[1] DBG2OLC [三代基因测序组装软件: An ultra efficient de Novo genome assembler for the 3rd generation sequencing technologies (PacBio & Oxford Nanopore)]. Available at: https://sites.google.com/site/dbg2olc/ https://sourceforge.net/projects/dbg2olc/ [2] Sparc (三代基因测序纠错软件: A sparsity-based consensus algorithm for long erroneous 3rdGS sequencing reads). Available at: https://sourceforge.net/projects/sparc-consensus/ https://github.com/yechengxi/Sparc [3] SparseAssembler (二代基因测序组装软件: Sparse k-mer Graph for Memory Efficient de novo Genome Assembly). The core algorithm (Sparse k-mer) was used in BGI’s SoapDenovo-II, the updated version of BGI’s flagship software SoapDenovo. Available at: https://sites.google.com/site/sparseassembler/ https://sourceforge.net/projects/sparseassembler/ 关于以上软件的相关报道和介绍: http://news.sciencenet.cn/htmlnews/2016/7/350187.shtm http://yn.xinhuanet.com/topic/2015-01/14/c_133919243.htm http://yndaily.yunnan.cn/html/2015-01/03/content_924003.htm http://ccwb.yunnan.cn/html/2016-06/15/content_1069115.htm http://stock.591hx.com/article/2016-06-17/0000988031s.shtml http://guba.eastmoney.com/news,cjpl,434957158.html http://news.hongzhoukan.com/16/0701/hl221824.html http://finance.qq.com/a/20160620/016790.htm http://news.cnstock.com/industry/sid_zxk/201608/3870020.htm http://stock.hexun.com/2016-06-23/184540860.html http://finance.ifeng.com/a/20160617/14498467_0.shtml http://www.cfi.net.cn/p20160619000072.html [4] Ma, ZS. Towards a Unified Theory for Reliability, Survivability, and Resilience of Complex Networks. (Monograph), Springer (in Press). [5] Ma, ZS. et al. An Introduction to Bioinformatics. (Monograph in Chinese), Science Press, Beijing, China (in Press) [6] Ma ZS et al (2016) A Brief Review on the Ecological Network Analysis with Applications in the Emerging Medical Ecology. (Invited book chapter) http://link.springer.com/protocol/10.1007/8623_2016_204 [7] Ye CX & ZS Ma (2016) Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads. PeerJ. 4:e2016; DOI 10.7717/peerj.2016 https://peerj.com/articles/2016/ [8] Ye CX, C Hill, J Ruan, ZS Ma (2016) DBG2OLC: Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies. http://www.nature.com/articles/srep31900 [9] Li LW & ZS Ma (2016) Testing the Neutral Theory of Biodiversity with Human Microbiome Datasets. Scientific Reports. 6, Article No. 31448 (2016) http://www.nature.com/articles/srep31448 [10] Ma ZS, LW Li, Wendy Li, Jie Li, HJ Chen (2016) Integrated network-diversity analyses suggest suppressive effect of Hodgkin’s lymphoma and slightly relieving effect of chemotherapy on human milk microbiome. Scientific Reports, vol. 6, Article Number 28048, doi:10.1038/srep28048 http://www.nature.com/articles/srep28048 [11] Ma ZS et al. (2015) Network analysis suggests a potentially ‘evil’ alliance of opportunistic pathogens inhibited by a cooperative network in human milk bacterial communities. Scientific Reports 5, Article number: 8275 http://www.nature.com/articles/srep08275 [12] Ma ZS (2015) Power law analysis of the human microbiome. Molecular Ecology, vol. 24, DOI: 10.1111/mec.13394. [13] Ma ZS (2015) Towards computational models of animal cognition, an introduction for computer scientists. Cognitive Systems Research 33:42-69 [14] Ma ZS (2015) Towards computational models of animal communication, an introduction for computer scientists. Cognitive Systems Research 33:70-99 [15] Ye CX, Hill C, Ruan J, Ma ZS* (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/ [16] 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. [17] Guan Q & Ma ZS* (2014). Ecological analysis of the human milk microbiome. Chinese Science Bulletin 59(22): 2205-2212. http://www.eurekalert.org/pub_releases/2014-09/scp-ahb090214.php [18] 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 [19] Zhang ZG, Geng JW, Tang XD, Fan H, Xu JC, Wen XJ, ZS Ma*, P. Shi* (2014) Spatial heterogeneity and co-occurrence patterns of human mucosal associated intestinal microbiota. The ISME Journal, doi:10.1038/ismej.2013.185 [20] Ma, ZS (2013) Stochastic Populations, Power Law, and Fitness Aggregation in Genetic Algorithms. Fundamenta Informaticae, vol. 122, pp173-206. [21] 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. [22] Ma, ZS (2012) Chaotic populations in Genetic Algorithms. Applied Soft Computing, 12(8): 2409-2424. [23] Ma, ZS (2012) A unified definition for reliability, survivability and resilience inspired by the handicap principle and ecological stability. I. J. of Critical Infrastructures, 8(2):242-272. [24] Ma, ZS. et al (2012). A Bird's Eye View of Microbial Community Dynamics. In “Microbial Ecological Theory: Current Perspectives.” Caister Academic Press, Editor: eds. by Lesley A. Ogilvie and Penny R. Hirsch. [25] Ma, ZS (2012) 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 [26] Ye, CX, ZS Ma, CH. Cannon, M Pop and DW. Yu. 2012. Exploiting sparseness in de novo genome assembly. BMC Bioinformatics, 13(Suppl 6):S1. [27] Gajer, P, RM. Brotman, G Bai, J Sakamoto, UME Schütte, X Zhong, SSK Koenig, L Fu, ZS Ma, X Zhou, Z Abdo, LJ Forney and J Ravel. (2012) Temporal Dynamics of the Human Vaginal Microbiota. Science Translational Medicine. 4:(132): 132ra52. [28] Ma, ZS & AW 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. [29] Ma, ZS (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. [30] Ma, ZS (2011) Did we miss some evidence of chaos in laboratory insect populations? Population Ecology, 53:405–412. [31] Ma, ZS (2011) Frailty modeling for risk analysis in network security and survivability. I. J. Computer and Information Security, 4:276-294. [32] Ma, ZS 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. [33] Ye, CX., C. Cannon, ZS Ma*, DW. Yu, and M. Pop* (2011) SparseAssembler2: Sparse k-mer Graph for Memory Efficient Genome Assembly. http://adsabs.harvard.edu/cgi-bin/bib_query?arXiv:1108.3556 [34] Ma, ZS, et al (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. [35] Ma, ZS (2010) Is Strategic Information Warfare Really Asymmetric? —a New Perspective from the Handicap Principle. Journal of Information Warfare, 9(3): 51-61. [36] Ma, ZS (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 [37] Ma, ZS 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. [38] Ma ZS (2010) An integrated approach to network intrusion detection with block clustering analysis, generalised logistic regression and linear discriminant analysis I. J. Information and Computer Security. DOI: http://dx.doi.org/10.1504/IJICS.2010.03186 [39] Ma ZS (2010) Towards an Extended Evolutionary Game Theory with Survival Analysis and Agreement Algorithms for Modeling Uncertainty, Vulnerability, and Deception. Springer Lecture Notes in Artificial Intelligence, vol. 5855, pp 608-618 [40] Ma ZS (2010) Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature. Springer Lecture Notes in Artificial Intelligence, vol. 5855, pp 195-205 [41] Ma ZS (2010) A New Extended Evolutionary Game Theory Approach to Strategic Information Warfare Research. J. of Information Warfare, vol. 8(2). [42] Ma, ZS 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 |