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Principal Investigator
Computational Biology and Medical Ecology Lab
Zhanshan (Sam) Ma   Ph.D.  
Title Principal Investigtor
Phone +86 871 65183700
Fax +86 871 65183700
E-mail samma@uidaho.edu; ma@mail.kiz.ac.cn
Address Kunming Institute of Zoology, the Chinese Academy of Sciences No. 32 Jiaochang Donglu, Kunming, Yunnan, 650223, P.R.China
Zip Code 650223
 
   Education and Appointments:

Prof. Zhanshan (Sam) Ma received his double Ph.Ds in Computer Science and Entomology in 2008 and 1997, respectively, both from the University of Idaho, USA. In November 2010, he was retained as a Professor and Principal Investigator (PI) by Kunming Institute of Zoology (KIZ), the Chinese Academy of Sciences (CAS) through “The Elite 100 PI Program” of the CAS. Prior to joining in KIZ, he was a Research Scientist (in Computational Biology & Computer Science) at the University of Idaho. He was a senior network and software engineer from 1998 to 2006 in the computer industry in Silicon Valley, USA. Dr. Ma has been keeping dual-track publishing in both Computer Science and Biology with more than 80 peer-refereed papers in premier platforms such as IEEE Transactions on Reliability, Science Translational Medicine, The ISME Journal. He is a member of London-based “Faculty 1000 of Biology and Medicine”.  

  Professional Services

 Faculty of 1000 Biology & Medicine (www.f1000.com) 

   Research Interests:

Genome Assembly, Computational Intelligence and Evolutionary Computing 

Network Biology (Metagenomic Networks, Cancer Gene Regulatory Networks) 

Medical Ecology of Human Microbiome and Personalized Medicine   

Reliability, Survivability and Resilience of Complex Networks

  Supported Projects:

(1) The Chinese Academy of Sciences (CAS) startup funding for the “One-Hundred Talented PI Plan” (PI, Year 2010-2014) 

(2) The CAS startup funding for the “Exceptional Overseas Technologist Program” (PI, 2011-2014) 

(3) National Science Foundation of China (NFSC) grant: “The Ecological Theater and the Evolutionary Computing Play” (PI, 2012-2015) 

(4) National Science Foundation of China (NFSC) grant: Reliability, survivability and resilience of complex networks (PI, 2015-2018) 

(5) National Science Foundation of China (NFSC) grant: “Rapid biodiversity measurement with metagenetics.” (2012-2015) (PI: Douglas Yu) 

(6) Special Funding for the “Exceptional Scientists in Science and Technology” by Yunnan Province:  “GP-GPU Computing for Computational Bioinformatics and Personalized Medicine” (PI, 2012-2015) 

(7) Innovative Research Initiative of the Synergy between the Natural and Computational Evolutions of CAS-Yunan Province (PI, 2012-2015) 

(8) Funding for the “Top Talents from Overseas” of Yunnan Province (PI, 2012-2015) 

  Public Services:
  Honors:
  Selected Publications:

 (Last Five Years)

[1] Ma, ZS. Towards a Unified Theory for Reliability, Survivability, and Resilience of Complex Networks. (Monograph), Springer (in Press).      

[2] Ma, ZS. et al. An Introduction to Bioinformatics. (Monograph in Chinese), Science Press, Beijing, China (in Press)      

[3] Ye CX*, Hill C, Koren S. Ruan J, Ma ZS*, Yorke JA, Zimin A* (2014). DBG2OLC: efficient assembly of large genomes using the compressed overlap graph.  

    Paper: http://adsabs.harvard.edu/cgi-bin/bib_query?arXiv:1410.2801   

    Software: http://sites.google.com/site/dbg2olc/,      

[4] Ma ZS (2014a). Towards computational models of animal cognition, an introduction for computer scientists. Cognitive Systems Research 33:42-69      

[5]  Ma ZS (2014b). Towards computational models of animal communication, an introduction for computer scientists. Cognitive Systems Research 33:70-99      

[6] Li H, Ye DD, Wang X, Settles ML, Wang J, Zhou L, Dong P, Ma ZS* (2014) Soil bacterial communities of different natural forest types in China. Plant and Soil 383:203-216.      

[7] Guan Q & Ma ZS* (2014). Ecological analysis of the human milk microbiome.  Chinese Science Bulletin 59(22): 2205-2212.   

[8]  Ma, ZS, Liexun Yang, Ronald P. Neilson, Andrew Hess, Richard Millar. 2014. A Survivability-Centered Research Agenda for Cloud Computing Supported Emergency Response and Management Systems. 17pp. The 35th IEEE-AIAA Aerospace Conference (Aerospace 2014), Big Sky, Montana, USA, March 7-15th, 2014. doi: 10.1109/AERO.2014.6836515       

[9] Zhang ZG, Geng JW, Tang XD, Fan H, Xu JC, Wen XJ, Zhanshan (Sam) Ma*, Peng Shi*. 2013. Spatial heterogeneity and co-occurrence patterns of human mucosal associated intestinal microbiota. The ISME Journal, doi:10.1038/ismej.2013.185  

[10] Ma ZS, Guan Q., Ye CX, Zhang CC, Foster JA, and Forney, LJ. Network analysis reveals a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities. http://adsabs.harvard.edu/cgi-bin/bib_query?arXiv:1410.0649  AAAS’s EurekAlert: http://www.eurekalert.org/pub_releases/2014-09/scp-ahb090214.php       

[11] Ma, ZS. 2013. Stochastic Populations, Power Law, and Fitness Aggregation in Genetic Algorithms. Fundamenta Informaticae, vol. 122, pp173-206.      

[12] Ma, ZS. 2013. First passage time and first passage percolation models for analyzing network resilience and effective strategies in strategic information warfare research. I. J. Information and Computer Security. 5(4): 334-358.      

[13] Ma, Z. S. 2012. Chaotic populations in Genetic Algorithms. Applied Soft Computing, 12(8): 2409-2424.       

[14] Ma, Z. S. 2012. A unified definition for reliability, survivability and resilience inspired by the handicap principle and ecological stability. International Journal of Critical Infrastructures, 8(2):242-272.       

[15] Ma, Z. S. et al. 2012. A Bird's Eye View of Microbial Community Dynamics. In “Microbial Ecological Theory: Current Perspectives.” Caister Academic Press, Editor: Lesley A. Ogilvie and Penny R. Hirsch.      

[16] Ye, Chengxi, Zhanshan (Sam) Ma, Charles H. Cannon, Mihai Pop and Douglas W. Yu. 2012. Exploiting sparseness in de novo genome assembly. BMC Bioinformatics, 13(Suppl 6):S1.      

[17] Gajer, Pawel, Rebecca M. Brotman, Guoyun Bai, Joyce Sakamoto, Ursel M. E. Schütte, Xue Zhong, Sara S. K. Koenig, Li Fu, Zhanshan (Sam) Ma, Xia Zhou, Zaid Abdo, Larry J. Forney and Jacques Ravel. 2012. Temporal Dynamics of the Human Vaginal Microbiota.  Science Translational Medicine. 4:(132): 132ra52.      

[18] Ma, Z. S. A Note on Extending Taylor’s Power Law for Characterizing Human Microbial Communities: Inspiration from Comparative Studies on the Distribution Patterns of Insects and Galaxies, and as a Case Study for Medical Ecology and Personalized Medicine. http://adsabs.harvard.edu/abs/2012arXiv1205.3504M      

[19] Ye, D, D, M. M., Fan, Q. Guan, H. J. Chen, & Z. S. Ma*. 2012. A review on the bioinformatics pipelines for metagenomic research [text in Chinese]. Zoological Research, 33(6): 574-85.      

[20] Ma, Z. S. & A. W. Krings. 2011. Dynamic hybrid fault modeling and extended evolutionary Game theory for reliability, survivability and fault tolerance analyses. IEEE Transactions on Reliability. vol. 60(1):180-196.      

[21] Ma, Z. S. 2011. Ecological ‘theater’ for evolutionary computing ‘play’: some insights from population ecology and evolutionary ecology. I. Journal of Bio-Inspired Computing 4(1):31-55.      

[22] Ma, Z. S. 2011. Did we miss some evidence of chaos in laboratory insect populations? Population Ecology, 53:405–412.      

[23] Ma, Z. S. 2011. Frailty modeling for risk analysis in network security and survivability. I. J. Computer and Information Security, 4:276-294.       

[24] Ma, Z. S. et al. 2011. Insect navigation and communication in flight and migration: a potential model for joining and collision avoidance in MAVs (Micro-Aerial Vehicle) and mobile robots fleet control. Proc. of the 32nd IEEE-AIAA Aerospace Conference. 14pp, Big Sky, Montana, USA.      

[25] Ye, C. X., Z. S. Ma, C. Canon, M. Pop, D. W. Yu. 2011. SparseAssembler: de novo Assembly with the Sparse de Bruijn Graph. http://arxiv.org/abs/1106.2603      

[26] Ye, C. X., C. Cannon, Z. S. Ma, D. W. Yu, and M. Pop. 2011. SparseAssembler2: Sparse k-mer Graph for Memory Efficient Genome Assembly. http://arxiv.org/abs/1108.3556.      

[27] Ma, Z. S., H. J. Chen, J. J. Zhang, A. W. Krings, F. Sheldon. 2011. Has the cyber warfare threat been overstated? A cheap talk game-theoretic perspective on the Google-hacking claim. The 7th Cyberspace Sciences and Information Intelligence Research Workshop, 7th CSIIRW11. October 14-16, 2011. Oak Ridge National Lab, Oak Ridge, USA.      

[28] Ma, Z. S. 2010. Is Strategic Information Warfare Really Asymmetric? —a New Perspective from the Handicap Principle. Journal of Information Warfare, 9(3): 51-61.      

[29] Ma, Z. S. (2010) Survival Analysis Approach to Life Table Analysis and Hypothesis Testing for Russian Wheat Aphid Populations. Bulletin of Entomological Research. vol.100(3): 315-324      

[30] Ma, Z. S., et al. (2010) Logics in Animal Cognition: Are They Important to Brain Computer Interfaces (BCI) and Future Space Missions? Proc. 31st IEEE-AIAA Aerospace Conference 2010, 8pp. Big Sky, Montana, USA.      

[31] Zhou, X. et al. 2010. Recent Advances in Understanding the Microbiology of the Female Reproductive Tract and the Causes of Premature Birth. Infectious Diseases in Obstetrics and Gynecology, vol. 2010, Article ID 737425, 10 pages.      

[32] Ma, Z. S., et al. (2011). Caring about trees in the forest: incorporating frailty in risk analysis for personalized medicine. Personalized Medicine, 8(6): 681-688      

    Previous publications in computer science may be found in DBLP and MathSciNet library  

    http://www.informatik.uni-trier.de/~ley/pers/hd/m/Ma:Zhanshan_=Sam=   

    http://genealogy.math.ndsu.nodak.edu/id.php?id=132255  

  Research Team:

Staff

Dandan YeResearch Associate, M.S. in Computer Science 

Yanlin Jia, Research Associate, M.S in Mathematics 

Ping DongResearch Associate, B.S. Probability and Statistics      

Graduate Students 

Qiong Guan; Mengmeng Fan; Lianwei Li; Yali Wang; Huayang Tang (Computer Science, Co-major Adviser); Benbo You; Juan Hu (Mathematics, Co-major Adviser)  

Visiting Professors 

Dr. Sharron Quisenberry,  Vice President of Research,  Professor of Entomology,  Iowa State University, Ames, Iowa, USA 

Ye Chengxi, PhD Candidate Department of Computer Science University of Maryland, USA 

Dr. Cheng Le, Executive Director of BGI-Yunnan, Associate Director of China National GeneBank, BGI Shenzhen, China     

Dr. Frederick T. Sheldon,  Senior Research Staff Member, Computational Sciences & Engineering Division, 

      Oak Ridge National Laboratory, Oak Ridge, Tennessee, USA 

Dr. Ronald P. Neilson,  USDA Bioclimatologist, Professor of Global Climate Changes, Oregon State University, Corvallis, Oregon, USA 

 
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