Measurably evolving populations

[1]  Anne-Mieke Vandamme,et al.  Genetic Variability and Molecular Evolution of the Human Respiratory Syncytial Virus Subgroup B Attachment G Protein , 2005, Journal of Virology.

[2]  M. Kimura Molecular evolutionary clock and the neutral theory , 2005, Journal of Molecular Evolution.

[3]  J. Felsenstein Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[4]  Anne-Mieke Vandamme,et al.  Molecular Evolution and Circulation Patterns of Human Respiratory Syncytial Virus Subgroup A: Positively Selected Sites in the Attachment G Glycoprotein , 2004, Journal of Virology.

[5]  Edward C Holmes,et al.  Comparative population dynamics of mosquito-borne flaviviruses. , 2003, Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases.

[6]  Carsten Wiuf,et al.  Diverse Plant and Animal Genetic Records from Holocene and Pleistocene Sediments , 2003, Science.

[7]  D. Nickle,et al.  Evolutionary Indicators of Human Immunodeficiency Virus Type 1 Reservoirs and Compartments , 2003, Journal of Virology.

[8]  Michael J. Sanderson,et al.  R8s: Inferring Absolute Rates of Molecular Evolution, Divergence times in the Absence of a Molecular Clock , 2003, Bioinform..

[9]  S. Sampling theory for neutral alleles in a varying environment , 2003 .

[10]  M. Whitlock,et al.  Estimating effective population size and migration rates from genetic samples over space and time. , 2003, Genetics.

[11]  J. Taubenberger,et al.  Characterization of the 1918 “Spanish” Influenza Virus Matrix Gene Segment , 2002, Journal of Virology.

[12]  L. Orlando,et al.  Ancient DNA and the population genetics of cave bears (Ursus spelaeus) through space and time. , 2002, Molecular biology and evolution.

[13]  John Wakeley,et al.  Estimating Divergence Times from Molecular Data on Phylogenetic and Population Genetic Timescales , 2002 .

[14]  Andrew Rambaut,et al.  GENIE: estimating demographic history from molecular phylogenies , 2002, Bioinform..

[15]  Hirohisa Kishino,et al.  Divergence time and evolutionary rate estimation with multilocus data. , 2002, Systematic biology.

[16]  L. Waits,et al.  Ancient DNA analyses reveal high mitochondrial DNA sequence diversity and parallel morphological evolution of late pleistocene cave bears. , 2002, Molecular biology and evolution.

[17]  T. Stadejek,et al.  Identification of radically different variants of porcine reproductive and respiratory syndrome virus in Eastern Europe: towards a common ancestor for European and American viruses. , 2002, The Journal of general virology.

[18]  Alexei J Drummond,et al.  Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. , 2002, Genetics.

[19]  Masami Hasegawa,et al.  Estimation of effective population size of HIV-1 within a host: a pseudomaximum-likelihood approach. , 2002, Genetics.

[20]  C. Millar,et al.  Rates of Evolution in Ancient DNA from Adélie Penguins , 2002, Science.

[21]  B. Shapiro,et al.  Dynamics of Pleistocene Population Extinctions in Beringian Brown Bears , 2002, Science.

[22]  Jean-Marie Cornuet,et al.  Likelihood-based estimation of the effective population size using temporal changes in allele frequencies: a genealogical approach. , 2002, Genetics.

[23]  Sudhir Kumar,et al.  Mutation rates in mammalian genomes , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[24]  Masami Hasegawa,et al.  A viral sampling design for testing the molecular clock and for estimating evolutionary rates and divergence times , 2002, Bioinform..

[25]  D. Nickle,et al.  Curiously Modern DNA for a ``250 Million-Year-Old'' Bacterium , 2002, Journal of Molecular Evolution.

[26]  M. Sanderson Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. , 2002, Molecular biology and evolution.

[27]  Edward C. Holmes,et al.  Rates of Molecular Evolution in RNA Viruses: A Quantitative Phylogenetic Analysis , 2002, Journal of Molecular Evolution.

[28]  R. Webster,et al.  Emergence of influenza A viruses. , 2001, Philosophical transactions of the Royal Society of London. Series B, Biological sciences.

[29]  Jonathan P. Bollback,et al.  Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology , 2001, Science.

[30]  D. Labuda,et al.  Phylogenetic and familial estimates of mitochondrial substitution rates: study of control region mutations in deep-rooting pedigrees. , 2001, American journal of human genetics.

[31]  P. Donnelly,et al.  Estimating recombination rates from population genetic data. , 2001, Genetics.

[32]  J. Hein,et al.  A molecular clock dates the common ancestor of European-type porcine reproductive and respiratory syndrome virus at more than 10 years before the emergence of disease. , 2001, Virology.

[33]  A. Rodrigo,et al.  The inference of stepwise changes in substitution rates using serial sequence samples. , 2001, Molecular biology and evolution.

[34]  O. Pybus,et al.  The Epidemic Behavior of the Hepatitis C Virus , 2001, Science.

[35]  T. Pupko,et al.  The Permian bacterium that isn't. , 2001, Molecular biology and evolution.

[36]  Peter Beerli,et al.  Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach , 2001, Proceedings of the National Academy of Sciences of the United States of America.

[37]  W. Bruno,et al.  Performance of a divergence time estimation method under a probabilistic model of rate evolution. , 2001, Molecular biology and evolution.

[38]  Jon A Yamato,et al.  Maximum likelihood estimation of recombination rates from population data. , 2000, Genetics.

[39]  O. Pybus,et al.  An integrated framework for the inference of viral population history from reconstructed genealogies. , 2000, Genetics.

[40]  A. Lapedes,et al.  Timing the ancestor of the HIV-1 pandemic strains. , 2000, Science.

[41]  J. Taubenberger,et al.  Characterization of the 1918 "Spanish" influenza virus neuraminidase gene. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[42]  P. Donnelly,et al.  The mutation rate in the human mtDNA control region. , 2000, American journal of human genetics.

[43]  J. Huelsenbeck,et al.  A compound poisson process for relaxing the molecular clock. , 2000, Genetics.

[44]  Andrew Rambaut,et al.  Estimating the rate of molecular evolution: incorporating non-contemporaneous sequences into maximum likelihood phylogenies , 2000, Bioinform..

[45]  R. Griffiths,et al.  Inference from gene trees in a subdivided population. , 2000, Theoretical population biology.

[46]  J. Margolick,et al.  Consistent Viral Evolutionary Changes Associated with the Progression of Human Immunodeficiency Virus Type 1 Infection , 1999, Journal of Virology.

[47]  J. Drake,et al.  Mutation rates among RNA viruses. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[48]  S. Pääbo,et al.  Nuclear DNA sequences from late Pleistocene megafauna. , 1999, Molecular biology and evolution.

[49]  T. Leitner,et al.  The molecular clock of HIV-1 unveiled through analysis of a known transmission history. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[50]  E. G. Shpaer,et al.  Coalescent estimates of HIV-1 generation time in vivo. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[51]  J. Taubenberger,et al.  Origin and evolution of the 1918 "Spanish" influenza virus hemagglutinin gene. , 1999, Proceedings of the National Academy of Sciences of the United States of America.

[52]  K. Crandall The evolution of HIV , 1999 .

[53]  R. Webster,et al.  A pandemic warning? , 1997, Nature.

[54]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[55]  W. Fitch,et al.  Long term trends in the evolution of H(3) HA1 human influenza type A. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[56]  Mark R. Wilson,et al.  A high observed substitution rate in the human mitochondrial DNA control region , 1997, Nature Genetics.

[57]  Stephen M. Krone,et al.  The genealogy of samples in models with selection. , 1997, Genetics.

[58]  Jon A Yamato,et al.  Estimating effective population size and mutation rate from sequence data using Metropolis-Hastings sampling. , 1995, Genetics.

[59]  R. Webster,et al.  Evolution of influenza A virus PB2 genes: implications for evolution of the ribonucleoprotein complex and origin of human influenza A virus , 1990, Journal of virology.

[60]  R. Hudson Gene genealogies and the coalescent process. , 1990 .

[61]  P. Sharp,et al.  Rates and dates of divergence between AIDS virus nucleotide sequences. , 1988, Molecular biology and evolution.

[62]  J. Holland,et al.  Rapid evolution of RNA viruses. , 1987, Annual review of microbiology.

[63]  W. Fitch,et al.  Evolution of human influenza A viruses over 50 years: rapid, uniform rate of change in NS gene. , 1986, Science.

[64]  N. Saitou,et al.  Polymorphism and evolution of influenza A virus genes. , 1986, Molecular biology and evolution.

[65]  Katherine Spindler,et al.  Rapid evolution of RNA genomes. , 1982, Science.

[66]  D. Reanney The evolution of RNA viruses. , 1982, Annual review of microbiology.

[67]  C. J-F,et al.  THE COALESCENT , 1980 .

[68]  M. Kimura,et al.  The neutral theory of molecular evolution. , 1983, Scientific American.

[69]  W. K. Hastings,et al.  Monte Carlo Sampling Methods Using Markov Chains and Their Applications , 1970 .

[70]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[71]  Yun-Xin Fu Estimating Mutation Rate and Generation Time from Longitudinal Samples of DNA Sequences , 2022 .