List of works - Murray Cox

A Core Gene Set Describes the Molecular Basis of Mutualism and Antagonism in Epichloë spp.

scientific article published in March 2015

A flexible theoretical representation for the temporal dynamics of structured populations as paths on polytope complexes

scientific article published on 12 October 2014

A new deep branch of eurasian mtDNA macrohaplogroup M reveals additional complexity regarding the settlement of Madagascar

scientific article

A novel DNA sequence database for analyzing human demographic history

scientific article published on 20 May 2008

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

scientific article

A small cohort of Island Southeast Asian women founded Madagascar

scientific article

Accuracy of molecular dating with the rho statistic: deviations from coalescent expectations under a range of demographic models

scientific article

Accuracy of molecular dating with the rho statistic: deviations from coalescent expectations under a range of demographic models. 2008.

scientific article published in December 2009

An interspecific fungal hybrid reveals cross-kingdom rules for allopolyploid gene expression patterns

scientific article

Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian-Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates.

scientific article published on 27 January 2010

Autosomal resequence data reveal Late Stone Age signals of population expansion in sub-Saharan African foraging and farming populations

scientific article (publication date: 29 July 2009)

Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover

scientific article published on 25 April 2019

Camellia plant resistance and susceptibility to petal blight disease are defined by the timing of defence responses

scientific article published on 30 March 2020

Chromosome-Level Reference Genome of Venturia effusa, Causative Agent of Pecan Scab

scientific article published on 02 December 2019

Climate change influenced female population sizes through time across the Indonesian archipelago

scientific article

Coevolution of languages and genes on the island of Sumba, eastern Indonesia

scientific article

Complete mitochondrial DNA sequences provide new insights into the Polynesian motif and the peopling of Madagascar

scientific article published on 23 December 2009

Complex Patterns of Admixture across the Indonesian Archipelago

scientific article published in October 2017

Conservation and expansion of a necrosis-inducing small secreted protein family from host-variable phytopathogens of the Sclerotiniaceae

scientific article published on 15 February 2020

Contrasting signatures of population growth for mitochondrial DNA and Y chromosomes among human populations in Africa.

scientific article published on 18 December 2007

Correction: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

scientific article published on 22 December 2015

Correction: The Guanine Nucleotide Exchange Factor RIC8 Regulates Conidial Germination through Gα Proteins in Neurospora crassa

scientific article published on 14 March 2013

Correlated Transcriptional Responses Provide Insights into the Synergy Mechanisms of the Furazolidone, Vancomycin, and Sodium Deoxycholate Triple Combination in Escherichia coli

scientific article published in 2021

Cross-species transcriptomics identifies core regulatory changes differentiating the asymptomatic asexual and virulent sexual life cycles of grass-symbiotic <i>Epichloë</i> fungi

scientific article published in 2022

Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity

scientific article published on 18 September 2019

Dense sampling of bird diversity increases power of comparative genomics

scientific article published on 11 November 2020

Disruption of signaling in a fungal-grass symbiosis leads to pathogenesis

scientific article

Dothistromin genes at multiple separate loci are regulated by AflR

article

Draft Genome Sequence of the Filamentous Fungus Penicillium paxilli (ATCC 26601)

scientific article

Draft Genome Sequences of Three Strains of Geobacillus stearothermophilus Isolated from a Milk Powder Manufacturing Plant

scientific article published on 15 October 2015

Epichloë hybrida, sp. nov., an emerging model system for investigating fungal allopolyploidy.

scientific article

Evolution of virulence in a novel family of transmissible mega‐plasmids

scientific article published in 2021

Exploring molecular signaling in plant-fungal symbioses using high throughput RNA sequencing

scientific article

Fragmentation of an aflatoxin-like gene cluster in a forest pathogen

scientific article

Fungal endophyte infection of ryegrass reprograms host metabolism and alters development

scientific article

Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with global and local ancestries

scientific article published on 16 December 2021

Genetic continuity across a deeply divergent linguistic contact zone in North Maluku, Indonesia

scientific article

Genetic patterning at Austronesian contact zones ⬇️

2003 doctoral thesis by Murray Paul Cox at University of Otago

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago

scientific article published on 26 May 2020

Genome-wide gene expression dynamics of the fungal pathogen Dothistroma septosporum throughout its infection cycle of the gymnosperm host Pinus radiata.

scientific article published on 28 April 2015

Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi

scientific article

Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi

scientific article published on 06 November 2019

High Frequency Haplotypes are Expected Events, not Historical Figures.

scientific article

HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species.

scientific article

Indonesian mitochondrial DNA and its opposition to a Pleistocene era origin of proto-Polynesians in island southeast Asia.

scientific article

Inferring human population sizes, divergence times and rates of gene flow from mitochondrial, X and Y chromosome resequencing data

scientific article

Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow

scientific article

Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles

scientific article published on 29 January 2018

Isolation, contact and social behavior shaped genetic diversity in West Timor

scientific article

Kinship structures create persistent channels for language transmission

scientific article published on 20 November 2017

Major east-west division underlies Y chromosome stratification across Indonesia

scientific article

Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations

scientific article

Molecular Cloning and Functional Analysis of Gene Clusters for the Biosynthesis of Indole-Diterpenes in Penicillium crustosum and P. janthinellum. ⬇️

scientific article published on 23 July 2015

Mycelial biomass and concentration of loline alkaloids driven by complex population structure in Epichloë uncinata and meadow fescue (Schedonorus pratensis)

scientific article published on 15 May 2020

Māori oral traditions record and convey indigenous knowledge of marine and freshwater resources

Opportunities for modern genetic technologies to maintain and enhance Aotearoa New Zealand’s bioheritage

scientific article

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci

scientific article published in 2013

Population growth of Mexican free-tailed bats (Tadarida brasiliensis mexicana) predates human agricultural activity

scientific article

Recombination-filtered genomic datasets by information maximization.

scientific article published on 22 May 2007

Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia.

scientific article published on 28 September 2016

Reconstructing Past Admixture Processes from Local Genomic Ancestry Using Wavelet Transformation.

scientific article published on 7 April 2015

Reconstructing Social Prehistory from Genomic Data in the Indo-Pacific Region ⬇️

2017 doctoral thesis by Murray Paul Cox at University of Otago

Reconstructing past changes in locus-specific recombination rates

scientific article published on 25 February 2013

Regime shifts in Balinese subaks.

scientific article

Relaxed Observance of Traditional Marriage Rules Allows Social Connectivity without Loss of Genetic Diversity.

scientific article published on 12 May 2015

Repeat elements organize 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae

article

SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations.

scientific article

Semi-automatic selection of summary statistics for ABC model choice

scientific article

Sex-biased evolutionary forces shape genomic patterns of human diversity

scientific article published in 2008

Sex-linked genetic diversity originates from persistent sociocultural processes at microgeographic scales

scientific article published on 28 August 2019

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data ⬇️

scientific article published on September 27, 2010

Testing for archaic hominin admixture on the X chromosome: model likelihoods for the modern human RRM2P4 region from summaries of genealogical topology under the structured coalescent

scientific article

The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific

scientific article

The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry

scientific article

The guanine nucleotide exchange factor RIC8 regulates conidial germination through Gα proteins in Neurospora crassa

scientific article

The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes

article

Warfare induces post-marital residence change

scientific article published on 03 May 2019

What triggers grass endophytes to switch from mutualism to pathogenism?

scientific article published on 16 October 2010

Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture

scientific article published in 2021

Y-chromosome diversity is inversely associated with language affiliation in paired Austronesian- and Papuan-speaking communities from Solomon Islands

scientific article

List of works by Murray Cox

A Core Gene Set Describes the Molecular Basis of Mutualism and Antagonism in Epichloë spp.

A flexible theoretical representation for the temporal dynamics of structured populations as paths on polytope complexes

A new deep branch of eurasian mtDNA macrohaplogroup M reveals additional complexity regarding the settlement of Madagascar

A novel DNA sequence database for analyzing human demographic history

A recent bottleneck of Y chromosome diversity coincides with a global change in culture

A small cohort of Island Southeast Asian women founded Madagascar

Accuracy of molecular dating with the rho statistic: deviations from coalescent expectations under a range of demographic models

Accuracy of molecular dating with the rho statistic: deviations from coalescent expectations under a range of demographic models. 2008.

An interspecific fungal hybrid reveals cross-kingdom rules for allopolyploid gene expression patterns

Autosomal and X-linked single nucleotide polymorphisms reveal a steep Asian-Melanesian ancestry cline in eastern Indonesia and a sex bias in admixture rates.

Autosomal resequence data reveal Late Stone Age signals of population expansion in sub-Saharan African foraging and farming populations

Breaking Free: The Genomics of Allopolyploidy-Facilitated Niche Expansion in White Clover

Camellia plant resistance and susceptibility to petal blight disease are defined by the timing of defence responses

Chromosome-Level Reference Genome of Venturia effusa, Causative Agent of Pecan Scab

Climate change influenced female population sizes through time across the Indonesian archipelago

Coevolution of languages and genes on the island of Sumba, eastern Indonesia

Complete mitochondrial DNA sequences provide new insights into the Polynesian motif and the peopling of Madagascar

Complex Patterns of Admixture across the Indonesian Archipelago

Conservation and expansion of a necrosis-inducing small secreted protein family from host-variable phytopathogens of the Sclerotiniaceae

Contrasting signatures of population growth for mitochondrial DNA and Y chromosomes among human populations in Africa.

Correction: The Genomes of the Fungal Plant Pathogens Cladosporium fulvum and Dothistroma septosporum Reveal Adaptation to Different Hosts and Lifestyles But Also Signatures of Common Ancestry

Correction: The Guanine Nucleotide Exchange Factor RIC8 Regulates Conidial Germination through Gα Proteins in Neurospora crassa

Correlated Transcriptional Responses Provide Insights into the Synergy Mechanisms of the Furazolidone, Vancomycin, and Sodium Deoxycholate Triple Combination in Escherichia coli

Cross-species transcriptomics identifies core regulatory changes differentiating the asymptomatic asexual and virulent sexual life cycles of grass-symbiotic <i>Epichloë</i> fungi

Denisovan, modern human and mouse TNFAIP3 alleles tune A20 phosphorylation and immunity

Dense sampling of bird diversity increases power of comparative genomics

Disruption of signaling in a fungal-grass symbiosis leads to pathogenesis

Dothistromin genes at multiple separate loci are regulated by AflR

Draft Genome Sequence of the Filamentous Fungus Penicillium paxilli (ATCC 26601)

Draft Genome Sequences of Three Strains of Geobacillus stearothermophilus Isolated from a Milk Powder Manufacturing Plant

Epichloë hybrida, sp. nov., an emerging model system for investigating fungal allopolyploidy.

Evolution of virulence in a novel family of transmissible mega‐plasmids

Exploring molecular signaling in plant-fungal symbioses using high throughput RNA sequencing

Fragmentation of an aflatoxin-like gene cluster in a forest pathogen

Fungal endophyte infection of ryegrass reprograms host metabolism and alters development

Genetic architecture of gene regulation in Indonesian populations identifies QTLs associated with global and local ancestries

Genetic continuity across a deeply divergent linguistic contact zone in North Maluku, Indonesia

Genetic patterning at Austronesian contact zones ⬇️

Genome-wide DNA methylation and gene expression patterns reflect genetic ancestry and environmental differences across the Indonesian archipelago

Genome-wide gene expression dynamics of the fungal pathogen Dothistroma septosporum throughout its infection cycle of the gymnosperm host Pinus radiata.

Genomic Data Quality Impacts Automated Detection of Lateral Gene Transfer in Fungi

Greater genetic and regulatory plasticity of retained duplicates in Epichloë endophytic fungi

High Frequency Haplotypes are Expected Events, not Historical Figures.

HyLiTE: accurate and flexible analysis of gene expression in hybrid and allopolyploid species.

Indonesian mitochondrial DNA and its opposition to a Pleistocene era origin of proto-Polynesians in island southeast Asia.

Inferring human population sizes, divergence times and rates of gene flow from mitochondrial, X and Y chromosome resequencing data

Intergenic DNA sequences from the human X chromosome reveal high rates of global gene flow

Investigating the origins of eastern Polynesians using genome-wide data from the Leeward Society Isles

Isolation, contact and social behavior shaped genetic diversity in West Timor

Kinship structures create persistent channels for language transmission

Major east-west division underlies Y chromosome stratification across Indonesia

Mitochondrial DNA and the Y chromosome suggest the settlement of Madagascar by Indonesian sea nomad populations

Molecular Cloning and Functional Analysis of Gene Clusters for the Biosynthesis of Indole-Diterpenes in Penicillium crustosum and P. janthinellum. ⬇️

Mycelial biomass and concentration of loline alkaloids driven by complex population structure in Epichloë uncinata and meadow fescue (Schedonorus pratensis)

Māori oral traditions record and convey indigenous knowledge of marine and freshwater resources

Opportunities for modern genetic technologies to maintain and enhance Aotearoa New Zealand’s bioheritage

Plant-symbiotic fungi as chemical engineers: multi-genome analysis of the clavicipitaceae reveals dynamics of alkaloid loci

Population growth of Mexican free-tailed bats (Tadarida brasiliensis mexicana) predates human agricultural activity

Recombination-filtered genomic datasets by information maximization.

Reconstructing Demography and Social Behavior During the Neolithic Expansion from Genomic Diversity Across Island Southeast Asia.

Reconstructing Past Admixture Processes from Local Genomic Ancestry Using Wavelet Transformation.

Reconstructing Social Prehistory from Genomic Data in the Indo-Pacific Region ⬇️

Reconstructing past changes in locus-specific recombination rates

Regime shifts in Balinese subaks.

Relaxed Observance of Traditional Marriage Rules Allows Social Connectivity without Loss of Genetic Diversity.

Repeat elements organize 3D genome structure and mediate transcription in the filamentous fungus Epichloë festucae

SMARTPOP: inferring the impact of social dynamics on genetic diversity through high speed simulations.

Semi-automatic selection of summary statistics for ABC model choice

Sex-biased evolutionary forces shape genomic patterns of human diversity

Sex-linked genetic diversity originates from persistent sociocultural processes at microgeographic scales

SolexaQA: At-a-glance quality assessment of Illumina second-generation sequencing data ⬇️

Testing for archaic hominin admixture on the X chromosome: model likelihoods for the modern human RRM2P4 region from summaries of genealogical topology under the structured coalescent

The Indonesian archipelago: an ancient genetic highway linking Asia and the Pacific

The genomes of the fungal plant pathogens Cladosporium fulvum and Dothistroma septosporum reveal adaptation to different hosts and lifestyles but also signatures of common ancestry

The guanine nucleotide exchange factor RIC8 regulates conidial germination through Gα proteins in Neurospora crassa

The ratio of human X chromosome to autosome diversity is positively correlated with genetic distance from genes

Warfare induces post-marital residence change

What triggers grass endophytes to switch from mutualism to pathogenism?

Widespread Denisovan ancestry in Island Southeast Asia but no evidence of substantial super-archaic hominin admixture