Publications of Allen G. Rodrigo    :recent first  combined  bibtex listing:

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Papers Published

  1. Ross, Howard A. and Nickle, David C. and Liu, Yi and Heath, Laura and Jensen, Mark A. and Rodrigo, Allen G. and Mullins, James I., Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes., Evolutionary bioinformatics online, vol. 2 (January, 2006), pp. 53--76 [19455202]  [abs].
  2. Ewing, Greg and Rodrigo, Allen, Estimating population parameters using the structured serial coalescent with Bayesian MCMC inference when some demes are hidden., Evolutionary bioinformatics online, vol. 2 (February, 2006), pp. 227--235 [19455215]  [abs].
  3. Poss, Mary and Ross, Howard A. and Painter, Sally L. and Holley, David C. and Terwee, Julie A. and Vandewoude, Sue and Rodrigo, Allen, Feline lentivirus evolution in cross-species infection reveals extensive G-to-A mutation and selection on key residues in the viral polymerase., Journal of virology, vol. 80 no. 6 (March, 2006), pp. 2728--2737 [16501082], [doi]  [abs].
  4. Ewing, Greg and Rodrigo, Allen and {SMBE Tri-National Young Investigators}, Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Coalescent-based estimation of population parameters when the number of demes changes over time., Molecular biology and evolution, vol. 23 no. 5 (May, 2006), pp. 988--996 [16495347], [doi]  [abs].
  5. Guindon, St{\'e}phane and Black, Mik and Rodrigo, Allen and {SMBE Tri-National Young Investigators}, Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Control of the false discovery rate applied to the detection of positively selected amino acid sites., Molecular biology and evolution, vol. 23 no. 5 (May, 2006), pp. 919--926 [16423864], [doi]  [abs].
  6. Hayward, Jessica J. and Taylor, John and Rodrigo, Allen G., Phylogenetic analysis of feline immunodeficiency virus in feral and companion domestic cats of New Zealand., Journal of virology, vol. 81 no. 6 (March, 2007), pp. 2999--3004 [17192306], [doi]  [abs].
  7. Poss, Mary and Idoine, Adam and Ross, Howard A. and Terwee, Julie A. and VandeWoude, Sue and Rodrigo, Allen, Recombination in feline lentiviral genomes during experimental cross-species infection., Virology, vol. 359 no. 1 (March, 2007), pp. 146--151 [17046045], [doi]  [abs].
  8. Goode, Matthew G. and Rodrigo, Allen G., SQUINT: a multiple alignment program and editor., Bioinformatics (Oxford, England), vol. 23 no. 12 (June, 2007), pp. 1553--1555 [17485434], [doi]  [abs].
  9. Lim, Seng Gee and Cheng, Yan and Guindon, Stephane and Seet, Bee Leng and Lee, Lay Yong and Hu, Peizhen and Wasser, Shanthi and Peter, Frank Josef and Tan, Theresa and Goode, Matthew and Rodrigo, Allen Gerard, Viral quasi-species evolution during hepatitis Be antigen seroconversion., Gastroenterology, vol. 133 no. 3 (September, 2007), pp. 951--958 [17854598], [doi]  [abs].
  10. Goode, Matthew and Guindon, St{\'e}phane and Rodrigo, Allen, Modelling the evolution of protein coding sequences sampled from Measurably Evolving Populations., Genome informatics. International Conference on Genome Informatics, vol. 21 (2008), pp. 150--164 [19425155]  [abs].
  11. Steel, Mike and Rodrigo, Allen, Maximum likelihood supertrees., Systematic biology, vol. 57 no. 2 (April, 2008), pp. 243--250 [18398769], [doi]  [abs].
  12. Poss, Mary and Ross, Howard and Rodrigo, Allen and Terwee, Julie and Vandewoude, Sue and Biek, Roman, The molecular biology and evolution of feline immunodeficiency viruses of cougars., Veterinary immunology and immunopathology, vol. 123 no. 1-2 (May, 2008), pp. 154--158 [18295904], [doi]  [abs].
  13. Hayward, Jessica J. and Rodrigo, Allen G., Recombination in feline immunodeficiency virus from feral and companion domestic cats., Virology journal, vol. 5 (June, 2008), pp. 76 [18559113], [doi]  [abs].
  14. Rodrigo, Allen and Bertels, Frederic and Heled, Joseph and Noder, Raphael and Shearman, Helen and Tsai, Peter, The perils of plenty: what are we going to do with all these genes?, Philosophical transactions of the Royal Society of London. Series B, Biological sciences, vol. 363 no. 1512 (December, 2008), pp. 3893--3902 [18852100], [doi]  [abs].
  15. Bordewich, Magnus and Rodrigo, Allen G. and Semple, Charles, Selecting taxa to save or sequence: desirable criteria and a greedy solution., Systematic biology, vol. 57 no. 6 (December, 2008), pp. 825--834 [19085326], [doi]  [abs].
  16. Rodrigo, Allen G. and Tsai, Peter and Shearman, Helen, On the use of bootstrapped topologies in coalescent-based Bayesian MCMC inference: a comparison of estimation and computational efficiencies., Evolutionary bioinformatics online, vol. 5 (July, 2009), pp. 97--105 [19812730]  [abs].
  17. SH Wu, MA Black, RA North, KR Atkinson, AG Rodrigo, A statistical model to identify differentially expressed proteins in 2D PAGE gels., PLoS computational biology, vol. 5 no. 9 (September, 2009), pp. e1000509 [doi]  [abs].
  18. Li, Wai Lok Sibon and Rodrigo, Allen G., Covariation of branch lengths in phylogenies of functionally related genes., PloS one, vol. 4 no. 12 (December, 2009), pp. e8487 [20041191], [doi]  [abs].
  19. E. J. Marks, A.G. Rodrigo and D. H. Brunton, Using logistic regression models to predict breeding success in male Adelie penguins (Pygoscelis adeliae)., Polar Biology, vol. 33 (2010), pp. 1083 - 1094 .
  20. E. J. Marks, A.G. Rodrigo and D. H. Brunton, Ecstatic Display Calls of the Adelie penguin honestly predict male condition and breeding success., Behaviour, vol. 147 (2010), pp. 165-184 .
  21. Abbott, William G. H. and Tsai, Peter and Leung, Euphemia and Trevarton, Alex and Ofanoa, Malakai and Hornell, John and Gane, Edward J. and Munn, Stephen R. and Rodrigo, Allen G., Associations between HLA class I alleles and escape mutations in the hepatitis B virus core gene in New Zealand-resident Tongans., Journal of virology, vol. 84 no. 1 (January, 2010), pp. 621--629 [19846510], [doi]  [abs].
  22. Hayward, Jessica J. and Rodrigo, Allen G., The distribution of feline immunodeficiency virus in tissue compartments of feral domestic cats., Archives of virology, vol. 155 no. 3 (March, 2010), pp. 411--416 [20112119], [doi] .
  23. JJ Hayward, AG Rodrigo, Molecular epidemiology of feline immunodeficiency virus in the domestic cat (Felis catus)., Veterinary immunology and immunopathology, vol. 134 no. 1-2 (March, 2010), pp. 68-74 [doi]  [abs].
  24. SY Ho, R Lanfear, L Bromham, MJ Phillips, J Soubrier, AG Rodrigo, A Cooper, Time-dependent rates of molecular evolution., Molecular ecology, vol. 20 no. 15 (August, 2011), pp. 3087-101 [doi]  [abs].
  25. BG Warner, P Tsai, AG Rodrigo, M 'ofanoa, EJ Gane, SR Munn, WG Abbott, Evidence for reduced selection pressure on the hepatitis B virus core gene in hepatitis B e antigen-negative chronic hepatitis B., The Journal of general virology, vol. 92 no. Pt 8 (August, 2011), pp. 1800-8 [doi]  [abs].
  26. S Schmitt, P Tsai, J Bell, J Fromont, M Ilan, N Lindquist, T Perez, A Rodrigo, PJ Schupp, J Vacelet, N Webster, U Hentschel, MW Taylor, Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges., The ISME journal (October, 2011) [doi]  [abs].
  27. Wu, S. H., Koelle, K., Rodrigo, A. G., Coalescent entanglement and the conditional dependence of the times-to-common-ancestry of mutually exclusive pairs of individuals., Journal of Heredity (2012) [doi] .
  28. Wu, S. H., Black, M. A., North, R. A., Rodrigo, A. G., A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels., BMC Bioinformatics, vol. 13 (2012), pp. 137 .
  29. Delaney, N. F., Balenger, S., Bonneaud, C., Marx, C. J., Hill, G. E., Ferguson-Noel, N., Tsai, P., Rodrigo, A., & Edwards, S. V., Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum., PLoS Genetics, vol. 8 (2012), pp. e1002511 .

Papers Accepted

  1. Allen Rodrigo, Susan Alberts, Karen Cranston, Joel Kingsolver, Hilmar Lapp, Craig McClain, Robin Smith, Todd Vision, Jory Weintraub, and Brian Wiegmann, Science incubators: synthesis centers and their role in the research ecosystem, PLoS Biology (In press.) .
  2. Cheng, Y., Guindon, S., Rodrigo, A., Wee, L. Y., Inoue, M., Thompson, A., Locarnini, S., Lim, S. G., Cumulative viral evolutionary changes in chronic Hepatitis B Virus infection precedes HBeAg seroconversion., Gut (In press) .
  3. Cheng, Y., Guindon, S., Hu, P. Z., Rodrigo, A., Lim, S. G., Viral Quasispecies Evolution in Chronic Hepatitis B Patients Treated with Lamivudine., Journal of Hepatology (In press.) .

Book Chapter

  1. A.G. Rodrigo, The Coalescent, in The Phylogenetic Handbook, 2nd Edition, edited by Philippe Lemey, Marco Salemi, Anne-Mieke Vandamme (2009), Cambridge University Press .

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