Publications

Publications  |  Highlights

2017

Journal

Fan Xu, Mingshu Zhang, Wenting He, Renmin Han, Fudong Xue, Zhiyong Liu, Fa Zhang, Jennifer Lippincott-Schwartz, Pingyong Xu.
Live cell single moleculeguided Bayesian localization super resolution microscopy.
Cell Research, 2017, 27(5): 713-716.

Yu Chen Zihao Wang Jingrong Zhang Lun Li Xiaohua Wan Fei Sun Fa Zhang
Accelerating electron tomography reconstruction algorithm ICON with GPU. 
Biophysics Reports, 2017: 1-7.

Conference

Yu Chen Zihao Wang Lun Li Xiaohua Wan Fei Sun Fa Zhang.
A Fully Automatic Geometric Parameters Determining Method for Electron Tomography.
International Symposium on Bioinformatics Research and Applications. Springer, Cham, 2017: 385-389.

Xiang Shi, Lin Wang, Fa Zhang, Kai Zheng and Zhiyong Liu.
PABO: Congestion Mitigation via Packet Bounce.
IEEE International Conference on Communications, 2017, accepted.

Mingzhe Zhang, Lunkai Zhang, Lei Jiang, Zhiyong Liu, Frederic T. Chong.
Balancing Performance and Lifetime of MLC PCM by Using a Region Retention Monitor. 
2017 IEEE International Symposium on High Performance Computer Architecture (HPCA 2017), pp.385-396, February 4-8, 2017, Austin, TX, USA.

Zihao Wang, Yu Chen, Jingrong Zhang, Lun Li, Xiaohua Wan, Zhiyong Liu, Fei Sun, Fa Zhang.
Accelerating Electron Tomography Reconstruction Algorithm ICON Using the Intel Xeon Phi Coprocessor on Tianhe-2 Supercomputer.
International Symposium on Bioinformatics Research and Applications. Springer, Cham, 2017: 258-269.

Youshi Wang, Fa Zhang, Rui Wang, Yangguang Shi, Hua Guo, and Zhiyong Liu.
Real-Time Task Scheduling for Joint Energy Efficiency Optimization in Data Centers. [slides]
The 22nd IEEE Symposium on Computers and Communications, 2017, accepted.

2016

Journal

Hong Shan, Zihao Wang, Fa Zhang, Yong Xiong, Chang-Cheng Yin,Fei Sun.[abstract]

A local-optimization refinement algorithm in single particle analysis for macromolecular complex with multiple rigid modules.

Protein & cell, 2016, 7(1): 46-62.


Fa Zhang, Yu Chen, Fei Ren, Xuan Wang, Zhiyong Liu, Xiaohua Wan .[abstract]

A two-phase improved correlation method for automatic particle selection in Cryo-EM.

IEEE/ACM Transactions on Computational Biology and Bioinformatics. 2015 Mar., In Press.


Yuchen Deng, Yu Chen, Yan Zhang, Shengliu Wang, Fa Zhang,  Fei Sun.[abstract]  ICON: 3D reconstruction with ‘missing-information’ restoration in biological electron tomography. Journal of Structural Biology,2016, 195(1):100-112


Yu Chen , Yan Zhang , Kai Zhang , Yuchen Deng ,  Shengliu Wang , Fa Zhang, Fei Sun. [abstract] FIRT: filtered iterative reconstruction technique with information restoration. Journal of Structural Biology,2016,195(1):49-61


Biyu Zhou, Fa Zhang, Lin Wang, Chenying Hou, Antonio Fernández Anta, Athanasios V. Vasilakos, Youshi Wang, Jie Wu, Zhiyong Liu. [abstract] HDEER: A Distributed Routing Scheme for Energy-Efficient Networking. IEEE Journal on Selected Areas in Communications (JSAC),January 2016,34(6)


Conference

Mingzhe Zhang, Yangguang ShiFa ZhangZhiyong Liu.
A rapid method for Network-on-Chip design space exploration.
7th International Green and Sustainable Computing Conference (IGSC 2016) pp.1-8, November 7-9, 2016, Hangzhou, China.

2015

Journal

Renmin Han, Liansan Wang, Zhiyong Liu, Fei Sun, Fa Zhang. [abstract] A novel fully automatic scheme for fiducial marker-based alignment in electron tomography.

Journal of Structural Biology, 2015, 192(3):403-417

Ziying Zhou, Yugang Li, Fa Zhang, Xiaohua Wan. [abstract] FASART: An iterative reconstruction algorithm with inter-iteration adaptive NAD filter. Bio-Medical Materials and Engineering,  2015, 26(s1): S1409-S1415


Yangguang Shi, Fa Zhang, Jie Wu, Zhiyong Liu. [abstract] Randomized oblivious integral routing for minimizing power cost. Theoretical Computer Science, 23 November 2015 , Volume 607, Part 2, Pages 221-246, ISSN 0304-3975.


Dawei Zang, Zheng Cao, Xiaoli Liu, Lin Wang, Zhan Wang, Ningsun Sun. [abstract] PROP: Using PCIe-based RDMA to Accelerate Rack-scale Communications in Data Centers. In Proc. of the 21st IEEE International Conference on Parallel and Distributed Systems (ICPADS 2015),2015: 465-472


Xibo Jin, Fa Zhang, Lin Wang, Songlin Hu, Biyu Zhou, Zhiyong Liu. [abstract] A Joint Optimization of Operational Cost and Performance Interference in Cloud Data Centers. In IEEE Transactions on Cloud Computing (TCC), 2015.


Kai Zheng, Lin Wang, Baohua Yang, Yi Sun, Yue Zhang, Steve Uhlig.[abstract] LazyCtrl: Scalable Network Control for Cloud Data Centers. In Proc. of the 35th IEEE International Conference on Distributed Computing Systems (ICDCS 2015), 2015: 788-789

Jordi Arjona Aroca, Antonio Fernández Anta, Miguel A. Mosteiro, Christopher Thraves, Lin Wang.[abstract] Power-efficient Assignment of Virtual Machines to Physical Machines. Future Generation Computer Systems (FGCS), 2015, 54(C):82-94.

Jin Xibo, Zhang Fa, Fan Liya, Ying Song, Zhiyong Liu.[abstract] Scheduling for energy minimization on restricted parallel processors. Journal of Parallel and Distributed Computing, April,2015, 81-82: 36-46

Renmin Han, Lianshan Wang, Fan Xu, Yongdeng Zhang, Mingshu Zhang, Zhiyong Liu, Fei Ren, Fa Zhang. [abstract]Drift Correction for Single-molecule Imaging by Molecular Constraint Field, A distance Minimum Metric. BMC Biophysics, Jan 13,2015, 8(1): 1-14

Fan Xu, Mingshu Zhang, Zhiyong Liu, Pingyong Xu, Fa Zhang. [abstract]

Bayesian Localization Microscopy Based on Intensity Distribution of Fluorophores. Protein & Cell,March, 2015, 6(3): 211-220


Fa Zhang, Jingrong Zhang, Albert Lawrence, Fei Ren, Xuan Wang, Zhiyong Liu, Xiaohua Wan. [abstract]

BSIRT: A Block-Iterative SIRT Parallel Algorithm Using Curvilinear Projection Model. IEEE Transactions on Nanobioscience, March,2015, 4(2):229-236


Conference

Youshi Wang, Fa Zhang, Zhiyong Liu.[abstract]

Truthful Strategy and Resource Integration for Multi-tenant Data Center Demand Response. In Proceeding of the 9th International Frontiers of Algorithmics Workshop (FAW) 2015. pp. 259-270, July 3-5, 2015, Guilin, China


Lin Wang, Antonio Fernández Anta, Fa Zhang, Jie Wu, Zhiyong Liu.[abstract]


2014

Journal

Ruijuan Chen, Xiaohua Wan, Ilkay Altintas, Jianwu Wang, Daniel Crawl, Sébastien Phan, Albert Lawrence, Mark Ellisman.[abstract] EPiK-a Workflow for Electron Tomography in Kepler. Procedia Computer Science (ICCS 2014),May, 2014, 29: 2295-2305 (co-first author).


Shaoli Liu, Tianshi Chen, Ling Li, Xi Li, Mingzhe Zhang, Chao Wang, Haibo Meng, Xuehai Zhou, and Yunji Chen.[abstract] FreeRider: Non-local Adaptive Network-on-Chip Routing with Packet-Carried Propagation of Congestion Information. IEEE Transactions on Parallel and Distributed Systems, August,2014, 2015, 26(1):2272-2285.


Dawei Zang, Zheng Cao, Zhan Wang, Xiaoli Liu, Lin Wang, and Ninghui Sun.[abstract] Decentralized NIC-switching Architecture Using SR-IOV PCIe Network Devices. IEEE Micro, July,2014, 34(5): 42-50.


Renmin Han, Fa Zhang, Xiaohua Wan, Jose-Jesus Fernández, Fei Sun, Zhiyong Liu. [abstract] A marker-free automatic alignment method based on scale-invariant features. Journal of Structural Biology, April ,2014,186(1): 167-180


Lin Wang, Fa Zhang, Jordi Arjona Aroca, Athanasios V. Vasilakos, Kai Zheng, Chenying Hou, Dan Li, and Zhiyong Liu.[abstract] GreenDCN: a General Framework for Achieving Network Energy Efficiency in Data Centers. IEEE Journal on Selected Areas in Communications (JSAC), vol. 32(1), pp. 4-15, January 2014.


Yu Chen, Fei Ren, Xiaohua Wan, et. al.[abstract] An Improved Correlation Method Based on Rotation Invariant Feature for Automatic Particle Selection. International Symposium on Bioinformatics Research and Applications (ISBRA’ 2014): 114-125.


Jingrong Zhang, Xiaohua Wan, Fa Zhang,Fei Ren, Xuan Wang, Zhiyong Liu. A Parallel Scheme for Three-Dimensional Reconstruction in Large-Field Electron Tomography. ISBRA 2014: 102-113.June 28-30, 2014.[abstract]


Conference

Lunkai Zhang, Dmitri B. Strukov, Hebatallah Saadeldeen, Dongrui Fan, Mingzhe Zhang, Diana Franklin.[abstract] SpongeDirectory: flexible sparse directories utilizing multi-level memristors. In Proceeding of the 23rd international conference on Parallel architectures and compilation (PACT) 2014. pp. 61-74, August 24-27, 2014, Edmonton, Canada


Yangguang Shi, Fa Zhang, Zhiyong Liu.[abstract] Polylogarithmic Competitive Algorithm for Energy Minimization in Optical WDM Networks. IEEE 22nd International Conference on Network Protocols (ICNP)2014 . pp. 197-202,  Oct 21-24,2014 .


Lin Wang, Fa Zhang, Kai Zheng, Athanasios V. Vasilakos, Shaolei Ren, and Zhiyong Liu.[abstract] Energy-Efficient Flow Scheduling and Routing with Hard Deadlines in Data Center Networks. Proceedings of the 34th International Conference on Distributed Computing Systems (ICDCS 2014), Madrid, Spain. June 30 2014-July 3 2014.


Jordi Arjona Aroca, Antonio Fernández Anta, Miguel A. Mosteiro, Christopher Thraves, and Lin Wang.[abstract] Power-efficient Assignment of Virtual Machines to Physical Machines. Proceedings of the 33th ACM Symposium on Principles of Distributed Computing (PODC 2014), workshop on Adaptive Resource Management and Scheduling for Cloud Computing, Paris, France, July 2014.


Biyu Zhou, Lin Wang, Fa Zhang, Xibo Jin, and Zhiyong Liu.[abstract]  DEER: a Distributed Routing Scheme forAchieving Network Energy Efficiency. Proceedings of the 20th IEEE International Workshop on Local and Metropolitan Area Networks (LANMAN 2014), Reno, NV, USA, May 2014.


Yangguang Shi, Fa Zhang, Zhiyong Liu.[abstract] Oblivious Integral Routing for Minimizing the Quadratic Polynomial Cost. Frontiers in Algorithmics – 8th International Workshop, FAW 2014, Zhangjiajie, China, June 28-30, 2014. Proceedings. Volume 8497 of Lecture Notes in Computer Science, pages 216-228, Springer, 2014.


 

2013

Journal

Lin Wang, Fa Zhang, Athanasios V. Vasilakos, Chenying Hou, and Zhiyong Liu.[abstract]

ACM SIGMETRICS Performance Evaluation Review, vol. 41(3), pp. 107-112, December 2013.

Mingzhe Zhang, Da Wang, Xiaochun Ye, Liqiang He, Dongrui Fan, Zhiyong Liu.[abstract] A Path-Adaptive Opto-electronic Hybrid NoC for Chip Multi-processor. TrustCom/ISPA/IUCC 2013: 1198-1205. 16-18 July 2013.


Mingzhe Zhang, Da Wang, Xiaochun Ye, Liqiang He, Dongrui Fan, Zhiyong Liu.[abstract] Energy-Performance Modeling and Optimization of Parallel Computing in On-Chip Networks. TrustCom/ISPA/IUCC 2013: 879-886.16-18 July 2013.


Xiaochun Ye, Dongrui Fan, Ninghui Sun, Shibin Tang, Mingzhe Zhang, Hao Zhang[abstract] 2013 IEEE International Symposium on Low Power Electronics and Design (ISLPED): 273-278.4-6.Sept,2013 SimICT: A fast and flexible framework for performance and power evaluation of large-scale architecture.


Xiaohua Wan, Sebastien Phan, Albert Lawrence, Fa Zhang, Renmin Han, Zhiyong Liu, Mark Ellisman. Iterative Methods in Large Field Electron Microscope Tomography. SIAM J. Sci. Comput, 35(5), S402–S419.October,2013.[abstract]


Chenying Hou, Fa Zhang, Antonio Fernández Anta, Lin Wang, Zhiyong Liu. [abstract] A hop-by-hop energy efficient distributed routing scheme. ACM SIGMETRICS Performance Evaluation Review,41(3): 101-106 .December 2013


GongMing Wang, Fa Zhang, Qi Chu, LiYa Fan, Fei Sun, ZhiYong Liu.   A fast calculation strategy of density function in ISAF reconstruction algorithm. SCIENCE CHINA Information Sciences 56(9): 1-12 .September 2013.[abstract]


Conference

Lunkai Zhang, Mingzhe Zhang, Lingjun Fan, Da Wang, Paolo Ienne.[abstract] Spontaneous Reload Cache: Mimicking a Larger Cache with Minimal Hardware Requirement. NAS 2013: 31-40.


Xibo Jin, Fa Zhang, Ying Song, Liya Fan and Zhiyong Liu.[abstract] Energy-Efficient Scheduling with Time and Processors Eligibility Restrictions. The 19th International European Conference on Parallel and Distributed Computing, EuroPar 2013, Aachen, Germany, Aug 26-30, 2013.


Lin Wang, Fa Zhang, Chenying Hou, Jordi Arjona Aroca, and Zhiyong Liu.[abstract] Incorporating Rate Adaptation into Green Networking for Future Data Centers. the 12th Proceedings of the 12th IEEE International Symposium on Network Computing and Applications (NCA 2013), Cambridge, MA USA, Aug 22-24, 2013.


Yangguang Shi, Fa Zhang, Zhiyong Liu.[abstract] A Universally Stable and Energy-Efficient Scheduling Protocol For Packet Switching Network. the 12th IEEE International Symposium on Network Computing and Applications (NCA), Cambridge, MA USA, Aug 22-24, 2013.


Lin Wang, Fa Zhang, and Zhiyong Liu.[abstract] Improving the Network Energy Efficiency in MapReduce Systems. Proceedings of the 22th International Conference on Computer Communications and Networks (ICCCN 2013), Nassau, Bahamas, July 30 – Aug 2, 2013.


Xibo Jin, Fa Zhang and Zhiyong Liu.[abstract] Discrete Min-Energy Scheduling on Restricted Parallel Processors. The 27th IEEE International Parallel and Distributed Processing Symposium Workshops & PhD Forum, IPDPS 2013, Boston, MA USA, May 20-24, 2013.


Xibo Jin, Fa Zhang, Songlin Hu and Zhiyong Liu.[abstract] Risk Management for Virtual Machines Consolidation in Data Centers. In Proceedings of IEEE Global Communications Conference, GlobeCom 2013, Atlanta, GA USA, Dec 9-13, 2013.


2012

Journal

Xiaohua Wan, Fa Zhang, Qi Chu, Zhiyong Liu.[abstract] High-performance blobbased iterative three-dimensional reconstruction in electron tomography using multi-GPUs. BMC bioinformatics , 2012, 13. (SCI, IF is 3.028).


Gongming Wang, Fa Zhang, Fei Sun, Zhiyong Liu.[abstract] An Accelerated ISAF Algorithm with the Fast Mapping Strategy. Journal of Computers, Vol 7, No 2 (2012), 528-533, Feb 2012.


Liya Fan, Fa Zhang, Gongming Wang, Zhiyong Liu.[abstract] An effective approximation algorithm for the Malleable Parallel Task Scheduling problem. J. Parallel Distrib. Comput. 72(5): 693-704 (2012). May,2012.


Conference

Fa Zhang, Qiaoxia Zhao.[abstract] Runtime Reconstruction of Simulation Models for Dynamic Structure Systems. Asia Simulation Conference 2012, Shanghai, China, October 27-30, 2012. Proceedings, Part III.


Xiaohua Wan, Sebastien Phan, Albert Lawrence, et. al.[abstract] Iterative methods in large field electron microscope tomography. Twelfth Copper Mountain Conference on Iterative Methods, Mar. 2012.


Lin Wang, Antonio Fernández Anta, Fa Zhang, Chenying Hou, and Zhiyong Liu.[abstract] Energy-efficient Network Routing with Discrete Cost Functions. Theory and Applications of Models of Computation (TAMC), 307-318, LNCS vol. 7287, Beijing China, May 16-22, 2012.


Mingzhe Zhang, Liqiang He, Dongrui Fan.[abstract] Self-Correction Trace Model: A Full-System Simulator for Optical Network-on-Chip. IPDPS Workshops 2012: 242-247.


2011

Journal

Xiaohua Wan, Fa Zhang, Qi Chu et. al.[abstract] Three-dimensional Reconstruction Using an Adaptive Simultaneous Algebraic Reconstruction Technique in Electron Tomography. Journal of Structural Biology.June,2011 (SCI, IF is 3.497).


Conference

Chenying Hou, Fa Zhang, Lin Wang, Zhiyong Liu. [abstract] Time-Slot Energy-Efficient Scheduling Algorithm for Capacity Limited Networks. 2011 IEEE/ACM International Conference on Green Computing and Communications (GreenCom).4-5 Aug,2011.


Xiaohua Wan, Fa Zhang, Qi Chu et. al.[abstract] High-performance Blob-based Iterative Reconstruction of Electron Tomography on Multi-GPUs. International Symposium on Bioinformatics Research and Applications (EI, ISBRA’ 2011) 6674: 61-72.May 27-29.


2010

Journal

万晓华,张法,刘志勇.[abstract] 电子断层三维重构迭代算法及其基于GPUs 的高效并行. China Computer Federation (CCF’ 2010).October,2010.


Yan Jia, Ziyang Chen, Xuan Wang, Fa Zhang.[abstract] Protein Sequence Alignment Algorithm Based on Hybrid Profile Information. BIOCOMP 2010: 220-224.


Conference

Qi Chu, Fa Zhang, Kai Zhang, Xiaohua Wan, Mingwei Chen, Zhiyong Liu.[abstract] An accurate, automatic method for markerless alignment of electron tomographic images. BIBM 2010: 393-396.18-21 Dec,2010.


Xiaohua Wan, Fa Zhang, Qi Chu, Zhiyong Liu.[abstract] Three-dimensional reconstruction of electron tomography using graphic processing units (GPUs). International Workshop of GPU Solutions to Multi-scale Problems in Science and Engineering (GPU-SMP’ 2010).July 26-29,2010.


2009

Journal

万晓华,张法,刘志勇.[abstract] 一种冷冻电子断层三维重构的并行迭代算法 《微电子学与计算机》.August,2009.


Liya Fan, Fa Zhang, Gongming Wang, Zhiyong Liu.[abstract] A framework to refine particle clusters produced by EMAN. Bioinformatics.June,2009.


Liya Fan, Fa Zhang, Gongming Wang, Bo Yuan, Zhiyong Liu.[abstract] A Self-adaptive Greedy Scheduling Scheme for a Multi-Objective Optimization on Identical Parallel Machines. 10th Conference on Software Engineering, Artificial Intelligence, Networking and Parallel/Distributed Computing (SNPD 2009): 43-55.May 27–29, 2009.


Conference

Liya Fan, Fa Zhang, Gongming Wang, Zhiyong Liu.[abstract] An effective scheduling algorithm for Linear Makespan Minimization on Unrelated Parallel Machines. 2009 International Conference on  High Performance Computing (HiPC): 40-49.16-19 Dec,2009.


Xiaohua Wan, Fa Zhang, Zhiyong Liu.[abstract] Modified simultaneous Algebraic Reconstruction Technique and its Parallelization in Cryo-electron Tomography. International Conference on Parallel and Distributed Systems (EI, ICPADS’2009).8-11 Dec,2009.


2008

Journal

Xinyu Que, Fa Zhang, Shengzhong Feng, Bo Yuan, Zhiyong Liu. [abstract]
An improvement method based on OrthoMCL by adding the domain information.
BIOCOMP 2008: 418-423.

2007

Journal


2006

Journal


2004

Journal

Fa Zhang, Xiangzhen Qiao, Zhiyong Liu.[abstract]
Parallel divide and conquer bio-sequence comparison based on smith-waterman algorithm.
Science in China Series F: Information Sciences 47(2): 221-231.March 2004.
 

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