Publications

Peer Reviewed Articles 

[95]      Ho C, Wu S, Amos JD, Colvin L, Smith SD, Wilks AB, Demarco CT, Brinkley C, Denny TN, Schmitz JE, Rodrigo AG, Permar SR. (2013). Transient compartmentalization of simian immunodeficiency virus variants in the breast milk of african green monkeys. Journal of Virology 87:11292-9

[94]       Ping L-H, Jabara CB, Rodrigo AG, Hudelson SE, Piwowar-Manning E, et al. (2013) HIV-1 Transmission during Early Antiretroviral Therapy: Evaluation of Two HIV-1 Transmission Events in the HPTN 052 Prevention Study. PLoS ONE 8: e71557.

[93]          Thrimawithana, A. H., Ortiz-Catedral, L., Rodrigo, A. G., and Hauber, M. E. (2013) Reduced Total Genetic Diversity Following Translocations? A Metapopulation Approach. Conservation Genetics 14:1043-1055

[92]            Cheng, Y., Guindon, S., Rodrigo, A., Wee, L. Y., Inoue, M., Thompson, A., Locarnini, S., Lim, S. G. (2013). Cumulative viral evolutionary changes in chronic Hepatitis B Virus infection precedes HBeAg seroconversion.  Gut 62:1347-55

[91]            Yan, C., Guindon, S., Rodrigo, A. and Lim, S. G. (2013). Increased viral quasispecies evolution in HBeAg seroconverter patients treated with oral nucleoside therapy. Journal of Hepatology 58:217-224

[90]            Allen Rodrigo, Susan Alberts, Karen Cranston, Joel Kingsolver, Hilmar Lapp, Craig McClain, Robin Smith, Todd Vision, Jory Weintraub, and Brian Wiegmann. (2013). Science incubators: synthesis centers and their role in the research ecosystem. PLoS Biology 11:e1001468.

[89]            Wu, S. H., Koelle, K., Rodrigo, A. G. (2013). Coalescent entanglement and the conditional dependence of the times-to-common-ancestry of mutually exclusive pairs of individuals.  Journal of Heredity 104:86-91

[88]            Wu, S. H., Black, M. A., North, R. A., Rodrigo, A. G. (2012). A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels. BMC Bioinformatics 13:137

[87]            Delaney, N. F., Balenger, S., Bonneaud, C., Marx, C. J., Hill, G. E., Ferguson-Noel, N., Tsai, P., Rodrigo, A., & Edwards, S. V. (2012). Ultrafast evolution and loss of CRISPRs following a host shift in a  novel wildlife pathogen, Mycoplasma gallisepticum. PLoS Genetics 8: e1002511

[86]           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. (2012). Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges. ISME Journal 6:564-76

[85]            Ho SY, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, Cooper A. (2011) Time-dependent rates of molecular evolution. Molecular Ecology 20:3087-3101

[84]          Warner BG, Tsai P, Rodrigo AG, ‘ofanoa M, Gane EJ, Munn SR, Abbott WG. (2011). Evidence for reduced selection pressure on the hepatitis B virus core gene in hepatitis B e antigen-negative chronic hepatitis B. Journal of General Virology 92:1800-1808.

[83]            Marks, E. J., Rodrigo, A. G., and Brunton, D. H. (2010). Using logistic regression models to predict breeding success in male Adelie penguins (Pygoscelis adeliae). Polar Biology 33:1083–1094.

[82]           Abbott, W. G. H., Tsai, P., Leung, E., Trevarton, A., ‘Ofanoa, M., Hornell, J., Gane, E. J., Munn, S.R., and Rodrigo, A. G. (2010) Associations between HLA Class I Alleles and Escape Mutations in the Hepatitis B Virus Core Gene in New Zealand-Resident Tongans.  Journal of Virology 84:621-629

[81]           Marks E. J., Rodrigo A. G. and Brunton D. H (2010) Ecstatic Display Calls of the Adelie penguin honestly predict male condition and breeding success. Behaviour 147:165-184.

[80]          Hayward, J. and Rodrigo, A. G. (2010). The distribution of feline immunodeficiency virus in tissue compartments of feral domestic cats. Archives of Virology 155:411-416.

[79]           Hayward, J. H. and Rodrigo, A. G. (2010).  Molecular epidemiology of feline immunodeficiency virus in the domestic cat (Felis catus). Veterinary Immunology and Immunopathology 134:68-74

[78]           Li, Wai-Lok and Rodrigo, A. G. (2009). Covariation of branch lengths in phylogenies of functionally related genes. PLoS ONE. 4:e8487

[77]          Wu, S.H., Black, M.A., North, R. A., Atkinson, K.,R. and Rodrigo, A. G. (2009).  A statistical model to identify differentially expressed proteins in 2D PAGE gels. PLoS Computational Biology 5: e1000509.

[76]          Rodrigo, A. G., Tsai, P., and Shearman, H. (2009).  On the use of bootstrapped topologies in coalescent-based Bayesian MCMC inference: a comparison of estimation and computational efficiencies.  Evolutionary Bioinformatics 5:97-105.

[75]           Langhoff, P., Authier, A., Buckley, T. R., Dugdale, J. S., Rodrigo, A., and Newcomb, R.D. (2009). DNA barcoding of the endemic New Zealand leafroller moth genera, Ctenopseustis and Planotortrix.  Molecular Ecology Notes 9:691-698

[74]           Goode, M., Guindon, S. and Rodrigo, A. G. (2008). Modelling the evolution of protein coding sequences sampled from Measurably Evolving Populations. Genome Informatics 21:150-164

[73]           Bordewich, M., Rodrigo, A. G., Semple, C. (2008).  Selecting taxa to save or sequence: desirable criteria and a greedy solution. Systematic Biology 57: 825-834

[72]            Rodrigo, A. G., Bertels, F., Heled, J., Noder, R., Shearman, H., and Tsai, P. (2008).  The perils of plenty: what are we going to do with all these genes?  Phil. Trans. Roy. Soc. B 363:3893-902

[71]            Hayward, J. J. and Rodrigo, A. G. (2008) Recombination in feline immunodeficiency virus from feral and companion domestic cats.  Virology Journal 5:76.

[70]            Steel, M. A. and Rodrigo, A. G. (2008). Maximum likelihood supertrees. Systematic Biology. 57:243-250

[69]            Poss, M., H. A. Ross, A. G. Rodrigo, J. A. Terwee and S. VandeWoude. (2008). The molecular biology and evolution of feline immunodeficiency viruses of cougars. Veterinary Immunology and Immunopathology 123:154-158

[68]            Lim SG, Cheng Y, Guindon S, Seet BL, Lee LY, Hu P, Wasser S, Tan T, Goode M, Rodrigo A. (2007) Viral quasispecies evolution in chronic hepatitis B: new light on an old story. Gastroenterology 33:951-8

[67]            Goode, M. and Rodrigo, A. G. (2007) SQUINT: A multiple alignment program and editor. Bioinformatics 23:1553-1555

[66]            Jess Hayward, John Taylor, Allen Rodrigo (2007) Phylogenetic Analysis of Feline Immunodeficiency Virus in Domestic Cats of New Zealand. Journal of Virology 81:2999-3004

[65]            Mary Poss, Adam  Idoine, Howard A  Ross, Julie A Terwee, Sue VandeWoude, Allen Rodrigo. (2007). Recombination in feline lentiviral genomes during experimental cross-species infection. Virology 359:146-151

[64]            Gregory Ewing and Allen G. Rodrigo. (2006) Estimating Population Parameters using the Structured Serial Coalescent with Bayesian MCMC Inference when some Demes are Hidden. Evolutionary Bioinformatics 2:239-247

[63]           Gregory Ewing and Allen G. Rodrigo. (2006). Coalescent-based estimation of population parameters when the number of demes changes over time. Molecular Biology and Evolution 23:988-996.

[62]           Mary Poss, Howard A. Ross, Sally L. Painter, David C. Holley, Julie A. Terwee, Sue Vandewoude, and Allen G. Rodrigo. (2006). Feline lentivirus evolution in cross-species infection reveals high error burdens and selection on key residues in the viral polymerase. Journal of Virology 80:2728-2737

[61]           Stéphane Guindon, Mik Black, and Allen Rodrigo (2006). Control of the false discover rate applied to the detection of positively detected sites. Molecular Biology and Evolution 23:919-926.

[60]           Howard A. Ross, David C. Nickle, Yi Liu, Laura Heath, Mark A. Jensen, Allen G. Rodrigo and James I. Mullins. (2006) Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes. Evolutionary Bioinformatics Online 2:18-41

[59]           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. (2005). 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. 79:11214-24.

[58]           Welch, D., Nicholls, G., Rodrigo, A. G., Solomon, W. (2005).  Integrating Genealogy and Epidemiology: The Ancestral Infection and Selection Graph as a Model for Reconstructing Host Virus Histories.  Theoretical Population Biology 68:65-75.

[57]            Meintjes, P. and Rodrigo, A. G. (2005). Evolution of Relative Synonymous Codon Usage in Human Immunodeficiency Virus Type-1. Journal of Bioinformatics and Computational Biology 3:157-168.

[56]           Olshen, A. B., Cosman, P. C., Rodrigo, A. G., Bickel, P. J., and Olshen, R. A. (2005). Vector quantization of amino acids: analysis of the HIV V3 loop region. Journal of Statistical Planning and Inference 130:277-298

[55]            James I Mullins, David C Nickle, Laura Heath, Allen G Rodrigo, and Gerald H Learn.  (2004) Immunogen sequence: the fourth tier of AIDS vaccine design.  Expert Review of Vaccines.Suppl 1:159-162

[54]            Ewing, G., Nicholls, G. and Rodrigo, A. (2004). Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations (MEPs). Genetics 168:2407-2420

[53]            Shriner, D., Rodrigo, A. G, Nickle, D. C., and  Mullins, J. I. (2004). Pervasive Genomic Recombination of HIV-1 In Vivo.  Genetics 167:1573-1587

[52]            Guindon, S., Rodrigo, A. G., Dyer, K., Huelsenbeck, J. P. (2004)  Modeling the site-specific variation of selection patterns along lineages. Proceedings of the National Academy of Sciences, USA 101:12957-12962

[51]           Rodrigo, A. G., M. Goode, R. Forsberg, H. Ross, & A. Drummond. (2003) Inferring Evolutionary Rates Using Serially Sampled Sequences from Several Populations. Molecular Biology and Evolution 20:2010-2018.

[50]           Drummond, A.J., O.G. Pybus, A. Rambaut, R. Forsberg & A.G. Rodrigo. 2003. Measurably evolving populations. Trends in Ecology and Evolution 18:481-488.

[49]           Roman Biek, Allen G. Rodrigo, David Holley, Alexei Drummond, Charles R. Anderson, Jr. Howard A. Ross, and Mary Poss (2003). Epidemiology, Genetic Diversity, and Evolution of Endemic Feline Immunodeficiency Virus in a Population of Wild Cougars. Journal of Virology 77:9578-9589

[48]           Jon P. Anderson, Gerald H. Learn , Allen G. Rodrigo, Xi He, Yang Wang, Hillard Weinstock, Marcia L. Kalish, Kenneth E. Robbins, Leroy Hood, and James I. Mullins. (2003). Predicting demographic group structures based on DNA sequence data. Molecular Biology and Evolution 20:1168-1180.

[47]           H. A. Ross, G. M. Lento, M. L. Dalebout, M. Goode, P. McLaren, G. Ewing, A. G. Rodrigo, S. Lavery, and C. S. Baker (2003).DNA Surveillance: Web-based molecular identification of whales, dolphins and porpoises. Journal of Heredity 94:111-114

[46]           David C. Nickle, Mark A. Jensen, Geoffrey S. Gottlieb, Daniel Shriner, Gerald H. Learn, Allen G. Rodrigo, James I. Mullins.  (2003). Consensus and ancestral state HIV vaccines. Science 299:1515-1517

[45]           Ross, H. A., and Rodrigo, A. G. (2002). Immune-mediated positive selection drives Human Immunodeficiency Virus Type 1 molecular variation and predicts disease duration. Journal of Virology 76: 11715-11720.

[44]           Liu, S.-L., Mittler, J. E., Nickle, D. C., Mulvania, T. M., Shriner, D., Rodrigo, A G., Kosloff, B., He, X., Corey, L.and Mullins, J. I. (2002). Selection for Human Immunodeficiency Virus Type 1 recombinants in a patient with rapid progression to AIDS.  Journal of Virology 76:10674-10684

[43]           Drummond, A., Nicholls, G.K., Rodrigo A.G. and Solomon.W. (2002) Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics 161:1307-1320

[42]         Turner, S. J., Saul, D. J., Rodrigo, A. G., and Lewis, G. D. (2002). A heteroduplex method for detection of targeted sub-populations of bacterial communities.  FEMS Microbiology Letters 208:9-13

[41]         Drummond, A., Forsberg, R., and Rodrigo, A.G. (2001). Estimating stepwise changes in substitution rates using serial samples. Molecular Biology and Evolution 18:1365-1371.

[40]         Anderson, J.P., Rodrigo, A.G,, Learn, G.H., Wang, Y., Weinstock, H., Kalish, M., Robbins, K.E., Hood, L., and Mullins, J.I. (2001). Substitution Model of Sequence Evolution for the Human Immunodeficiency Virus Type I Subtype B gp120 Gene over the C2-V5 Region. Journal of Molecular Evolution 53:55-62

[39]         Rouzine, I.M., Rodrigo, A., and Coffin, J.M. (2001). Transition between Stochastic Evolution and Deterministic Evolution in the Presence of Selection: General Theory and Application to Virology. Microbiol. Mol. Biol. Rev. 65:151-185.

[38]         Goldman, N., Anderson, J.P., and Rodrigo, A.G. (2000) Likelihood-Based Tests of Topologies in Phylogenetics. Systematic Biology 49:652-670.

[37]         Anderson, J.P., Rodrigo, A.G., Learn G.H., Madan, A., Delahunty, C., Coon, M., Girard, M., Osmanov, S., Hood, L., and Mullins, J.I. (2000). Testing the Hypothesis of a Recombinant Origin of Human Immunodeficiency Virus Type I Subtype E. Journal of Virology 74:10752-10765.

[36]         Kliks, S., Contag, C.H., Corliss, H., Learn, G., Rodrigo, A., Wara, D., Mullins, J.I., and Levy J.A. (2000). Genetic analysis of viral variants selected in transmission of human immunodeficiency viruses to newborns. AIDS Research and Human Retroviruses 16:1223-1233.

[35]         Drummond, A. and Rodrigo, A.G. (2000). Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA (sUPGMA). Molecular Biology and Evolution 17:1807-1815.

[34]         Shankarappa, R., Margolick, R. B., Gange, S. J., Rodrigo, A. G., Upchurch, D., Farzadegan, H., Gupta, P., Rinaldo, C. R., Learn, G. H., He, X., Huang, X.-L., and Mullins, J. I. (1999) Consistent viral evolutionary changes associated with progression of HIV-1 infection. Journal of Virology 73:10489-10502.

[33]         Rodrigo, A. G. (1999) HIV evolutionary genetics [Commentary]. Proceedings of the National Academy of Sciences, USA 96: 10559-10561

[32]         Melvin, A. J., A. G. Rodrigo, K. M. Mohan, P. A. Lewis, L. Manns-Arcuino, R. W. Coombs, J. I. Mullins, and L. M. Frenkel. (1999). HIV-1 dynamics in children. J. Acquir. Immune Defic. Syndr. Hum. Retrovirol. 20: 468-473

[31]         Dodd-Wilson, S. L., Crowhurst, R. N., Rodrigo, A. G., Samuels, G. J., Hill, R. A. and Stewart, A. (1999). Examination of Trichoderma phylogenies derived from ribosomal DNA sequence data. Mycological Research.

[30]         Rodrigo, A. G., Shpaer, E. G., Delwart, E. L., Iversen, A. K. N., Gallo, M. V., Jxrgen Brojatsch, J., Hirsch, M. S., Walker, B. D., and Mullins, J. I. (1999). Coalescent estimates of HIV-1 generation time in vivo. Proceedings of the National Academy of Sciences, USA. 96:2187-2191

[29]         Rodrigo, A.G. (1998). Combinability of phylogenies and bootstrap confidence envelopes. Systematic Biology 47:727-733.

[28]         Poss, M., Rodrigo, A. G., Gosink, J. J., Learn, G. H., Panteleeff, D. D., Martin, Jr., H. L., Bwayo, J., Kreiss, J. K., and Overbaugh, J. (1998). 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 72:8240-8251.

[27]         B. Shankarappa, P. Gupta, G. H. Learn Jr., A. G. Rodrigo, C. R. Rinaldo Jr., M. C. Gorry, J. I. Mullins, P. L. Nara, and G. D. Ehrlich. (1998). Evolution of Human Immunodeficiency Virus Type 1 envelope sequences in infected individuals with differing disease progression profiles. Virology 241:251-259.

[26]         Rodrigo, A. G. (1997). Dynamics of non-syncytium-inducing and syncytium-inducing Type 1 Human Immunodeficiency Viruses during primary infection. AIDS Research and Human Retroviruses 17:1447-1451

[25]         Bachmann, M. H., C. Matthieson-Dubard, G. H. Learn, A. G. Rodrigo, D. L. Sodora, E. A. Hoover, and J. I. Mullins. (1997). Genetic diversity of Feline Immunodeficiency Virus: Dual infection, recombination and distinct evolutionary rates between envelope gene subtypes. Journal of Virology 71:4241-4253.

[24]         Rodrigo, A. G., Goracke, P. C., Rowhanian, K., and Mullins, J. I. (1997). Quantitation of target molecules from PCR-based limiting dilution assays. AIDS Research and Human Retroviruses 13:737-742.

[23]         Ardern, S. L., Lambert, D. M., Rodrigo, A. G., and McLean, I. G. (1997). The effects of bottleneck events on minisatellite DNA variation in robins. Journal of Heredity 88:179-186

[22]         Rodrigo, A. G., and Mullins, J. I. (1996). HIV-1 molecular evolution and the measure of selection. AIDS Research and Human Retroviruses 12:1681-1685.

[21]         Bickel, P. J., Cosman, P. C., Olshen, R. A., Spector, P. C., Rodrigo, A. G., and Mullins, J. I. (1996). Covariability of V3 loop amino acids. AIDS Research and Human Retroviruses 12:1401-1411.

[20]         Liu, S.-L., Rodrigo, A. G., Shankarappa, R., Learn, G. H., Zhao, L. P., Li, H., Davidov, O., and Mullins, J. I. (1996). HIV quasispecies diversity and resampling. Science 273:415-416.

[19]         Rodrigo, A. G. (1996). On combining cladograms. Taxon 45:267-274.

[18]         Iversen, A. K. N., Shpaer, E. G., Rodrigo, A. G., Hirsch, M. S., Walker, B. D., Sheppard, H. W., Merigan, T. C., and Mullins, J. I. (1995). Persistence of attenuated Rev genes in an HIV-1 infected asymptomatic individual. Journal of Virology 69:5743-5753.

[17]         Delwart, E. L., Herring, B., Rodrigo, A. G., and Mullins, J. I. (1995). Genetic subtyping of Human Immunodeficiency Virus using a Heteroduplex Mobility Assay. PCR Methods and Applications. 4:5202-5216.

[16]         Rodrigo, A. G., Bergquist, P. R., and Bergquist, P. L. (1994). Inadequate support for an evolutionary link between the Metazoa and the Fungi. Systematic Biology 43:578-584

[15]         McArdle, B. and Rodrigo, A. G. (1994). Estimating the ancestral states of continuous-valued characters using squared changes parsimony: an analytic solution. Systematic Biology 43: 584-595.

[14]         Rodrigo, A. G., Borges, K. M., and Bergquist, P. L. (1994). Pulsed-field gel electrophoresis of genomic digests of Thermus strains and its implications for taxonomic and evolutionary studies. International Journal of Systematic Bacteriology 44:547-552.

[13]         Rodrigo, A. G., Bergquist, P. R., Bergquist, P. L., and Reeves, R. A. (1994). Are sponges animals? An investigation into the vagaries of phylogenetic inference. Sponges in Time amd Space: Proceedings of the 4th International Porifera Congress (eds. R. W. M. van Soest, T. M. G. van Kempen and J.-C. Braekman). A. A. Balkema, Rotterdam, The Netherlands.

[12]         Rainey, F. A., Donnison, A. M., Janssen, P. H., Saul, D. J., Rodrigo, A., Bergquist, P. L., Daniel, R. M., Stackebrandt, E. and Morgan, H. W. (1994). Description of Caldicellulosiruptor saccharolyticus gen. nov., sp. nov.: an obligately anaerobic, extremely thermophilic, cellulolytic bacterium. FEMS Microbiological Letters 120:263-266.

[11]         Saul, D. J., Rodrigo, A. G., Reeves, R. A., Williams, L. C., Borges, K. M., Morgan, H. W., and Bergquist, P. L. (1993). Phylogeny of twenty Thermus isolates constructed from 16S rRNA gene sequence data. International Journal of Systematic Bacteriology 43:754-760.

[10]         Rodrigo, A. G., Kelly-Borges, M., Bergquist, P. R., and Bergquist, P. L. (1993). A randomization test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree. New Zealand Journal of Botany 31:257-268.

[9]           Rodrigo, A. G. (1993). A comment on Baum’s method for combining phylogenetic trees. Taxon 42:631-636.

[8]           Rodrigo, A. G. (1993). Calibrating the bootstrap test of monophyly. International Journal of Parasitology 23:507-514.

[7]           Rodrigo, A. G. (1992). A modification of Wheeler’s combinatorial weights procedure. Cladistics 8:165-170.

[6]           Rodrigo, A. G. (1992). Two optimality criteria for selecting subsets of most parsimonious trees. Systematic Biology 41:33-40.

[5]           Roberts, M., Rodrigo, A. G., McArdle, B. H., and Charleston, W. A. (1992). The effect of habitat on the helminth parasites of an island population of the Polynesian rat (Rattus exulans). Journal of Zoology, London 227:109-125.

[4]           Rodrigo, A. G. and Jackson, R. R. (1992). Four jumping spider genera of the Cocalodes-group are monophyletic with genera of the Spartaeinae (Araneae: Salticidae). New Zealand Natural Sciences 19:61-67.

[3]           Rodrigo, A. G. (1990). Formulae for the number of band combinations for different colour-banding strategies. New Zealand Journal of Zoology 17:285-288.

[2]           Rodrigo, A. G. (1989). Surficial sediment-heavy metal associations in the Avon-Heathcote Estuary, New Zealand. New Zealand Journal of Marine and Freshwater Research 23:255-262.

[1]           Rodrigo, A. G. (1989). An information-rich character weighting procedure for parsimony analysis. New Zealand Natural Sciences 16:97-103.

(ii) Edited volume

Rodrigo, A. G. and Learn, G. H. (2000) Computational and Evolutionary Analysis of HIV Molecular Sequences. Kluwer Academic Publishers, Boston, USA.

 (iii) Book chapters

[11]        Rodrigo, A. G. (2009) The coalescent. In The Phylogenetics Handbook 2nd Edition (eds. Salemi, M., Vandamme A.M, and Lemey, P). Cambridge University Press.

[10]        Rodrigo, A. G., Ewing G., and Drummond, A. (2007). The evolutionary analysis of Measurably Evolving Populations using serially sampled gene sequences. In Mathematics of Evolution and Phylogenetics (eds. O. Gascuel and M. A. Steel). Oxford University Press.

[9]          Goode, M., and Rodrigo, A. G. (2004) Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences.  In Current Protocols in Bioinformatics (ed. A. Baxevanis). J. Wiley.

[8]          A.J. Drummond, G.K. Nicholls, A.G. Rodrigo, W. Solomon. (2003). ‘Genealogies from time-stamped sequence data’ pages 151-174 of Tools for Constructing Chronologies (Eds. C. Buck and A. Millard) Springer Lecture Notes in Statistics, v171.

[7]          Ross, H. A. and Rodrigo, A. G. (2004) An assessment of matrix representation with compatibility in supertree construction. In “Phylogenetic supertrees” (ed. Olaf Bininda-Emonds). Kluwer Academic Press.

[6]          Anderson, J. P., Rain, M., Shriner, D., Rodrigo, A. G., Wang, Y., Nickle, D., Learn, G. H., Naugler, W. E., and Mullins, J. I. (2001). The Genetics of HIV-1. In The Human Immunodeficiency Virus: Biology, Immunology and Therapy (ed. E. A. Emini). Princeton University Press

[5]          Poss, M, R. Biek and A. Rodrigo. (2001). Virus Evolution and Population Dynamics. In: Conservation Medicine: Ecological Health in Practice, Oxford University Press, Oxford, UK.

[4]          Beerli, P., Grassly, N. C., Kuhner, M. K., Nickle, D., Pybus, O., Rain, M., Rambaut, A., Rodrigo, A. G., and Wang, Y. (2000). Population genetics of HIV:  parameter estimation using genealogy-based methods. In Computational and Evolutionary Analysis of HIV Molecular Sequences (eds. A. G. Rodrigo and G. H. Learn).  Kluwer Academic Publishers, Boston, USA.

[3]          Rodrigo, A. G., Hanley, E. J., Goracke, P. C., and Learn, G. H. (2000).  Sampling and processing HIV molecular sequences: a computational evolutionary biologist’s perspective.  In Computational and Evolutionary Analysis of HIV Molecular Sequences (eds. A. G. Rodrigo and G. H. Learn).  Kluwer Academic Publishers, Boston, USA.

[2]          Rodrigo, A. G. and Felsenstein, J. (1999).  Coalescent Approaches to HIV-1 Population Genetics. In The Evolution of HIV (ed. Crandall, K.A.).  Johns Hopkins University Press.

[1]          Delwart, E. L., Herring, B., Rodrigo, A. G., and Mullins, J. I. (1995). Genetic subtyping of Human Immunodeficiency Virus using a Heteroduplex Mobility Assay. In PCR Primer, A Laboratory Manual (eds. Dieffenbach, C. W. and Dveksler, G. S.). Cold Spring Harbor Laboratory Press, NY.

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