Summer Studentship Reports
2009 - 2010
Student: Amali Thrimawithana
Supervisors: Dr. Emma Marks and Louis Ranjard
Captive gentoo penguin vocal variation: A comparison within family groups and between the sexes
Student: Christoph Knapp
Supervisors: Assoc. Prof. Cristin Print
Developing modules for GenePattern
Student: Thomas Garden
Supervisors: Dr. Howard Ross & Dr. Craig Millar
DNA Barcoding the Birds of New Zealand – How reliable will be this identification system?
Bioinformatics of disease
Mehta S., Shelling A., Muthukaruppan A., Lasham A., Blenkiron C., Laking G. and Print C. (In press 2010). Predictive and Prognostic Molecular Markers for Cancer Medicine. Therapeutic Advances in Medical Oncology.
Jeffs A, Glover A, Slobbe L, He S, Woolley A, PRINT C, Baguley B, and Eccles M (2010). A gene expression signature of invasion in metastatic melanoma cells.PLoS ONE; 24(12).
Tamada Y, Imoto S, Araki H, Nagasaki M, PRINT C, Charnock-Jones D S and Miyano S. Estimating Genome-Wide Gene Networks Using Nonparametric Bayesian Network Models on Massively Parallel Computers. (In press 2010) IEEE/ACM Transactions on Computational Biology and Bioinformatics.
Ohlsson Teague E, PRINT C and Hull L. The role of microRNAs in endometriosis and associated conditions. (2010) Hum Reprod Update, 16(2):142-65
Cultural Evolution
Marks E. J., Rodrigo A. G. & Brunton D. H (In press). Ecstatic Display Calls of the Adélie penguin honestly predict male condition and breeding success. Behaviour.
Ranjard, L. and Ross, H. A., (2008), Unsupervised bird song syllable classification using evolving neural networks., The Journal of the Acoustical Society of America 123(6): 4358-4368
Ranjard, L. and Ross, H. A., (2007), A method for bird song segmentation and pairwise distance measure of syllables and songs., Proceedings of the Fourth International Conference on Bio-Acoustics, Loughborough, UK, 10-12 April 2007, 185-192
Phylogeography
Robins, J. H., M. Hingston, E. Matisoo-Smith, H. A. Ross (2007): Identifying Rattus species using mitochondrial DNA. Molecular Ecology Notes, 7 (5), 717-729.
Genomics
Ross, H. A. and Shearman H. (2008). Validation of mtDNA control-region sequences in GenBank for large baleen whales. International Whaling Commission. SC/60/SD6: 1-16
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? Philosophical Transactions of the Royal Society B 363: 3893-902
Robins, J. H., McLenachan, P. A., Phillips, M. J., Craig, L., Ross, H. A. and Matisoo-Smith, E. (2008). Dating of divergences within the Rattus genus phylogeny using whole mitochondrial genomes. Molecular Phylogenetics and Evolution 49: 460-466
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
Poss, M., Idoine, A., Ross, H. A., Terwee, J. A., VandeWoude, S. and Rodrigo, A. G., (2007), Recombination in feline lentiviral genomes during experimental cross-species infection., Virology 359:146-151.
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.
Rat Genome Sequencing Project Consortium, (2004), Genome sequence of the brown Norway rat yields insights into mammalian evolution., Nature 428, 493-521
Evolutionary Bioinformatics
Anderson, M. G., H. A. Ross, D. H. Brunton, and M. E. Hauber. (In press). Begging call matching between a specialist brood parasite and its host: A comparative approach to detect co-evolution. Biological Journal of the Linnean Society.
Gillman, L. N., D. J. Keeling, H. A. Ross, and S. D. Wright. (In press). Latitude, elevation and the tempo of molecular evolution in mammals. Proceedings of the Royal Society B-Biological Sciences.
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.
http://www.la-press.com/on-the-use-of-bootstrapped-topologies-in-coalescent-based-bayesian-mcm-a1574
Rodrigo, A. G. (2009) The coalescent. In The Phylogenetics Handbook 2nd Edition (eds. Salemi, M., Vandamme A.M, and Lemey, P). Cambridge University Press.
Thierer, T. and Bryant, D. and Steel, M., (2008), Counting ancestral reconstructions in a fixed phylogeny. Annals of Combinatorics. 12(1) 123--132.
Poss, M. and Ross, H. A. (2008). Evolution of the long terminal repeat and regulatory genes of feline immunodeficiency virus genomes from naturally infected cougars. Virology 370(1): 55-62
Poss, M., Ross, H., Rodrigo, A., Terwee, J., VandeWoude, S., and Biek, R. (2008). The molecular biology and evolution of feline immunodeficiency viruses of cougars. Veterinary Immunology and Immunopathology 123: 154-158
Heled, J. and Drummond, A. J. (2008). Bayesian inference of population size history from multiple loci. BMC Evolutionary Biology 8: 289
Drummond, A. J. and Suchard, M. A. (2008). Fully Bayesian tests of neutrality using genealogical summary statistics. BMC Genetics 9: 68
Bruen, T. and Bryant, D., (2008), A subdivision approach to maximum parsimony. Annals of Combinatorics 12: 45--51
Bruen, T. and Bryant, D., (2008), Parsimony via consensus. Systematic Biology 57:251--256
Atkinson, Q. D., Gray, R. D. and Drummond, A. J. (2008). mtDNA Variation predicts population size in humans and reveals a major southern Asian chapter in human prehistory. Molecular Biology and Evolution 25: 468-474
Atkinson, Q. D., Gray, R. D. and Drummond, A. J. (In Press). Bayesian coalescent inference of major human mitochondrial DNA haplogroup expansions in Africa. Proceedings of the Royal Society of London B
Steel, M. and Rodrigo, A., (2008), Maximum Likelihood Supertrees., Systematic Biology 57:243-250
Drummond, A. J. and Rambaut, A., (2007), BEAST: Bayesian evolutionary analysis by sampling trees., BMC Evolutionary Biology 7: 214-221
Shapiro, B., Ho, S. Y. W.,Phillips, M. J., Cooper, A. and Drummond, A. J., (2007), Evidence for Time Dependency of Molecular Rate Estimates., Systematic Biology 56:515-522.
Lemey, P., Kosakovsky Pond, S. L., Drummond, A. J., Pybus, O. G. and Shapiro, B., (2007), Synonymous Substitution Rates Predict HIV Disease Progression as a Result of Underlying Replication Dynamics., PLoS Comput Biol 3:e29.
Lim, S. G., Cheng, Y., Guindon, S., Seet, B. L., Lee, L. Y., Hu, P., Wasser, S., Tan, T., Goode, M. and Rodrigo, A. G., (2007), Viral quasispecies evolution in chronic hepatitis B: new light on an old story., Gastroenterology 33:951-958.
Pybus, O. G., Rambaut, A., Belshaw, R., Freckleton, R. P., Drummond, A. J. and Holmes, E. C., (2007), Phylogenetic Evidence for Deleterious Mutation Load in RNA Viruses and Its Contribution to Viral Evolution., Mol Biol Evol 24:845-852.
Rodrigo, A. G., Ewing, G. and Drummond, A. J., (2007), The evolutionary analysis of Measurably Evolving Populations using serially sampled gene sequences. Mathematics of Evolution and Phylogenetics (eds. O. Gascuel and M. A. Steel), Oxford University Press.
Ross, H. A. and Poss, M., (2007), Evolution of the long terminal repeat and regulatory genes of feline immunodeficiency virus genomes from naturally infected courgars., Virology Available online 29 September 2007.
Bruen, T., Philiipe, H. and Bryant, D., (2006), A quick and robust statistical test to detect the presence of recombination., Genetics 172:2665-2681.
Bryant, D., (2006), Radiation and network breaking in Polynesian Language Evolution. in Forster, P. and Renfrew, C. (eds)Phylogenetics and the Prehistory of Languages.
Drummond, A. J., Ho, S. Y. W., Phillips, M. J. and Rambaut, A., (2006), Relaxed phylogenetics and dating with confidence., PLoS Biol 4:e88.
Edwards, C. T. T., Holmes, E. C., Pybus, O. G., Wilson, D. J., Viscidi, R. P., Abrams, E. J., Phillips, R. E. and Drummond, A. J., (2006), Evolution of the HIV-1 envelope gene is dominated by purifying selection., Genetics 174:1441-1453.
Edwards, C. T. T., Holmes, E. C., Wilson, D. J., Viscidi, R. P., Abrams, E. J., Phillips, R. E. and Drummond, A. J., (2006), Population genetic estimation of the loss of genetic diversity during horizontal transmission of HIV-1., BMC Evol Biol 6:28.
Ewing, G. and Rodrigo, A. G., (2006), Estimating Population Parameters using the Structured Serial Coalescent with Bayesian MCMC Inference when some Demes are Hidden., Evolutionary Bioinformatics Online 2:239-247.
Ewing, G. and Rodrigo, A. G., (2006), Coalescent-based estimation of population parameters when the number of demes changes over time., Molecular Biology and Evolution 33:951-958.
Hon, C. C., Lam, T. Y., Drummond, A. J., Rambaut, A., Lee, Y. F., Yip, C. W., Zeng, F., Lam, P. Y., Ng, P. T. and Leung, F. C., (2006), Phylogenetic analysis reveals a correlation between the expansion of very virulent infectious bursal disease virus and reassortment of its genome segment B., Journal of Virology 80:8503-8509.
Huson, D. and Bryant, D., (2006), Application of Phylogenetic Networks in Evolutionary Studies., Molecular Biology and Evolution 23:254-267.
Lepage, T., Lawi, S., Tupper, P. and Bryant, D., (2006), Continuous and Tractable Models for the Variation of Evolutionary Rates., Mathematical Biosciences 199:216-233.
Shapiro, B., Rambaut, A. and Drummond, A. J., (2006), Choosing appropriate substitution models for the phylogenetic analysis of protein-coding sequences., Mol Biol Evol 23:7-9.
Pyrc, K., Dijkman, R., Deng, L., Jebbink, M. F., Ross, H. A., Berkhout, B. and Van Der Hoek, L., (2006), Mosaic structure of human coronavirus NL63, one thousand years of evolution., Journal of Molecular Biology 365:964-973.
Murugan, S. and Ross, H. A., (2006), Using phylogenetic analyses and reference datasets to validate the species identities of cetacean sequences in GenBank., Molecular Phylogenetics and Evolution 40:866-871.
Ross, H. A., D. C. Nickle, Y. Liu, L. Heath, M. A. Jensen, A. G. Rodrigo and J. I. Mullins, (2006), Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes., Evolutionary Bioinformatics Online 2:18-41.
Welch, D., Nicholls, G. K., Rodrigo, A. G. and 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.
Shapiro, A., Rambaut, A. and Drummond, A. J., (2005), Choosing Appropriate Substitution Models for the Phylogenetic Analysis of Protein-Coding Sequences., Mol Biol Evol. 2005 Sep 21
Ewing, G., Nicholls, G. K. and Rodrigo, A. G., (2004), Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations (MEPs)., Genetics 168:2407-2420.
Guindon, S., Rodrigo, A. G., Dyer, K. and 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
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
Ross, H. A. and Rodrigo, A. G., (2004), An assessment of matrix representation with compatibility in supertree construction. Pp. 35-63 in O. R. P. Bininda-Emonds, ed. Phylogenetic Supertrees: Combining Information to Reveal the Tree of Life., Kluwer Academic Publishers, Boston.
Rodrigo, A. G., M. Goode, R. Forsberg, H. A. Ross and A. J. Drummond, (2003), Inferring Evolutionary Rates Using Serially Sampled Sequences from Several Populations., Molecular Biology and Evolution 20:2010-2018.
Ross, H. A., 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
Drummond, A. J., O. G. Pybus, A. Rambaut, R. Forsberg and A. G. Rodrigo, (2003), Measurably evolving populations., Trends in Ecology and Evolution 18:481-488.
Drummond, A. J., G. K. Nicholls, A. G. Rodrigo and 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.
Guindon, S. and Gascuel, O., (2003), A Simple, Fast, and Accurate Algorithm to Estimate Large Phylogenies by Maximum Likelihood., Syst. Biol. 52(5), 696-704.
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. [Supplementary Materials]
Robins, J. H., E. Matisoo-Smith and H. A. Ross, (2003), The origins of the feral pigs on the Auckland Islands., Proceedings of the Royal Society of New Zealand 33: 561-569.
Baker, C. S., M. L. Dalebout, S. Lavery and H. A. Ross, (2003), www.DNA-surveillance: Applied molecular taxonomy for species conservation and discovery., Trends in Ecology and Evolution 18: 271-272.
Baker, C. S., H. A. Ross and S. Lavery, (2002), Molecular taxonomy for conservation., Species 38: 12-13.
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
Drummond, A. J., 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
Guindon, S. and O. Gascuel, (2002), Efficient biased estimation of evolutionary distances when substitution rates vary across sites., Molecular Biology and Evolution, 19(4): 534-543, 2002.
Guindon, S. and G. Perriere, (2001), Intragenomic Base Content Variation Is a Potential Source of Biases When Searching for Horizontally Transferred Genes., Molecular Biology and Evolution, September 1, 2001; 18(9): 1838 - 1840.
Genetic Epidemiology
Wright, S. D., L. N. Gillman, H. A. Ross, and D. J. Keeling. (In press). Slower tempo of microevolution in island birds: implications for conservation biology. Evolution.
Langhoff, P., Authier, A., Buckley, T. R., Dugdale, J. S., Rodrigo, A., and Newcomb, R.D. (In press). DNA barcoding of the endemic New Zealand leafroller moth genera, Ctenopseustis and Planotortrix. Molecular Ecology Notes.
http://www3.interscience.wiley.com/cgi-bin/fulltext/122217573/PDFSTART
Hayward, J. H. and Rodrigo, A. G. (In press). Molecular epidemiology of feline immunodeficiency virus in the domestic cat (Felis catus). Veterinary Immunology and Immunopathology
Lemey P., Pond S. L. K., Drummond A. J., et al. (2008). Synonymous substitution rates predict HIV disease progression as a result of underlying replication dynamics. Infection Genetics and Evolution 8: S15-S16
Hon, C. C., Lam, T. Y., Shi, Z. L., Drummond, A. J., Yip, C. W., Zeng, F., Lam, P. Y. and Leung, F. C. (2008). Evidence of the recombinant origin of a bat SARS-like coronavirus and its implications on the direct ancestor of SARS coronavirus. Journal of Virology 82: 1819-1826
Hayward, J. J. and Rodrigo, A. G. (2008). Recombination in feline immunodeficiency virus from feral and companion domestic cats. Virology Journal 5: 76
Poss, M., Ross, H., Rodrigo, A., Terwee, J., VandeWoude, S., and Biek, R., (2008), The molecular biology and evolution of feline immunodeficiency viruses of cougars., Veterinary Immunology and Immunopathology 123: 154-158.
Hayward, J. J., Taylor, J. and Rodrigo, A. G., (2007), Phylogenetic Analysis of Feline Immunodeficiency Virus in Feral and Companion Domestic Cats of New Zealand, Journal of Virology 81:2999-3004
Poss, M., H. A. Ross, S. L. Painter, D. C. Holley, J. A. Terwee, S. VandeWoude and A. G. Rodrigo, (2006), 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 80:2728-2737.
Poss, M., Ross, H. A., Painter, S. L., Holley, D. C., Terwee, J. A., VandeWoude, S. and Rodrigo, A. G., (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.
Biek, R., A. G. Rodrigo, D. C. Holley, A. J. Drummond, C. R. Anderson, Jr., H. A. Ross and M. Poss, (2003), Epidemiology, Genetic Diversity, and Evolution of Endemic Feline Immunodeficiency Virus in a Population of Wild Cougars., Journal of Virology 77:9578-9589. [Supplementary Materials]
Anderson, J. P., G. H. Learn, A. G. Rodrigo, X. He, Y. Wang, H. Weinstock, M. L. Kalish, K. E. Robbins, L. Hood and J. I. Mullins, (2003), Predicting demographic group structures based on DNA sequence data., Molecular Biology and Evolution 20:1168-1180.
Applied Bioinformatics
Wu, S.H., Black, M.A., North, R. A., Atkinson, K.,R. and Rodrigo, A. G. (In press). A statistical model to identify differentially expressed proteins in 2D PAGE gels. PLoS Comp. Biol.
Ross, H. A., Murugan, S. and Li, W. L. S., (2008), Testing the Reliability of Genetic Methods of Species Identification via Simulation., Systematic Biology 57:216-230
Goode, M. and Rodrigo, A. G., (2007), SQUINT: A multiple alignment program and editor., Bioinformatics 23:1553-1555.
Biek, R., Drummond, A. J. and Poss, M., (2006), A virus reveals population structure and recent demographic history of its carnivore host., Science 311:538-541.
Bryant, D. and Lagergren, J., (2006), Compatibility of unrooted trees is FPT., Theoretical Computer Science 351:296-302.
Guindon, S., Black, A. and Rodrigo, A. G., (2006), Control of the false discover rate applied to the detection of positively detected sites., Molecular Biology and Evolution 23:919-926.
Guindon, S., Lethiec, F., Duroux, P. and Gascuel, O., (2005), PHYML Online--a web server for fast maximum likelihood-based phylogenetic inference., Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W557-9.
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.
Doria-Rose, N. A., Learn, G. H., Rodrigo, A. G., Nickle, D. C., Li, F., Mahalanabis, M., Hensel, M. T., McLaughlin, S., Edmonson, P. F., Montefiori, D., Barnett, S. W., Haigwood, N. L. and Mullins, J. I., (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.
Mullins, J. I., D. C. Nickle, L. Heath, A. G. Rodrigo and G. H. Learn, (2004), Immunogen sequence: the fourth tier of AIDS vaccine design., Expert Review of Vaccines. Suppl 1:159-162
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.
Nickle, D. C., M. A. Jensen, G. S. Gottlieb, D. Shriner, G. H. Learn, A. G. Rodrigo and J. I. Mullins, (2003), Consensus and ancestral state HIV vaccines., Science 299:1515-1517