List of works - Dan Nettleton

A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence

scientific article

A discussion of statistical methods for design and analysis of microarray experiments for plant scientists.

scientific article published in September 2006

A hidden Markov tree model for testing multiple hypotheses corresponding to Gene Ontology gene sets.

scientific article published on 27 March 2018

A hierarchical semiparametric model for incorporating intergene information for analysis of genomic data.

scientific article

A novel approach for characterizing expression levels of genes duplicated by polyploidy

scientific article

A systems biology approach toward understanding seed composition in soybean

scientific article

Accounting for host cell protein behavior in anion-exchange chromatography.

scientific article published on 24 August 2016

Accounting for spot matching uncertainty in the analysis of proteomics data from two-dimensional gel electrophoresis

Accounting for variability in the use of permutation testing to detect quantitative trait loci.

scientific article published in March 2000

Adjusting for gene-specific covariates to improve RNA-seq analysis

scientific article published in August 2023

Agrobacterium tumefaciens-mediated transformation of maize embryos using a standard binary vector system.

scientific article

All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents

scholarly article

Analysis of porcine transcriptional response to Salmonella enterica serovar Choleraesuis suggests novel targets of NFkappaB are activated in the mesenteric lymph node

scientific article

ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity of Avian Pathogenic Escherichia coli

scientific article published on 22 June 2015

Array-based genomic comparative hybridization analysis of field strains of Mycoplasma hyopneumoniae

scientific article

BarleyBase--an expression profiling database for plant genomics

scientific article

Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlate with fungal penetration and haustoria formation

scientific article published on 26 July 2011

Borrowing information across genes and experiments for improved error variance estimation in microarray data analysis

scientific article

Broadly Conserved Fungal Effector BEC1019 Suppresses Host Cell Death and Enhances Pathogen Virulence in Powdery Mildew of Barley (Hordeum vulgare L.).

scientific article published on 4 May 2015

Changes in genome content generated via segregation of non-allelic homologs

scientific article published on 30 August 2012

CmeR functions as a pleiotropic regulator and is required for optimal colonization of Campylobacter jejuni in vivo

scientific article

Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene.

scientific article

Combining classical trait and microarray data to dissect transcriptional regulation: a case study.

scientific article

Comparative gene expression profiles between heterotic and non-heterotic hybrids of tetraploid Medicago sativa

scientific article published on 13 August 2009

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

scientific article

Complexity and specificity of the maize (Zea mays L.) root hair transcriptome

scientific article published on 08 April 2017

Copy number variation detection using next generation sequencing read counts.

scientific article

Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning

article

Detecting Differentially Expressed Genes with RNA-seq Data Using Backward Selection to Account for the Effects of Relevant Covariates

scientific article

Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates

scientific article

Developmental transcript profiling of cyst nematode feeding cells in soybean roots.

scientific article

Discovery and Characterization of the 3-Hydroxyacyl-ACP Dehydratase Component of the Plant Mitochondrial Fatty Acid Synthase System

scientific article published on 15 February 2017

Distinct biphasic mRNA changes in response to Asian soybean rust infection.

scientific article published on August 2007

Distinct genetic architectures for phenotype means and plasticities in Zea mays. ⬇️

scientific article published on 4 September 2017

Distinct peripheral blood RNA responses to Salmonella in pigs differing in Salmonella shedding levels: intersection of IFNG, TLR and miRNA pathways

scientific article

Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines

scientific article

Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution

scientific article

Effects of ad libitum and restricted feed intake on growth performance and body composition of Yorkshire pigs selected for reduced residual feed intake.

scientific article published on 10 September 2010

Effects of ad libitum and restricted feeding on early production performance and body composition of Yorkshire pigs selected for reduced residual feed intake

scientific article published on 01 August 2011

Empirical Bayes analysis of RNA-seq data for detection of gene expression heterosis

scientific article (publication date: December 2015)

Endometrial gene expression profiling in pregnant Meishan and Yorkshire pigs on day 12 of gestation

scientific article

Estimating the number of true null hypotheses from a histogram of p values

article

Estimation and Testing of Gene Expression Heterosis

scientific article

Estimation of false discovery rate using sequential permutation p-values.

scientific article published on 4 February 2013

Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between markers and QTL

scientific article published on 01 August 2005

Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms

scientific article published on 01 February 2007

Exploring the information in p-values for the analysis and planning of multiple-test experiments.

scientific article published in June 2007

Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit

scientific article published on 13 October 2015

Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel

scientific article published on 19 September 2015

Flor Revisited (Again): eQTL and Mutational Analysis of NB-LRR Mediated Immunity to Powdery Mildew in Barley

Gene expression in intestinal mucosal biopsy specimens obtained from dogs with chronic enteropathy.

scientific article

Gene expression programs during shoot, root, and callus development in Arabidopsis tissue culture

scientific article

Gene mapping via bulked segregant RNA-Seq (BSR-Seq).

scientific article

Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations.

scientific article published on 29 April 2016

Genetic regulation of gene expression during shoot development in Arabidopsis.

scientific article

Genome-wide methylation profile following prenatal and postnatal dietary omega-3 fatty acid supplementation in pigs.

scientific article

Genomics, prior probability, and statistical tests of multiple hypotheses.

scientific article published on June 2004

Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.).

scientific article

Global transcriptional response of porcine mesenteric lymph nodes to Salmonella enterica serovar Typhimurium.

scientific article published on 17 May 2007

Helicobacter bilis Colonization Enhances Susceptibility to Typhlocolitis Following an Inflammatory Trigger

scientific article published on 19 April 2011

Hierarchical Modeling and Differential Expression Analysis for RNA-seq Experiments with Inbred and Hybrid Genotypes

scientific article published on 5 October 2015

High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes

scientific article (publication date: 2 December 2010)

Host-Induced Gene Silencing in Barley Powdery Mildew Reveals a Class of Ribonuclease-Like Effectors

article

Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis

scientific article published on 27 November 2007

Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves

scientific article (publication date: May 2009)

Identifying genes associated with a quantitative trait or quantitative trait locus via selective transcriptional profiling

scientific article published on 01 June 2006

Improved estimation of the noncentrality parameter distribution from a large number of t-statistics, with applications to false discovery rate estimation in microarray data analysis.

scientific article

Integrating comparative expression profiling data and association of SNPs with Salmonella shedding for improved food safety and porcine disease resistance

scientific article

Inter-chromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen.

scientific article

Interaction-dependent gene expression in Mla-specified response to barley powdery mildew

scientific article

Investigation of the efficacy of albumin removal procedures on porcine serum proteome profile.

scientific article

Linear mixed model selection for false discovery rate control in microarray data analysis

scientific article published on 12 June 2009

Metabolomic Profiling of Nicotiana Spp. Nectars Indicate That Pollinator Feeding Preference Is a Stronger Determinant Than Plant Phylogenetics in Shaping Nectar Diversity

scientific article published on 22 May 2020

Microarray analysis of vegetative phase change in maize

scientific article

Microarray gene expression profiles of fasting induced changes in liver and adipose tissues of pigs expressing the melanocortin-4 receptor D298N variant.

scientific article

Microbial community sequencing analysis of the calf eye microbiota and relationship to infectious bovine keratoconjunctivitis.

scientific article

Microdissection of shoot meristem functional domains

scientific article

Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome

scientific article (publication date: November 2009)

Mucosal gene expression profiles following the colonization of immunocompetent defined-flora C3H mice with Helicobacter bilis: a prelude to typhlocolitis.

scientific article published on 14 January 2009

Non-syntenic genes drive RTCS-dependent regulation of the embryo transcriptome during formation of seminal root primordia in maize (Zea mays L.).

scientific article published on January 2017

Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids.

scientific article published on 14 October 2014

Ontogeny of the maize shoot apical meristem

scientific article

Parallel genome-wide expression profiling of host and pathogen during soybean cyst nematode infection of soybean

scientific article published on 01 March 2007

Paternal dominance of trans-eQTL influences gene expression patterns in maize hybrids

scientific article published on 01 November 2009

Pooling mRNA in microarray experiments and its effect on power

scientific article published on 07 March 2007

Post-weaning blood transcriptomic differences between Yorkshire pigs divergently selected for residual feed intake

scientific article published on 22 January 2016

Proteomics-based, multivariate random forest method for prediction of protein separation behavior during cation-exchange chromatography ⬇️

scientific article published on June 12, 2012

QQS orphan gene and its interactor NF-YC4 reduce susceptibility to pathogens and pests

article

QQSorphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions

scientific article (publication date: 9 November 2015)

Quantitative and temporal definition of the Mla transcriptional regulon during barley-powdery mildew interactions

scientific article published on June 2011

Quantitative trait loci associated with adventitious shoot formation in tissue culture and the program of shoot development in Arabidopsis.

scientific article

Random Forest Prediction Intervals

scientific article published on 4 June 2019

Reverse engineering and analysis of large genome-scale gene networks

scientific article published on 4 October 2012

Roles of the HIF-1 hypoxia-inducible factor during hypoxia response in Caenorhabditis elegans.

scientific article published on 21 March 2005

Root Type-Specific Reprogramming of Maize Pericycle Transcriptomes by Local High Nitrate Results in Disparate Lateral Root Branching Patterns

scientific article published on 25 January 2016

Salmonella enterica serovar Typhimurium-infected pigs with different shedding levels exhibit distinct clinical, peripheral cytokine and transcriptomic immune response phenotypes.

scientific article published on 14 March 2014

Scanning microarrays at multiple intensities enhances discovery of differentially expressed genes.

scientific article published on 26 May 2006

Selective transcriptional profiling for trait-based eQTL mapping

scientific article published on 01 August 2006

Sequence mining and transcript profiling to explore cyst nematode parasitism

scientific article

SimSeq: a nonparametric approach to simulation of RNA-sequence datasets.

scientific article published on 26 February 2015

Single-Parent Expression Is a General Mechanism Driving Extensive Complementation of Non-syntenic Genes in Maize Hybrids.

scientific article published on 8 January 2018

Single-parent expression complementation contributes to phenotypic heterosis in maize hybrids

scientific article published in 2022

Spatial analysis of arabidopsis thaliana gene expression in response to Turnip mosaic virus infection.

scientific article published in April 2007

Spotted cotton oligonucleotide microarrays for gene expression analysis

scientific article

Stability of Single-Parent Gene Expression Complementation in Maize Hybrids upon Water Deficit Stress.

scientific article published on 20 December 2016

Stage-specific suppression of basal defense discriminates barley plants containing fast- and delayed-acting Mla powdery mildew resistance alleles

scientific article

Substantial contribution of genetic variation in the expression of transcription factors to phenotypic variation revealed by eRD-GWAS.

scientific article published on 17 October 2017

The Arabidopsis microRNA396-GRF1/GRF3 regulatory module acts as a developmental regulator in the reprogramming of root cells during cyst nematode infection.

scientific article

The B73 Maize Genome: Complexity, Diversity, and Dynamics

scientific article

The Soybean Rhg1 locus for resistance to the soybean cyst nematode Heterodera glycines regulates the expression of a large number of stress- and defense-related genes in degenerating feeding cells.

scientific article

The effect of selection for residual feed intake on general behavioral activity and the occurrence of lesions in Yorkshire gilts1

scientific article published on 10 September 2010

The knottin-like Blufensin family regulates genes involved in nuclear import and the secretory pathway in barley-powdery mildew interactions

scientific article

The maize brown midrib4 (bm4) gene encodes a functional folylpolyglutamate synthase

scientific article

Transcript-based cloning of RRP46, a regulator of rRNA processing and R gene-independent cell death in barley-powdery mildew interactions

scientific article published on 27 October 2009

Transcriptional analysis of the global regulatory networks active in Pseudomonas syringae during leaf colonization

scientific article

Transcriptional profiling of Mycoplasma hyopneumoniae during heat shock using microarrays.

scientific article published on January 2006

Transcriptional profiling of Mycoplasma hyopneumoniae during iron depletion using microarrays

scientific article published on 01 April 2006

Transcriptional profiling of myostatin-knockout mice implicates Wnt signaling in postnatal skeletal muscle growth and hypertrophy.

scientific article published on 19 January 2006

Transcriptional profiling using a novel cDNA array identifies differential gene expression during porcine embryo elongation.

scientific article published in June 2005

Transcriptional responses of Pseudomonas syringae to growth in epiphytic versus apoplastic leaf sites

scientific article published on 14 January 2013

Transcriptomic and anatomical complexity of primary, seminal, and crown roots highlight root type-specific functional diversity in maize (Zea mays L.).

scientific article

Transformation of maize with the p1 transcription factor directs production of silk maysin, a corn earworm resistance factor, in concordance with a hierarchy of floral organ pigmentation.

scientific article published in March 2005

Unique genome-wide transcriptome profiles of chicken macrophages exposed to Salmonella-derived endotoxin.

scientific article

Use of bioinformatic SNP predictions in differentially expressed genes to find SNPs associated with Salmonella colonization in swine.

scientific article published on 17 June 2011

Using Conformal Win Probability to Predict the Winners of the Canceled 2020 NCAA Basketball Tournaments

scientific article published on 21 December 2023

Validation of a first-generation long-oligonucleotide microarray for transcriptional profiling in the pig.

scientific article

List of works by Dan Nettleton

A Clade-Specific Arabidopsis Gene Connects Primary Metabolism and Senescence

A discussion of statistical methods for design and analysis of microarray experiments for plant scientists.

A hidden Markov tree model for testing multiple hypotheses corresponding to Gene Ontology gene sets.

A hierarchical semiparametric model for incorporating intergene information for analysis of genomic data.

A novel approach for characterizing expression levels of genes duplicated by polyploidy

A systems biology approach toward understanding seed composition in soybean

Accounting for host cell protein behavior in anion-exchange chromatography.

Accounting for spot matching uncertainty in the analysis of proteomics data from two-dimensional gel electrophoresis

Accounting for variability in the use of permutation testing to detect quantitative trait loci.

Adjusting for gene-specific covariates to improve RNA-seq analysis

Agrobacterium tumefaciens-mediated transformation of maize embryos using a standard binary vector system.

All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents

Analysis of porcine transcriptional response to Salmonella enterica serovar Choleraesuis suggests novel targets of NFkappaB are activated in the mesenteric lymph node

ArcA Controls Metabolism, Chemotaxis, and Motility Contributing to the Pathogenicity of Avian Pathogenic Escherichia coli

Array-based genomic comparative hybridization analysis of field strains of Mycoplasma hyopneumoniae

BarleyBase--an expression profiling database for plant genomics

Biphasic gene expression changes elicited by Phakopsora pachyrhizi in soybean correlate with fungal penetration and haustoria formation

Borrowing information across genes and experiments for improved error variance estimation in microarray data analysis

Broadly Conserved Fungal Effector BEC1019 Suppresses Host Cell Death and Enhances Pathogen Virulence in Powdery Mildew of Barley (Hordeum vulgare L.).

Changes in genome content generated via segregation of non-allelic homologs

CmeR functions as a pleiotropic regulator and is required for optimal colonization of Campylobacter jejuni in vivo

Code-assisted discovery of TAL effector targets in bacterial leaf streak of rice reveals contrast with bacterial blight and a novel susceptibility gene.

Combining classical trait and microarray data to dissect transcriptional regulation: a case study.

Comparative gene expression profiles between heterotic and non-heterotic hybrids of tetraploid Medicago sativa

Complementation contributes to transcriptome complexity in maize (Zea mays L.) hybrids relative to their inbred parents

Complexity and specificity of the maize (Zea mays L.) root hair transcriptome

Copy number variation detection using next generation sequencing read counts.

Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning

Detecting Differentially Expressed Genes with RNA-seq Data Using Backward Selection to Account for the Effects of Relevant Covariates

Detecting differential expression in RNA-sequence data using quasi-likelihood with shrunken dispersion estimates

Developmental transcript profiling of cyst nematode feeding cells in soybean roots.

Discovery and Characterization of the 3-Hydroxyacyl-ACP Dehydratase Component of the Plant Mitochondrial Fatty Acid Synthase System

Distinct biphasic mRNA changes in response to Asian soybean rust infection.

Distinct genetic architectures for phenotype means and plasticities in Zea mays. ⬇️

Distinct peripheral blood RNA responses to Salmonella in pigs differing in Salmonella shedding levels: intersection of IFNG, TLR and miRNA pathways

Divergent evolution of arrested development in the dauer stage of Caenorhabditis elegans and the infective stage of Heterodera glycines

Duplicate gene expression in allopolyploid Gossypium reveals two temporally distinct phases of expression evolution

Effects of ad libitum and restricted feed intake on growth performance and body composition of Yorkshire pigs selected for reduced residual feed intake.

Effects of ad libitum and restricted feeding on early production performance and body composition of Yorkshire pigs selected for reduced residual feed intake

Empirical Bayes analysis of RNA-seq data for detection of gene expression heterosis

Endometrial gene expression profiling in pregnant Meishan and Yorkshire pigs on day 12 of gestation

Estimating the number of true null hypotheses from a histogram of p values

Estimation and Testing of Gene Expression Heterosis

Estimation of false discovery rate using sequential permutation p-values.

Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between markers and QTL

Evaluation of linkage disequilibrium measures between multi-allelic markers as predictors of linkage disequilibrium between single nucleotide polymorphisms

Exploring the information in p-values for the analysis and planning of multiple-test experiments.

Extensive tissue-specific transcriptomic plasticity in maize primary roots upon water deficit

Extreme-phenotype genome-wide association study (XP-GWAS): a method for identifying trait-associated variants by sequencing pools of individuals selected from a diversity panel

Flor Revisited (Again): eQTL and Mutational Analysis of NB-LRR Mediated Immunity to Powdery Mildew in Barley

Gene expression in intestinal mucosal biopsy specimens obtained from dogs with chronic enteropathy.

Gene expression programs during shoot, root, and callus development in Arabidopsis tissue culture

Gene mapping via bulked segregant RNA-Seq (BSR-Seq).

Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations.

Genetic regulation of gene expression during shoot development in Arabidopsis.

Genome-wide methylation profile following prenatal and postnatal dietary omega-3 fatty acid supplementation in pigs.

Genomics, prior probability, and statistical tests of multiple hypotheses.

Global gene expression analysis of the shoot apical meristem of maize (Zea mays L.).

Global transcriptional response of porcine mesenteric lymph nodes to Salmonella enterica serovar Typhimurium.

Helicobacter bilis Colonization Enhances Susceptibility to Typhlocolitis Following an Inflammatory Trigger

Hierarchical Modeling and Differential Expression Analysis for RNA-seq Experiments with Inbred and Hybrid Genotypes

High-resolution genotyping via whole genome hybridizations to microarrays containing long oligonucleotide probes

Host-Induced Gene Silencing in Barley Powdery Mildew Reveals a Class of Ribonuclease-Like Effectors

Identification of differentially expressed gene categories in microarray studies using nonparametric multivariate analysis

Identification of the novel protein QQS as a component of the starch metabolic network in Arabidopsis leaves

Identifying genes associated with a quantitative trait or quantitative trait locus via selective transcriptional profiling

Improved estimation of the noncentrality parameter distribution from a large number of t-statistics, with applications to false discovery rate estimation in microarray data analysis.

Integrating comparative expression profiling data and association of SNPs with Salmonella shedding for improved food safety and porcine disease resistance

Inter-chromosomal Transfer of Immune Regulation During Infection of Barley with the Powdery Mildew Pathogen.

Interaction-dependent gene expression in Mla-specified response to barley powdery mildew

Investigation of the efficacy of albumin removal procedures on porcine serum proteome profile.

Linear mixed model selection for false discovery rate control in microarray data analysis

Metabolomic Profiling of Nicotiana Spp. Nectars Indicate That Pollinator Feeding Preference Is a Stronger Determinant Than Plant Phylogenetics in Shaping Nectar Diversity

Microarray analysis of vegetative phase change in maize

Microarray gene expression profiles of fasting induced changes in liver and adipose tissues of pigs expressing the melanocortin-4 receptor D298N variant.

Microbial community sequencing analysis of the calf eye microbiota and relationship to infectious bovine keratoconjunctivitis.

Microdissection of shoot meristem functional domains

Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome

Mucosal gene expression profiles following the colonization of immunocompetent defined-flora C3H mice with Helicobacter bilis: a prelude to typhlocolitis.