CAS Center for Excellence in Animal Evolution and Genetics

MA Zhanshan

2019-03-07 | | 【Print】

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). 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”.

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

Supported Subjects

(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)

Research Interest

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

Publications

[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. 　　