Allen Rodrigo

Allen Rodrigo
Director
 +61 2 6125 2204 (Office)

Profile

Biography

I did my doctoral research at the University of Canterbury, New Zealand, and postdoctoral work at the University of Auckland, Stanford University and the University of Washington, before returning to the University of Auckland in 1999. In 2002, I was appointed Professor of Bioinformatics and Computational Biology at the University of Auckland, and the founding Director of the Bioinformatics Institute.  I remained at Auckland until Jan 2010, after which I moved to Duke University to take up the Directorship of the US National Evolutionary Synthesis Center.  I joined the ANU as Director of the Research School of Biology in July 2015.

Research

Research interests

I am a computational evolutionary biologist with interests in phylogenetic reconstruction, statistical bioinformatics and evolutionary modelling.  In the past, I worked on the evolution of rapidly evolving viruses including HIV, FIV, and Hepatitis B Virus. We developed population genetic methods to study phylogenies where samples are taken at different times, and where there is an appreciable accumulation of substitutions over the sampling intervals. 

I continue to work on virus evolution and phylogenetic reconstruction, but recently the major focus in our lab has shifted to two new areas: modelling the evolution of microbiomes, and using phylogenetics to study the dynamics of cancerous tumours.  Our interest in microbiomes stems from the fact that there is little formal or quantitative theoretical work done on modelling how microbiome diversity is generated within and between hosts, and over time.  To fill this gap, we have started developing agent-based computational models that incorporate the simplest processes -- so-called "neutral" models of microbiome evolution. The resulting measures of within-host, between-host, and population-level diversities that are recovered from these models tell us what we can expect when stochastic forces and sampling effects alone operate on microbes and their hosts.

Tumours are populations of cells that (typically) have a higher rate of genomic mutation than background. Some cancerous tumours spread, others do not. Those that do may lead to cancerous growths in other organs, and this is a bad outcome.  Since the cells in a tumour typically grow out of one progenitor cell, it is possible to trace the phylogeny of a sample of tumour cells, if enough genetic sequences are obtained. Phylogenetic trees, in turn, bear the imprint of the dynamics of the population from which individuals have been sampled: trees of individuals from rapidly growing populations look quite different to trees of individuals from slow growing populations.  Our goal is to determine whether we can use phylogenies to distinguish "bad" tumours from the rest.  To do this, we first have to develop reasonably sophisticated models of tumour development, and then validate these models against samples obtained from the lab. We are working with collaborators who are collecting the experimental data.

Publications

1. Abbott WGH, Tsai P, Leung E, Trevarton A, Ofanoa M, Hornell J, et al. Associations between HLA Class I Alleles and Escape Mutations in the Hepatitis B Virus Core Gene in New Zealand-Resident Tongans. Journal of Virology. 2010;84(1):621-9. doi: 10.1128/JVI.01471-09. PubMed PMID: WOS:000272564300058.

2. Anderson J, Learn G, Rodrigo A, He X, Wang Y, Weinstock H, et al. Predicting demographic group structures based on DNA sequence data. Molecular Biology and Evolution. 2003;20(7):1168-80. doi: 10.1093/molbev/msg128. PubMed PMID: WOS:000183848700017.

3. Anderson J, Rodrigo A, Learn G, Madan A, Delahunty C, Coon M, et al. Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E. Journal of Virology. 2000;74(22):10752-65. doi: 10.1128/JVI.74.22.10752-10765.2000. PubMed PMID: WOS:000090083800051.

4. Anderson J, Rodrigo A, Learn G, Wang Y, Weinstock H, Kalish M, et al. 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. 2001;53(1):55-62. PubMed PMID: WOS:000169544200007.

5. Ardern S, Lambert D, Rodrigo A, McLean I. The effects of population bottlenecks on multilocus DNA variation in robins. Journal of Heredity. 1997;88(3):179-86. PubMed PMID: WOS:A1997XC31900003.

6. Bachmann M, MathiasonDubard C, Learn G, Rodrigo A, Sodora D, Mazzetti P, et al. Genetic diversity of feline immunodeficiency virus: Dual infection, recombination, and distinct evolutionary rates among envelope sequence clades. Journal of Virology. 1997;71(6):4241-53. PubMed PMID: WOS:A1997WZ57100008.

7. Bickel P, Cosman P, Olshen R, Spector P, Rodrigo A, Mullins J. Covariability of V3 loop amino acids. Aids Research and Human Retroviruses. 1996;12(15):1401-11. doi: 10.1089/aid.1996.12.1401. PubMed PMID: WOS:A1996VM09500003.

8. Biek R, Rodrigo A, Holley D, Drummond A, Anderson C, Ross H, et al. Epidemiology, genetic diversity, and evolution of endemic feline immunodeficiency virus in a population of wild cougars. Journal of Virology. 2003;77(17):9578-89. doi: 10.1128/JVI.77.17.9578-9589.2003. PubMed PMID: WOS:000184776800045.

9. Bordewich M, Rodrigo AG, Semple C. Selecting Taxa to Save or Sequence: Desirable Criteria and a Greedy Solution. Systematic Biology. 2008;57(6):825-34. doi: 10.1080/10635150802552831. PubMed PMID: WOS:000261667300001.

10. Cheng Y, Guindon S, Hu P, Rodrigo A, Lim SG. VIRAL QUASISPECIES EVOLUTION PATTERN IN CHRONIC HEPATITIS B PATIENTS WITH LAMIVUDINE TREATMENT. Hepatology. 2009;50(4):976A. PubMed PMID: WOS:000270456001456.

11. Cheng Y, Guindon S, Rodrigo A, Lim SG. Increased viral quasispecies evolution in HBeAg seroconverter patients treated with oral nucleoside therapy. Journal of Hepatology. 2013;58(2):217-24. PubMed PMID: WOS:000315069900005.

12. Cheng Y, Guindon S, Rodrigo A, Wee LY, Inoue M, Thompson AJV, et al. Cumulative viral evolutionary changes in chronic hepatitis B virus infection precedes hepatitis B e antigen seroconversion. Gut. 2013;62(9):1347-55. doi: 10.1136/gutjnl-2012-302408. PubMed PMID: WOS:000323164200020.

13. Delaney NF, Balenger S, Bonneaud C, Marx CJ, Hill GE, Ferguson-Noel N, et al. Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum. Plos Genetics. 2012;8(2). doi: 10.1371/journal.pgen.1002511. PubMed PMID: WOS:000300725500030.

14. DELWART E, HERRING B, RODRIGO A, MULLINS J. GENETIC SUBTYPING OF HUMAN-IMMUNODEFICIENCY-VIRUS USING A HETERODUPLEX MOBILITY ASSAY. Pcr-Methods and Applications. 1995;4(5):S202-S16. PubMed PMID: WOS:A1995RM62900016.

15. Dodd S, Crowhurst R, Rodrigo A, Samuels G, Hill R, Stewart A. Examination of Trichoderma phylogenies derived from ribosomal DNA sequence data. Mycological Research. 2000;104:23-34. doi: 10.1017/S0953756299001100. PubMed PMID: WOS:000085404000005.

16. Doria-Rose N, Learn G, Rodrigo A, Nickle D, Li F, Mahalanabis M, et al. 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. 2005;79(17):11214-24. doi: 10.1128/JVI.79.17.11214-11224.2005. PubMed PMID: WOS:000231303900037.

17. Drummond A, Nicholls G, Rodrigo A, Solomon W. Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. Genetics. 2002;161(3):1307-20. PubMed PMID: WOS:000177192500032.

18. Drummond A, Pybus O, Rambaut A, Forsberg R, Rodrigo A. Measurably evolving populations. Trends in Ecology & Evolution. 2003;18(9):481-8. doi: 10.1016/S0169-5347(03)00216-7. PubMed PMID: WOS:000185311800014.

19. Drummond A, Forsberg R, Rodrigo A. The inference of stepwise changes in substitution rates using serial sequence samples. Molecular Biology and Evolution. 2001;18(7):1365-71. PubMed PMID: WOS:000169846400019.

20. Drummond A, Nicholls G, Rodrigo A, Solomon W, Buck C, Millard A. Genealogies from time-stamped sequence data. Tools For Constructing Chronologies: Crossing Disciplinary Boundaries. 2003;177:149-71. PubMed PMID: CCC:000223049300007.

21. Drummond A, Rodrigo A. Reconstructing genealogies of serial samples under the assumption of a molecular clock using serial-sample UPGMA. Molecular Biology and Evolution. 2000;17(12):1807-15. PubMed PMID: WOS:000166051900005.

22. Ewing G, Rodrigo A. Estimating Population Parameters using the Structured Serial Coalescent with Bayesian MCMC Inference when some Demes are Hidden. Evolutionary Bioinformatics. 2006;2:227-35. PubMed PMID: WOS:000205733800019.

23. 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. 2004;168(4):2407-20. doi: 10.1534/genetics.104.030411. PubMed PMID: WOS:000226483300055.

24. Ewing G, Rodrigo A. Coalescent-based estimation of population parameters when the number of demes changes over time. Molecular Biology and Evolution. 2006;23(5):988-96. doi: 10.1093/molbev/msj111. PubMed PMID: WOS:000237320800019.

25. Goldman N, Anderson J, Rodrigo A. Likelihood-based tests of topologies in phylogenetics. Systematic Biology. 2000;49(4):652-70. PubMed PMID: WOS:000165797000003.

26. Goode MG, Rodrigo AG. SQUINT: a multiple alignment program and editor. Bioinformatics. 2007;23(12):1553-5. doi: 10.1093/bioinformatics/btm128. PubMed PMID: WOS:000248271700016.

27. Goode M, Guindon S, Rodrigo A, Arthur J, Ng S. Modelling the evolution of protein coding sequences sampled from Measurably Evolving Populations. Genome Informatics 2008, Vol 21. 2008;21:150-64. PubMed PMID: WOS:000263559100013.

28. Goode M, Rodrigo AG. Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences. Current protocols in bioinformatics / editoral board, Andreas D Baxevanis [et al]. 2004;Chapter 6:Unit 6.8. doi: 10.1002/0471250953.bi0608s05. PubMed PMID: MEDLINE:18428729.

29. 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. 2006;23(5):919-26. doi: 10.1093/molbev/msj095. PubMed PMID: WOS:000237320800011.

30. Guindon S, Rodrigo A, Dyer K, Huelsenbeck J. Modeling the site-specific variation of selection patterns along lineages. Proceedings of the National Academy of Sciences of the United States of America. 2004;101(35):12957-62. doi: 10.1073/pnas.0402177101. PubMed PMID: WOS:000223694700034.

31. Hayward JJ, Rodrigo AG. Recombination in feline immunodeficiency virus from feral and companion domestic cats. Virology Journal. 2008;5. doi: 10.1186/1743-422X-5-76. PubMed PMID: WOS:000258511700001.

32. Hayward JJ, Rodrigo AG. Molecular epidemiology of feline immunodeficiency virus in the domestic cat (Felis catus). Veterinary Immunology and Immunopathology. 2010;134(1-2):68-74. doi: 10.1016/j.vetimm.2009.10.011. PubMed PMID: WOS:000275625700010.

33. Hayward JJ, Rodrigo AG. The distribution of feline immunodeficiency virus in tissue compartments of feral domestic cats. Archives of Virology. 2010;155(3):411-6. doi: 10.1007/s00705-010-0598-z. PubMed PMID: WOS:000274939600016.

34. Hayward JJ, Taylor J, Rodrigo AG. Phylogenetic analysis of feline immunodeficiency virus in feral and companion domestic cats of New Zealand. Journal of Virology. 2007;81(6):2999-3004. doi: 10.1128/JVI.02090-06. PubMed PMID: WOS:000244850800044.

35. Ho C, Wu S, Amos JD, Colvin L, Smith SD, Wilks AB, et al. Transient Compartmentalization of Simian Immunodeficiency Virus Variants in the Breast Milk of African Green Monkeys. Journal of Virology. 2013;87(20):11292-9. doi: 10.1128/JVI.01643-13. PubMed PMID: WOS:000325275800033.

36. Ho SYW, Lanfear R, Bromham L, Phillips MJ, Soubrier J, Rodrigo AG, et al. Time-dependent rates of molecular evolution. Molecular Ecology. 2011;20(15):3087-101. doi: 10.1111/j.1365-294X.2011.05178.x. PubMed PMID: WOS:000292963100003.

37. IVERSEN A, SHPAER E, RODRIGO A, HIRSCH M, WALKER B, SHEPPARD H, et al. PERSISTENCE OF ATTENUATED REV GENES IN A HUMAN-IMMUNODEFICIENCY-VIRUS TYPE 1-INFECTED ASYMPTOMATIC INDIVIDUAL. Journal of Virology. 1995;69(9):5743-53. PubMed PMID: WOS:A1995RN98600064.

38. Kliks S, Contag C, Corliss H, Learn G, Rodrigo A, Wara D, et al. Genetic analysis of viral variants selected in transmission of human immunodeficiency viruses to newborns. Aids Research and Human Retroviruses. 2000;16(13):1223-33. doi: 10.1089/08892220050116998. PubMed PMID: WOS:000088921400004.

39. 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. Molecular Ecology Resources. 2009;9(3):691-8. doi: 10.1111/j.1755-0998.2009.02537.x. PubMed PMID: WOS:000265897200002.

40. Li WLS, Rodrigo AG. Covariation of Branch Lengths in Phylogenies of Functionally Related Genes. Plos One. 2009;4(12). doi: 10.1371/journal.pone.0008487. PubMed PMID: WOS:000273105200019.

41. Lim SG, Cheng Y, Guindon S, Seet BL, Lee LY, Hu P, et al. Viral quasispecies evolution in chronic hepatitis B: new light on an old story. Journal of Clinical Virology. 2006;36:S18. doi: 10.1016/S1386-6532(06)80064-8. PubMed PMID: WOS:000239067300055.

42. Lim SG, Cheng Y, Guindon S, Seet BL, Lee LY, Hu P, et al. Viral quasi-species evolution during hepatitis be antigen Seroconversion. Gastroenterology. 2007;133(3):951-8. doi: 10.1053/j.gastro.2007.06.011. PubMed PMID: WOS:000249326900028.

43. Lim SG, Cheng Y, Guindon S, Seet BL, Lee LY, Hu P, et al. Viral quasispecies evolution in chronic hepatitis B: New light on an old story. Hepatology. 2006;44(4):539A-40A. PubMed PMID: WOS:000241362302041.

44. Liu S, Mittler J, Nickle D, Mulvania T, Shriner D, Rodrigo A, et al. Selection for human immunodeficiency virus type 1 recombinants in a patient with rapid progression to AIDS. Journal of Virology. 2002;76(21):10674-84. doi: 10.1128/JVI.76.21.10674-10684.2002. PubMed PMID: WOS:000178512300010.

45. Liu S, Rodrigo A, Shankarappa R, Learn G. HIV quasispecies and resampling. Science. 1996;273(5274):415-6. doi: 10.1126/science.273.5274.415. PubMed PMID: WOS:A1996UY98300005.

46. Marks EJ, Rodrigo AG, Brunton DH. Ecstatic display calls of the Adelie penguin honestly predict male condition and breeding success. Behaviour. 2010;147(2):165-84. doi: 10.1163/000579509X12512863752751. PubMed PMID: WOS:000275079400002.

47. Marks EJ, Rodrigo AG, Brunton DH. Using logistic regression models to predict breeding success in male Ad,lie penguins (Pygoscelis adeliae). Polar Biology. 2010;33(8):1083-94. doi: 10.1007/s00300-010-0793-0. PubMed PMID: WOS:000280074800009.

48. MCARDLE B, RODRIGO A. ESTIMATING THE ANCESTRAL STATES OF A CONTINUOUS-VALUED CHARACTER USING SQUARED-CHANGE PARSIMONY - AN ANALYTICAL SOLUTION. Systematic Biology. 1994;43(4):573-8. doi: 10.2307/2413555. PubMed PMID: WOS:A1994QE10000010.

49. Mckenney EA, Rodrigo A, Yoder AD. Species-specific assembly of the gut microbiota in lemurs. Integrative and Comparative Biology. 2014;54:E137. PubMed PMID: WOS:000333049501080.

50. Mckenney E, Wu S, Yoder AD, Rodrigo A. MMAP: A Pipeline for Metagenomic Analysis of Complex Microbial Populations. Integrative and Comparative Biology. 2013;53:E331. PubMed PMID: WOS:000316991402381.

51. McKenney EA, Rodrigo A, Yoder AD. Patterns of Gut Bacterial Colonization in Three Primate Species. Plos One. 2015;10(5). doi: 10.1371/journal.pone.0124618. PubMed PMID: WOS:000354544200045.

52. Meintjes PL, Rodrigo AG. Evolution of relative synonymous codon usage in Human Immunodeficiency Virus type-1. Journal of bioinformatics and computational biology. 2005;3(1):157-68. doi: 10.1142/S0219720005000953. PubMed PMID: MEDLINE:15751118.

53. Melvin A, Rodrigo A, Mohan K, Lewis P, Manns-Arcuino L, Coombs R, et al. HIV-1 dynamics in children. Journal of Acquired Immune Deficiency Syndromes. 1999;20(5):468-73. PubMed PMID: WOS:000079892400009.

54. Mullins JI, Nickle DC, Heath L, Rodrigo AG, Learn GH. Immunogen sequence: the fourth tier of AIDS vaccine design. Expert review of vaccines. 2004;3(4 Suppl):S151-9. doi: 10.1586/14760584.3.4.S151. PubMed PMID: MEDLINE:15285713.

55. Nickle D, Jensen M, Gottlieb G, Shriner D, Learn G, Rodrigo A, et al. Consensus and ancestral state HIV vaccines. Science. 2003;299(5612):1515-7. PubMed PMID: WOS:000181367900015.

56. Olsen A, Cosman P, Rodrigo A, Bickel P, Olshen R. Vector quantization of amino acids: Analysis of the HIV V3 loop region. Journal of Statistical Planning and Inference. 2005;130(1-2):277-98. doi: 10.1016/j.jspi.2003.10.010. PubMed PMID: WOS:000226645200017.

57. Ping L-H, Jabara CB, Rodrigo AG, Hudelson SE, Piwowar-Manning E, Wang L, et al. HIV-1 Transmission during Early Antiretroviral Therapy: Evaluation of Two HIV-1 Transmission Events in the HPTN 052 Prevention Study. Plos One. 2013;8(9). doi: 10.1371/journal.pone.0071557. PubMed PMID: WOS:000325025200004.

58. Poss M, Idoine A, Ross HA, Terwee JA, VandeWoude S, Rodrigo A. Recombination in feline lentiviral genomes during experimental cross-species infection. Virology. 2007;359(1):146-51. doi: 10.1016/j.virol.2006.08.026. PubMed PMID: WOS:000244735700016.

59. Poss M, Ross HA, Painter SL, Holley DC, Terwee JA, VandeWoude S, et al. Feline lentivirus evolution in cross-species infection reveals extensive G-to-A mutation and selection on key residues in the viral polymerase (vol 80, pg 2728, 2006). Journal of Virology. 2006;80(17):8845. doi: 10.1128/JVI.01230-06. PubMed PMID: WOS:000239934500054.

60. 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. 2008;123(1-2):154-8. doi: 10.1016/j.vetimm.2008.01.022. PubMed PMID: WOS:000256208000021.

61. Poss M, Rodrigo A, Gosink J, Learn G, Panteleeff D, Martin H, et al. 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. 1998;72(10):8240-51. PubMed PMID: WOS:000075864100062.

62. RAINEY F, DONNISON A, JANSSEN P, SAUL D, RODRIGO A, BERGQUIST P, et al. DESCRIPTION OF CALDICELLULOSIRUPTOR-SACCHAROLYTICUS GEN-NOV, SP-NOV - AN OBLIGATELY ANAEROBIC, EXTREMELY THERMOPHILIC, CELLULOLYTIC BACTERIUM. Fems Microbiology Letters. 1994;120(3):263-6. doi: 10.1016/0378-1097(94)90481-2. PubMed PMID: WOS:A1994NX64000008.

63. ROBERTS M, RODRIGO A, MCARDLE B, CHARLESTON W. THE EFFECT OF HABITAT ON THE HELMINTH-PARASITES OF AN ISLAND POPULATION OF THE POLYNESIAN RAT (RATTUS-EXULANS). Journal of Zoology. 1992;227:109-25. PubMed PMID: WOS:A1992HV68600009.

64. RODRIGO A. SURFICIAL SEDIMENT-HEAVY METAL ASSOCIATIONS IN THE AVON-HEATHCOTE ESTUARY, NEW-ZEALAND. New Zealand Journal of Marine and Freshwater Research. 1989;23(2):255-62. PubMed PMID: WOS:A1989AL60400012.

65. RODRIGO A. SPECIFIC AND GENERAL FORMULAS FOR THE NUMBER OF BAND COMBINATIONS FOR DIFFERENT COLOR-BANDING REGIMES. New Zealand Journal of Zoology. 1990;17(2):285-8. PubMed PMID: WOS:A1990EB24700013.

66. RODRIGO A. 2 OPTIMALITY CRITERIA FOR SELECTING SUBSETS OF MOST PARSIMONIOUS TREES. Systematic Biology. 1992;41(1):33-40. doi: 10.2307/2992504. PubMed PMID: WOS:A1992JL28900004.

67. RODRIGO A. A MODIFICATION TO WHEELER COMBINATORIAL WEIGHTS CALCULATIONS. Cladistics-the International Journal of the Willi Hennig Society. 1992;8(2):165-70. doi: 10.1111/j.1096-0031.1992.tb00062.x. PubMed PMID: WOS:A1992JM48000007.

68. RODRIGO A. A COMMENT ON BAUM METHOD FOR COMBINING PHYLOGENETIC TREES. Taxon. 1993;42(3):631-6. doi: 10.2307/1222540. PubMed PMID: WOS:A1993LU73300010.

69. RODRIGO A. CALIBRATING THE BOOTSTRAP TEST OF MONOPHYLY. International Journal For Parasitology. 1993;23(4):507-14. doi: 10.1016/0020-7519(93)90040-6. PubMed PMID: WOS:A1993LT66500011.

70. Rodrigo A. On combining cladograms. Taxon. 1996;45(2):267-74. doi: 10.2307/1224667. PubMed PMID: WOS:A1996UN42800008.

71. Rodrigo A. Dynamics of syncytium-inducing and non-syncytium-inducing type 1 human immunodeficiency viruses during primary infection. Aids Research and Human Retroviruses. 1997;13(17):1447-51. doi: 10.1089/aid.1997.13.1447. PubMed PMID: WOS:A1997YH23600001.

72. Rodrigo A. Combinability of phylogenies and bootstrap confidence envelopes. Systematic Biology. 1998;47(4):727-33. doi: 10.1080/106351598260716. PubMed PMID: WOS:000077592700015.

73. Rodrigo A. HIV evolutionary genetics. Proceedings of the National Academy of Sciences of the United States of America. 1999;96(19):10559-61. doi: 10.1073/pnas.96.19.10559. PubMed PMID: WOS:000082574100006.

74. RODRIGO A, BERGQUIST P, BERGQUIST P. INADEQUATE SUPPORT FOR AN EVOLUTIONARY LINK BETWEEN THE METAZOA AND THE FUNGI. Systematic Biology. 1994;43(4):578-84. doi: 10.2307/2413556. PubMed PMID: WOS:A1994QE10000011.

75. RODRIGO A, BERGQUIST P, BERGQUIST P, REEVES R, VanSoest R, VanKempen T, et al. ARE SPONGES ANIMALS - AN INVESTIGATION INTO THE VAGARIES OF PHYLOGENETIC INFERENCE. Sponges in Time and Space. 1994:47-54. PubMed PMID: WOS:A1994BA35E00007.

76. RODRIGO A, BORGES K, BERGQUIST P. PULSED-FIELD GEL-ELECTROPHORESIS OF GENOMIC DIGESTS OF THERMUS STRAINS AND ITS IMPLICATIONS FOR TAXONOMIC AND EVOLUTIONARY STUDIES. International Journal of Systematic Bacteriology. 1994;44(3):547-52. PubMed PMID: WOS:A1994NW04300023.

77. Rodrigo A, Felsenstein J, Crandall K. Coalescent approaches to HIV population genetics. Evolution of Hiv. 1999:233-72. PubMed PMID: CCC:000081571300008.

78. Rodrigo A, Goode M, Forsberg R, Ross H, Drummond A. Inferring evolutionary rates using serially sampled sequences from several populations. Molecular Biology and Evolution. 2003;20(12):2010-8. doi: 10.1093/molbev/msg215. PubMed PMID: WOS:000187969400007.

79. Rodrigo A, Goracke P, Rowhanian K, Mullins J. Quantitation of target molecules from polymerase chain reaction-based limiting dilution assays. Aids Research and Human Retroviruses. 1997;13(9):737-42. doi: 10.1089/aid.1997.13.737. PubMed PMID: WOS:A1997XC32400002.

80. RODRIGO A, KELLYBORGES M, BERGQUIST P, BERGQUIST P. A RANDOMIZATION TEST OF THE NULL HYPOTHESIS THAT 2 CLADOGRAMS ARE SAMPLE ESTIMATES OF A PARAMETRIC PHYLOGENETIC TREE. New Zealand Journal of Botany. 1993;31(3):257-68. PubMed PMID: WOS:A1993MJ35600008.

81. Rodrigo A, Mullins J. Human immunodeficiency virus type 1 molecular evolution and the measure of selection. Aids Research and Human Retroviruses. 1996;12(18):1681-5. doi: 10.1089/aid.1996.12.1681. PubMed PMID: WOS:A1996VY70800004.

82. Rodrigo A, Shpaer E, Delwart E, Iversen A, Gallo M, Brojatsch J, et al. Coalescent estimates of HIV-1 generation time in vivo. Proceedings of the National Academy of Sciences of the United States of America. 1999;96(5):2187-91. doi: 10.1073/pnas.96.5.2187. PubMed PMID: WOS:000078956600069.

83. 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. 2009;5:97-105. PubMed PMID: WOS:000271316700009.

84. Rodrigo A, Alberts S, Cranston K, Kingsolver J, Lapp H, McClain C, et al. Science Incubators: Synthesis Centers and Their Role in the Research Ecosystem. Plos Biology. 2013;11(1). doi: 10.1371/journal.pbio.1001468. PubMed PMID: WOS:000314648700008.

85. 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 of the Royal Society B-Biological Sciences. 2008;363(1512):3893-902. doi: 10.1098/rstb.2008.0173. PubMed PMID: WOS:000260886700002.

86. Ross H, Lento G, Dalebout M, Goode M, Ewing G, McLaren P, et al. DNA Surveillance: Web-based molecular identification of whales, dolphins, and porpoises. Journal of Heredity. 2003;94(2):111-4. doi: 10.1093/jhered/esg027. PubMed PMID: WOS:000182628400001.

87. Ross H, Rodrigo A. Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration. Journal of Virology. 2002;76(22):11715-20. doi: 10.1128/JVI.76.22.11715-11720.2002. PubMed PMID: WOS:000178822400055.

88. Ross HA, Nickle DC, Liu Y, Heath L, Jensen MA, Rodrigo AG, et al. Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes. Evolutionary Bioinformatics. 2006;2:53-76. PubMed PMID: WOS:000205733800006.

89. Rouzine I, Rodrigo A, Coffin J. Transition between stochastic evolution and deterministic evolution in the presence of selection: General theory and application to virology. Microbiology and Molecular Biology Reviews. 2001;65(1):151-+. doi: 10.1128/MMBR.65.1.151-185.2001. PubMed PMID: WOS:000167343200007.

90. SAUL D, RODRIGO A, REEVES R, WILLIAMS L, BORGES K, MORGAN H, et al. PHYLOGENY OF 20 THERMUS ISOLATES CONSTRUCTED FROM 16S RIBOSOMAL-RNA GENE SEQUENCE DATA. International Journal of Systematic Bacteriology. 1993;43(4):754-60. PubMed PMID: WOS:A1993MC21000016.

91. Schmitt S, Tsai P, Bell J, Fromont J, Ilan M, Lindquist N, et al. Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges. Isme Journal. 2012;6(3):564-76. doi: 10.1038/ismej.2011.116. PubMed PMID: WOS:000300883200009.

92. Shankarappa R, Gupta P, Learn G, Rodrigo A, Rinaldo C, Gorry M, et al. Evolution of human immunodeficiency virus type 1 envelope sequences in infected individuals with differing disease progression profiles. Virology. 1998;241(2):251-9. doi: 10.1006/viro.1997.8996. PubMed PMID: WOS:000072301800008.

93. Shankarappa R, Margolick J, Gange S, Rodrigo A, Upchurch D, Farzadegan H, et al. Consistent viral evolutionary changes associated with the progression of human immunodeficiency virus type 1 infection. Journal of Virology. 1999;73(12):10489-502. PubMed PMID: WOS:000083699300090.

94. Shriner D, Rodrigo A, Nickle D, Mullins J. Pervasive genomic recombination of HIV-1 in vivo. Genetics. 2004;167(4):1573-83. doi: 10.1534/genetics.103.023382. PubMed PMID: WOS:000223720300005.

95. Steel M, Rodrigo A. Maximum likelihood supertrees. Systematic Biology. 2008;57(2):243-50. doi: 10.1080/10635150802033014. PubMed PMID: WOS:000255690200005.

96. Thrimawithana AH, Ortiz-Catedral L, Rodrigo A, Hauber ME. Reduced total genetic diversity following translocations? A metapopulation approach. Conservation Genetics. 2013;14(5):1043-55. doi: 10.1007/s10592-013-0494-7. PubMed PMID: WOS:000325127100012.

97. Turner S, Saul D, Rodrigo A, Lewis G. A heteroduplex method for detection of targeted sub-populations of bacterial communities. Fems Microbiology Letters. 2002;208(1):9-13. doi: 10.1111/j.1574-6968.2002.tb11052.x. PubMed PMID: WOS:000174920500002.

98. Warner BG, Tsai P, Rodrigo AG, 'Ofanoa M, Gane EJ, Munn SR, et al. 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. 2011;92:1800-8. doi: 10.1099/vir.0.030478-0. PubMed PMID: WOS:000293488800008.

99. Warner BG, Abbott WGH, Rodrigo AG. Frequency-dependent selection drives HBeAg seroconversion in chronic hepatitis B virus infection. Evolution, medicine, and public health. 2014;2014(1):1-9. doi: 10.1093/emph/eot023. PubMed PMID: MEDLINE:24481244.

100. Welch D, Nicholls G, 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. 2005;68(1):65-75. doi: 10.1016/j.tpb.2005.03.003. PubMed PMID: WOS:000230981100008.

101. 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. 2009;5(9). doi: 10.1371/journal.pcbi.1000509. PubMed PMID: WOS:000270800100014.

102. Wu SH, Black MA, North RA, Rodrigo AG. A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels. Bmc Bioinformatics. 2012;13. doi: 10.1186/1471-2105-13-137. PubMed PMID: WOS:000311489900001.

103. 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. 2013;104(1):86-91. doi: 10.1093/jhered/ess074. PubMed PMID: WOS:000312885900009.

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