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        計算與進化生物學研究中心

          計算與進化生物學研究中心 2007年8月23日在北京成立。該中心的成立旨在加強北京地區生物學、數學、統計學和計算學科研人員的合作與交流。該中心起始階段為跨單位、跨學科的開放性非實體機構,設立在中國科學院動物研究所。目前研究中心邀請了中科院動物研究所、中科院植物研究所、中科院北京基因組研究所、中科院遺傳與發育生物學研究所、中科院微生物研究所、中科院數學與系統科學研究院應用數學研究所等機構的14名中國科學家作為中心成員;同時還邀請了英國倫敦大學學院、美國加州大學、美國北卡羅萊那州立大學、美國亞利桑那州立大學、美國杜克大學、瑞士伯爾尼大學、丹麥哥本哈根大學、歐洲生物信息研究所等機構的10位國外專家作為客座教授參與研究中心的合作與交流。

        Publications from the Center:

        • Ziheng Yang and Bruce Rannala (2012) Molecular phylogenetics: principles and practice.  NATURE REVIEWS GENETICS, VOLUME 13: 303-314.
        • Zhang C, Rannala B, Yang Z (2012) Robustness of Compound Dirichlet Priors for Bayesian Inference of Branch Lengths. Systematic Biology (advance published online, 2012). doi: 10.1093/sysbio/sys030
        • Cressman R , Song JW , Zhang BY , Tao Y (2012) Cooperation and evolutionary dynamics in the public goods game with institutional incentives . JOURNAL OF THEORETICAL BIOLOGY 299: 144-151.
        • Xia LX , Zheng XD , Zheng WJ, Zhang GQ , Wang HL , Tao Y , Chen DH (2012)The Niche-Dependent Feedback Loop Generates a BMP Activity Gradient to Determine the Germline Stem Cell Fate. CURRENT BIOLOGY 22: 515-521.
        • Rannala B, Zhu T, Yang Z (2012) Tail Paradox, Partial Identifiability, and Influential Priors in Bayesian Branch Length Inference. MOLECULAR BIOLOGY AND EVOLUTION 29: 325-335.
        • Chen J, Wu YC, Chen X, Ji YJ, Zhang DX (2011) A simple and reliable method for discriminating between Helicoverpa armigera and Helicoverpa assulta (Lepidoptera: Noctuidae). INSECT SCIENCE 18: 629-634.
        • Zhang C, Zhang D-X, Zhu T, Yang Z (2011) Evaluation of a Bayesian coalescent method of species delimitation. Syst Biol 60:747-761.
        • Groussin M, Pawlowski J, Yang Z (2011) Bayesian relaxed clock estimation of divergence times in Foraminifera. Mol Phylogenet Evol 61:157-166.
        • Zang LL, Zou XH, Zhang FM (2011) Phylogeny and species delimitation of the C-genome diploid species in Oryza. JOURNAL OF SYSTEMATICS AND EVOLUTION 49: 386-395
        • dos Reis M, Yang Z (2011) Approximate likelihood calculation for Bayesian estimation of divergence times. Mol Biol Evol 28:2161?-2172.
        • Leng L, Zhang DX (2011) Measuring population differentiation using G(ST) or D? A simulation study with microsatellite DNA markers under a finite island model. Mol Ecol 20:2494-2509.
        • Zheng XD, Yang XQ, Tao Y (2011) Bistability, Probability Transition Rate and First-Passage Time in an Autoactivating Positive-Feedback Loop. PLOS ONE 6: e17104
        • Yang Z, dos Reis M (2011) Statistical properties of the branch-site test of positive selection. Mol Biol Evol 28:1217-1228.
        • Zheng XD; Tao Y (2011) Stochastic Analysis of Gene Expression. YEAST GENETIC NETWORKS: METHODS AND PROTOCOLS 734: 123-151.
        • Huang ZS, Zhang DX (2010) CVhaplot: a consensus tool for statistical haplotyping. Mol Ecol Resour 10:1066–1070.
        • Yang Z, Rannala B (2010) Bayesian species delimitation using multilocus sequence data. Proc Natl Acad Sci USA 107:9264-9269.
        • Zheng XD, Tao Y (2010) Effects of bidirectional regulation on noises in gene networks. PHYSICAL CHEMISTRY CHEMICAL PHYSICS 12: 2418-2426
        • Zhang DX, Yan LN, Ji YJ, Hewitt GM, Huang ZS (2009) Unexpected relationships of substructured populations in Chinese Locusta migratoria. BMC Evol Biol 9:144. doi:10.1186/1471-2148-9-144.
        • Huang ZS, Ji YJ, Zhang DX (2009) Internal algorithm variability and among-algorithm discordance in statistical haplotype reconstruction. Mol Ecol 18:1556-1559.
        • Ji T, Zhang BY, Sun YH, Tao Y (2009) Evolutionary dynamics of fearfulness and boldness. JOURNAL OF THEORETICAL BIOLOGY 256: 637-643.
        • Zheng XD, Tao Y (2008) Additivity of noise propagation in a protein cascade. JOURNAL OF CHEMICAL PHYSICS 128: 165104.
        • Huang ZS, Ji YJ, Zhang DX (2008) Haplotype reconstruction for scnp DNA: a consensus vote approach with extensive sequence data from populations of the migratory locust (Locusta migratoria). Mol Ecol 17:1930-1947.
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