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List of works by Allen Gerard Rodrigo

A Bayesian model for classifying all differentially expressed proteins simultaneously in 2D PAGE gels.

scientific article

A Comment on Baum's Method for Combining Phylogenetic Trees

scientific article (publication date: August 1993)

A MODIFICATION TO WHEELER'S COMBINATORIAL WEIGHTS CALCULATIONS

scientific article published in 1992

A heteroduplex method for detection of targeted sub-populations of bacterial communities

scientific article published on 01 February 2002

A randomisation test of the null hypothesis that two cladograms are sample estimates of a parametric phylogenetic tree ⬇️

article

A statistical model to identify differentially expressed proteins in 2D PAGE gels

scientific article

An assembly-free method of phylogeny reconstruction using short-read sequences from pooled samples without barcodes

scientific article published on 13 September 2021

An information-rich character weighting procedure for parsimony analysis

scholarly article

Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges ⬇️

scientific article

Associations between HLA class I alleles and escape mutations in the hepatitis B virus core gene in New Zealand-resident Tongans

scientific article published on January 2010

Bamboo Specialists from Two Mammalian Orders (Primates, Carnivora) Share a High Number of Low-Abundance Gut Microbes

scientific article published on 29 November 2017

Calibrating the bootstrap test of monophyly

scientific article published in July 1993

Can Stomach Content and Microbiomes of Tuna Provide Near Real-Time Detection of Ecosystem Composition in the Pacific Ocean?

scientific article published on 06 May 2022

Coalescent Entanglement and the Conditional Dependence of the Times to Common Ancestry of Mutually Exclusive Pairs of Individuals

scientific article published on 16 October 2012

Coalescent estimates of HIV-1 generation time in vivo

scientific article (publication date: 2 March 1999)

Combinability of Phylogenies and Bootstrap Confidence Envelopes

scientific article published on 01 December 1998

Computational Evaluation of the Strict Master and Random Template Models of Endogenous Retrovirus Evolution

scientific article

Consensus and Ancestral State HIV Vaccines

scientific article published in Science

Control of the False Discovery Rate Applied to the Detection of Positively Selected Amino Acid Sites

article

Correction to: Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage

scientific article published on 22 January 2020

Correction: Ultrafast Evolution and Loss of CRISPRs Following a Host Shift in a Novel Wildlife Pathogen, Mycoplasma gallisepticum.

scientific article

Covariability of V3 loop amino acids.

scientific article published in October 1996

Covariation of branch lengths in phylogenies of functionally related genes

scientific article (publication date: 29 December 2009)

Cumulative viral evolutionary changes in chronic hepatitis B virus infection precedes hepatitis B e antigen seroconversion

scientific article published on 15 December 2012

DNA barcoding of the endemic New Zealand leafroller moth genera, Ctenopseustis and Planotortrix

scientific article published on 25 February 2009

DNA surveillance: web-based molecular identification of whales, dolphins, and porpoises.

scientific article

Dynamics of Syncytium-Inducing and Non-Syncytium-Inducing Type 1 Human Immunodeficiency Viruses during Primary Infection ⬇️

scientific article published on November 20, 1997

Ecstatic display calls of the Adélie penguin honestly predict male condition and breeding success

scholarly article

Editorial foreword

scientific article published on 01 January 2004

Effective machine-learning assembly for next-generation amplicon sequencing with very low coverage

scientific article published on 11 December 2019

Epidemiology, genetic diversity, and evolution of endemic feline immunodeficiency virus in a population of wild cougars

scientific article

Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data

scientific article (publication date: July 2002)

Estimating population parameters using the structured serial coalescent with Bayesian MCMC inference when some demes are hidden.

scientific article published on January 2006

Estimating the Ancestral States of a Continuous-Valued Character Using Squared-Change Parsimony: An Analytical Solution

article

Estimation of evolutionary parameters using short, random and partial sequences from mixed samples of anonymous individuals.

scientific article published on 4 November 2015

Evidence for reduced selection pressure on the hepatitis B virus core gene in hepatitis B e antigen-negative chronic hepatitis B.

scientific article published on 20 April 2011

Evolution of human immunodeficiency virus type 1 envelope sequences in infected individuals with differing disease progression profiles.

scientific article published in February 1998

Evolution of relative synonymous codon usage in Human Immunodeficiency Virus type-1.

scientific article published in February 2005

Examination of Trichoderma phylogenies derived from ribosomal DNA sequence data

article

Feeding strategy shapes gut metagenomic enrichment and functional specialization in captive lemurs

scientific article published on 28 November 2017

Feline Lentivirus Evolution in Cross-Species Infection Reveals Extensive G-to-A Mutation and Selection on Key Residues in the Viral Polymerase.

scientific article published in September 2006

Feline lentivirus evolution in cross-species infection reveals extensive G-to-A mutation and selection on key residues in the viral polymerase

scientific article

Four jumping spider genera of the Cocalodes-group are monophyletic with genera of the Spartaeinae (Araneae: Salticidae)

scholarly article

Frequency-dependent selection drives HBeAg seroconversion in chronic hepatitis B virus infection

scientific article published on 13 December 2013

Genealogies from Time-Stamped Sequence Data

Genetic analysis of viral variants selected in transmission of human immunodeficiency viruses to newborns

scientific article published on September 2000

HIV Quasispecies and Resampling

scientific article published in Science

HIV evolutionary genetics.

scientific article

HIV-1 transmission during early antiretroviral therapy: evaluation of two HIV-1 transmission events in the HPTN 052 prevention study

scientific article

HaploJuice : accurate haplotype assembly from a pool of sequences with known relative concentrations

scientific article published on 22 October 2018

Human immunodeficiency virus type 1 molecular evolution and the measure of selection

scientific article published in December 1996

Identifying predictors of time-inhomogeneous viral evolutionary processes

scientific article published on July 2016

Immune-mediated positive selection drives human immunodeficiency virus type 1 molecular variation and predicts disease duration.

scientific article published on November 2002

Immunogen sequence: the fourth tier of AIDS vaccine design

scientific article

Inadequate Support for an Evolutionary Link Between the Metazoa and the Fungi

scientific article published in 1994

Increased viral quasispecies evolution in HBeAg seroconverter patients treated with oral nucleoside therapy ⬇️

scientific article published on September 27, 2012

Inferring evolutionary rates using serially sampled sequences from several populations

scientific article published on 29 August 2003

Integrating genealogy and epidemiology: the ancestral infection and selection graph as a model for reconstructing host virus histories.

scientific article published in July 2005

Maximum likelihood supertrees

scientific article published in April 2008

Measurably evolving populations

scientific article published in 2003

Modeling the site-specific variation of selection patterns along lineages

scholarly article

Modelling the evolution of protein coding sequences sampled from Measurably Evolving Populations.

scientific article published in January 2008

Models of microbiome evolution incorporating host and microbial selection.

scientific article published on 25 September 2017

Molecular epidemiology of feline immunodeficiency virus in the domestic cat (Felis catus).

scientific article

Neutral Models of Microbiome Evolution

scientific article published on 22 July 2015

Neutral models of short-term microbiome dynamics with host subpopulation structure and migration limitation.

scientific article published on 27 April 2018

On Combining Cladograms

scientific article (publication date: May 1996)

On the use of bootstrapped topologies in coalescent-based Bayesian MCMC inference: a comparison of estimation and computational efficiencies

scientific article published on 31 July 2009

Patterns of gut bacterial colonization in three primate species

scientific article published on 13 May 2015

Pervasive genomic recombination of HIV-1 in vivo

scientific article

Phylogenetic analysis of feline immunodeficiency virus in feral and companion domestic cats of New Zealand

scientific article published on 27 December 2006

Predicting demographic group structures based on DNA sequence data

scientific article

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Coalescent-based estimation of population parameters when the number of demes changes over time

scientific article published on 22 February 2006

Quantitation of target molecules from polymerase chain reaction-based limiting dilution assays

scientific article published in June 1997

Reassembling haplotypes in a mixture of pooled amplicons when the relative concentrations are known: A proof-of-concept study on the efficient design of next-generation sequencing strategies.

scientific article

Recombination in feline immunodeficiency virus from feral and companion domestic cats

scientific article published on 17 June 2008

Recombination in feline lentiviral genomes during experimental cross-species infection

scientific article published on 12 October 2006

SQUINT: a multiple alignment program and editor

article

Science incubators: synthesis centers and their role in the research ecosystem

scientific article

Selecting taxa to save or sequence: desirable criteria and a greedy solution

scientific article

Selection for human immunodeficiency virus type 1 recombinants in a patient with rapid progression to AIDS.

scientific article published on November 2002

Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes

scientific article published on January 2006

Specific and general formulae for the number of band combinations for different colour-banding regimes

Surficial sediment‐heavy metal associations in the Avon‐Heathcote Estuary, New Zealand

article

Synthesis Centers as Critical Research Infrastructure

article

Testing the hypothesis of a recombinant origin of human immunodeficiency virus type 1 subtype E.

scientific article

The Evolutionary Value of Helpful Microbes: A Response to Shapira.

scientific article

The distribution of feline immunodeficiency virus in tissue compartments of feral domestic cats

scientific article published on 29 January 2010

The molecular biology and evolution of feline immunodeficiency viruses of cougars

scientific article published on 19 January 2008

The perils of plenty: what are we going to do with all these genes?

scientific article (publication date: 27 December 2008)

The principles and methods of phylogenetic systematics and its application to the taxonomy of the Pronocephalidae Looss, 1902 (Platyhelminthes: Digenea) ⬇️

1990 doctoral thesis by Allen Gerard Rodrigo at University of Canterbury

Time-dependent rates of molecular evolution

scientific article published on 08 July 2011

Transient compartmentalization of simian immunodeficiency virus variants in the breast milk of african green monkeys

scientific article published on 07 August 2013

Transition between stochastic evolution and deterministic evolution in the presence of selection: general theory and application to virology.

scientific article

Two Optimality Criteria for Selecting Subsets of Most Parsimonious Trees

scientific article published in 1992

Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum

scientific article

Using PEBBLE for the evolutionary analysis of serially sampled molecular sequences

scientific article published in May 2004

Using logistic regression models to predict breeding success in male Adélie penguins (Pygoscelis adeliae)

Using temporally spaced sequences to simultaneously estimate migration rates, mutation rate and population sizes in measurably evolving populations.

scientific article published on December 2004

ViPRA-Haplo: <i>De Novo</i> Reconstruction of Viral Populations Using Paired End Sequencing Data

scientific article published on 07 March 2024

Viral Quasi-Species Evolution During Hepatitis Be Antigen Seroconversion

article

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