List of Publications

System Software

  1. G. Almasi, C. J. Archer, C. Chris Erway, P. Heidelberger, X. Martorell, J. E. Moreira, B. Steinmacher-Burow, Y. Zheng, "Optimization of MPI Collective Communication on BlueGene/L Systems", Proceedings of the 19th Annual International Conference on Supercomputing, ICS 2005, June 20-22, 2005, Cambridge, Massachusetts, USA, pp. 253-262.
  2. Barton, C., Casçaval, C., Almási, G., Zheng, Y., Farreras, M., Chatterje, S., and Amaral, J. N., "Shared memory programming for large scale machines", In Proceedings of the 2006 ACM SIGPLAN Conference on Programming Language Design and Implementation (Ottawa, Ontario, Canada, June 11 - 14, 2006). PLDI '06. ACM Press, New York, NY, 108-117.
  3. Ali R. Butt, Troy A. Johnson, Yili Zheng, Y. Charlie Hu, "Kosha: A Peer-to-Peer Enhancement for the Network File System", Proceedings of Supercomputing (SC) 2004, November 2004, Pittsburgh, P.A., pp. 51.
  4. Ali R. Butt, Troy A. Johnson, Yili Zheng, Y. Charlie Hu, "Kosha: A Peer-to-Peer Enhancement for the Network File System", Journal of Grid Computing, Special Issue on Peer-to-Peer and Grid Computing, Volume 4 (3), pp. 323-341, September 2006. .
  5. Brian Armstrong, Hansang Bae, Rudolf Eigenmann, Faisal Saied, Mohamed Sayeed, Yili Zheng, "HPC Benchmarking and Performance Evaluation With Realistic Applications", SPEC Benchmark Workshop 2006, January 23, 2006, Austin, Texas.
  6. Brian Armstrong, Hansang Bae, Rudolf Eigenmann, Faisal Saied, Mohamed Sayeed, Yili Zheng, "Measuring HPC Performance With Real Applications" (In submission)

Statistical Image Processing and High Performance Computing in Biomedical Applications

  1. Zhye Yin, Yili Zheng, Peter C. Doerschuk, "An ab initio algorithm for low-resolution 3-D reconstruction from cryo electron microscope images", J. Structural Biology, vol. 133, pp. 132-142 (2001)
  2. Zhye Yin, Yili Zheng, Peter C. Doerschuk, Padmaja Natarajan, John E. Johnson, "A statistical approach to computer processing of cryo electron microscope images: virion classification and 3-D reconstruction", J. Structural Biology, vol. 144, pp. 24-50 (2003)
  3. Zhye Yin, Yili Zheng, Peter C. Doerschuk, "3-D reconstructions from cryo electron microscope images: an ab initio algorithm", Proceedings of the Optical Society of America Topical Meeting on Signal Recovery and Synthesis, November 2001, pp. 77-79.
  4. Zhye Yin, Yili Zheng, Peter C. Doerschuk, "Robustness of 3-D maximum likelihood reconstructions of viruses from cryo electron microscope images", Proceedings of the IEEE 2002 International Conference on Acoustics, Speech, and Signal Processing, May 2002, vol. IV, pp. 3249-3252.
  5. Zhye Yin, Yili Zheng, Peter C. Doerschuk, "A statistical model for cryo electron microscope images and 3-D reconstruction and experimental design", Proceedings of the IEEE 2002 International Symposium on Biomedical Imaging: Macro to Nano, July 2002, pp. 673-676.
  6. Yili Zheng, Zhye Yin, Peter C. Doerschuk, "3-D maximum likelihood reconstructions of viruses from cryo electron microscope images and parallel computation", Proceeding of the IEEE 2002 International Conference on Image Processing, September 2002, vol. II, pp. 617-620.
  7. Zhye Yin, Yili Zheng, Peter C. Doerschuk, "Computational 3-D Reconstructions by Optimization for Cryo-Electron Microscopy", Proceedings of the Electronic Imaging 2003 Symposium, January 20-24, 2003, Santa Clara, CA, SPIE Vol. 5016, pp. 71-79.
  8. Zhye Yin, Yili Zheng, Peter C. Doerschuk, "Inverse problems in computational biology", Proceedings of the Electronic Imaging 2004 Symposium, January 18-22, 2004, San Jose, CA.
  9. Junghoon Lee, Yili Zheng, Peter C. Doerschuk, "A fast algorithm for 3-D reconstruction from unoriented projections and cryo electron microscopy of viruses",  Electronic Imaging 2006.
  10. Junghoon Lee, Yili Zheng, Peter C. Doerschuk, Jinghua Tang, John E. Johnson, "Maximum likelihood 3-D reconstruction of multiple viruses from mixtures of cryo electron microscope images", in Computational Imaging III, edited by Charles A. Bouman and Eric L. Miller, Proceedings of SPIE-IS&T Electronic Imaging, SPIE vol. 5674, pp. 336-343, 2005; IS&T/SPIE Symposium on Electronic Imaging 2005, January 16-20, 2005, San Jose, CA.
  11. Junghoon Lee, Yili Zheng, Peter C. Doerschuk, "Computing the 3-D structure of viruses from unoriented cryo electron microscope images: a fast algorithm for a statistical approach", Engineering in Medicine and Biology Society, 2006. EMBS '06. 28th Annual International Conference of the IEEE, pp. 2538-2541.
  12. Yili Zheng, Peter C. Doerschuk, John E. Johnson, Using multi-core, multi-cpu, PC clusters for statistical 3-D virus reconstructions from cryo electron microscopy images, accepted to SIAM Conference on Parallel Processing 2008.   
  13. Yili Zheng, Peter C. Doerschuk, "A Parallel Software Toolkit for Statistical 3-D Virus Reconstructions from Cryo Electron Microscopy Images Using Computer Clusters with Multi-core Shared-Memory Nodes", accepted to IEEE International Parallel and Distributed Processing Symposium (IPDPS) 2008 (acceptance rate 105/410).

Posters and Presentations

  1. TAP List, SPEC Booth in Supercomputing 2002.
  2. Zhye Yin, Yili Zheng, Peter C. Doerschuk, John E. Johnson, "Statistical classification and 3-D reconstruction of multiple virion types from mixtures of boxed cryo electron microscopy images", Mont Diego Workshop, The Scripps Research Institute, La Jolla, CA, March 28-29, 2003. No proceedings.
  3. Yili Zheng, Peter C. Doerschuk, John E Johnson, "Automatic statistical symmetry classification of phage P22 portal electron microscopy images", BMES Annual Meeting, Los Angeles, CA, 2007

Technical Reports

  1. Ali Raza Butt, Troy A. Johnson, Yili Zheng, Y. Charlie Hu, "Hoard: A Peer-to-Peer Enhancement for the Network File System", Technical Report TR-ECE-03-08, School of ECE, Purdue University, 2003.

Thesis

  1. Yili Zheng, “Parallel implementations of 3-D reconstruction algorithms for cryo electron microscopy: A comparative. study,” MS. thesis, School of ECE, Purdue University, 2002