Publications of Allen G Rodrigo    :chronological  alphabetical  combined  bibtex listing:

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Papers Published

  1. Wu, SH; Rodrigo, AG, Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals., BMC Bioinformatics, vol. 16 (November, 2015), pp. 357 [doi]  [abs].
  2. Nunn, CL; Alberts, SC; McClain, CR; Meshnick, SR; Vision, TJ; Wiegmann, BM; Rodrigo, AG, Linking Evolution, Ecology, and Health: TriCEM, BioScience (BioOne), vol. 65 no. 8 (August, 2015), pp. 748-749 [doi] .
  3. McKenney, EA; Rodrigo, A; Yoder, AD, Patterns of gut bacterial colonization in three primate species., PloS one, vol. 10 no. 5 (January, 2015), pp. e0124618 [doi]  [abs].
  4. Ho, C; Wu, S; Amos, JD; Colvin, L; Smith, SD; Wilks, AB; Demarco, CT; Brinkley, C; Denny, TN; Schmitz, JE; Rodrigo, AG; Permar, SR, Transient compartmentalization of simian immunodeficiency virus variants in the breast milk of african green monkeys., Journal of virology, vol. 87 no. 20 (October, 2013), pp. 11292-11299 [23926337], [doi]  [abs].
  5. Wu, S; Koelle, K; Rodrigo, A, Coalescent entanglement and the conditional dependence of the times to common ancestry of mutually exclusive pairs of individuals., Journal of Heredity, vol. 104 no. 1 (January, 2013), pp. 86-91 [23077234], [doi]  [abs].
  6. Thrimawithana, AH; Ortiz-Catedral, L; Rodrigo, A; Hauber, ME, Reduced total genetic diversity following translocations? A metapopulation approach, Conservation Genetics, vol. 14 no. 5 (2013), pp. 1043-1055 [doi]  [abs].
  7. Ping, L-H; Jabara, CB; Rodrigo, AG; Hudelson, SE; Piwowar-Manning, E; Wang, L; Eshleman, SH; Cohen, MS; Swanstrom, R, HIV-1 transmission during early antiretroviral therapy: evaluation of two HIV-1 transmission events in the HPTN 052 prevention study., PloS one, vol. 8 no. 9 (2013), pp. e71557 [24086252], [doi]  [abs].
  8. S Wu, K Koelle, A Rodrigo, Coalescent entanglement and the conditional dependence of the times to common ancestry of mutually exclusive pairs of individuals., The Journal of heredity, vol. 104 no. 1 (October, 2012), pp. 86-91 [doi]  [abs].
  9. Wu, SH; Black, MA; North, RA; Rodrigo, AG, A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels., BMC Bioinformatics, vol. 13 (June, 2012), pp. 137 [22712439], [doi]  [abs].
  10. Cheng, Y; Guindon, S; Rodrigo, A; Lim, SG, Increased viral quasispecies evolution in HBeAg seroconverter patients treated with oral nucleoside therapy, Journal of Hepatology, vol. 58 no. 2 (2012), pp. 217-224 [doi]  [abs].
  11. Cheng, Y; Guindon, S; Hu, PZ; Rodrigo, A; Lim, SG, Viral Quasispecies Evolution in Chronic Hepatitis B Patients Treated with Lamivudine., Journal of Hepatology (2012) .
  12. Delaney, NF; Balenger, S; Bonneaud, C; Marx, CJ; Hill, GE; Ferguson-Noel, N; Tsai, P; Rodrigo, A; Edwards, SV, Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma Gallisepticum, PLoS genetics, vol. 8 no. 2 (2012), pp. e1002511 [doi]  [abs].
  13. Cheng, Y; Guindon, S; Rodrigo, A; Wee, LY; Inoue, M; Thompson, AJV; Locarnini, S; Lim, SG, Cumulative viral evolutionary changes in chronic hepatitis B virus infection precedes hepatitis B e antigen seroconversion, Gut, vol. 62 no. 9 (2012), pp. 1347-1355 [doi]  [abs].
  14. Rodrigo, A; Alberts, S; Cranston, K; Kingsolver, J; Lapp, H; McClain, C; Smith, R; Vision, T; Weintraub, J; Wiegmann, B, Science incubators: synthesis centers and their role in the research ecosystem, PLoS Biology, vol. 11 no. 1 (2012), pp. e1001468 [repository], [doi]  [abs].
  15. Schmitt, S; Tsai, P; Bell, J; Fromont, J; Ilan, M; Lindquist, N; Perez, T; Rodrigo, A; Schupp, PJ; Vacelet, J; Webster, N; Hentschel, U; Taylor, MW, Assessing the complex sponge microbiota: Core, variable and species-specific bacterial communities in marine sponges, The ISME Journal, vol. 6 no. 3 (2012), pp. 564-576 [doi]  [abs].
  16. Warner, BG; Tsai, P; Rodrigo, AG; 'ofanoa, M; Gane, EJ; Munn, SR; Abbott, WGH, 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. 1800-1808 [21508187], [doi]  [abs].
  17. Ho, SYW; Lanfear, R; Bromham, L; Phillips, MJ; Soubrier, J; Rodrigo, AG; Cooper, A, Time-dependent rates of molecular evolution., Molecular Ecology, vol. 20 no. 15 (August, 2011), pp. 3087-3101 [21740474], [doi]  [abs].
  18. Hayward, JJ; Rodrigo, AG, 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 [19896220], [doi]  [abs].
  19. Hayward, JJ; Rodrigo, AG, 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] .
  20. Abbott, WGH; Tsai, P; Leung, E; Trevarton, A; Ofanoa, M; Hornell, J; Gane, EJ; Munn, SR; Rodrigo, AG, 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].
  21. Marks, EJ; Rodrigo, AG; Brunton, DH, Ecstatic display calls of the Adélie penguin honestly predict male condition and breeding success, Behaviour, vol. 147 no. 2 (2010), pp. 165-184 [doi]  [abs].
  22. Marks, EJ; Rodrigo, AG; Brunton, DH, Using logistic regression models to predict breeding success in male Adélie penguins (Pygoscelis adeliae), Polar Biology, vol. 33 no. 8 (2010), pp. 1083-1094 [doi]  [abs].
  23. Li, WLS; Rodrigo, AG, Covariation of branch lengths in phylogenies of functionally related genes., PloS one, vol. 4 no. 12 (December, 2009), pp. e8487 [20041191], [doi]  [abs].
  24. Wu, SH; Black, MA; North, RA; Atkinson, KR; Rodrigo, AG, A statistical model to identify differentially expressed proteins in 2D PAGE gels., PLoS computational biology, vol. 5 no. 9 (September, 2009), pp. e1000509 [19763172], [doi]  [abs].
  25. Rodrigo, AG; Tsai, P; Shearman, H, 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].
  26. Langhoff, P; Authier, A; Buckley, TR; Dugdale, JS; Rodrigo, A; Newcomb, RD, DNA barcoding of the endemic New Zealand leafroller moth genera, Ctenopseustis and Planotortrix: DNA BARCODING, Molecular Ecology Resources, vol. 9 no. 3 (2009), pp. 691-698 [doi]  [abs].
  27. Bordewich, M; Rodrigo, AG; Semple, C, Selecting taxa to save or sequence: desirable criteria and a greedy solution., Systematic Biology (OUP), vol. 57 no. 6 (December, 2008), pp. 825-834 [19085326], [doi]  [abs].
  28. Hayward, JJ; Rodrigo, AG, Recombination in feline immunodeficiency virus from feral and companion domestic cats., Virology Journal, vol. 5 (June, 2008), pp. 76 [18559113], [doi]  [abs].
  29. Goode, M; Guindon, S; Rodrigo, A, 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].
  30. Steel, M; Rodrigo, A, Maximum likelihood supertrees, Systematic Biology (OUP), vol. 57 no. 2 (2008), pp. 243-250 [18398769], [doi]  [abs].
  31. Poss, M; Ross, H; Rodrigo, A; Terwee, J; VandeWoude, S; Biek, R, The molecular biology and evolution of feline immunodeficiency viruses of cougars, Veterinary Immunology and Immunopathology, vol. 123 no. 1-2 (2008), pp. 154-158 [18295904], [doi]  [abs].
  32. Rodrigo, A; Bertels, F; Heled, J; Noder, R; Shearman, H; Tsai, P, The perils of plenty: What are we going to do with all these genes?, Philosophical Transactions B, vol. 363 no. 1512 (2008), pp. 3893-3902 [18852100], [doi]  [abs].
  33. Lim, SG; Cheng, Y; Guindon, S; Seet, BL; Lee, LY; Hu, P; Wasser, S; Peter, FJ; Tan, T; Goode, M; Rodrigo, AG, Viral quasi-species evolution during hepatitis Be antigen seroconversion., Gastroenterology, vol. 133 no. 3 (September, 2007), pp. 951-958 [17854598], [doi]  [abs].
  34. Goode, MG; Rodrigo, AG, SQUINT: a multiple alignment program and editor., Bioinformatics, vol. 23 no. 12 (June, 2007), pp. 1553-1555 [17485434], [doi]  [abs].
  35. Hayward, JJ; Taylor, J; Rodrigo, AG, 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].
  36. Ross, HA; Nickle, DC; Liu, Y; Heath, L; Jensen, MA; Rodrigo, AG; Mullins, JI, Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes., Evolutionary bioinformatics online, vol. 2 (January, 2007), pp. 53-76 [19455202]  [abs].
  37. Poss, M; Idoine, A; Ross, HA; Terwee, JA; VandeWoude, S; Rodrigo, A, Recombination in feline lentiviral genomes during experimental cross-species infection, Virology, vol. 359 no. 1 (2007), pp. 146-151 [17046045], [doi]  [abs].
  38. Ewing, G; Rodrigo, A, 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].
  39. Poss, M; Ross, HA; Painter, SL; Holley, DC; Terwee, JA; VandeWoude, S; Rodrigo, A, Erratum: 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 (2006) 80, 6 (2728-2737)), Journal of virology, vol. 80 no. 17 (2006), pp. 8845- [doi] .
  40. Poss, M; Ross, HA; Painter, SL; Holley, DC; Terwee, JA; Vandewoude, S; Rodrigo, A, 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 (2006), pp. 2728-2737 [16501082], [doi]  [abs].
  41. Guindon, S; Black, M; Rodrigo, A, Control of the false discovery rate applied to the detection of positively selected amino acid sites, Molecular Biology and Evolution, vol. 23 no. 5 (2006), pp. 919-926 [16423864], [doi]  [abs].
  42. Ewing, G; Rodrigo, A, Coalescent-based estimation of population parameters when the number of demes changes over time, Molecular Biology and Evolution, vol. 23 no. 5 (2006), pp. 988-996 [16495347], [doi]  [abs].
  43. Doria-Rose, NA; Learn, GH; Rodrigo, AG; Nickle, DC; Li, F; Mahalanabis, M; Hensel, MT; McLaughlin, S; Edmonson, PF; Montefiori, D; Barnett, SW; Haigwood, NL; Mullins, JI, Human immunodeficiency virus type 1 subtype B ancestral envelope protein is functional and elicits neutralizing antibodies in rabbits similar to those elicited by a circulating subtype B envelope., Journal of virology, vol. 79 no. 17 (September, 2005), pp. 11214-11224 [16103173], [doi]  [abs].
  44. Meintjes, PL; Rodrigo, AG, Evolution of relative synonymous codon usage in Human Immunodeficiency Virus type-1., Journal of Bioinformatics & Computational Biology, vol. 3 no. 1 (February, 2005), pp. 157-168 [15751118]  [abs].
  45. Olshen, AB; Cosman, PC; Rodrigo, AG; Bickel, PJ; Olshen, RA, Vector quantization of amino acids: Analysis of the HIV V3 loop region, Journal of Statistical Planning and Inference, vol. 130 no. 1-2 (2005), pp. 277-298 [doi]  [abs].
  46. Welch, D; Nicholls, GK; Rodrigo, A; Solomon, W, Integrating genealogy and epidemiology: The ancestral infection and selection graph as a model for reconstructing host virus histories, Theoretical Population Biology, vol. 68 no. 1 (2005), pp. 65-75 [doi]  [abs].
  47. Guindon, S; Rodrigo, AG; Dyer, KA; Huelsenbeck, JP, Modeling the site-specific variation of selection patterns along lineages., Proceedings of the National Academy of Sciences of USA, vol. 101 no. 35 (August, 2004), pp. 12957-12962 [15326304], [doi]  [abs].
  48. Shriner, D; Rodrigo, AG; Nickle, DC; Mullins, JI, Pervasive genomic recombination of HIV-1 in vivo., Genetics, vol. 167 no. 4 (August, 2004), pp. 1573-1583 [15342499], [doi]  [abs].
  49. Goode, M; Rodrigo, AG, Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences., Current Protocols in Bioinformatics, vol. Chapter 6 (May, 2004), pp. Unit-6.8 [18428729], [doi]  [abs].
  50. Rodrigo, A, Applied Bioinformatics: Foreword, Applied Bioinformatics, vol. 3 no. 4 (2004), pp. 201-204 [doi] .
  51. Mullins, JI; Nickle, DC; Heath, L; Rodrigo, AG; Learn, GH, Immunogen sequence: The fourth tier of AIDS vaccine design, Expert Review of Vaccines, vol. 3 no. 4 SUPPL. (2004), pp. S151-S159 [doi]  [abs].
  52. Ewing, G; Nicholls, G; Rodrigo, A, Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations, Genetics, vol. 168 no. 4 (2004), pp. 2407-2420 [doi]  [abs].
  53. Rodrigo, AG; Goode, M; Forsberg, R; Ross, HA; Drummond, A, Inferring evolutionary rates using serially sampled sequences from several populations., Molecular Biology and Evolution, vol. 20 no. 12 (December, 2003), pp. 2010-2018 [12949147], [doi]  [abs].
  54. Biek, R; Rodrigo, AG; Holley, D; Drummond, A; Anderson, CR; Ross, HA; Poss, M, Epidemiology, genetic diversity, and evolution of endemic feline immunodeficiency virus in a population of wild cougars., Journal of virology, vol. 77 no. 17 (September, 2003), pp. 9578-9589 [12915571]  [abs].
  55. Anderson, JP; Learn, GH; Rodrigo, AG; He, X; Wang, Y; Weinstock, H; Kalish, ML; Robbins, KE; Hood, L; Mullins, JI, Predicting demographic group structures based on DNA sequence data., Molecular Biology and Evolution, vol. 20 no. 7 (July, 2003), pp. 1168-1180 [12777527], [doi]  [abs].
  56. Nickle, DC; Jensen, MA; Gottlieb, GS; Shriner, D; Learn, GH; Rodrigo, AG; Mullins, JI, Consensus and ancestral state HIV vaccines., Science, vol. 299 no. 5612 (March, 2003), pp. 1515-1518 [12624248], [doi] .
  57. Ross, HA; Lento, GM; Dalebout, ML; Goode, M; Ewing, G; McLaren, P; Rodrigo, AG; Lavery, S; Baker, CS, DNA surveillance: web-based molecular identification of whales, dolphins, and porpoises., Journal of Heredity, vol. 94 no. 2 (March, 2003), pp. 111-114 [12721222]  [abs].
  58. Drummond, AJ; Pybus, OG; Rambaut, A; Forsberg, R; Rodrigo, AG, Measurably evolving populations, Trends in Ecology and Evolution, vol. 18 no. 9 (2003), pp. 481-488 [doi]  [abs].
  59. Ross, HA; Rodrigo, AG, Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration., Journal of virology, vol. 76 no. 22 (November, 2002), pp. 11715-11720 [12388731]  [abs].
  60. Liu, S-L; Mittler, JE; Nickle, DC; Mulvania, TM; Shriner, D; Rodrigo, AG; Kosloff, B; He, X; Corey, L; Mullins, JI, Selection for human immunodeficiency virus type 1 recombinants in a patient with rapid progression to AIDS., Journal of virology, vol. 76 no. 21 (November, 2002), pp. 10674-10684 [12368309]  [abs].
  61. Drummond, AJ; Nicholls, GK; Rodrigo, AG; Solomon, W, Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data., Genetics, vol. 161 no. 3 (July, 2002), pp. 1307-1320 [12136032]  [abs].
  62. Turner, SJ; Saul, DJ; Rodrigo, AG; Lewis, GD, A heteroduplex method for detection of targeted sub-populations of bacterial communities., Fems Microbiology Letters, vol. 208 no. 1 (February, 2002), pp. 9-13 [11934486]  [abs].
  63. Drummond, A; Forsberg, R; Rodrigo, AG, The inference of stepwise changes in substitution rates using serial sequence samples., Molecular Biology and Evolution, vol. 18 no. 7 (July, 2001), pp. 1365-1371 [11420374]  [abs].
  64. Anderson, JP; Rodrigo, AG; Learn, GH; Wang, Y; Weinstock, H; Kalish, ML; Robbins, KE; Hood, L; Mullins, JI, Substitution model of sequence evolution for the human immunodeficiency virus type 1 subtype B gp120 gene over the C2-V5 region., Journal of Molecular Evolution, vol. 53 no. 1 (July, 2001), pp. 55-62 [11683323]  [abs].
  65. Rouzine, IM; Rodrigo, A; Coffin, JM, Transition between stochastic evolution and deterministic evolution in the presence of selection: General theory and application to virology, Microbiology and Molecular Biology Reviews, vol. 65 no. 1 (2001), pp. 151-185 [doi]  [abs].
  66. Drummond, A; Rodrigo, AG, Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA., Molecular Biology and Evolution, vol. 17 no. 12 (December, 2000), pp. 1807-1815 [11110896]  [abs].
  67. Goldman, N; Anderson, JP; Rodrigo, AG, Likelihood-based tests of topologies in phylogenetics., Systematic Biology (OUP), vol. 49 no. 4 (December, 2000), pp. 652-670 [12116432]  [abs].
  68. Anderson, JP; Rodrigo, AG; Learn, GH; Madan, A; Delahunty, C; Coon, M; Girard, M; Osmanov, S; Hood, L; Mullins, JI, Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E., Journal of virology, vol. 74 no. 22 (November, 2000), pp. 10752-10765 [11044120]  [abs].
  69. Kliks, S; Contag, CH; Corliss, H; Learn, G; Rodrigo, A; Wara, D; Mullins, JI; Levy, JA, Genetic analysis of viral variants selected in transmission of human immunodeficiency viruses to newborns, AIDS Research and Human Retroviruses, vol. 16 no. 13 (2000), pp. 1223-1233 [doi]  [abs].
  70. Dodd, SL; Crowhurst, RN; Rodrigo, AG; Samuels, GJ; Hill, RA; Stewart, A, Examination of Trichoderma phylogenies derived from ribosomal DNA sequence data, Mycological Research, vol. 104 no. 1 (2000), pp. 23-34 [doi]  [abs].
  71. Shankarappa, R; Margolick, JB; Gange, SJ; Rodrigo, AG; Upchurch, D; Farzadegan, H; Gupta, P; Rinaldo, CR; Learn, GH; He, X; Huang, XL; Mullins, JI, Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection., Journal of virology, vol. 73 no. 12 (December, 1999), pp. 10489-10502 [10559367]  [abs].
  72. Rodrigo, AG, HIV evolutionary genetics., Proceedings of the National Academy of Sciences of USA, vol. 96 no. 19 (September, 1999), pp. 10559-10561 [10485860] .
  73. Melvin, AJ; Rodrigo, AG; Mohan, KM; Lewis, PA; Manns-Arcuino, L; Coombs, RW; Mullins, JI; Frenkel, LM, HIV-1 dynamics in children., Journal of acquired immune deficiency syndromes and human retrovirology : official publication of the International Retrovirology Association, vol. 20 no. 5 (April, 1999), pp. 468-473 [10225229]  [abs].
  74. Rodrigo, AG; Shpaer, EG; Delwart, EL; Iversen, AK; Gallo, MV; Brojatsch, J; Hirsch, MS; Walker, BD; Mullins, JI, Coalescent estimates of HIV-1 generation time in vivo., Proceedings of the National Academy of Sciences of USA, vol. 96 no. 5 (March, 1999), pp. 2187-2191 [10051616]  [abs].
  75. Rodrigo, AG, Combinability of phylogenies and bootstrap confidence envelopes., Systematic Biology (OUP), vol. 47 no. 4 (December, 1998), pp. 727-733 [12066315] .
  76. Poss, M; Rodrigo, AG; Gosink, JJ; Learn, GH; de Vange Panteleeff, D; Martin, HL; Bwayo, J; Kreiss, JK; Overbaugh, J, Evolution of envelope sequences from the genital tract and peripheral blood of women infected with clade A human immunodeficiency virus type 1., Journal of virology, vol. 72 no. 10 (October, 1998), pp. 8240-8251 [9733867]  [abs].
  77. Shankarappa, R; Gupta, P; Learn, GH; Rodrigo, AG; Rinaldo, CR; Gorry, MC; Mullins, JI; Nara, PL; Ehrlich, GD, Evolution of human immunodeficiency virus type 1 envelope sequences in infected individuals with differing disease progression profiles., Virology, vol. 241 no. 2 (February, 1998), pp. 251-259 [9499799], [doi]  [abs].
  78. Rodrigo, AG, Dynamics of syncytium-inducing and non-syncytium-inducing type 1 human immunodeficiency viruses during primary infection., AIDS Research and Human Retroviruses, vol. 13 no. 17 (November, 1997), pp. 1447-1451 [9390743], [doi]  [abs].
  79. Rodrigo, AG; Goracke, PC; Rowhanian, K; Mullins, JI, Quantitation of target molecules from polymerase chain reaction-based limiting dilution assays., AIDS Research and Human Retroviruses, vol. 13 no. 9 (June, 1997), pp. 737-742 [9171217], [doi]  [abs].
  80. Bachmann, MH; Mathiason-Dubard, C; Learn, GH; Rodrigo, AG; Sodora, DL; Mazzetti, P; Hoover, EA; Mullins, JI, Genetic diversity of feline immunodeficiency virus: dual infection, recombination, and distinct evolutionary rates among envelope sequence clades., Journal of virology, vol. 71 no. 6 (June, 1997), pp. 4241-4253 [9151811]  [abs].
  81. Ardern, SL; Lambert, DM; Rodrigo, AG; McLean, IG, The effects of population bottlenecks on multilocus DNA variation in robins, Journal of Heredity, vol. 88 no. 3 (1997), pp. 179-186  [abs].
  82. Rodrigo, AG; Mullins, JI, Human immunodeficiency virus type 1 molecular evolution and the measure of selection., AIDS Research and Human Retroviruses, vol. 12 no. 18 (December, 1996), pp. 1681-1685 [8959243], [doi]  [abs].
  83. Bickel, PJ; Cosman, PC; Olshen, RA; Spector, PC; Rodrigo, AG; Mullins, JI, Covariability of V3 loop amino acids., AIDS Research and Human Retroviruses, vol. 12 no. 15 (October, 1996), pp. 1401-1411 [8893048], [doi]  [abs].
  84. Liu, SL; Rodrigo, AG; Shankarappa, R; Learn, GH; Hsu, L; Davidov, O; Zhao, LP; Mullins, JI, HIV quasispecies and resampling., Science, vol. 273 no. 5274 (July, 1996), pp. 415-416 [8677432] .
  85. Iversen, AK; Shpaer, EG; Rodrigo, AG; Hirsch, MS; Walker, BD; Sheppard, HW; Merigan, TC; Mullins, JI, Persistence of attenuated rev genes in a human immunodeficiency virus type 1-infected asymptomatic individual., Journal of virology, vol. 69 no. 9 (September, 1995), pp. 5743-5753 [7637019]  [abs].
  86. Delwart, EL; Herring, B; Rodrigo, AG; Mullins, JI, Genetic subtyping of human immunodeficiency virus using a heteroduplex mobility assay., Genome Research, vol. 4 no. 5 (April, 1995), pp. S202-S216 [7580909] .
  87. Rainey, FA; Donnison, AM; Janssen, PH; Saul, D; Rodrigo, A; Bergquist, PL; Daniel, RM; Stackebrandt, E; Morgan, HW, Description of Caldicellulosiruptor saccharolyticus gen. nov., sp. nov: An obligately anaerobic, extremely thermophilic, cellulolytic bacterium, Fems Microbiology Letters, vol. 120 no. 3 (1994), pp. 263-266 [doi]  [abs].
  88. Mcardle, B; Rodrigo, AG, Estimating the ancestral states of a continuous-valued character using squared-change parsimony: An analytical solution, Systematic Biology, vol. 43 no. 4 (1994), pp. 573-578 .
  89. Rodrigo, AG; Bergquist, PR; Bergquist, PL, Inadequate support for an evolutionary link between the metazoa and the fungi, Systematic Biology, vol. 43 no. 4 (1994), pp. 578-584 .
  90. Rodrigo, AG; Borges, KM; Bergquist, PL, Pulsed-field gel electrophoresis of genomic digests of Thermus strains and its implications for taxonomic and evolutionary studies, International Journal of Systematic Bacteriology, vol. 44 no. 3 (1994), pp. 547-552  [abs].
  91. Saul, DJ; Rodrigo, AG; Reeves, RA; Williams, LC; Borges, KM; Morgan, HW; Bergquist, PL, Phylogeny of twenty Thermus isolates constructed from 16S rRNA gene sequence data., International journal of systematic bacteriology, vol. 43 no. 4 (October, 1993), pp. 754-760 [8240955], [doi]  [abs].
  92. Rodrigo, AG, Calibrating the bootstrap test of monophyly., International Journal for Parasitology, vol. 23 no. 4 (July, 1993), pp. 507-514 [8354601]  [abs].
  93. Roberts, M; Rodrigo, A; McArdle, B; Charleston, WAG, The effect of habitat on the helminth parasites of an island population of the Polynesian rat (Rattus exulans), Journal of Zoology, vol. 227 no. 1 (1992), pp. 109-125  [abs].
  94. Rodrigo, AG, Two optimality criteria for selecting subsets of most parsimonious trees, Systematic Biology (OUP), vol. 41 no. 1 (1992), pp. 33-40  [abs].
  95. Rodrigo, AG, A modification to Wheeler's combinatorial weights calculations, Cladistics, vol. 8 no. 2 (1992), pp. 165-170 .
  96. Rodrigo, AG, Surficial sediment-heavy metal associations in the Avon-Heathcote Estuary, New Zealand, New Zealand Journal of Marine & Freshwater Research, vol. 23 no. 2 (1989), pp. 255-262  [abs].

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 .