메뉴 건너뛰기




Volumn 9, Issue 3, 2008, Pages 155-159

Simulation of genomes: A review

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; COALESCENT SIMULATION; COMPUTER PROGRAM; COMPUTER SIMULATION; DATA ANALYSIS SOFTWARE; DEMOGRAPHY; FORWARD SIMULATION; GENE LINKAGE DISEQUILIBRIUM; GENE SEQUENCE; GENETIC CONSERVATION; GENETIC VARIABILITY; GENOME; HAPLOTYPE; PHYLOGENY; POPULATION GENETICS; REVIEW; SIMULATION; SIMULATOR;

EID: 46049089628     PISSN: 13892029     EISSN: None     Source Type: Journal    
DOI: 10.2174/138920208784340759     Document Type: Review
Times cited : (46)

References (40)
  • 1
  • 2
    • 34047236641 scopus 로고    scopus 로고
    • Simulations provide support for the common disease-common variant hypothesis
    • Peng, B., Kimmel, A Simulations provide support for the common disease-common variant hypothesis. Genetics 2007, 175: 763-776.
    • (2007) Genetics , vol.175 , pp. 763-776
    • Peng, B.1    Kimmel, A.2
  • 3
    • 0034791032 scopus 로고    scopus 로고
    • Islands of linkage disequilibrium
    • Goldstein, D.B. Islands of linkage disequilibrium. Nat. Genet. 2001, 29: 109-111.
    • (2001) Nat. Genet , vol.29 , pp. 109-111
    • Goldstein, D.B.1
  • 4
    • 79959524146 scopus 로고    scopus 로고
    • A haplotype map of the human genome
    • International-HapMap-Consortium
    • International-HapMap-Consortium. A haplotype map of the human genome. Nature 2005, 437: 1299-320.
    • (2005) Nature , vol.437 , pp. 1299-1320
  • 5
    • 33746331248 scopus 로고    scopus 로고
    • The International HapMap Project
    • International-HapMap-Consortium
    • International-HapMap-Consortium. The International HapMap Project. Nature 2003, 426: 189-96.
    • (2003) Nature , vol.426 , pp. 189-196
  • 6
    • 35348983887 scopus 로고    scopus 로고
    • A second generation human haplotype map of over 3.1 million SNPs
    • International-HapMap-Consortium
    • International-HapMap-Consortium. A second generation human haplotype map of over 3.1 million SNPs. Nature 2007, 449: 851-61.
    • (2007) Nature , vol.449 , pp. 851-861
  • 10
    • 33847232971 scopus 로고    scopus 로고
    • Significant variation in haplotype block structure but conservation in tagSNP patterns among global populations
    • Gu, S., Pakstis, A.J., Li, H., Speed, W.C., Kidd, J.R., Kidd, K.K. Significant variation in haplotype block structure but conservation in tagSNP patterns among global populations. Eur. J. Hum. Genet. 2007, 15: 302-312.
    • (2007) Eur. J. Hum. Genet , vol.15 , pp. 302-312
    • Gu, S.1    Pakstis, A.J.2    Li, H.3    Speed, W.C.4    Kidd, J.R.5    Kidd, K.K.6
  • 11
    • 34047215035 scopus 로고    scopus 로고
    • Ancestral alleles.and population origins: Inferences depend on mutation rate
    • Rogers, A.R., Wooding, S., Huff, C.D., Batzer, M.A., Jorde, L.B. Ancestral alleles.and population origins: inferences depend on mutation rate. Mole. Biol. Evol. 2007, 24: 990-7.
    • (2007) Mole. Biol. Evol , vol.24 , pp. 990-997
    • Rogers, A.R.1    Wooding, S.2    Huff, C.D.3    Batzer, M.A.4    Jorde, L.B.5
  • 12
    • 34548725013 scopus 로고    scopus 로고
    • Brief communication: The Thule migration: rejecting population histories using computer simulation
    • Marchani, E.E., Rogers, A.R., O'Rourke, D.H. Brief communication: the Thule migration: rejecting population histories using computer simulation. Am. J. Phys. Anthropol. 2007, 134: 281-4.
    • (2007) Am. J. Phys. Anthropol , vol.134 , pp. 281-284
    • Marchani, E.E.1    Rogers, A.R.2    O'Rourke, D.H.3
  • 14
    • 0001935493 scopus 로고
    • Gene genealogies and the coalescent process
    • Hudson, R.R. Gene genealogies and the coalescent process. Oxf. Surv. Evol. Biol. 1990, 7: 1-44.
    • (1990) Oxf. Surv. Evol. Biol , vol.7 , pp. 1-44
    • Hudson, R.R.1
  • 15
    • 46049091705 scopus 로고    scopus 로고
    • Nordborg, M. Coalescent theory. In: Handbook of Statistical Genetics. D.J. Balding, M.J.B., and C. Cannings (Editor) J. Wiley, Chichester; 2003.
    • Nordborg, M. Coalescent theory. In: Handbook of Statistical Genetics. D.J. Balding, M.J.B., and C. Cannings (Editor) J. Wiley, Chichester; 2003.
  • 16
    • 0036245438 scopus 로고    scopus 로고
    • Genealogical trees, coalescent theory and the analysis of genetic polymorphisms
    • Rosenberg, N.A., Nordborg, M. Genealogical trees, coalescent theory and the analysis of genetic polymorphisms. Nat. Rev. Genet. 2002, 3: 380-90.
    • (2002) Nat. Rev. Genet , vol.3 , pp. 380-390
    • Rosenberg, N.A.1    Nordborg, M.2
  • 17
    • 0033180294 scopus 로고    scopus 로고
    • Coalescing into the 21st century: An overview and prospects of coalescent theory
    • Fu, Y.-X., Li, W.-H. Coalescing into the 21st century: An overview and prospects of coalescent theory. Theor. Popul. Biol. 1999, 56: 1-10.
    • (1999) Theor. Popul. Biol , vol.56 , pp. 1-10
    • Fu, Y.-X.1    Li, W.-H.2
  • 18
    • 0036184745 scopus 로고    scopus 로고
    • Generating samples under a Wright-Fisher neutral model of genetic variation
    • Hudson, R.R. Generating samples under a Wright-Fisher neutral model of genetic variation. Bioinformatics 2002, 18: 337-338.
    • (2002) Bioinformatics , vol.18 , pp. 337-338
    • Hudson, R.R.1
  • 19
    • 1342288606 scopus 로고    scopus 로고
    • SPLATCHE: A program to simulate genetic diversity taking into account environmental heterogeneity
    • Currat, M., Ray, N., Excoffier, L. SPLATCHE: a program to simulate genetic diversity taking into account environmental heterogeneity. Mol. Ecol. Notes 2004, 4: 139-142.
    • (2004) Mol. Ecol. Notes , vol.4 , pp. 139-142
    • Currat, M.1    Ray, N.2    Excoffier, L.3
  • 20
    • 85142187087 scopus 로고    scopus 로고
    • Spencer, C.C., Coop, G. SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics 2004, 20: 3673-5.
    • Spencer, C.C., Coop, G. SelSim: a program to simulate population genetic data with natural selection and recombination. Bioinformatics 2004, 20: 3673-5.
  • 21
    • 33751319883 scopus 로고    scopus 로고
    • Perfect simulation from nonneutral population genetic models: Variable population size and population subdivision
    • Fearnhead, P. Perfect simulation from nonneutral population genetic models: Variable population size and population subdivision. Genetics 2006, 174: 1397-1406.
    • (2006) Genetics , vol.174 , pp. 1397-1406
    • Fearnhead, P.1
  • 22
    • 27644455774 scopus 로고    scopus 로고
    • Mailund, T., Schierup, M.H., Pedersen, C.N., Mechlenborg, P.J., Madsen, J.N., Schauser, L. CoaSim: a flexible environment for simulating genetic data under coalescent models. BMC Bioinformatics 2005, 6: 252.
    • Mailund, T., Schierup, M.H., Pedersen, C.N., Mechlenborg, P.J., Madsen, J.N., Schauser, L. CoaSim: a flexible environment for simulating genetic data under coalescent models. BMC Bioinformatics 2005, 6: 252.
  • 23
    • 85142154693 scopus 로고    scopus 로고
    • Hellenthal G., Stephens, M. msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics 2007, 23: 520-1.
    • Hellenthal G., Stephens, M. msHOT: modifying Hudson's ms simulator to incorporate crossover and gene conversion hotspots. Bioinformatics 2007, 23: 520-1.
  • 25
    • 34547830810 scopus 로고    scopus 로고
    • GENOME: A rapid coalescent-based whole genome simulator
    • Liang, L., Zollner, S., Abecasis, G.R. GENOME: a rapid coalescent-based whole genome simulator. Bioinformatics 2007, 23: 1565-7.
    • (2007) Bioinformatics , vol.23 , pp. 1565-1567
    • Liang, L.1    Zollner, S.2    Abecasis, G.R.3
  • 26
    • 33748202027 scopus 로고    scopus 로고
    • Positive selection versus demography: Evolutionary inferences based on an unusual haplotype structure in Drosophila simulans
    • Quesada, H., Ramos-Onsins, S.E., Rozas, J., Aguade, M. Positive selection versus demography: evolutionary inferences based on an unusual haplotype structure in Drosophila simulans. Mol. Biol. Evol. 2006, 23: 1643-7.
    • (2006) Mol. Biol. Evol , vol.23 , pp. 1643-1647
    • Quesada, H.1    Ramos-Onsins, S.E.2    Rozas, J.3    Aguade, M.4
  • 27
    • 0030928378 scopus 로고    scopus 로고
    • Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees
    • Rambaut, A., Grassly, N.C. Seq-Gen: an application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees. Comput. Appl. Biosci. 1997, 13: 235-238.
    • (1997) Comput. Appl. Biosci , vol.13 , pp. 235-238
    • Rambaut, A.1    Grassly, N.C.2
  • 28
    • 34547803197 scopus 로고    scopus 로고
    • PAML 4: Phylogenetic analysis by maximum likelihood
    • Yang, Z. PAML 4: phylogenetic analysis by maximum likelihood. Mol. Biol. Evol. 2007, 24: 1586-91.
    • (2007) Mol. Biol. Evol , vol.24 , pp. 1586-1591
    • Yang, Z.1
  • 29
    • 33646348730 scopus 로고    scopus 로고
    • coalescent simulation
    • Marjoram, P., Wall, J.D. Fast "coalescent" simulation. BMC Genet. 2006, 7: 16.
    • (2006) BMC Genet , vol.7 , pp. 16
    • Marjoram, P.1    Wall, J.D.F.2
  • 30
    • 0032912338 scopus 로고    scopus 로고
    • Population dynamics of HIV-1 inferred from gene sequences
    • Grassly, N.C., Harvey, P.H., Holmes, E.C. Population dynamics of HIV-1 inferred from gene sequences. Genetics 1999, 151: 427-438.
    • (1999) Genetics , vol.151 , pp. 427-438
    • Grassly, N.C.1    Harvey, P.H.2    Holmes, E.C.3
  • 31
    • 0034491799 scopus 로고    scopus 로고
    • SIMCOAL: A general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography
    • Excoffier, L., Novembre, J., Schneider, S. SIMCOAL: a general coalescent program for the simulation of molecular data in interconnected populations with arbitrary demography. J. Hered. 2000, 91: 506-9.
    • (2000) J. Hered , vol.91 , pp. 506-509
    • Excoffier, L.1    Novembre, J.2    Schneider, S.3
  • 32
    • 85142201042 scopus 로고    scopus 로고
    • Anderson, C.N., Ramakrishnan, U., Chan, Y.L., Hadly, E.A. Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bioinformatics 2005, 21: 1733-4.
    • Anderson, C.N., Ramakrishnan, U., Chan, Y.L., Hadly, E.A. Serial SimCoal: a population genetics model for data from multiple populations and points in time. Bioinformatics 2005, 21: 1733-4.
  • 33
    • 0035213313 scopus 로고    scopus 로고
    • Haplotype evolution and linkage disequilibrium: A simulation study
    • Calafell, F., Grigorenko, E.L., Chikanian, A.A., Kidd, K.K. Haplotype evolution and linkage disequilibrium: A simulation study. Hum. Hered. 2001, 51: 85-96.
    • (2001) Hum. Hered , vol.51 , pp. 85-96
    • Calafell, F.1    Grigorenko, E.L.2    Chikanian, A.A.3    Kidd, K.K.4
  • 34
    • 34047228125 scopus 로고    scopus 로고
    • Forward-Time Simulations of Human Populations with Complex Diseases
    • Peng, B., Amos, C.I., Kimmel, M. Forward-Time Simulations of Human Populations with Complex Diseases. PLoS Genet. 2007, 3: e47.
    • (2007) PLoS Genet , vol.3
    • Peng, B.1    Amos, C.I.2    Kimmel, M.3
  • 35
    • 13744261515 scopus 로고    scopus 로고
    • The limits of theoretical population genetics
    • Wakeley, J. The limits of theoretical population genetics. Genetics 2005, 169: 1-7.
    • (2005) Genetics , vol.169 , pp. 1-7
    • Wakeley, J.1
  • 36
    • 46049101385 scopus 로고    scopus 로고
    • Hey, J. FPG: A computer program for forward population genetics simulation. http://Iifesci.rutgers.edu/~heylab/HeylabSoftware.htm#FPG.
    • Hey, J. FPG: A computer program for forward population genetics simulation. http://Iifesci.rutgers.edu/~heylab/HeylabSoftware.htm#FPG.
  • 37
    • 0034952180 scopus 로고    scopus 로고
    • Balloux, F. EASYPOP version 1.7, a computer program for population genetics simulations. J. Hered. 2001, 92: 301-2
    • Balloux, F. EASYPOP (version 1.7): a computer program for population genetics simulations. J. Hered. 2001, 92: 301-2.
  • 38
    • 85142175991 scopus 로고    scopus 로고
    • Peng, B., Kimmel, M. simuPOP: a forward-time population genetics simulation environment. Bioinformatics 2005, 21: 3686-7.
    • Peng, B., Kimmel, M. simuPOP: a forward-time population genetics simulation environment. Bioinformatics 2005, 21: 3686-7.


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.