Bryant, David, Bouckaert, Remco, Rosenberg, Noah
We introduce a method for inferring species trees, divergence dates, and population sizes directly from unlinked binary loci. The method produces results identical to a full, multiple species,...
Species delimitation and phylogeny of a New Zealand plant species radiation (2009)
Meudt, Heidi M, Lockhart, Peter J, Bryant, David
Abstract Background Delimiting species boundaries and reconstructing the evolutionary relationships of late Tertiary and Quaternary species radiations is difficult. One recent approach emphasizes the...
Properties of Consensus Methods for Inferring Species Trees from Gene Trees (2009)
Degnan, James H., DeGiorgio, Michael, Bryant, David, Rosenberg, Noah A.
Consensus methods provide a useful strategy for summarizing information from a collection of gene trees. An important application of consensus methods is to combine gene trees to estimate a species...
Design and prototyping of an aircraft to maximize the triaviation score (2009)
This thesis describes some of the processes and results obtained during the design and prototyping of a single seat experimental aircraft. The major aim was to maximise the Triaviation score of the...
Design and prototyping of an aircraft to maximize the triaviation score (2009)
This thesis describes some of the processes and results obtained during the design and prototyping of a single seat experimental aircraft. The major aim was to maximise the Triaviation score of the...
On the uniqueness of the selection criterion in neighbor-joining (2008)
The Neighbor-Joining (NJ) method of Saitou and Nei is the most widely used distance based method in phylogenetic analysis. Central to the method is the selection criterion, the formula used to choose...
Computing the Distribution of a Tree Metric (2008)
The Robinson-Foulds (RF) distance is by far the most widely used measure of dissimilarity between trees. Although the distribution of these distances has been investigated for twenty years, an...
Hadamard Phylogenetic Methods and the n-taxon process (2008)
The Hadamard transform of \cite{Hendy89a, Hendy89} provides a way to work with stochastic models for sequence evolution without having to deal with the complications of tree space and the graphical...
17 Extending Tree Models to Split Networks (2008)
In this chapter we take statistical models designed for trees and adapt them for split networks, a more general class of mathematical structures. The models we propose provide natural swing-bridges...
David Bryant, Flavia Filimon, Russell D. Gray
truth is rarely pure and never simple". The idea that much of recent human history might reflect pure trees of phylogenetic descent is appealing simple. It has stimulated numerous...
SplitsTree 4.0- Computation of phylogenetic trees and networks (2008)
The goal of phylogenetic analysis is to determine the order and approximate timing of speciation events in the evolution of a given set of species. In the classic theory of phylogenetic analysis the...
Expertise, Cognitive Ability, and Age Effects on Pilot Communication (2008)
Daniel G. Morrow, William E. Menard, Heather E. Ridolfo, Thomas Teller, David Bryant
We investigated whether expertise reduced age-related declines in pilot communication, using multiple expertise measures and laboratory tasks varying in domain rel-evance. Younger, middle-aged, and...
Whitianga, New Zealand Whitianga ‘08 NEW ZEALAND PHYLOGENETICS CONFERENCE Participants (2008)
John Beck, David Bryant, Michael Charleston, Alan Cooper, Beata Faller, Mareike Fischer, ...
revisited
Parsimony via Consensus (2008)
Bruen, Trevor C., Bryant, David
The parsimony score of a character on a tree equals the number of state changes required to fit that character onto the tree. We show that for unordered, reversible characters this score equals the...
Algorithmic aspects of tree (2007)
Sebastian Böcker, Gk Strukturbildungsprozesse, Fsp Mathematisierung, David Bryant, ...
‡ Mike Steel thanks the New Zealand Marsden Fund (UOC-MIS-003) for supporting this research 1 2 BÖCKER, BRYANT, DRESS, STEEL Proposed running head: Tree amalgamation
Abstract. A consensus tree method takes a collection of phylogenetic trees and outputs a single “representative ” tree. The first consensus method was proposed by Adams in 1972. Since then a...
David Bryant, Flavia Filimon, Russell D. Gray
truth is rarely pure and never simple". The idea that much of recent human history might reflect pure trees of phylogenetic descent is appealing simple. It has stimulated numerous...
Huang, Da Wei, Sherman, Brad T., Tan, Qina, Kir, Joseph, Liu, David, Bryant, David, ...
All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies. The newly updated DAVID Bioinformatics Resources...
Consistency of the Neighbor-Net Algorithm (2007)
Bryant, David, Moulton, Vincent, Spillner, Andreas
Abstract Background Neighbor-Net is a novel method for phylogenetic analysis that is currently being widely used in areas such as virology, bacteriology, and plant evolution. Given an input distance...
A fresh look at maximum parsimony (2007)
This paper has been withdrawn due to a problem in one of the figures.
Consistency of the Neighbor-Net Algorithm (2007)
Bryant, David, Moulton, Vincent, Spillner, Andreas
An open access copy of this article is available and complies with the copyright holder/publisher conditions.
Nucleic Acids Research Advance Access published June 18, 2007 (2007)
Da Wei Huang, Brad T. Sherman, Qina Tan, Joseph Kir, David Liu, ...
annotation database and novel algorithms to better extract biology from large gene lists
A General Comparison of Relaxed Molecular Clock Models (2007)
Lepage, Thomas, Bryant, David, Philippe, Hervé, Lartillot, Nicolas
Several models have been proposed to relax the molecular clock in order to estimate divergence times. However, it is unclear which model has the best fit to real data and should therefore be used to...
Conditioned Genome Reconstruction: How to Avoid Choosing the Conditioning Genome (2007)
Spencer, Matthew, Bryant, David, Susko, Edward
Genome phylogenies can be inferred from data on the presence and absence of genes across taxa. Logdet distances may be a good method, because they allow expected genome size to vary across the tree....
Accounting for Gene Rate Heterogeneity in Phylogenetic Inference (2007)
Bevan, Rachel B., Bryant, David, Lang, B. Franz
Traditionally, phylogenetic analyses over many genes combine data into a contiguous block. Under this concatenated model, all genes are assumed to evolve at the same rate. However, it is clear that...
Faunce, Thomas A, Walters, Haydn, Williams, Trevor, Bryant, David, Jennings, Martin, Musk, Bill
Abstract On 22 June 2005 the Senate of the Commonwealth of Australia voted to establish an inquiry into workplace harm related to toxic dust and emerging technologies (including nanoparticles). The...
Application of Phylogenetic Networks in Evolutionary Studies (2006)
Huson, Daniel H., Bryant, David
The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known...
Thomas A Faunce, Hayden Walters, Trevor Williams, David Bryant, Martin Jennings, Bill Musk
On 22 June 2005 the Senate of the Commonwealth of Australia voted to establish an inquiry into workplace harm related to toxic dust and emerging technologies (including nanoparticles). The inquiry...
Thomas A Faunce, Hayden Walters, Trevor Williams, David Bryant, Martin Jennings, Bill Musk
On 22 June 2005 the Senate of the Commonwealth of Australia voted to establish an inquiry into workplace harm related to toxic dust and emerging technologies (including nanoparticles). The inquiry...
Zeeberg, Barry R, Qin, Haiying, Narasimhan, Sudarshan, Sunshine, Margot, Cao, Hong, Kane, David W, ...
Abstract Background We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for...
Continuous and Tractable models for the Variation of Evolutionary Rates (2005)
Lepage, Thomas, Lawi, Stephan, Tupper, Paul, Bryant, David
We propose a continuous model for evolutionary rate variation across sites and over the tree and derive exact transition probabilities under this model. Changes in rate are modelled using the CIR...
Site Interdependence Attributed to Tertiary Structure in Amino Acid Sequence Evolution (2005)
Nicolas Rodrigue, Nicolas Lartillot, David Bryant, Herve Philippe
Standard likelihood-based frameworks in phylogenetics consider the process of evolution of a sequence site by site. Assuming that sites evolve independently greatly simplifies the required...
Application of Phylogenetic Networks in Evolutionary Studies (2005)
Huson, Daniel H., Bryant, David
The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known...
Application of Phylogenetic Networks in Evolutionary Studies (2005)
Huson, Daniel H., Bryant, David
The evolutionary history of a set of taxa is usually represented by a phylogenetic tree, and this model has greatly facilitated the discussion and testing of hypotheses. However, it is well known...
Bevan, Rachel B., Lang, B. Franz, Bryant, David
In phylogenetic analyses with combined multigene or multiprotein data sets, accounting for differing evolutionary dynamics at different loci is essential for accurate tree prediction. Existing...
Biogeographic Interpretation of Splits Graphs: Least Squares Optimization of Branch Lengths (2005)
Winkworth, Richard C., Bryant, David, Lockhart, Peter J., Havell, David, Moulton, Vincent
Although most often used to represent phylogenetic uncertainty, network methods are also potentially useful for describing the phylogenetic complexity expected to characterize recent species...
Thesis (Ph.D.)--University of Durham, 2004.
The Splits in the Neighborhood of a Tree (2004)
A phylogenetic tree represents historical evolutionary relationships between different species or organisms. The space of possible phylogenetic trees is both complex and exponentially large. Here we...
A Lower Bound for the Breakpoint Phylogeny Problem (2004)
Breakpoint phylogenies methods have been shown to be an effective tool for extracting phylogenetic information from gene order data. Currently, the only practical breakpoint phylogeny algorithms for...
Supertree methods for ancestral divergence dates and other applications (2004)
David Bryant, Charles Semple, Mike Steel
Abstract: There are many ways to combine rooted phylogenetic trees with overlapping leaf sets into a single “supertree”. The most widely used method is MRP (matrix representation with parsimony...
Esser, Christian, Ahmadinejad, Nahal, Wiegand, Christian, Rotte, Carmen, Sebastiani, Federico, Gelius-Dietrich, Gabriel, ...
Analyses of 55 individual and 31 concatenated protein data sets encoded in Reclinomonas americana and Marchantia polymorpha mitochondrial genomes revealed that current methods for constructing...
Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks (2004)
Bryant, David, Moulton, Vincent
We present Neighbor-Net, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei. Neighbor-Net provides a snapshot of the...
Esser, Christian, Ahmadinejad, Nahal, Wiegand, Christian, Rotte, Carmen, Sebastiani, Federico, Gelius-Dietrich, Gabriel, ...
Analyses of 55 individual and 31 concatenated protein data sets encoded in Reclinomonas americana and Marchantia polymorpha mitochondrial genomes revealed that current methods for constructing...
Esser, Christian, Ahmadinejad, Nahal, Wiegand, Christian, Rotte, Carmen, Sebastiani, Federico, Gelius-Dietrich, Gabriel, ...
Analyses of 55 individual and 31 concatenated protein data sets encoded in Reclinomonas americana and Marchantia polymorpha mitochondrial genomes revealed that current methods for constructing...
David Bryant, Vincent Moulton, David Bryant
Neighbor-Net: An agglomerative method for the construction of phylogenetic networks
Distance Corrections on Recombinant Sequences (2003)
David Bryant, Daniel Huson, Tobias Kloepper, Kay Nieselt-struwe
Sequences that have evolved under recombination have a `mosaic' structure, with di#erent portions of the alignment having evolved on di#erent trees. In this paper we study the e#ect of mosaic...
Distance corrections for recombinant sequences (2003)
David Bryant, Daniel Huson, Kay Nieselt-struwe
Abstract. Sequences that have evolved under recombination have a ‘mosaic ’ structure, with different portions of the alignment having evolved on different trees. In this paper we study the effect...
Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks (2003)
Bryant, David, Moulton, Vincent
We present Neighbor-Net, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei. Neighbor-Net provides a snapshot of the...
Neighbor-Net: An Agglomerative Method for the Construction of Phylogenetic Networks (2003)
Bryant, David, Moulton, Vincent
We present Neighbor-Net, a distance based method for constructing phylogenetic networks that is based on the Neighbor-Joining (NJ) algorithm of Saitou and Nei. Neighbor-Net provides a snapshot of the...
Constructing optimal trees from quartets (2001)
We present fast new algorithms for constructing phylogenetic trees from quartets Ž resolved trees on four leaves.. The problem is central to divide-and-conquer approaches to phylogenetic analysis...
Constructing optimal trees from quartets (2001)
We present fast new algorithms for constructing phylogenetic trees from quartets (resolved trees on four leaves). The problem is central to divide and conquer approaches to phylogenetic analysis and...
Optimal Agreement Supertrees (2001)
David Bryant Lirmm, David Bryant
An agreement supertree of a collection of unrooted phylogenetic trees {T1 , T2 , . . . , Tk} with leaf sets ), L(T2), . . . , L(Tk ) is an unrooted tree T with leaf set ) # # L(Tk ) such that each...
Early eukaryote evolution based on mitochondrial gene order breakpoints (2000)
David Sankoff, David Bryant, Mélanie Deneault, B. Franz, Lang Gertraud Burger
The comparison of the gene orders in a set of genomes can be used to infer their phylogenetic relationships and to reconstruct ancestral gene orders. For three genomes this is done by solving the...
Early eukaryote evolution based on mitochondrial gene order breakpoints (2000)
David Sankoff, David Bryant, Mélanie Deneault, B. Franz, Lang Gertraud Burger
The comparison of the gene orders in a set of genomes can be used to infer their phylogenetic relationships and to reconstruct ancestral gene orders. For three genomes this is done by solving the...
Algorithmic aspects of tree (2000)
Sebastian Böcker, Gk Strukturbildungsprozesse, Fsp Mathematisierung, David Bryant, ...
‡ Mike Steel thanks the New Zealand Marsden Fund (UOC-MIS-003) for supporting this research 1 2 BÖCKER, BRYANT, DRESS, STEEL Proposed running head: Tree amalgamation
Computing the quartet distance between evolutionary trees (2000)
David Bryant, John Tsang, Paul Kearney, Ming Li
The comparison of evolutionary trees is a fundamental problem in evolutionary biology. Di erent evolutionary hypotheses (or con icting phylogenies) arise
Computing the quartet distance between evolutionary trees (2000)
David Bryant, John Tsang, Paul Kearney, Ming Li
The comparison of evolutionary trees is a fundamen-tal problem in evolutionary biology. Different evolu-tionary hypotheses (or conflicting phylogenies) arise
David Sankoff, Mélanie Deneault, David Bryant, Claude Lemieux, Monique Turmel
Normalizing the number of breakpoints between two genomes, previously reduced by deleting the genes specific to one or the other, gives a rapidly calculated in-dex of gene order evolution which is...
A practical algorithm for recovering the best supported edges of an evolutionary tree (2000)
Vincent Berry, David Bryant, Tao Jiang, Paul Kearney, Ming Li, Todd Wareham, ...
It is now routine for biologists to conduct evolutionary analyses of large DNA and protein sequence datasets. A computational bottleneck in these analyses is the recovery of the topology of the...
Computing the Quartet Distance Between Evolutionary Trees (2000)
David Bryant, John Tsang, Paul Kearney, Ming Li
this paper, we study the quartet metric, which is based on common subtrees induced by four leaves. This metric has several attractive properties, though its use has been limited by the time required...
Vincent Berry, David Bryant, Tao Jiang, Paul Kearney, Ming Li, Todd Wareham, ...
) Vincent Berry David Bryant y Tao Jiang z Paul Kearney x Ming Li -- Todd Wareham k Haoyong Zhang Abstract It is now routine for biologists to conduct evolutionary analyses of large DNA and protein...
The Complexity of Calculating Exemplar (2000)
Distances David Bryant, David Bryant
Traditional methods for estimating rearrangement distances between genomes assume that there is at most one copy of each gene in each genome. In the case that there are multiple genes from the same...
Algorithmic Aspects of Tree Amalgamation (2000)
Sebastian Böcker, David Bryant, Mike A. Steel
this paper, we consider the question ofdetermining whether the collection of input trees uniquely determines a possible supertree. Webeg4 by introducing some terminologM We will view (leaf-labeled)...
Early eukaryote evolution based on mitochondrial gene order breakpoints (2000)
David Sankoff, David Bryant, Mdlanie Deneault, B. Franz, Lang Gertraud Burger
We present a general heuristic for the median problem for induced breakpoints on genomes with unequal gene con-tent and incorporate this into a routine for estimating op-timal gene orders for the...
Promoter Methylation and Silencing of the Retinoic Acid Receptor-ß Gene in Lung Carcinomas (2000)
Virmani, Arvind K., Rathi, Asha, Zöchbauer-Müller, Sabine, Sacchi, Nicoletta, Fukuyama, Yasuro, Bryant, David, ...
Background: Retinoic acid plays an important role in lung development and differentiation, acting primarily via nuclear receptors encoded by the retinoic acid receptor-&bgr; (RAR&bgr;) gene. Because...
A polynomial time algorithm for constructing the refined Buneman tree (1999)
We present a polynomial time algorithm for computing the refined Buneman tree, thereby making it applicable for tree reconstruction on large data sets. The refined Buneman tree retains many of the...
The complexity of the breakpoint median problem. Centre de Recherches Mathematiques (1998)
The breakpoint median problems arise in the problem of determining phylogenetic history from comparative genome data. We prove that the breakpoint median problems, and a number of related and...
Rapid Evaluation of Least-Squares and Minimum-Evolution Criteria on Phylogenetic Trees (1998)
We present fast new algorithms for evaluating trees with respect to least squares and minimum evolution (ME), the most commonly used criteria for inferring phylogenetic trees from distance data. The...
Phylogenetics is the study and identification of evolutionary patterns and structures in nature; this thesis explores the mathematics of these structures. The basic objects of study are the leaf...
Thesis (Ph. D.)--King's College, University of London, 1981.
Zeeberg, Barry R, Qin, Haiying, Narasimhan, Sudarshan, Sunshine, Margot, Cao, Hong, Kane, David W, ...
Faunce, Thomas A, Walters, Haydn, Williams, Trevor, Bryant, David, Jennings, Martin, Musk, Bill
On 22 June 2005 the Senate of the Commonwealth of Australia voted to establish an inquiry into workplace harm related to toxic dust and emerging technologies (including nanoparticles). The inquiry...
A Simple and Robust Statistical Test for Detecting the Presence of Recombination
Bruen, Trevor C., Philippe, Hervé, Bryant, David
Recombination is a powerful evolutionary force that merges historically distinct genotypes. But the extent of recombination within many organisms is unknown, and even determining its presence within...
Zeeberg, Barry R, Qin, Haiying, Narasimhan, Sudarshan, Sunshine, Margot, Cao, Hong, Kane, David W, ...
A Simple and Robust Statistical Test for Detecting the Presence of Recombination
Bruen, Trevor C., Philippe, Hervé, Bryant, David
Recombination is a powerful evolutionary force that merges historically distinct genotypes. But the extent of recombination within many organisms is unknown, and even determining its presence within...
Faunce, Thomas A, Walters, Haydn, Williams, Trevor, Bryant, David, Jennings, Martin, Musk, Bill
On 22 June 2005 the Senate of the Commonwealth of Australia voted to establish an inquiry into workplace harm related to toxic dust and emerging technologies (including nanoparticles). The inquiry...
Huang, Da Wei, Sherman, Brad T., Tan, Qina, Kir, Joseph, Liu, David, Bryant, David, ...
All tools in the DAVID Bioinformatics Resources aim to provide functional interpretation of large lists of genes derived from genomic studies. The newly updated DAVID Bioinformatics Resources...