List of works - Matthew L Settles

A 2cM genome-wide scan of European Holstein cattle affected by classical BSE.

scientific article

A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae)

scientific article published in February 2016

A forward genetic screen reveals that calcium-dependent protein kinase 3 regulates egress in Toxoplasma

scientific article

A whole genome association analysis identifies loci associated withMycobacterium aviumsubsp.paratuberculosisinfection status in US holstein cattle

scientific article published on 24 April 2009

Alterations in the developing testis transcriptome following embryonic vinclozolin exposure

scientific article

An improved algorithm for the detection of genomic variation using short oligonucleotide expression microarrays

scientific article

Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio)

scientific article

Breeding swarms

Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures

scientific article published on 17 December 2014

Draft Genome Sequence of Pseudomonas moraviensis R28-S.

scientific article published on 20 February 2014

Draft Genome Sequence of Pseudomonas sp. nov. H2.

scientific article

Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio).

scientific article published on 26 August 2008

Elevated dairy fat intake in lactating women alters milk lipid and fatty acids without detectible changes in expression of genes related to lipid uptake or synthesis

scientific article published on 19 January 2015

Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome

scientific article

Epigenetic transgenerational inheritance of vinclozolin induced mouse adult onset disease and associated sperm epigenome biomarkers

scientific article

Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance

scientific article published on 14 December 2015

Experimental sink removal induces stress responses, including shifts in amino acid and phenylpropanoid metabolism, in soybean leaves

scientific article published on 23 November 2011

Fecal Microbial Community Structure Is Stable over Time and Related to Variation in Macronutrient and Micronutrient Intakes in Lactating Women

scientific article published on 26 August 2015

Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp

scientific article

Full Mitochondrial Genome Sequence of the Sugar Beet Wireworm Limonius californicus (Coleoptera: Elateridae), a Common Agricultural Pest

scientific article

GSEA-SNP identifies genes associated with Johne's disease in cattle

scientific article published on 13 August 2010

Genome-wide scan identifies loci associated with classical BSE occurrence

scientific article

Genome-wide transcriptional response of Silurana (Xenopus) tropicalis to infection with the deadly chytrid fungus

scientific article

Global analysis of phase variation in Myxococcus xanthus

scientific article

Identification of loci associated with tolerance to Johne's disease in Holstein cattle.

scientific article published in February 2011

Influence of organic loading rate and solid retention time on polyhydroxybutyrate production from hybrid poplar hydrolysates using mixed microbial cultures

scientific article

Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

scientific article

MasABK proteins interact with proteins of the type IV pilin system to affect social motility of Myxococcus xanthus

scientific article

Maternal bisphenol a exposure impacts the fetal heart transcriptome

scientific article (publication date: 2014)

Meta-analysis of transcripts associated with race-specific resistance to stripe rust in wheat demonstrates common induction of blue copper-binding protein, heat-stress transcription factor, pathogen-induced WIR1A protein, and ent-kaurene synthase tr

scientific article

Meta-analysis of two genome-wide association studies of bovine paratuberculosis

scientific article (publication date: 2012)

Microbiota of the seminal fluid from healthy and infertile men.

scientific article published on 29 August 2013

Mitochondrial Genome Sequence of the Galápagos Endemic Land Snail Naesiotus nux.

scientific article

OTUbase: an R infrastructure package for operational taxonomic unit data

scientific article

Only skin deep: shared genetic response to the deadly chytrid fungus in susceptible frog species

scientific article

PRNP haplotype associated with classical BSE incidence in European Holstein cattle

scientific article

Phase variation in Myxococcus xanthus yields cells specialized for iron sequestration

scientific article

Prenatal exposure to BPA alters the epigenome of the rat mammary gland and increases the propensity to neoplastic development

scientific article

Sex-specific transcriptional responses of the zebrafish (Danio rerio) brain selenoproteome to acute sodium selenite supplementation

scientific article published on 04 June 2013

Sexual dimorphism in hepatic gene expression and the response to dietary carbohydrate manipulation in the zebrafish (Danio rerio)

scientific article

Soil bacterial communities of different natural forest types in Northeast China

article

Substrate-specific gene expression in Batrachochytrium dendrobatidis, the chytrid pathogen of amphibians

scientific article

Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus

scientific article published on 10 May 2008

The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards

scientific article published on 12 September 2015

The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation

scientific article

Transcriptome analysis of high-temperature adult-plant resistance conditioned by Yr39 during the wheat-Puccinia striiformis f. sp. tritici interaction

scientific article

Vaginal microbiome changes with levonorgestrel intrauterine system placement.

scientific article

Vaginal microbiota of adolescent girls prior to the onset of menarche resemble those of reproductive-age women

scientific article published on 24 March 2015

mcaGUI: microbial community analysis R-Graphical User Interface (GUI).

scientific article

List of works by Matthew L Settles

A 2cM genome-wide scan of European Holstein cattle affected by classical BSE.

A Phylogenomic Approach Based on PCR Target Enrichment and High Throughput Sequencing: Resolving the Diversity within the South American Species of Bartsia L. (Orobanchaceae)

A forward genetic screen reveals that calcium-dependent protein kinase 3 regulates egress in Toxoplasma

A whole genome association analysis identifies loci associated withMycobacterium aviumsubsp.paratuberculosisinfection status in US holstein cattle

Alterations in the developing testis transcriptome following embryonic vinclozolin exposure

An improved algorithm for the detection of genomic variation using short oligonucleotide expression microarrays

Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio)

Breeding swarms

Breeding swarms

Comparative analysis of microbial community of novel lactic acid fermentation inoculated with different undefined mixed cultures

Draft Genome Sequence of Pseudomonas moraviensis R28-S.

Draft Genome Sequence of Pseudomonas sp. nov. H2.

Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio).

Elevated dairy fat intake in lactating women alters milk lipid and fatty acids without detectible changes in expression of genes related to lipid uptake or synthesis

Epigenetic transgenerational actions of vinclozolin on promoter regions of the sperm epigenome

Epigenetic transgenerational inheritance of vinclozolin induced mouse adult onset disease and associated sperm epigenome biomarkers

Evolutionary Paths That Expand Plasmid Host-Range: Implications for Spread of Antibiotic Resistance

Experimental sink removal induces stress responses, including shifts in amino acid and phenylpropanoid metabolism, in soybean leaves

Fecal Microbial Community Structure Is Stable over Time and Related to Variation in Macronutrient and Micronutrient Intakes in Lactating Women

Fine-scale analysis of 16S rRNA sequences reveals a high level of taxonomic diversity among vaginal Atopobium spp

Full Mitochondrial Genome Sequence of the Sugar Beet Wireworm Limonius californicus (Coleoptera: Elateridae), a Common Agricultural Pest

GSEA-SNP identifies genes associated with Johne's disease in cattle

Genome-wide scan identifies loci associated with classical BSE occurrence

Genome-wide transcriptional response of Silurana (Xenopus) tropicalis to infection with the deadly chytrid fungus

Global analysis of phase variation in Myxococcus xanthus

Identification of loci associated with tolerance to Johne's disease in Holstein cattle.

Influence of organic loading rate and solid retention time on polyhydroxybutyrate production from hybrid poplar hydrolysates using mixed microbial cultures

Large-scale analysis of antisense transcription in wheat using the Affymetrix GeneChip Wheat Genome Array

MasABK proteins interact with proteins of the type IV pilin system to affect social motility of Myxococcus xanthus

Maternal bisphenol a exposure impacts the fetal heart transcriptome

Meta-analysis of transcripts associated with race-specific resistance to stripe rust in wheat demonstrates common induction of blue copper-binding protein, heat-stress transcription factor, pathogen-induced WIR1A protein, and ent-kaurene synthase tr

Meta-analysis of two genome-wide association studies of bovine paratuberculosis

Microbiota of the seminal fluid from healthy and infertile men.

Mitochondrial Genome Sequence of the Galápagos Endemic Land Snail Naesiotus nux.

OTUbase: an R infrastructure package for operational taxonomic unit data

Only skin deep: shared genetic response to the deadly chytrid fungus in susceptible frog species

PRNP haplotype associated with classical BSE incidence in European Holstein cattle

Phase variation in Myxococcus xanthus yields cells specialized for iron sequestration

Prenatal exposure to BPA alters the epigenome of the rat mammary gland and increases the propensity to neoplastic development

Sex-specific transcriptional responses of the zebrafish (Danio rerio) brain selenoproteome to acute sodium selenite supplementation

Sexual dimorphism in hepatic gene expression and the response to dietary carbohydrate manipulation in the zebrafish (Danio rerio)

Soil bacterial communities of different natural forest types in Northeast China

Substrate-specific gene expression in Batrachochytrium dendrobatidis, the chytrid pathogen of amphibians

Surveying expression level polymorphism and single-feature polymorphism in near-isogenic wheat lines differing for the Yr5 stripe rust resistance locus

The population genomics of rapid adaptation: disentangling signatures of selection and demography in white sands lizards

The role of clonal interference in the evolutionary dynamics of plasmid-host adaptation

Transcriptome analysis of high-temperature adult-plant resistance conditioned by Yr39 during the wheat-Puccinia striiformis f. sp. tritici interaction

Vaginal microbiome changes with levonorgestrel intrauterine system placement.

Vaginal microbiota of adolescent girls prior to the onset of menarche resemble those of reproductive-age women

mcaGUI: microbial community analysis R-Graphical User Interface (GUI).