071007-遗传学
081203-计算机应用技术

计算生物学，生物信息学，医学生态学
计算智能和进化计算
网络软件可靠性和可存活性

2006-03--2008-05   University of Idaho   PhD in Computer Science
1992-05--1997-12   University of Idaho   PhD in Entomology, MSc in Computer Science

   

2010-11~现在, 中科院动物研究所, 研究员
2008-06~2010-11,University of Idaho, Research Scientist
2006-03~2008-05,University of Idaho, PhD in Computer Science
1998-01~2006-03,Micron Technology, Tumbleweed Communications Corp., Senior Network/Software Engineer
1992-05~1997-12,University of Idaho, PhD in Entomology, MSc in Computer Science

2020-07-01-今,PeerJ Computer Science, Associate Editor
2009-04-01-今,Member of Faculty 1000 of Biology and Medicine,

   

（1） 哈佛大学 Bullard 学者奖, , 其他, 2020
（2） 国家教委“霍英东优秀青年教师基金奖”, , 部委级, 1992

（ 1 ） 一种基于多样性指数和区域范围关系的幂法则标度模型预测微生物群落结构的方法, 2021, 第 1 作者, 专利号: 201710949841.0

（ 2 ） 一种基于多样性指数与时空关系的幂法则标度模型预测微生物群落结构的变化的方法, 2021, 第 1 作者, 专利号: 201711289534.0

（ 3 ） 201911299411.4, 2019, 第 1 作者, 专利号: 201911299411.4

（ 4 ） 201911351370.9, 2019, 第 1 作者, 专利号: 201911351370.9

（ 5 ） 用于组装基因组序列的方法、系统及装置, 2019, 第 2 作者, 专利号: ZL 201510084489.X

（ 6 ） 201911299315.X, 2019, 第 1 作者, 专利号: 201911299315.X

（ 7 ） 201820827933.3, 2018, 第 1 作者, 专利号: 201820827933.3

（ 8 ） 201810159081.8, 2018, 第 1 作者, 专利号: 201810159081.8

（ 9 ） 201810159082.2, 2018, 第 1 作者, 专利号: 201810159082.2

（ 10 ） 201710063855.2, 2017, 第 1 作者, 专利号: 201710063855.2

（ 11 ） 201711223008.4, 2017, 第 1 作者, 专利号: 201711223008.4

（ 12 ） 201710066344.6, 2017, 第 1 作者, 专利号: 201710066344.6

（ 13 ） 用于高性能计算机的微型空调制冷系统, 2015, 第 1 作者, 专利号: ZL 2014 2 0517804.4

（ 14 ） 多显卡组合驱动的多显示器系统, 2015, 第 1 作者, 专利号: ZL201420517805.9

   

（1） Cross-Scale Analyses of Animal and Human Gut Microbiome Assemblies from Metacommunity to Global Landscape, mSystems, 2021, 第 1 作者
（2） Population-level diversity-disease relationship (P-DDR) in the human microbiome associated diseases, Computational and Structural Biotechnology Journal, 2021, 通讯作者
（3） Spatial Heterogeneity Analysis of the Human Virome with Taylor's Power Law, Computational and Structural Biotechnology Journal, 2021, 第 1 作者
（4） A unified survival-analysis approach to insect population development and survival times, Scientific Reports, 2021, 第 1 作者
（5） In silico trio-biomarkers for bacterial vaginosis revealed by species dominance network analysis, Computational and Structural Biotechnology Journal, 2021, 第 1 作者
（6） Inter-Individual Diversity Scaling Analysis of the Human Virome with Classic Diversity-Area Relationship (DAR) Modeling, Frontiers in Genetics, 2021, 通讯作者
（7） Ecological and network analyses identify four microbial species with potential significance for the diagnosis/treatment of ulcerative colitis (UC), BMC Microbiology, 2021, 通讯作者
（8） FBA Ecological Guild: Trio of Firmicutes-Bacteroidetes Alliance against Actinobacteria in Human Oral Microbiome, Scientific Reports, 2020, 通讯作者
（9） Defining individual-level genetic diversity and similarity profiles, Scientific Reports, 2020, 第 1 作者
（10） Network analysis of the hot spring microbiome sketches possible niche differentiations among ecological guilds, Ecological Modelling, 2020, 通讯作者
（11） Species sorting and neutral theory analyses reveal archaeal and bacterial communities are assembled differently in hot springs, Frontiers in Bioengineering and Biotechnology, 2020, 通讯作者
（12） Estimating the optimum coverage and quality of amplicon sequencing with Taylor's power law, Frontiers in Bioengineering and Biotechnology, 2020, 第 1 作者
（13） Assessing and interpreting the metagenome heterogeneity with power law, Frontiers in Microbiology, 2020, 第 1 作者
（14） Critical Network Structures and Medical Ecology Mechanisms Underlying Human Microbiome-Associated Diseases, iScience, 2020, 第 1 作者
（15） Heterogeneity-disease relationship in the human microbiome associated diseases, FEMS Microbiology Ecology, 2020, 第 1 作者
（16） Testing the Anna Karenina Principle in Human Microbiome-Associated Diseases, iScience, 2020, 第 1 作者
（17） Human reproductive system microbiomes exhibited significantly different heterogeneity scaling with gut microbiome, but the intra-system scaling is invariant, Oikos, 2020, 第 1 作者
（18） Niche-neutral theoretic approach to mechanisms underlying biodiversity and biogeography of human microbiomes, Evolutionary Applications, 2020, 第 1 作者
（19） A theoretic approach to the mechanism of gut microbiome translocation in SIV-infected Asian macaques, FEMS Microbiology Ecology, 2020, 通讯作者
（20） Dominance network analysis of the healthy human vaginal microbiome not dominated by Lactobacillus species, Computational and Structural Biotechnology Journal, 2020, 通讯作者
（21） Predicting the Outbreak Risks and Inflection Points of COVID‐19 Pandemic with Classic Ecological Theories, Advanced Science, 2020, 第 1 作者
（22） Dominance network analysis provides a new framework for studying the diversity–stability relationship, Ecological Monographs, 2019, 第 1 作者
（23） Diversity-disease relationships and shared species analyses for human microbiome-associated diseases, The ISME Journal, 2019, 第 1 作者
（24） A new DTAR (diversity–time–area relationship) model demonstrated with the indoor microbiome, Journal of Biogeography, 2019, 第 1 作者
（25） Comparative Power Law Analysis for the Spatial Heterogeneity Scaling of the Hot-Spring Microbiomes, Molecular Ecology, 2019, 通讯作者
（26） Hybrid assembly of ultra-long Nanopore® reads augmented with 10×genomics® contigs: Demonstrated with a human genome., Genomics, 2019, 通讯作者
（27） Global Microbiome Diversity Scaling in Hot Springs With DAR (Diversity-Area Relationship) Profiles, Frontiers in Microbiology, 2019, 通讯作者
（28） Semen Microbiome Biogeography: An Analysis Based on a Chinese Population Study, Frontiers in Microbiology, 2019, 通讯作者
（29） How and Why Men and Women Differ in Their Microbiomes: Medical Ecology and Network Analyses of the Microgenderome, Advanced Science, 2019, 第 1 作者
（30） Diversity scaling of human vaginal microbial communities, Zoological Research, 2019, 通讯作者
（31） Diversity time-period and diversity-time-area relationships exemplified by the human microbiome, Scientific Reports, 2018, 第 1 作者
（32） A cross-scale neutral theory approach to the influence of obesity on community assembly of human gut microbiome, Frontiers in Microbiology, 2018, 通讯作者
（33） A unified concept of dominance applicable at both community and species scale, Ecosphere, 2018, 第 1 作者
（34） Extending species-area relationships (SAR) to diversity-area relationships (DAR), Ecology and Evolution, 2018, 第 1 作者
（35） Sketching the human microbiome biogeography with DAR (diversity-area relationship) profiles, Microbial Ecology, 2018, 第 1 作者
（36） Assessing and interpreting the within-Body biogeography of human microbiome diversity, Frontiers in Microbiology, 2018, 第 1 作者
（37） Measuring metagenome diversity and similarity with Hill numbers, Molecular Ecology Resources, 2018, 第 1 作者
（38） The P/N (Positive-to-negative links) ratio in complex networks— a promising in silico biomarkers for detecting changes occurring in the human microbiome., Microbial Ecology, 2017, 第 1 作者
（39） Trios— promising in silico biomarkers for differentiating the effect of disease on the human microbiome network, Scientific Reports, 2017, 第 1 作者
（40） Quantifying the human vaginal community state types (CSTs) with the species specificity index., PeerJ, 2017, 第 1 作者
（41） Does colorectal cancer significantly influence the assembly of gut microbial communities?, PeerJ, 2017, 通讯作者
（42） Oral microbial community assembly under the influence of periodontitis., Plos One, 2017, 通讯作者
（43） CPPred-RF: A Sequence-based Predictor for Identifying Cell-Penetrating Peptides and Their Uptake EfficiencyJournal of Proteome, Journal of Proteome, 2017, 通讯作者
（44） Reconstructing evolutionary trees in parallel for massive sequences, BMC Systems Biology, 2017, 通讯作者
（45） Sparc: a sparsity-based consensus algorithm for long erroneous sequencing reads, PeerJ, 2016, 通讯作者
（46） Integrated network-diversity analyses suggest suppressive e ect of Hodgkin’s lymphoma and slightly relieving e ect of chemotherapy on human milk microbiome, Scientific Reports, 2016, 通讯作者
（47） A Brief Review on the Ecological Network Analysis 1 with Applications in the Emerging Medical Ecology, Springer Methods & Protocol, 2016, 通讯作者
（48） Scientific Reports, 2015, 第 1 作者
（49） Cognitive System Research, 2015, 第 1 作者
（50） Cognitive System Research, 2015, 第 1 作者
（51） Power Law Analysis of the Human Microbiome, Molecular Ecology, 2015, 通讯作者
（52） A Survivability-Centered Research Agenda for Cloud Computing Supported Emergency Response and Management Systems., IEEE-AIAA Aerospace, 2014, 第 1 作者
（53） The ISME Journal, 2014, 通讯作者
（54） Spatial heterogeneity and co-occurrence patterns of human mucosal associated intestinal microbiota, The ISME Journal, 2013, 通讯作者
（55） Stochastic populations, power law and fitness aggregation in Genetic Algorithms. Fundamenta Informaticae, Fundamenta Informaticae, 2013, 第 1 作者
（56） Chaotic populations in Genetic Algorithms., Applied Soft Computing, 2012, 第 1 作者
（57） A unified definition for reliability, survivability and resilience inspired by the handicap principle and ecological stability, International Journal of Critical Infrastructures,, 2012, 第 1 作者
（58） A Bird Eye View of Microbial Community Dynamics, Microbial Ecological Theory , 2012, 第 1 作者
（59） Exploiting sparseness in de novo genome assembly, BMC Bioinformatics, 2012, 第 2 作者
（60） Temporal Dynamics of the Human Vaginal Microbiota, Science Translational Medicine, 2012, 通讯作者
（61） 宏基因组研究的生物信息学平台现状, 动物学研究, 2012, 通讯作者
（62） Insect Navigation and Communication in Flight and Migration: A Potential Model for Joining and Collision Avoidance in MAV (Micro-Aerial Vehicle) and Mobile Robots Fleet Control., Proceedings of The 32nd IEEE-AIAA AeroSpace Conference, 2011, 第 1 作者
（63） SparseAssembler: de novo Assembly with the Sparse de Bruijn Graph , CoRR abs/1106.2603, 2011, 第 2 作者
（64） Dynamic hybrid fault modeling and extended evolutionary game theory for reliability, survivability and fault tolerance analyses. , IEEE Transactions on Reliability. , 2011, 第 1 作者
（65） Did we miss some evidence of chaos in laboratory insect populations, Population Ecology, 2011, 第 1 作者
（66） Ecological ‘theatre’ for evolutionary computing ‘play’: some insights from population and evolutionary ecology., I.J. Bio-Inspired Computing, 2011, 第 1 作者
（67） Frailty modeling for risk analysis in network security and survivability, I. J. of Information and Computer Security, 2011, 第 1 作者
（68） Recent advances in understanding the microbiology of the female reproductive tract and the causes of premature birth. , Infectious Diseases of Obstetrics and Gynecology., 2010, 通讯作者
（69） Survival Analysis Approach to Life Table Analysis and Hypothesis Testing for Russian Wheat Aphid Populations., Bulletin of Entomological Research, 2010, 第 1 作者
（70） Insect Sensory Systems Inspired Computing and Communications., Ad Hoc Networks, 2009, 第 1 作者
（71） Towards a Population Dynamics Theory for Evolutionary Computing: Learning from Biological Population Dynamics in Nature., Springer Lecture Notes in Artificial Intelligence, 2009, 第 1 作者

（ 1 ） Book Chapter: Measuring Microbiome Diversity with Hill Numbers., Metagenomics: Perspecitives, Methods, and Applications., Elsevier, 2017-07, 第 5 作者
（ 2 ） 《生物信息学：计算技术和软件导论》, Bioinformatics: Computing and Software, 科学出版社, 2017-09, 第 1 作者

   

（ 1 ） ****, 负责人, 中国科学院计划, 2011-01--2013-12
（ 2 ） 遗传资源国家重点试验室启动基金, 负责人, 其他国际合作项目, 2011-07--2012-07
（ 3 ） 云南省引进高端科技人才项目, 负责人, 地方任务, 2012-10--2014-11
（ 4 ） 网络系统可存活性理论的扩展及实证研究, 负责人, 国家任务, 2014-01--2018-12
（ 5 ） 云岭产业技术领军人才项目, 负责人, 地方任务, 2015-10--2021-12
（ 6 ） 菌群多样性与疾病关系的生态机制及病因研究, 负责人, 国家任务, 2020-01--2023-12
（ 7 ） 基因大数据信息技术及其应用, 负责人, 其他国际合作项目, 2017-01--2021-12
（ 8 ） 遗传资源与进化国家重点实验室自主课题, 负责人, 其他国际合作项目, 2021-01--2022-12
（ 9 ） 遗传资源与进化国家重点实验室开放课题, 负责人, 其他国际合作项目, 2021-01--2023-12