-540-21988-9, Springer-Verlag Heidelberg, 2004
Logue MW, Park J, Ni J, Cremer J, Segre A, Knosp B, Beck S, Vieland V., “Interactive visualization tools for genetic data,” ASHG 54th Annual Meeting, American Society of Human Genetics, 2004. p528
Juw Won Park, Jun Ni, James Cremer, Mark Logue, “Multidimensional Multivariate Visualization: Directed Visualization on Linkage Analysis, International Conference on Bioinformatics and its Applications (ICBA’04), December 16-19, 2004, Nova Southeastern University, Fort Lauderdale, Florida, USA
Xiaoxu Han, Jun Ni, James Cremer, Xiaoqian Jiang, “An Improved Protein-Folding Algorithm In the HP Model,” submitted to International Conference on Bioinformatics and its Applications (ICBA’04), December 16-19, 2004, Nova Southeastern University, Fort Lauderdale, Florida, USA
Juw Won Park, Mark Logue, Jun Ni, James Cremer, Alberto Segre, Veronica Vieland, “Scientific Visualization of Multidimensional Data: Genetic Likelihood Visualization,” presented at High Performance Computing and Applications (HPCA2004), Shanghai, China, August 8-10, 2004, Lecture Note in Computer Science, Springer-Verlag Heidelberg, Germany, ISBN 3-540-25785-3, 2004
Jun Ni, Ge Wang, Shaowen Wang, Tiange Zhuang, Weiqin Tong, “Grid-enhanced International Digital Library (GridIDL) for Medical Imaging,” submitted to High Performance Computing and Applications (HPCA2004), Shanghai, China, August 8-10, 2004, Lecture Note in Computer Science, Springer-Verlag Heidelberg, Germany, ISBN 3-540-25785-3,2004
Xiaoxu Han, Jun Ni, Zhihong Wang, Xiaoqian Jiang, “ P-LZB, A Real-Time Parallel Local Z-Buffer Rendering Algorithm of Large Geometric Datasets,” submitted to High Performance Computing and Applications (HPCA2004), Shanghai, China, August 8-10, 2004, Lecture Note in Computer Science, Springer-Verlag Heidelberg, Germany, ISBN 3-540-25785-3, 2004
Xiaoxu Han, James Cremer, Zhihong Wang, Jun Ni, “LZB, A Hybrid Algorithm of Local Ray-casting and Z-buffering for Large Geometric Datasets,” presented at the International Workshop on Visualization and Visual Steering (VVS'’04), in conjunction with GCC2004, Wu Han, China, Oct. 21-24, 2004 GCC2004, Lecture Note in Computer Science, Vol. 3252, pp 720-727, Springer-Verlag Heidelberg, Germany, 2004
Jun Ni, Chinglong Lin, Yongxiang Zhang, Tao He, Shaowen Wang, Body Knosp, “Parallelism of Lattice Boltzmann Method (LBM) for Lid-driven Cavity Flows,” High Performance Computing and Applications (HPCA2004), Shanghai, China, August 8-10, 2004, Lecture Note in Computer Science, Springer-Verlag Heidelberg, Germany, ISBN 3-540-25785-3, 2004
Jun Ni, Tao He, Lili Huang, Shaowen Wang, Boyd Knosp, and C Lin, “Distributed Computation for Diffusion Problem in a P2P-Enhanced Computing System,” in the conference proceeding of 2nd International Workshop of Grid and Cooperative Computing (GCC2003), Shanghai, China, 2003; Lecture Note in Computer Science, Volume 3032, pp. 428 – 435, 2004, ISBN: 3-540-21988-9, Springer-Verlag Heidelberg, 2004
Jun Ni, Ching-long Lin, Yongxiang Zhang, Tao He, Shaowen Wang, and Boyd M. Knosp “Performance Evaluation of a Parallel Lattice Boltzmann Method for Cavity Flows Using Cluster Computing,” The 2004 International Conference on Parallel and Distributed Processing Techniques and Applications (PDPTA'04), Las Vegas, Nevada, USA, June 21 - 24, 2004, pp. 10-16, Vol. I, ISBN: 1-932415-23-8, CSREA Press, 2004
Jun Ni, Tao He, Ge Wang, Shaowen Wang, and Boyd Knosp, “Scenario of Application Layers for Grid-enhanced International Digital Library in Medical Imaging,” The 2005 International Conference on Grid Computing and Applications (GCA'05), The 2005 World Congress in Applied Computing, Les Vegas, June, 2005, (GCA’05), ISBN 1-932415-57-2, CSREA Press, 2005
Shaowen Wang, Shaoping Xiao, and Jun Ni, “A Grid-based Bridging Domain Multiple-scale Method for Computational Nanotechnology,” presented at The First International Workshop On Computational Nano-science and Technology, 2005 (CNST’05), Lecture Note in Computer Science (LNCS), ISBN: 0302-9743, vol. 3516, pp. 326, Springer-Verlag Heidelberg, Germany, 2005
Jun Ni, Tao He, Joe DeMaria, Shaowen Wang, and Boyd Knosp, “Parallel Numerical Integration on a P2P/Grid Computing Environment,” The 2005 International Conference on Grid Computing and Applications (GCA'05), The 2005 World Congress in Applied Computing, Les Vegas, June, 2005, (GCA’05), ISBN 1-932415-57-2, CSREA Press, 2005
Shaowen Wang, Marc P. Armstrong, Jun Ni, Yan Liu, “GISolve: A Grid-based Problem Solving Environment for Computationally Intensive Geographic Information Analysis,” in IEEE/NSF’s Challenges of Large Applications in Distributed Environments (CLADE|05), July 24, 2005, Research Triangle Park, NC, USA
Shaowen Wang, Marc P. Armstrong, Jun Ni, Yan Liu, “GISolve: A Grid-based Problem Solving Environment for Computationally Intensive Geographic Information Analysis,” submitted to Challenges of Large Applications in Distributed Environments 2005, CLADE 2005, in conjunction with HPDC held in Research Triangle Park, NC, in July 2005
Nianmin Yao, Wenbin Yao, Shaobin Cai, and Jun Ni, “A New Scheduling Algorithm for Servers,” IMSCCS|06, J. Ni, J. Dongarra, Y. Zheng, G. Gu, W. Gentzsch, and H. Jin (eds.), IEEE Computer Society Press, Los Alamitos, California, USA, 2006, ISBN: 0-7695-2581-4
Wenbin Yao, Nianmin Yao, Shaobin Cai, and Jun Ni, “A Verification Environment for CMP Architecture Design,” IMSCCS|06, J. Ni, J. Dongarra, Y. Zheng, G. Gu, W. Gentzsch, and H. Jin (eds.), IEEE Computer Society Press, Los Alamitos, California, USA, 2006, ISBN: 0-7695-2581-4
Tao He, Jun Ni, and Ge Wang, “A Heterogeneous Windows Cluster System for Medical Image Reconstruction,” in the Processing of the First International Multi-symposiums on Computer and Computational Sciences (IMSCCS|06), IEEE Computer Society Press, Los Alamitos, California, USA, ISBN 0-7695-2581-4, Vol. 1, pp. 410-415, 2006
Tao He, Jun Ni, Junjun Deng, Hengyong Yu, and Ge Wang, “Deployment of One-Sided Communication Technique for Parallel Computing in Katsevich CT Image Reconstruction,” in the Processing of the First International Multi-symposiums on Computer and Computational Sciences (IMSCCS|06), IEEE Computer Society Press, Los Alamitos, California, USA, ISBN 0-7695-2581-4, Vol. 1, pp. 416-423, 2006
Jun Ni, Junjun Deng, Hengyong Yu, Tao He, and Ge Wang, Analysis of Performance Evaluation of Parallel Katsevich Algorithm for 3-D CT Image Reconstruction, in the Processing of the First International Multi-symposiums on Computer and Computational Sciences (IMSCCS|06), IEEE Computer Society Press, Los Alamitos, California, USA, ISBN 0-7695-2581-4, Vol. 1, pp. 258-265, 2006
Shaoping Xiao, Jun Ni, and Shaowen Wang, “The Need of High-performance Computing in Computational Nano- Mechanics and Materials Science,” in Proceeding of The Second Workshop of High Performance Computing for Nanotechnology,” IEEE Computer Society Press, Los Alamitos, California, USA (in Press), 2006
Jun Ni, Shaoping Xiao, and Shaowen Wang, “Modeling and Simulations of Nanostructure Materials Processing,” in Proceeding of the First Workshop of High Performance Computing for Nanotechnology,” IEEE Computer Society Press, Los Alamitos, California, USA (In Press), 2006
Daming Xu and Jun Ni, “A Numerical Approach of Direct-SIMPLE deduced Pressure Equations to Simulations of Transport Phenomena during Shaped Casting,” in the Processing of the First International Multi-symposiums on Computer and Computational Sciences (IMSCCS|06), IEEE Computer Society Press, Los Alamitos, California, USA, ISBN 0-7695-2581-4, Vol. 2
Ransom Briggs, Shaowen Wang, Sukumar Ghosh, Eric Shook, Anand Padmanabhan, Shaoping Xiao, Jun Ni, “A High-Throughput Virtual Organization Job Execution System (VOJES): Using the Open Science Grid for Reliability Analyses of Carbon Nanotubes,” in Challenges of Large Applications in Distributed Environments (CLADE 2007), Monterey Bay, California, USA
Wang, T., Ni J., “Speedup Analysis for Parallel Implementation of Model of Response Accuracy and Response Time in Computerized Testing,” ICCS 2007, Part III, Lecture Note in Computer Science, Vol. 4489, pp. 34-41, Springer-Verlag Berlin Heidelberg Publisher (2007)
Yanxia Wu, Guochang Gu, Kehui Wang, Jun Ni, “Control Flow Checking Algorithm using Soft-based Intra-/Inter-block Assigned-Signature,” Proceeding of the Second International Multi-symposiums of Computer and Computational Sciences (IMSCCS|07), University of Iowa, Iowa City, USA, Aug. 13-15, 2007, IEEE Computer Society Press, Los Alamitos, California, USA, Vol. 1, pp. 412-415
Song Han, Guochang Gu, and Jun Ni, “A Mobile Ad hoc Network with Mobile Satellite Communication Base Station,” Proceeding of the Second International Multi-symposiums of Computer and Computational Sciences (IMSCCS|07), University of Iowa, Iowa City, USA, Aug. 13-15, 2007, IEEE Computer Society Press, Los Alamitos, California, USA, Vol. 1, pp. 512-516.
Xianbo Lang, Guochang Gu, Hongxun Yao, and Jun Ni, “An Image Classification Method Based on a SK Sub-Vector Multi-Hierarchy Clustering Algorithm,” Proceeding of the Second International Multi-symposiums of Computer and Computational Sciences (IMSCCS|07), University of Iowa, Iowa City, USA, Aug. 13-15, 2007, IEEE Computer Society Press, Los Alamitos, California, USA, pp. 182-186
Chen Ying, Guochang Gu, Tianyang Lv, Shaobin Huang, Jun Ni, “The Linear Correlation Analysis of Numeric Attributes for Government Data,” Proceeding of the Second International Multi-symposiums of Computer and Computational Sciences (IMSCCS|07), University of Iowa, Iowa City, USA, Aug. 13-15, 2007, IEEE Computer Society Press, Los Alamitos, California, USA, Vol. 1, pp. 521-524
Chunna Cao, Wenbin Yao, Jun Ni, “An Improved RED Algorithm Combines with Queue Length and Sending Rate Inspection,” Proceeding of the Second International Multi-symposiums of Computer and Computational Sciences (IMSCCS|07), University of Iowa, Iowa City, USA, Aug. 13-15, 2007, IEEE Computer Society Press, Los Alamitos, California, USA, Vol. 1, pp. 421-424
Linzhi Ning, Wenbin Yao, Jun Ni, Nianmin Yao, “Fault-Tolerance CMP Architecture based on SMT Technology,” Proceeding of the Second International Multi-symposiums of Computer and Computational Sciences (IMSCCS|07), University of Iowa, Iowa City, USA, Aug. 13-15, 2007, IEEE Computer Society Press, Los Alamitos, California, USA, Vol. 1, pp. 425-429
Fei Gu, Hang Chen, Jun Ni, and Zhengge Huang, “Protein Structural Class Prediction by Combining Conditional Probability with Information Content,” Proceeding of the Second International Multi-symposiums of Computer and Computational Sciences (IMSCCS|07), University of Iowa, Iowa City, USA, Aug. 13-15, 2007, IEEE Computer Society Press, Los Alamitos, California, USA, Vol. 1, pp. 38-43
Yongqiang Zhao, Minglu Li, and Jun Ni, “Adaptive Nonlinear Diffusion Model for Vessel Image Enhancement,” Proceeding of the Second International Multi-symposiums of Computer and Computational Sciences (IMSCCS|07), University of Iowa, Iowa City, USA, Aug. 13-15, 2007, IEEE Computer Society Press, Los Alamitos, California, USA, Vol. 1, pp. 170-176
Ying Chen, Jiadong Wang, Jun Ni, and Lu Zhang, “Octree Data Structure in Image-based CAS for Noise Surgery in Otolaryngology,” Proceeding of the Second International Multi-symposiums of Computer and Computational Sciences (IMSCCS|07), University of Iowa, Iowa City, USA, Aug. 13-15, 2007, IEEE Computer Society Press, Los Alamitos, California, USA, Vol. 1, pp. 123-128
Tingjun Yang, Zhengge Huang, Xingsheng Lin, Jianjun Chen, and Jun Ni, “A Parallel Algorithm for Binary-Tree-Based String Rewriting in L-system,” Proceeding of the Second International Multi-symposiums of Computer and Computational Sciences (IMSCCS|07), University of Iowa, Iowa City, USA, Aug. 13-15, 2007, IEEE Computer Society Press, Los Alamitos, California, USA, Vol. 1, pp. 245-252
Tao He, Jun Ni, Alberto M Segre, Shaowen Wang, and Boyd M. Knosp, “SkipMard: A Multi-attribute Peer-to-Peer Resource Discovery Approach, Proceeding of the Second International Multi-symposiums of Computer and Computational Sciences (IMSCCS|07), University of Iowa, Iowa City, USA, Aug. 13-15, 2007, IEEE Computer Society Press, Los Alamitos, California, USA, Vol. 1, pp. 266-273
Bo Qiang, Jun Ni, and Laurie Fajardo, “Parallel Monte Carlo Algorithm for Simulation of Photon Migration inside Biological Tissues,” RSNA|07, Chicago, USA, Scientific Paper, Nov. 25-30, 2007, SSQ16-02, pp. 596
Haiwei Pan, Qilong Han, Guisheng Yin, Wei Zhang, Jianzhong Li, Jun Ni, “A ROI-Based Mining Method with Medical Domain Knowledge Guidance,” ICICSE|08, IEEE CS Press, 2008 (in press)
Yingjie Xia, Guanghua Song, Yao Zheng, Jun Ni, Mingzhe Zhu, “A Small World Overlay P2P Transfer System with Role-based and Reputation-based Access Control Policies, ICICSE|08, IEEE CS Press, 2008 (in press)
Kent Lee, Jun Ni, Tom Halverson, Eric Van Wyk, and Judith Brown, “Is MVE the Right Environment for Your Visualization Application,” Computer Graphics, Vol. 29, No. 2, May 1995, pp. 49-51
Youping Deng, Jun Ni and Chaoyang Zhang, “Development of computations in bioscience and bioinformatics and its application,” BMC Bioinformatics, 2006, 7 (Suppl 4): S19
Longde Yin, Chun-Hsi Huang, Jun Ni, “Clustering of Gene Expression Data: Performance and Similarity Analysis,” BMC Bioinformatics, 2006, 7 (Suppl 4): S1
Lili Huang, Ge Wang, S. Kao, and Jun Ni, “VoluMeasureTM: A Portable Java program for Stereological Volume Measurement,” Radiology, November 2002, Vol. 225 (P)
Xiang Li, Jun Ni and Ge Wang, “Parallel Iterative Cone Beam CT Image Reconstruction on a PC Cluster,” Journal of X-Ray Science and Technology, 13(2005) 1-10.
Junjun Deng, Hengyong Yu, Jun Ni, Shiyi Zhao, Lihe Wang, and Ge Wang, “A Parallel Katsevich algorithm for 3-D CT Image Reconstruction,” Journal of Supercomputing, Volume 38, Number 1/October, 2006, pp. 35–47, Springer/Kluwer Academic Publisher
Jun Ni, Xiang Li, Ge Wang, “Parallel Computing Techniques for Computed Tomography,” Current Medical Imaging Reviews, 2006, Vol. 2, No. 4, pp. 1-10, Bentham Science Publishers
Jun Ni, Junjun Deng, Hengyong Yu, Tao He, Ge Wang, “Analytical Model for Performance Evaluation of Parallel Katsevich Algorithm for 3-D CT Image Reconstruction,” Int. Journal on Computational Science and Engineering, Inderscience Publisher (accepted)
Junjun Deng, Hengyong Yu, Jun Ni, Lihe Wang, and Ge Wang, “Parallelism of Iterative CT Algorithm based on Local Reconstruction,” Journal of Supercomputing, Springer (in press)
Shaoping Xiao, Shaowen Wang, Jun Ni, Ransom Briggs, Maciej Rysz, “Reliability Analysis of Carbon Nanotubes Using Molecular Dynamics with the Aid of Grid Computing, Journal of Computational and Theoretical Nanosciences (in press)
Shaoping Xiao, Jun Ni, Shaowen Wang, “The Bridging Domain Multiscale Method and its High Performance Computing Implementation,” Journal of Computational and Theoretical Nanosciences (in press)
Bo Qiang, Jun Ni, and Laurie Fajardo, “Parallel Monte Carlo Algorithm for Simulation of Photon Migration inside Biological Tissues,” RSNA|07, Chicago, USA, Scientific Paper, Nov. 25-30, 2007, SSQ16-02, pp. 596
Fei Gu, Hang Chen, Jun Ni, and Zhengge Huang, “Protein structural class prediction based on an improved statistical strategy, BMC Bioinformatics (supple), 2008 (in press)
Hiroyuki Mishima, Andrew C. Lidral, and Jun Ni, “Application of the Linux-based Cluster for Exhaustive Window Haplotype Analysis Computation using FBAT and Unphased Programs,” BMC Bioinformatics (supple), 2008 (in press)
Guoqing Lu and Jun Ni, Highlighting computations in bioscience and bioinformatics, BMC Bioinformatics (supple), 2008 (in press)
Published Application Software
Jun Ni, Lili Huang, Ge Wang, and S. Kao, “VoluMeasureTM: A Portable Java program for Stereological Volume Measurement,” Education Exhibition, Radiological Society of North American Scientific Assembly and Annual Meeting, Chicago, Nov. 2002
Instructional software, “Stereotactic Atlas of the Macaca Mulatta Thalamus and Adjacent Basal Ganglia Nuclei,” I. A. Ilinsky, K. K. Ilinsky, and Boyd Knosp, Kluwer Academic/Plenum Publishers, 2002
