List of works - Murray Cox

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

scientific article published on September 27, 2010

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

scientific article published in 2013

Recombination-filtered genomic datasets by information maximization

scientific article published on 22 May 2007

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

scientific article

Genomic analyses inform on migration events during the peopling of Eurasia

scientific article (publication date: 13 October 2016)

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

Sex-biased evolutionary forces shape genomic patterns of human diversity

scientific article published in 2008

Major east-west division underlies Y chromosome stratification across Indonesia

scientific article

A novel DNA sequence database for analyzing human demographic history

scientific article published on 20 May 2008

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

article

Genomic insights into the peopling of the Southwest Pacific

scientific article (publication date: 3 October 2016)

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

scientific article

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

scientific article

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

scientific article

What triggers grass endophytes to switch from mutualism to pathogenism?

scientific article published on 16 October 2010

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

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

scientific article

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

scientific article published on 18 December 2007

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

scientific article

Fungal endophyte infection of ryegrass reprograms host metabolism and alters development

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

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)

A small cohort of Island Southeast Asian women founded Madagascar

scientific article

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

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

Male dominance rarely skews the frequency distribution of Y chromosome haplotypes in human populations

scholarly article

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

scientific article published in March 2015

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

scientific article

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

scientific article

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

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

scientific article

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

scientific article

Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo

scientific article

Multiple Deeply Divergent Denisovan Ancestries in Papuans

scientific article published on 11 April 2019

Complex Patterns of Admixture across the Indonesian Archipelago

scientific article published in October 2017

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

scientific article

The Case of the Missing Ancient Fungal Polyploids

scientific article published on 26 September 2016

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

scientific article published in April 2005

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

scientific article

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

article

Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy

scientific article

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

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

scientific article

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

scientific article

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

scientific article published on 7 April 2015

Semi-automatic selection of summary statistics for ABC model choice

scientific article

Dothistromin genes at multiple separate loci are regulated by AflR

article

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

scientific article

A Polynesian motif on the Y chromosome: population structure in remote Oceania

scientific article

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

scientific article

List of works by Murray Cox

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

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

Recombination-filtered genomic datasets by information maximization

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

Genomic analyses inform on migration events during the peopling of Eurasia

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

Sex-biased evolutionary forces shape genomic patterns of human diversity

Major east-west division underlies Y chromosome stratification across Indonesia

A novel DNA sequence database for analyzing human demographic history

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

Genomic insights into the peopling of the Southwest Pacific

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

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

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

What triggers grass endophytes to switch from mutualism to pathogenism?

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

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

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

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

Fungal endophyte infection of ryegrass reprograms host metabolism and alters development

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

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

A small cohort of Island Southeast Asian women founded Madagascar

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

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

Male dominance rarely skews the frequency distribution of Y chromosome haplotypes in human populations

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

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

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

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

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

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

Malagasy Genetic Ancestry Comes from an Historical Malay Trading Post in Southeast Borneo

Multiple Deeply Divergent Denisovan Ancestries in Papuans

Complex Patterns of Admixture across the Indonesian Archipelago

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

The Case of the Missing Ancient Fungal Polyploids

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

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

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

Contrasting Linguistic and Genetic Origins of the Asian Source Populations of Malagasy

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

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

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

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

Semi-automatic selection of summary statistics for ABC model choice

Dothistromin genes at multiple separate loci are regulated by AflR

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

A Polynesian motif on the Y chromosome: population structure in remote Oceania

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