Allen G Rodrigo

Summary

Affiliation: University of Auckland
Country: New Zealand

Publications

  1. ncbi The perils of plenty: what are we going to do with all these genes?
    Allen Rodrigo
    Allan Wilson Centre for Molecular Evolution and Bioinformatics Institute, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
    Philos Trans R Soc Lond B Biol Sci 363:3893-902. 2008
  2. ncbi Inferring evolutionary rates using serially sampled sequences from several populations
    Allen G Rodrigo
    Computational and Evolutionary Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland, New Zealand
    Mol Biol Evol 20:2010-8. 2003
  3. ncbi Recombination in feline immunodeficiency virus from feral and companion domestic cats
    Jessica J Hayward
    Bioinformatics Institute, Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
    Virol J 5:76. 2008
  4. ncbi A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels
    Steven H Wu
    Bioinformatics Institute, University of Auckland, Private Bag, 92019, Auckland, New Zealand
    BMC Bioinformatics 13:137. 2012
  5. ncbi Molecular epidemiology of feline immunodeficiency virus in the domestic cat (Felis catus)
    Jessica J Hayward
    Bioinformatics Institute, Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
    Vet Immunol Immunopathol 134:68-74. 2010
  6. ncbi Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences
    Matthew Goode
    Bioinformatics Institute and The Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand
    Curr Protoc Bioinformatics . 2004
  7. ncbi Evolution of relative synonymous codon usage in Human Immunodeficiency Virus type-1
    Peter L Meintjes
    Bioinformatics Institute and Computational and Evolutionary Biology Lab, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
    J Bioinform Comput Biol 3:157-68. 2005
  8. ncbi Modeling the site-specific variation of selection patterns along lineages
    Stephane Guindon
    Bioinformatics Institute, Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Private Bag 92019, Auckland, New Zealand
    Proc Natl Acad Sci U S A 101:12957-62. 2004
  9. ncbi Phylogenetic analysis of feline immunodeficiency virus in feral and companion domestic cats of New Zealand
    Jessica J Hayward
    Bioinformatics Institute, Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland Mail Centre, Auckland 1142, New Zealand
    J Virol 81:2999-3004. 2007
  10. ncbi A heteroduplex method for detection of targeted sub-populations of bacterial communities
    Susan J Turner
    School of Biological Sciences, University of Auckland, Private Bag 92 019, Auckland, New Zealand
    FEMS Microbiol Lett 208:9-13. 2002

Collaborators

Detail Information

Publications22

  1. ncbi The perils of plenty: what are we going to do with all these genes?
    Allen Rodrigo
    Allan Wilson Centre for Molecular Evolution and Bioinformatics Institute, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
    Philos Trans R Soc Lond B Biol Sci 363:3893-902. 2008
    ..Finally, we discuss new sequencing technologies, the types of data available and the efficacy of alignment-free methods to estimate pairwise distances for phylogenetic analyses...
  2. ncbi Inferring evolutionary rates using serially sampled sequences from several populations
    Allen G Rodrigo
    Computational and Evolutionary Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland, New Zealand
    Mol Biol Evol 20:2010-8. 2003
    ..An example data set comprising HIV-1 partial envelope sequences from six patients on highly active antiretroviral therapy is analyzed...
  3. ncbi Recombination in feline immunodeficiency virus from feral and companion domestic cats
    Jessica J Hayward
    Bioinformatics Institute, Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
    Virol J 5:76. 2008
    ..We investigated recombination in Feline Immunodeficiency Virus from naturally-infected New Zealand domestic cats (Felis catus) by sequencing regions of the gag, pol and env genes...
  4. ncbi A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels
    Steven H Wu
    Bioinformatics Institute, University of Auckland, Private Bag, 92019, Auckland, New Zealand
    BMC Bioinformatics 13:137. 2012
    ....
  5. ncbi Molecular epidemiology of feline immunodeficiency virus in the domestic cat (Felis catus)
    Jessica J Hayward
    Bioinformatics Institute, Allan Wilson Centre for Molecular Ecology and Evolution, School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland 1142, New Zealand
    Vet Immunol Immunopathol 134:68-74. 2010
    ..We studied the tissue distribution of FIV(Fca) in feral domestic cats, finding the first case of FIV compartmentalisation, a phenomenon well documented in HIV-1 patients...
  6. ncbi Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences
    Matthew Goode
    Bioinformatics Institute and The Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland, New Zealand
    Curr Protoc Bioinformatics . 2004
    ..The alternate and support protocols describe the simulation capabilities of PEBBLE, and general use of the PEBBLE application, respectively...
  7. ncbi Evolution of relative synonymous codon usage in Human Immunodeficiency Virus type-1
    Peter L Meintjes
    Bioinformatics Institute and Computational and Evolutionary Biology Lab, School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland, New Zealand
    J Bioinform Comput Biol 3:157-68. 2005
    ..However, closer examination of the data revealed that the apparent trend towards human RSCU can be attributed to the homogenization of the codon usage by mutation pressure rather than host adaptation...
  8. ncbi Modeling the site-specific variation of selection patterns along lineages
    Stephane Guindon
    Bioinformatics Institute, Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Private Bag 92019, Auckland, New Zealand
    Proc Natl Acad Sci U S A 101:12957-62. 2004
    ..We also provide strong evidence that the strength and the frequency of occurrence of selection might not be estimated accurately when the site-specific variation of selection regimes is ignored...
  9. ncbi Phylogenetic analysis of feline immunodeficiency virus in feral and companion domestic cats of New Zealand
    Jessica J Hayward
    Bioinformatics Institute, Allan Wilson Centre for Molecular Ecology and Evolution, University of Auckland, Auckland Mail Centre, Auckland 1142, New Zealand
    J Virol 81:2999-3004. 2007
    ..In addition, 17 sequences were identified that were distinct from all known FIV clades, and we tentatively suggest these belong to a novel subtype...
  10. ncbi A heteroduplex method for detection of targeted sub-populations of bacterial communities
    Susan J Turner
    School of Biological Sciences, University of Auckland, Private Bag 92 019, Auckland, New Zealand
    FEMS Microbiol Lett 208:9-13. 2002
    ..The utility of the method was tested by field studies in which stream biofilms could be characterised by heteroduplex profiles generated with heterotrophic and autotrophic reporter organisms representing target groups...
  11. ncbi SQUINT: a multiple alignment program and editor
    Matthew G Goode
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    Bioinformatics 23:1553-5. 2007
    ..AVAILABILITY: The software is freely available for download at http://www.cebl.auckland.ac.nz..
  12. ncbi Evidence for reduced selection pressure on the hepatitis B virus core gene in hepatitis B e antigen-negative chronic hepatitis B
    Brook G Warner
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    J Gen Virol 92:1800-8. 2011
    ..There is a subtle relaxation in selection pressure on the HBV core gene in e-CHB. This may be due to impaired antiviral immunity, and could contribute to the high levels of viral replication that cause liver inflammation in this disease...
  13. ncbi A statistical model to identify differentially expressed proteins in 2D PAGE gels
    Steven H Wu
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    PLoS Comput Biol 5:e1000509. 2009
    ..An R package, Slider (Statistical Likelihood model for Identifying Differential Expression in R), is freely available at http://www.cebl.auckland.ac.nz/slider.php...
  14. ncbi Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration
    Howard A Ross
    Computational and Evolutionary Biology Laboratory, School of Biological Sciences, University of Auckland, Auckland, New Zealand
    J Virol 76:11715-20. 2002
    ..Our study is consistent with the hypothesis that a broad and persistent immunologic response is associated with a slower rate of disease progression. In contrast, narrow, shifting immune responses characterize short-term progressors...
  15. ncbi Covariation of branch lengths in phylogenies of functionally related genes
    Wai Lok Sibon Li
    Bioinformatics Institute, University of Auckland, Auckland, New Zealand
    PLoS ONE 4:e8487. 2009
    ..We discuss the relevance of our findings as it relates to the use of phylogenetic methods in comparative genomics...
  16. ncbi Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
    Alexei J Drummond
    School of Biological Sciences, University of Auckland 1001, Auckland, New Zealand
    Genetics 161:1307-20. 2002
    ..We illustrate some of the important features of this approach on a genealogy of HIV-1 envelope (env) partial sequences...
  17. ncbi Selection for human immunodeficiency virus type 1 recombinants in a patient with rapid progression to AIDS
    Shan-Lu Liu
    Department of Microbiology, University of Washington, Seattle, Washington 98195, USA
    J Virol 76:10674-84. 2002
    ....
  18. ncbi Consensus and ancestral state HIV vaccines
    David C Nickle
    Science 299:1515-8; author reply 1515-8. 2003
  19. ncbi Predicting demographic group structures based on DNA sequence data
    Jon P Anderson
    Department of Molecular Biotechnology, Health Sciences Center, University of Washington, Seattle, USA
    Mol Biol Evol 20:1168-80. 2003
    ..Such predictions of demographic epidemiology based on sequence information may become valuable in assigning different treatment regimens to infected individuals...
  20. ncbi Pervasive genomic recombination of HIV-1 in vivo
    Daniel Shriner
    Department of Microbiology, University of Washington School of Medicine, Seattle, Washington 98195 8070, USA
    Genetics 167:1573-83. 2004
    ..Thus, recombination is a major evolutionary force affecting genetic variation within an HIV-1-infected individual, of the same order of magnitude as point mutational change...
  21. ncbi Epidemiology, genetic diversity, and evolution of endemic feline immunodeficiency virus in a population of wild cougars
    Roman Biek
    Wildlife Biology Program, University of Montana, Missoula, Montana 59812, USA
    J Virol 77:9578-89. 2003
    ..These results support the premise that FIVpco is well adapted to its cougar host and provide a basis for comparing lentivirus evolution in endemic and epidemic infections in natural hosts...
  22. ncbi Immunogen sequence: the fourth tier of AIDS vaccine design
    James I Mullins
    Department of Microbiology, University of Washington School of Medicine, Seattle, WA 98109 8070, USA
    Expert Rev Vaccines 3:S151-9. 2004
    ....