D. Bryant

发表

The Complexity of Calculating Exemplar Distances

D. Bryant, 2000 .

Application of phylogenetic networks in evolutionary studies.

D. Huson, D. Bryant, 2006, Molecular biology and evolution.

A Simple and Robust Statistical Test for Detecting the Presence of Recombination

D. Bryant, T. C. Bruen, H. Philippe, 2006, Genetics.

17 Extending Tree Models to Split Networks

D. Bryant, 2006 .

Untangling our past : languages, trees, splits and networks

R. Gray, Flavia Filimon, D. Bryant, 2005 .

Extension Operations on Sets of Leaf-Labeled Trees

M. Steel, D. Bryant, 1995 .

Rapid Evaluation of Least-Squares and Minimum-Evolution Criteria on Phylogenetic Trees

P. Waddell, D. Bryant, 1998 .

On the artefactual parasitic eubacteria clan in conditioned logdet phylogenies: heterotachy and ortholog identification artefacts as explanations

David Bryant, Edward Susko, Matthew Spencer, 2010, BMC Evolutionary Biology.

Conditioned genome reconstruction: how to avoid choosing the conditioning genome.

M. Spencer, D. Bryant, E. Susko, 2007, Systematic biology.

A genome phylogeny for mitochondria among alpha-proteobacteria and a predominantly eubacterial ancestry of yeast nuclear genes.

M. Steel, D. Penny, D. Bryant, 2004, Molecular biology and evolution.

Neighbor-net: an agglomerative method for the construction of phylogenetic networks.

V. Moulton, D. Bryant, 2002, Molecular biology and evolution.

Origins of major archaeal clades correspond to gene acquisitions from bacteria

Filipa L. Sousa, A. Janssen, J. McInerney, 2014, Nature.

A general comparison of relaxed molecular clock models.

D. Bryant, H. Philippe, N. Lartillot, 2007, Molecular biology and evolution.

Building trees, hunting for trees, and comparing trees : theory and methods in phylogenetic analysis

D. Bryant, 1997 .

Inferring species trees directly from biallelic genetic markers: bypassing gene trees in a full coalescent analysis.

David Bryant, Remco Bouckaert, Joseph Felsenstein, 2009, Molecular biology and evolution.

On the shape and fabric of human history

Simon J. Greenhill, David Bryant, Simon J Greenhill, 2010, Philosophical Transactions of the Royal Society B: Biological Sciences.

Biogeographic interpretation of splits graphs: least squares optimization of branch lengths.

Vincent Moulton, David Bryant, V. Moulton, 2005, Systematic biology.

Consistency of the Neighbor-Net Algorithm

V. Moulton, D. Bryant, A. Spillner, 2007, Algorithms for molecular biology : AMB.

Strengths and limitations of the minimum evolution principle.

O Gascuel, O. Gascuel, F. Denis, 2001, Systematic biology.

Phylogenetic Supertrees

Charles Semple, Mark A. Ragan, David Bryant, 2004, Computational Biology.

Properties of consensus methods for inferring species trees from gene trees.

David Bryant, Michael DeGiorgio, Noah A Rosenberg, 2008, Systematic biology.

Mathematics of Evolution and Phylogeny Library of Congress Cataloging in Publication Data (data Available)

Bernard M. E. Moret, Elchanan Mossel, D. Sankoff, 2004 .

Chapter 3.4 The Concatenation Question

Matthew W. Hahn, D. Bryant, M. Hahn, 2020 .

Flexible methods for estimating genetic distances from single nucleotide polymorphisms

D. Bryant, P. Lockhart, S. Joly, 2014, bioRxiv.

Matrix representations with parsimony or with distances: two sides of the same coin?

François-Joseph Lapointe, David Bryant, Mark Wilkinson, 2003, Systematic biology.

The Splits in the Neighborhood of a Tree

D. Bryant, 2004 .

Running Head : Parsimony by consensus

D. Bryant, T. C. Bruen, 2008 .

Parsimony via consensus.

David Bryant, D. Bryant, T. C. Bruen, 2007, Systematic biology.

The probability of monophyly of a sample of gene lineages on a species tree

David Bryant, Noah A Rosenberg, N. Rosenberg, 2016, Proceedings of the National Academy of Sciences.

Hadamard Phylogenetic Methods and the n-taxon Process

David Bryant, D. Bryant, 2008, Bulletin of mathematical biology.

The link between segregation and phylogenetic diversity

David Bryant, Steffen Klaere, D. Bryant, 2010, Journal of mathematical biology.

Estimating phylogenetic trees and networks using SplitsTree 4

Daniel H. Huson, David Bryant, D. Huson, 2004 .

Monte Carlo Strategies for Selecting Parameter Values in Simulation Experiments.

D. Bryant, J. Leigh, 2015, Systematic biology.

Parameter Exploration in Simulation Experiments: A Bayesian Framework

D. Bryant, J. Leigh, Jessica W. Leigh, 2012, 1205.4503.

Efficient Recycled Algorithms for Quantitative Trait Models on Phylogenies

C. Fox, M. Parry, D. Bryant, 2015, Genome biology and evolution.

Simulating gene trees under the multispecies coalescent and time-dependent migration

David Bryant, Alexei J Drummond, Joseph Heled, 2013, BMC Evolutionary Biology.

Bayesian Inference of Species Trees using Diffusion Models.

C. Fox, R. Bouckaert, D. Bryant, 2019, Systematic biology.

Counting Ancestral Reconstructions in a Fixed Phylogeny

M. Steel, D. Bryant, T. Thierer, 2008 .

Early eukaryote evolution based on mitochondrial gene order breakpoints

David Sankoff, David Bryant, Gertraud Burger, 2000, Annual International Conference on Research in Computational Molecular Biology.

Count does not recover major events of gene flux in real biological data

Joana C. Xavier, D. Bryant, P. Lockhart, 2018, bioRxiv.

The dimensions of species diversity

S. Higgins, D. Bryant, G. Jordan, 2018, bioRxiv.

The dimensionality of niche space allows bounded and unbounded processes to jointly influence diversification

S. Higgins, D. Bryant, G. Jordan, 2018, Nature Communications.

Geometry of Ranked Nearest Neighbour Interchange Space of Phylogenetic Trees

D. Bryant, Mareike Fischer, A. Gavryushkin, 2019, bioRxiv.

How Good Are Indirect Tests at Detecting Recombination in Human mtDNA?

D. J. White, Daniel J. White, N. Gemmell, 2013, G3: Genes, Genomes, Genetics.

Continuous and tractable models for the variation of evolutionary rates.

D. Bryant, P. Tupper, T. Lepage, 2005, Mathematical biosciences.

Correction: Investigating the Global Dispersal of Chickens in Prehistory Using Ancient Mitochondrial DNA Signatures

E. Matisoo-Smith, T. Ladefoged, D. Bryant, 2019, PloS one.

The link between segregation and phylogenetic diversity

D. Bryant, S. Klaere, 2011, Journal of Mathematical Biology.

Investigating the Global Dispersal of Chickens in Prehistory Using Ancient Mitochondrial DNA Signatures

E. Matisoo-Smith, T. Ladefoged, D. Bryant, 2012, PloS one.

Inferring species trees directly from SNP and AFLP data: full coalescent analysis without those pesky gene trees

N. Rosenberg, R. Bouckaert, D. Bryant, 2009 .

popart: full‐feature software for haplotype network construction

David Bryant, D. Bryant, J. Leigh, 2015 .

Likelihood calculation in molecular phylogenetics

David Bryant, Nicolas Galtier, Marie-Anne Poursat, 2007, Mathematics of Evolution and Phylogeny.

Site interdependence attributed to tertiary structure in amino acid sequence evolution.

D. Bryant, H. Philippe, N. Lartillot, 2005, Gene.

Distance Corrections on Recombinant Sequences

Daniel H. Huson, Kay Nieselt, Tobias H. Klöpper, 2003, WABI.

Genome Networks Root the Tree of Life between Prokaryotic Domains

David Bryant, Mayo Roettger, Tal Dagan, 2010, Genome biology and evolution.

On the Uniqueness of the Selection Criterion in Neighbor-Joining

David Bryant, D. Bryant, 2005, J. Classif..

NeighborNet: An Agglomerative Method for the Construction of Planar Phylogenetic Networks

Vincent Moulton, David Bryant, V. Moulton, 2002, WABI.

A Structured Family of Clustering and Tree Construction Methods

Vincent Berry, David Bryant, V. Berry, 2001, Adv. Appl. Math..

Failure to Recover Major Events of Gene Flux in Real Biological Data Due to Method Misapplication

Joana C. Xavier, D. Bryant, P. Lockhart, 2018, Genome biology and evolution.

Endosymbiotic origin and differential loss of eukaryotic genes

David Bryant, Chuan Ku, Shijulal Nelson-Sathi, 2015, Nature.

Reconstructing the pre-doubling genome

David Sankoff, Nadia El-Mabrouk, David Bryant, 1999, RECOMB.

Forty Years of Model-Based Phylogeography

David Bryant, Jamie Kydd, D. Bryant, 2013, Models and Algorithms for Genome Evolution.

Calculating the evolutionary rates of different genes: a fast, accurate estimator with applications to maximum likelihood phylogenetic analysis.

David Bryant, B Franz Lang, B. Lang, 2005, Systematic biology.

Compatibility of unrooted phylogenetic trees is FPT

David Bryant, Jens Lagergren, J. Lagergren, 2006, Theor. Comput. Sci..

Constructing Optimal Trees from Quartets

Mike A. Steel, David Bryant, M. Steel, 2001, J. Algorithms.

The Concatenation Question

David Bryant, Matthew W. Hahn, D. Bryant, 2020 .

A polynomial time algorithm for constructing the refined Buneman tree

Vincent Moulton, David Bryant, V. Moulton, 1999 .

Faster reliable phylogenetic analysis

Vincent Berry, David Bryant, V. Berry, 1999, RECOMB.

Computing the quartet distance between evolutionary trees

Ming Li, David Bryant, Paul E. Kearney, 2000, SODA '00.

A classification of consensus methods for phylogenetics

David Bryant, D. Bryant, 2001, Bioconsensus.

Microbial Phylogenetic Context Using Phylogenetic Outlines

D. Huson, D. Bryant, C. Bagci, 2021, Genome biology and evolution.

Phylogenetic context using phylogenetic outlines

D. Huson, D. Bryant, C. Bagci, 2021, bioRxiv.

Linearly independent split systems

David Bryant, Andreas W. M. Dress, A. Dress, 2007, Eur. J. Comb..

Consistency of the Neighbor-Net Algorithm

Vincent Moulton, Andreas Spillner, David Bryant, 2007, Algorithms for Molecular Biology.

A Comparison of Three Heuristic Methods for Solving the Parsing Problem for Tandem Repeats

David Bryant, Michael D. Hendy, Christopher P. Tuffley, 2012, BSB.

Discrete coalescent trees

D. Bryant, Mareike Fischer, A. Gavryushkin, 2021, Journal of mathematical biology.

Accounting for gene rate heterogeneity in phylogenetic inference.

David Bryant, B Franz Lang, B. Lang, 2007, Systematic biology.

A lower bound for the breakpoint phylogeny problem

David Bryant, D. Bryant, 2000, J. Discrete Algorithms.

Chloroplast Gene Order and the Divergence of Plants and Algae, from the Normalized Number of Induced Breakpoints

David Sankoff, David Bryant, Monique Turmel, 2000 .

Early eukaryote evolution based on mitochondrial gene order breakpoints

David Sankoff, David Bryant, Gertraud Burger, 2000, RECOMB '00.

Flexible methods for estimating genetic distances from single nucleotide polymorphisms

Peter J. Lockhart, Simon Joly, Dj Bryant, 2014, bioRxiv.

When Can Splits be Drawn in the Plane?

Andreas Spillner, David Bryant, Monika Balvociute, 2015, SIAM J. Discret. Math..

Failure toRecoverMajor EventsofGeneFlux inReal Biological Data Due to Method Misapplication

Joana C. Xavier, D. Bryant, P. Lockhart, 2018 .

How disturbance and dispersal influence intraspecific structure

D. Bryant, I. Davies, C. Fraser, 2018 .

MCMC estimation of Markov models for ion channels.

Edmund J Crampin, David Bryant, Colin Fox, 2011, Biophysical journal.

Acceleration of hidden Markov model fitting using graphical processing units, with application to low-frequency tremor classification

Ting Wang, David Bryant, Gene Stoltz, 2020, Comput. Geosci..

The complexity of the breakpoint median problem

David Bryant, D. Bryant, 1998 .

Computing the Distribution of a Tree Metric

M. Steel, D. Bryant, D. Bryant, 2008, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Species delimitation and phylogeny of a New Zealand plant species radiation

David Bryant, Heidi M. Meudt, D. Bryant, 2009, BMC Evolutionary Biology.

Supertree Methods for Ancestral Divergence Dates and other Applications

Charles Semple, David Bryant, Mike Steel, 2004 .

Investigating the global dispersal of chickens in prehistory using ancient mitochondrial DNA signatures.

E. Matisoo-Smith, T. Ladefoged, D. Bryant, 2012 .

Fast algorithms for constructing optimal trees from quartets

Mike A. Steel, David Bryant, M. Steel, 1999, SODA '99.

'Bureaucratic' set systems, and their role in phylogenetics

M. Steel, D. Bryant, 2011, Appl. Math. Lett..

The Geometry of the space of Discrete Coalescent Trees pdf

David Bryant, Alex Gavryushkin, Mareike Fischer, 2021, ArXiv.

Can We “Future‐Proof” Consensus Trees?†

David Bryant, Mike Steel, Andrew Francis, 2016, Systematic biology.

Parsimony and the rank of a flattening matrix

C. Fox, D. Bryant, J. Snyman, 2021, Journal of Mathematical Biology.

Algorithmic Aspects of Tree Amalgamation

Mike A. Steel, David Bryant, Andreas W. M. Dress, 2000, J. Algorithms.

Neighbor-net: an agglomerative method for the construction of phylogenetic networks.

V. Moulton, D. Bryant, 2004, Molecular biology and evolution.

The agreement problem for unrooted phylogenetic trees is FPT

Leo van Iersel, Steven Kelk, David Bryant, 2014, J. Graph Algorithms Appl..

Uncovering rate variation of lateral gene transfer during bacterial genome evolution

Weilong Hao, T. Pupko, D. Bryant, 2008, BMC Genomics.

A practical algorithm for recovering the best supported edges of an evolutionary tree (extended abstract)

Tao Jiang, Todd Wareham, Vincent Berry, 2000, SODA '00.

Special Issue: Mathematical and Computational Evolutionary Biology—2015

O. Gascuel, D. Bryant, 2017, Systematic biology.

Hunting for binary trees in binary character sets : efficient algorithms for extraction , enumeration and optimization

D. Bryant, 2014 .

Exact coalescent likelihoods for unlinked markers in finite-sites mutation models

N. Rosenberg, J. Felsenstein, R. Bouckaert, 2011, 1109.3525.

Correction: Investigating the Global Dispersal of Chickens in Prehistory Using Ancient Mitochondrial DNA Signatures

E. Matisoo-Smith, T. Ladefoged, D. Bryant, 2019, PLoS ONE.