List of works - Barbara Holland

A futile act? Thoughts on the reproductive biology of Candida albicans

scientific article published in 2004

A new phylogenetic protocol: Dealing with model misspecification and confirmation bias in molecular phylogenetics

article

A novel exploratory method for visual recombination detection

scientific article

A tensorial approach to the inversion of group-based phylogenetic models

scientific article

Analysis of Acorus calamus chloroplast genome and its phylogenetic implications.

scientific article

Analysis of Phylogenetics and Evolution with R

scholarly article by Barbara R. Holland et al published 1 August 2007 in Systematic Biology

Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization

scientific article

Benchmarking Methods of Protein Structure Alignment

scientific article published on 28 July 2020

Biogeography of circum-Antarctic springtails

scientific article published on 15 June 2010

Brenner's Encyclopedia of Genetics (Second Edition) – Copyright

copyright notice

Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand

scientific article

Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns

scientific article

Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes

scientific article

Detecting Selection on Temporal and Spatial Scales: A Genomic Time-Series Assessment of Selective Responses to Devil Facial Tumor Disease ⬇️

scientific article

Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants.

scientific article published on 22 April 2017

Distinguishing Between Convergent Evolution and Violation of the Molecular Clock for Three Taxa

scientific article published on 18 May 2018

Distribution of mutations distinguishing the most prevalent disease-causing Candida albicans genotype from other genotypes

scientific article published on 30 January 2009

Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods ⬇️

article

Estimating the relative roles of recombination and point mutation in the generation of single locus variants in Campylobacter jejuni and Campylobacter coli

scientific article published on June 2012

Evaluation of Monitoring Schemes for Wastewater-Based Epidemiology to Identify Drug Use Trends Using Cocaine, Methamphetamine, MDMA and Methadone.

scientific article

Evolutionary analyses of large data sets : trees and beyond

2001 doctoral thesis by Barbara Ruth Holland at Massey University

Extensive population decline in the Tasmanian devil predates European settlement and devil facial tumour disease

scientific article

Faster exact maximum parsimony search with XMP.

scientific article published on 27 March 2011

Gaps: An Elusive Source of Phylogenetic Information

scientific article published on 21 March 2012

Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences

scientific article

Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon.

scientific article published on February 2017

Habitat type and dispersal mode underlie the capacity for plant migration across an intermittent seaway.

scientific article

Heterozygosity and functional allelic variation in the Candida albicans efflux pump genes CDR1 and CDR2.

scientific article

Identifying cliques of convergent characters: concerted evolution in the cormorants and shags

scientific article published on 14 May 2010

Impact of genetic background on allele selection in a highly mutable Candida albicans gene, PNG2.

scientific article

Imputing supertrees and supernetworks from quartets

scientific article published in February 2007

Is the general time-reversible model bad for molecular phylogenetics?

scientific article published on 22 March 2012

Last hope for the doomed? Thoughts on the importance of a parasexual cycle for the yeast Candida albicans

scientific article

LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites

scientific article

LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites

scientific article published in 2009

Live bearing promotes the evolution of sociality in reptiles

scientific article published on 11 December 2017

Low-parameter phylogenetic inference under the general markov model

scientific article published on 22 August 2012

Maximum likelihood estimates of pairwise rearrangement distances

scientific article

Missing data and influential sites: choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice

scientific article (publication date: 2013)

Molecular epidemiology of Campylobacter jejuni isolates from wild-bird fecal material in children's playgrounds

scientific article published in December 2008

Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses

scientific article published on July 2003

Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach

scientific article published on 01 October 2000

Novel distances for dollo data

scientific article

Optimal alphabets for an RNA world

scientific article (publication date: 7 June 2003)

Optimizing automated AFLP scoring parameters to improve phylogenetic resolution

scientific article published in 2008

Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock--A Simulation Study

scholarly article by B. R. Holland et al published 1 April 2003 in Systematic Biology

Outgroup misplacement and phylogenetic inaccuracy under a molecular clock--a simulation study.

scientific article published in April 2003

Patterns of Reproductive Isolation in Eucalyptus-A Phylogenetic Perspective

scientific article published on 16 March 2015

Phylogenetic tree reconstruction accuracy and model fit when proportions of variable sites change across the tree

scientific article

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny

scientific article

Quantification of historical livestock importation into New Zealand 1860-1979.

scientific article published on 26 June 2014

Radiocarbon dating of Sacred Ibis mummies from ancient Egypt

scholarly article by Sally Wasef et al published December 2015 in Journal of Archaeological Science: Reports

Rates of evolution in ancient DNA from Adélie penguins.

scientific article

Reconciling molecules and morphology: molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria).

scientific article

Reconstructing past changes in locus-specific recombination rates

scientific article published on 25 February 2013

Searching factors causing implausible non-monophyly: ssu rDNA phylogeny of Isopoda Asellota (Crustacea: Peracarida) and faster evolution in marine than in freshwater habitats

scientific article

Selecting representative model micro-organisms

scientific article

Selective Advantages of a Parasexual Cycle for the Yeast Candida albicans

scientific article

Simulating and Summarizing Sources of Gene Tree Incongruence

scientific article

Sixty alleles of the ALS7 open reading frame in Candida albicans: ALS7 is a hypermutable contingency locus

scientific article

Supermatrices, supertrees and serendipitous scaffolding: inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data

scientific article

Testing the effect of metabolic rate on DNA variability at the intra-specific level

scientific article (publication date: 15 March 2010)

The Ancient Operational Code is Embedded in the Amino Acid Substitution Matrix and aaRS Phylogenies

scientific article published on 28 November 2019

The K-bit-swap

The MinMax Squeeze: guaranteeing a minimal tree for population data.

scientific article

The algebra of the general Markov model on phylogenetic trees and networks

scientific article published in April 2012

The emergence of predators in early life: there was no Garden of Eden

scientific article (publication date: 3 June 2009)

The identification of concerted convergence in insect heads corroborates palaeoptera

scientific article published on 23 November 2012

The problem of rooting rapid radiations

scientific article published on 23 August 2007

Treeness triangles: visualizing the loss of phylogenetic signal

scientific article published on 13 July 2007

Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks

scientific article

Upper bounds on maximum likelihood for phylogenetic trees

scientific article published on 01 October 2003

Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny

article

Using supernetworks to distinguish hybridization from lineage-sorting

scientific article

Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods

scientific article published in February 2005

List of works by Barbara Holland

A futile act? Thoughts on the reproductive biology of Candida albicans

A new phylogenetic protocol: Dealing with model misspecification and confirmation bias in molecular phylogenetics

A novel exploratory method for visual recombination detection

A tensorial approach to the inversion of group-based phylogenetic models

Analysis of Acorus calamus chloroplast genome and its phylogenetic implications.

Analysis of Phylogenetics and Evolution with R

Analysis of a mechanistic Markov model for gene duplicates evolving under subfunctionalization

Benchmarking Methods of Protein Structure Alignment

Biogeography of circum-Antarctic springtails

Brenner's Encyclopedia of Genetics (Second Edition) – Copyright

Campylobacter jejuni colonization and population structure in urban populations of ducks and starlings in New Zealand

Conflict amongst chloroplast DNA sequences obscures the phylogeny of a group of Asplenium ferns

Deciphering past human population movements in Oceania: provably optimal trees of 127 mtDNA genomes

Detecting Selection on Temporal and Spatial Scales: A Genomic Time-Series Assessment of Selective Responses to Devil Facial Tumor Disease ⬇️

Developing a statistically powerful measure for quartet tree inference using phylogenetic identities and Markov invariants.

Distinguishing Between Convergent Evolution and Violation of the Molecular Clock for Three Taxa

Distribution of mutations distinguishing the most prevalent disease-causing Candida albicans genotype from other genotypes

Estimating the relative rate of recombination to mutation in bacteria from single-locus variants using composite likelihood methods ⬇️

Estimating the relative roles of recombination and point mutation in the generation of single locus variants in Campylobacter jejuni and Campylobacter coli

Evaluation of Monitoring Schemes for Wastewater-Based Epidemiology to Identify Drug Use Trends Using Cocaine, Methamphetamine, MDMA and Methadone.

Evolutionary analyses of large data sets : trees and beyond

Extensive population decline in the Tasmanian devil predates European settlement and devil facial tumour disease

Faster exact maximum parsimony search with XMP.

Gaps: An Elusive Source of Phylogenetic Information

Genome BLAST distance phylogenies inferred from whole plastid and whole mitochondrion genome sequences

Genomic Scans across Three Eucalypts Suggest that Adaptation to Aridity is a Genome-Wide Phenomenon.

Habitat type and dispersal mode underlie the capacity for plant migration across an intermittent seaway.

Heterozygosity and functional allelic variation in the Candida albicans efflux pump genes CDR1 and CDR2.

Identifying cliques of convergent characters: concerted evolution in the cormorants and shags

Impact of genetic background on allele selection in a highly mutable Candida albicans gene, PNG2.

Imputing supertrees and supernetworks from quartets

Is the general time-reversible model bad for molecular phylogenetics?

Last hope for the doomed? Thoughts on the importance of a parasexual cycle for the yeast Candida albicans

LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites

LineageSpecificSeqgen: generating sequence data with lineage-specific variation in the proportion of variable sites

Live bearing promotes the evolution of sociality in reptiles

Low-parameter phylogenetic inference under the general markov model

Maximum likelihood estimates of pairwise rearrangement distances

Missing data and influential sites: choice of sites for phylogenetic analysis can be as important as taxon sampling and model choice

Molecular epidemiology of Campylobacter jejuni isolates from wild-bird fecal material in children's playgrounds

Mosaic genomes of the six major primate lentivirus lineages revealed by phylogenetic analyses

Multiple Maxima of Likelihood in Phylogenetic Trees: An Analytic Approach

Novel distances for dollo data

Optimal alphabets for an RNA world

Optimizing automated AFLP scoring parameters to improve phylogenetic resolution

Outgroup Misplacement and Phylogenetic Inaccuracy Under a Molecular Clock--A Simulation Study

Outgroup misplacement and phylogenetic inaccuracy under a molecular clock--a simulation study.

Patterns of Reproductive Isolation in Eucalyptus-A Phylogenetic Perspective

Phylogenetic tree reconstruction accuracy and model fit when proportions of variable sites change across the tree

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Improved consensus network techniques for genome-scale phylogeny

Quantification of historical livestock importation into New Zealand 1860-1979.

Radiocarbon dating of Sacred Ibis mummies from ancient Egypt

Rates of evolution in ancient DNA from Adélie penguins.

Reconciling molecules and morphology: molecular systematics and biogeography of Neotropical blennies (Acanthemblemaria).

Reconstructing past changes in locus-specific recombination rates

Searching factors causing implausible non-monophyly: ssu rDNA phylogeny of Isopoda Asellota (Crustacea: Peracarida) and faster evolution in marine than in freshwater habitats

Selecting representative model micro-organisms

Selective Advantages of a Parasexual Cycle for the Yeast Candida albicans

Simulating and Summarizing Sources of Gene Tree Incongruence

Sixty alleles of the ALS7 open reading frame in Candida albicans: ALS7 is a hypermutable contingency locus

Supermatrices, supertrees and serendipitous scaffolding: inferring a well-resolved, genus-level phylogeny of Styphelioideae (Ericaceae) despite missing data

Testing the effect of metabolic rate on DNA variability at the intra-specific level

The Ancient Operational Code is Embedded in the Amino Acid Substitution Matrix and aaRS Phylogenies

The K-bit-swap

The MinMax Squeeze: guaranteeing a minimal tree for population data.

The algebra of the general Markov model on phylogenetic trees and networks

The emergence of predators in early life: there was no Garden of Eden

The identification of concerted convergence in insect heads corroborates palaeoptera

The problem of rooting rapid radiations

Treeness triangles: visualizing the loss of phylogenetic signal

Untangling long branches: identifying conflicting phylogenetic signals using spectral analysis, neighbor-net, and consensus networks

Upper bounds on maximum likelihood for phylogenetic trees

Using Consensus Networks to Visualize Contradictory Evidence for Species Phylogeny

Using supernetworks to distinguish hybridization from lineage-sorting

Visualizing conflicting evolutionary hypotheses in large collections of trees: using consensus networks to study the origins of placentals and hexapods

Δ additive and Δ ultra-additive maps, Gromov's trees, and the Farris transform