(Last Five Years)
 Ma, ZS. Towards a Unified Theory for Reliability, Survivability, and Resilience of Complex Networks. (Monograph), Springer (in Press).
 Ma, ZS. et al. An Introduction to Bioinformatics. (Monograph in Chinese), Science Press, Beijing, China (in Press)
 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.
 Ma ZS (2014a). Towards computational models of animal cognition, an introduction for computer scientists. Cognitive Systems Research 33:42-69
 Ma ZS (2014b). Towards computational models of animal communication, an introduction for computer scientists. Cognitive Systems Research 33:70-99
 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.
 Guan Q & Ma ZS* (2014). Ecological analysis of the human milk microbiome. Chinese Science Bulletin 59(22): 2205-2212.
 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
 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
 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
 Ma, ZS. 2013. Stochastic Populations, Power Law, and Fitness Aggregation in Genetic Algorithms. Fundamenta Informaticae, vol. 122, pp173-206.
 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.
 Ma, Z. S. 2012. Chaotic populations in Genetic Algorithms. Applied Soft Computing, 12(8): 2409-2424.
 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.
 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.
 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.
 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.
 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
 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.
 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.
 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.
 Ma, Z. S. 2011. Did we miss some evidence of chaos in laboratory insect populations? Population Ecology, 53:405–412.
 Ma, Z. S. 2011. Frailty modeling for risk analysis in network security and survivability. I. J. Computer and Information Security, 4:276-294.
 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.
 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
 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.
 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.
 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.
 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
 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.
 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.
 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