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马占山  研究员
计算生物与医学生态学学科组
职  务:
学  历: 计算机科学和昆虫学双博士
电  话: +86 871 65183700
传  真: +86 871 65183700
电子邮件: ma@mail.kiz.ac.cn
通讯地址: 云南省昆明市教场东路32号    650223
其他主页:
  简  历

  马占山,研究员,博导,计算生物与医学生态学学科负责人。美国爱达荷大学计算机科学(2008年)和昆虫学(1997年)双博士、 计算机科学和计算生物学研究科学家。 2011年分别入选云南省高端科技人才海外高层次人才; 2015 年入选云岭产业领军人才 具有在美国硅谷等地近10年的涵盖电子、网络、软件、信息安全领域的计算机高级工程师经历; 美国人类微生物菌群宏基因组研究计划(Human Microbiome Project: HMP)主要研发科学家之一。是总部设在英国伦敦的“Faculty of 1000 Biology & Medicine”成员,  是目前该机构在微生物进化与基因组学(Microbial Evolution & Genomics)” 领域的唯一华人,也是整个微生物学科 (Microbiology) 在中国的唯一成员。 以第一和责任作者在计算机科学、工程数学、计算智能与人工智能 昆虫学、生态学、生物信息学、人体微生物菌群宏基因组等领域的重要期刊发表论文近百篇。并担任英国 I. J. Network Science (网络科学)期刊主编。在计算科学领域(非生物学领域)论文可见DBLP计算机科学数据库和MathSciNet 数学网数据库: 

  http://dblp.uni-trier.de/pers/hd/m/Ma:Zhanshan_=Sam= 

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

  研究方向

基因大数据科学、第三代基因测序软件技术; 

大数据精准医学、深度学习与人工智能算法  

肠道菌群、人体微生物菌群宏基因组学技术; 

网络安全可靠性、可存活性理论及其应用。 

  承担科研项目

(1)  国家自然科学基金(信息科学部):生态“舞台”与进化计算“演出”(20122015)  

(2)  国家自然科学基金(管理科学部):网络系统可存活性理论的扩展及实证研究(20152018 

(3)  国家自科学基金(生命科学部):基于Metagenetics技术建立快速高效的生物多样性检测法(20122015)   

(4)  云南省引进高端科技人才项目:面向“计算生物信息学和个性化医学(疗)”的“GP-GPU微型超算系统”。  

(5)  海外高层次人才引进计划 (2012-2015)  

(6)  云岭产业技术领军人才基金(2015-2019

  专家类别
研究员;云南省“高端科技人才”;“海外高层次人才”;云岭产业技术领军人才
  社会任职

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

  获奖及荣誉
  代表论著

[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, 53:405412.   

[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 

  研究团队

  李连伟 (生物信息学,医学生态学) 

  夏尧(生物信息学,医学生态学) 

  李杰(数学、计算生物学) 

  曾丹丹(计算机科学,计算生物学) 

  李文迪(生物信息学、医学) 

  彭淑琴(数理统计、生物信息学) 

  寇贺丹(数理统计、生物信息学) 

  史石岩(数学、计算生物学) 

  陈红菊(数学,客座) 

  叶承曦(计算机科学,客座)     

  客座教授 

  Prof. Aaron Ellison
  Senior Research Fellow
  Fellow of the Ecological Society of America
  Harvard University, USA 
  http://harvardforest.fas.harvard.edu/aaron-ellison
  Recipient of CAS PIFI (President’s International Fellowship Initiative)
  美国哈佛大学 Aaron Ellison 教授  

  Prof. Sharron Quisenberry  
  Vice President of Research and Economic Development  
  Fellow of the Entomological Society of America  
  Iowa State University, USA 
  美国衣阿华州立大学 Sharron Quisenberry 付校长
  
  Prof. Cheng Le (程乐) 
  MD, PhD (Connell University)  
  Vice Director of, 
  China National GeneBank
  中国国家基因库副主任 & 华大基因研究院
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