Allen G. Rodrigo, Peter Tsai, Helen Shearman
Coalescent-based Bayesian Markov chain Monte Carlo (MCMC) inference generates estimates of evolutionary parameters and their posterior probability distributions. As the number of sequences increases,...
Recombination in feline immunodeficiency virus from feral and companion domestic cats (2008)
Hayward, Jessica J, Rodrigo, Allen G
Abstract Background Recombination is a relatively common phenomenon in retroviruses. We investigated recombination in Feline Immunodeficiency Virus from naturally-infected New Zealand domestic cats (...
Department of Mathematics, (2008)
Alexei J. Drummond, Geoff K. Nicholls, Allen G. Rodrigo, Wiremu Solomon
Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data
Selecting Taxa to Save or Sequence: Desirable Criteria and a Greedy Solution (2008)
Bordewich, Magnus, Rodrigo, Allen G., Semple, Charles
Three desirable properties for any method of selecting a subset of evolutionary units (EUs) for conservation or for genomic sequencing are discussed. These properties are spread, stability, and...
Abstract Evolution of Relative Synonymous Codon Usage in Human (2007)
Immunodeficiency Virus Type, Peter L. Meintjes, Allen G. Rodrigo, Human Immunodeficiency
Mutation in HIV-1 is extremely rapid, a consequence of a low-fidelity viral reverse transcription process. The envelope gene has been shown to accumulate substitutions at a rate of approximately 1 %...
DNA Analysis using a Portable Robotic Instrument (2007)
Daksh Sadarangani, Bruce Macdonald, Allen G. Rodrigo, David Saul
Obtaining the sequence of nucleotides that constitute a gene or segment of DNA involves extracting DNA from a cell, amplifying the number of DNA molecules, purifying, tagging the ends of the...
SQUINT: a multiple alignment program and editor (2007)
Goode, Matthew G., Rodrigo, Allen G.
Summary: SQUINT is a sequence alignment tool, and combines both automated progressive sequence alignment with facilities for manual editing. The program imports nucleotide or amino acid sequence...
Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes (2006)
Howard A. Ross, David C. Nickle, Yi Liu, Laura Heath, Mark A. Jensen, Allen G. Rodrigo, ...
We characterized the variation in the reconstructed ancestor of 118 HIV-1 envelope gene sequences arising from the methods used for (a) estimating and (b) rooting the phylogenetic tree, and (c)...
Matthew G. Goode, Allen G. Rodrigo
Summary: SQUINT is a sequence alignment tool, and combines both automated progressive sequence alignment with facilities for manual editing. The program imports nucleotide or amino acid sequence...
Genealogies from Time-Stamped Sequence Data (2003)
Alexei Drummond, Geoff K. Nicholls, Allen G. Rodrigo, Wiremu Solomon
this paper we review recently published statistical methodology for genetic dating. Our explicit treatment of the uncertainty arising from imprecisely dated sequences, Section 6, is new, as is our...
Predicting Demographic Group Structures Based on DNA Sequence Data (2003)
Anderson, Jon P., Learn, Gerald H., Rodrigo, Allen G., He, Xi, Wang, Yang, Weinstock, Hillard, ...
The ability to infer relationships between groups of sequences, either by searching for their evolutionary history or by comparing their sequence similarity, can be a crucial step in hypothesis...
Inferring Evolutionary Rates Using Serially Sampled Sequences from Several Populations (2003)
Rodrigo, Allen G., Goode, Matthew, Forsberg, Roald, Ross, Howard A., Drummond, Alexei
The estimation of evolutionary rates from serially sampled sequences has recently been the focus of several studies. In this paper, we extend these analyses to allow the estimation of a joint rate of...
Predicting Demographic Group Structures Based on DNA Sequence Data (2003)
Anderson, Jon P., Learn, Gerald H., Rodrigo, Allen G., He, Xi, Wang, Yang, Weinstock, Hillard, ...
The ability to infer relationships between groups of sequences, either by searching for their evolutionary history or by comparing their sequence similarity, can be a crucial step in hypothesis...
Inferring Evolutionary Rates Using Serially Sampled Sequences from Several Populations (2003)
Rodrigo, Allen G., Goode, Matthew, Forsberg, Roald, Ross, Howard A., Drummond, Alexei
The estimation of evolutionary rates from serially sampled sequences has recently been the focus of several studies. In this paper, we extend these analyzes to allow the estimation of a joint rate of...
Predicting Demographic Group Structures Based on DNA Sequence Data (2003)
Anderson, Jon P., Learn, Gerald H., Rodrigo, Allen G., He, Xi, Wang, Yang, Weinstock, Hillard, ...
The ability to infer relationships between groups of sequences, either by searching for their evolutionary history or by comparing their sequence similarity, can be a crucial step in hypothesis...
Inferring Evolutionary Rates Using Serially Sampled Sequences from Several Populations (2003)
Rodrigo, Allen G., Goode, Matthew, Forsberg, Roald, Ross, Howard A., Drummond, Alexei
The estimation of evolutionary rates from serially sampled sequences has recently been the focus of several studies. In this paper, we extend these analyses to allow the estimation of a joint rate of...
The Inference of Stepwise Changes in Substitution Rates Using Serial Sequence Samples (2001)
Drummond, Alexei, Forsberg, Roald, Rodrigo, Allen G.
It is frequently true that molecular sequences do not evolve in a strictly clocklike manner. Instead, substitution rate may vary for a number of reasons, including changes in selection pressure and...
Examination of Trichoderma phylogenies derived from ribosomal DNA sequence data (2000)
Dodd, Sarah L., Crowhurst, Ross N., Rodrigo, Allen G., Samuels, Gary J., Hill, Robert A., Stewart, Alison
Ribosomal DNA sequences were assessed for their usefulness in distinguishing among Trichoderma isolates and for their robustness in resolving their phylogenetic relationships. DNA sequences from the...
Drummond, Alexei, Rodrigo, Allen G.
Reconstruction of evolutionary relationships from noncontemporaneous molecular samples provides a new challenge for phylogenetic reconstruction methods. With recent biotechnological advances there...
Likelihood-Based Tests of Topologies in Phylogenetics (2000)
Goldman, Nick, Anderson, Jon P., Rodrigo, Allen G.
Likelihood-based statistical tests of competing evolutionary hypotheses (tree topologies) have been available for approximately a decade. By far the most commonly used is the Kishino-Hasegawa test....
Inadequate Support for an Evolutionary Link between the Metazoa and the Fungi (1994)
Rodrigo, Allen G., Bergquist, Patricia R., Bergquist, Peter L.
Two Optimality Criteria for Selecting Subsets of most Parsimonious Trees (1992)
Two new optimality indices are developed for selecting subsets of trees from a set of most parsimonious trees. The optimal character compatibility index (OCCI) quantifies, for each most parsimonious...
Coalescent estimates of HIV-1 generation time in vivo
Rodrigo, Allen G., Shpaer, Eugene G., Delwart, Eric L., Iversen, Astrid K. N., Gallo, Michael V., Brojatsch, Jürgen, ...
The generation time of HIV Type 1 (HIV-1) in vivo has previously been estimated using a mathematical model of viral dynamics and was found to be on the order of one to two days per generation. Here,...
Poss, Mary, Rodrigo, Allen G., Gosink, John J., Learn, Gerald H., De Vange Panteleeff, Dana, Martin, Harold L., ...
The development of viral diversity during the course of human immunodeficiency virus type 1 (HIV-1) infection may significantly influence viral pathogenesis. The paradigm for HIV-1 evolution is based...
Testing the Hypothesis of a Recombinant Origin of Human Immunodeficiency Virus Type 1 Subtype E
Anderson, Jon P., Rodrigo, Allen G., Learn, Gerald H., Madan, Anup, Delahunty, Claire, Coon, Michael, ...
The human immunodeficiency virus type 1 (HIV-1) epidemic in Southeast Asia has been largely due to the emergence of clade E (HIV-1E). It has been suggested that HIV-1E is derived from a recombinant...
Shankarappa, Raj, Margolick, Joseph B., Gange, Stephen J., Rodrigo, Allen G., Upchurch, David, Farzadegan, Homayoon, ...
To understand the high variability of the asymptomatic interval between primary human immunodeficiency virus type 1 (HIV-1) infection and the development of AIDS, we studied the evolution of the...
Liu, Shan-Lu, Mittler, John E., Nickle, David C., Mulvania, Thera M., Shriner, Daniel, Rodrigo, Allen G., ...
Although human immunodeficiency virus type 1 (HIV-1) recombinants have been found with high frequency, little is known about the forces that select for these viruses or their importance to...
Ross, Howard A., Rodrigo, Allen G.
Using likelihood-based evolutionary methods, we demonstrate that the broad genetic diversity of human immunodeficiency virus type 1 (HIV-1) in an infected individual is a consequence of site-specific...
Biek, Roman, Rodrigo, Allen G., Holley, David, Drummond, Alexei, Anderson, Charles R., Ross, Howard A., ...
Within the large body of research on retroviruses, the distribution and evolution of endemic retroviruses in natural host populations have so far received little attention. In this study, the...
Modeling the site-specific variation of selection patterns along lineages
Guindon, Stéphane, Rodrigo, Allen G., Dyer, Kelly A., Huelsenbeck, John P.
The unambiguous footprint of positive Darwinian selection in protein-coding DNA sequences is revealed by an excess of nonsynonymous substitutions over synonymous substitutions compared with the...
Drummond, Alexei J, Nicholls, Geoff K, Rodrigo, Allen G, Solomon, Wiremu
Molecular sequences obtained at different sampling times from populations of rapidly evolving pathogens and from ancient subfossil and fossil sources are increasingly available with modern sequencing...
Pervasive genomic recombination of HIV-1 in vivo.
Shriner, Daniel, Rodrigo, Allen G, Nickle, David C, Mullins, James I
Recombinants of preexisting human immunodeficiency virus type 1 (HIV-1) strains are now circulating globally. To increase our understanding of the importance of these recombinants, we assessed...
Coalescent estimates of HIV-1 generation time in vivo
Rodrigo, Allen G., Shpaer, Eugene G., Delwart, Eric L., Iversen, Astrid K. N., Gallo, Michael V., Brojatsch, Jürgen, ...
The generation time of HIV Type 1 (HIV-1) in vivo has previously been estimated using a mathematical model of viral dynamics and was found to be on the order of one to two days per generation. Here,...
Poss, Mary, Rodrigo, Allen G., Gosink, John J., Learn, Gerald H., De Vange Panteleeff, Dana, Martin, Harold L., ...
The development of viral diversity during the course of human immunodeficiency virus type 1 (HIV-1) infection may significantly influence viral pathogenesis. The paradigm for HIV-1 evolution is based...
Testing the Hypothesis of a Recombinant Origin of Human Immunodeficiency Virus Type 1 Subtype E
Anderson, Jon P., Rodrigo, Allen G., Learn, Gerald H., Madan, Anup, Delahunty, Claire, Coon, Michael, ...
The human immunodeficiency virus type 1 (HIV-1) epidemic in Southeast Asia has been largely due to the emergence of clade E (HIV-1E). It has been suggested that HIV-1E is derived from a recombinant...
Shankarappa, Raj, Margolick, Joseph B., Gange, Stephen J., Rodrigo, Allen G., Upchurch, David, Farzadegan, Homayoon, ...
To understand the high variability of the asymptomatic interval between primary human immunodeficiency virus type 1 (HIV-1) infection and the development of AIDS, we studied the evolution of the...
Liu, Shan-Lu, Mittler, John E., Nickle, David C., Mulvania, Thera M., Shriner, Daniel, Rodrigo, Allen G., ...
Although human immunodeficiency virus type 1 (HIV-1) recombinants have been found with high frequency, little is known about the forces that select for these viruses or their importance to...
Ross, Howard A., Rodrigo, Allen G.
Using likelihood-based evolutionary methods, we demonstrate that the broad genetic diversity of human immunodeficiency virus type 1 (HIV-1) in an infected individual is a consequence of site-specific...
Biek, Roman, Rodrigo, Allen G., Holley, David, Drummond, Alexei, Anderson, Charles R., Ross, Howard A., ...
Within the large body of research on retroviruses, the distribution and evolution of endemic retroviruses in natural host populations have so far received little attention. In this study, the...
Modeling the site-specific variation of selection patterns along lineages
Guindon, Stéphane, Rodrigo, Allen G., Dyer, Kelly A., Huelsenbeck, John P.
The unambiguous footprint of positive Darwinian selection in protein-coding DNA sequences is revealed by an excess of nonsynonymous substitutions over synonymous substitutions compared with the...
Drummond, Alexei J, Nicholls, Geoff K, Rodrigo, Allen G, Solomon, Wiremu
Molecular sequences obtained at different sampling times from populations of rapidly evolving pathogens and from ancient subfossil and fossil sources are increasingly available with modern sequencing...
Pervasive genomic recombination of HIV-1 in vivo.
Shriner, Daniel, Rodrigo, Allen G, Nickle, David C, Mullins, James I
Recombinants of preexisting human immunodeficiency virus type 1 (HIV-1) strains are now circulating globally. To increase our understanding of the importance of these recombinants, we assessed...
Hayward, Jessica J., Taylor, John, Rodrigo, Allen G.
Nested PCR was used to amplify envelope V3-V6 gene fragments of feline immunodeficiency virus (FIV) from New Zealand cats. Phylogenetic analyses established that subtypes A and C predominate among...
Sources of variation in ancestral sequence reconstruction for HIV-1 envelope genes
Ross, Howard A., Nickle, David C., Liu, Yi, Heath, Laura, Jensen, Mark A., Rodrigo, Allen G., ...
We characterized the variation in the reconstructed ancestor of 118 HIV-1 envelope gene sequences arising from the methods used for (a) estimating and (b) rooting the phylogenetic tree, and (c)...
A Statistical Model to Identify Differentially Expressed Proteins in 2D PAGE Gels
Wu, Steven H., Black, Michael A., North, Robyn A., Atkinson, Kelly R., Rodrigo, Allen G.
Two dimensional polyacrylamide gel electrophoresis (2D PAGE) is used to identify differentially expressed proteins and may be applied to biomarker discovery. A limitation of this approach is the...
Rodrigo, Allen G., Tsai, Peter, Shearman, Helen
Coalescent-based Bayesian Markov chain Monte Carlo (MCMC) inference generates estimates of evolutionary parameters and their posterior probability distributions. As the number of sequences increases,...