List of works - David J. Lynn

A genome-wide association study for genetic susceptibility to Mycobacterium bovis infection in dairy cattle identifies a susceptibility QTL on chromosome 23.

scientific article published on 9 March 2016

A genome-wide association study for somatic cell score using the Illumina high-density bovine beadchip identifies several novel QTL potentially related to mastitis susceptibility

scientific article

A genomics approach to the detection of positive selection in cattle: adaptive evolution of the T-cell and natural killer cell-surface protein CD2.

scientific article

Analysis and Visualization of Dynamic Networks Using the DyNet App for Cytoscape

scientific article published on 31 August 2018

Analysis combining correlated glaucoma traits identifies five new risk loci for open-angle glaucoma

scientific article published on 15 February 2018

Avian beta-defensin nomenclature: a community proposed update

scientific article published on 23 April 2007

Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes.

scientific article

CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization

scientific article

Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks

scientific article published on 19 July 2016

Contrasting evolution of diversity at two disease-associated chicken genes

scientific article

Detecting the effects of selection at the population level in six bovine immune genes

scientific article

Discovery of alpha-defensins in basal mammals

scientific article published on 2 March 2007

DyNet: visualization and analysis of dynamic molecular interaction networks

scientific article

Dysregulated fibronectin trafficking by Hsp90 inhibition restricts prostate cancer cell invasion

scientific article published in February 2018

Effective adjunctive therapy by an innate defense regulatory peptide in a preclinical model of severe malaria

scientific article published in May 2012

Erratum to: 'Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis'.

scientific article published on 10 December 2015

Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus

scientific article

Evidence of positive selection on the Atlantic salmon CD3γδ gene

article

Evidence of positively selected sites in mammalian alpha-defensins

scientific article published on 12 February 2004

Fatty acid oxidation is an adaptive survival pathway induced in prostate tumors by heat shock protein 90 inhibition

scientific article published on 15 July 2020

Genome-wide association study of intraocular pressure uncovers new pathways to glaucoma

scientific article published on 27 July 2018

Genome-wide associations for milk production and somatic cell score in Holstein-Friesian cattle in Ireland

scientific article

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

scientific article

Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis

scientific article

HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.

scientific article

Identification of a human neonatal immune-metabolic network associated with bacterial infection

scientific article

Identification of novel response and predictive biomarkers to Hsp90 inhibitors through mass spectrometry-based proteomic profiling of patient-derived prostate tumor explants

scientific article published on 9 April 2018

In silico identification of components of the Toll-like receptor (TLR) signaling pathway in clustered chicken expressed sequence tags (ESTs)

scientific article published on 01 June 2003

Induction of a novel chicken Toll-like receptor following Salmonella enterica serovar Typhimurium infection.

scientific article

InnateDB: facilitating systems-level analyses of the mammalian innate immune response.

scientific article

InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation

scientific article

Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis

scientific article published on 19 October 2015

Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever

scientific article published on 23 May 2016

Linkage mapping of the locus for inherited ovine arthrogryposis (IOA) to sheep Chromosome 5

scientific article published on 22 January 2007

Messenger RNA sequence rather than protein sequence determines the level of self-synthesis and antigen presentation of the EBV-encoded antigen, EBNA1.

scientific article

MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking.

scientific article

MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model

scientific article

Modification of chicken avian beta-defensin-8 at positively selected amino acid sites enhances specific antimicrobial activity.

scientific article published on 5 May 2007

Network Visualization and Analysis of Spatially Aware Gene Expression Data with InsituNet

article

Next generation sequencing reveals the expression of a unique miRNA profile in response to a gram-positive bacterial infection

scientific article

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

scientific article (publication date: 29 June 2011)

Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures.

scientific article published on 19 December 2013

Profiling microRNA expression in bovine alveolar macrophages using RNA-seq

scientific article

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

scientific article

RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance

scientific article

Retinal Pigment Epithelial Cells are a Potential Reservoir for Ebola Virus in the Human Eye.

scientific article

The bovine lactation genome: insights into the evolution of mammalian milk

scientific article

The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults

scientific article

The genome sequence of taurine cattle: a window to ruminant biology and evolution

scientific article

The human transcriptome during nontyphoid Salmonella and HIV coinfection reveals attenuated NFkappaB-mediated inflammation and persistent cell cycle disruption

scientific article

The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep

scientific article

The miRNAome of the postpartum dairy cow liver in negative energy balance

scientific article

The non-specific and sex-differential effects of vaccines

scientific article published on 27 May 2020

The potential of the microbiota to influence vaccine responses.

scientific article published on September 2017

The synthetic form of a novel chicken beta-defensin identified in silico is predominantly active against intestinal pathogens

scientific article published on 3 March 2005

Towards a unified open access dataset of molecular interactions

scientific article published on 01 December 2020

Transcriptional response in the peripheral blood of patients infected with Salmonella enterica serovar Typhi

scientific article published on 11 December 2009

Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology

scientific article published on 18 June 2012

Using biological networks to integrate, visualize and analyze genomics data

scientific article

Using the Contextual Hub Analysis Tool (CHAT) in Cytoscape to Identify Contextually Relevant Network Hubs

scientific article published on 13 September 2017

Whole blood gene expression profiling of neonates with confirmed bacterial sepsis

scientific article

Whole exome sequencing implicates eye development, the unfolded protein response and plasma membrane homeostasis in primary open-angle glaucoma.

scientific article

Zika Virus Infection of Human Iris Pigment Epithelial Cells

scientific article published on 22 April 2021

List of works by David J. Lynn

A genome-wide association study for genetic susceptibility to Mycobacterium bovis infection in dairy cattle identifies a susceptibility QTL on chromosome 23.

A genome-wide association study for somatic cell score using the Illumina high-density bovine beadchip identifies several novel QTL potentially related to mastitis susceptibility

A genomics approach to the detection of positive selection in cattle: adaptive evolution of the T-cell and natural killer cell-surface protein CD2.

Analysis and Visualization of Dynamic Networks Using the DyNet App for Cytoscape

Analysis combining correlated glaucoma traits identifies five new risk loci for open-angle glaucoma

Avian beta-defensin nomenclature: a community proposed update

Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes.

CerebralWeb: a Cytoscape.js plug-in to visualize networks stratified by subcellular localization

Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks

Contrasting evolution of diversity at two disease-associated chicken genes

Detecting the effects of selection at the population level in six bovine immune genes

Discovery of alpha-defensins in basal mammals

DyNet: visualization and analysis of dynamic molecular interaction networks

Dysregulated fibronectin trafficking by Hsp90 inhibition restricts prostate cancer cell invasion

Effective adjunctive therapy by an innate defense regulatory peptide in a preclinical model of severe malaria

Erratum to: 'Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis'.

Evidence of balanced diversity at the chicken interleukin 4 receptor alpha chain locus

Evidence of positive selection on the Atlantic salmon CD3γδ gene

Evidence of positively selected sites in mammalian alpha-defensins

Fatty acid oxidation is an adaptive survival pathway induced in prostate tumors by heat shock protein 90 inhibition

Genome-wide association study of intraocular pressure uncovers new pathways to glaucoma

Genome-wide associations for milk production and somatic cell score in Holstein-Friesian cattle in Ireland

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds

Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with Mycobacterium bovis

HiQuant: Rapid Postquantification Analysis of Large-Scale MS-Generated Proteomics Data.

Identification of a human neonatal immune-metabolic network associated with bacterial infection

Identification of novel response and predictive biomarkers to Hsp90 inhibitors through mass spectrometry-based proteomic profiling of patient-derived prostate tumor explants

In silico identification of components of the Toll-like receptor (TLR) signaling pathway in clustered chicken expressed sequence tags (ESTs)

Induction of a novel chicken Toll-like receptor following Salmonella enterica serovar Typhimurium infection.

InnateDB: facilitating systems-level analyses of the mammalian innate immune response.

InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation

Integrated analysis of the local and systemic changes preceding the development of post-partum cytological endometritis

Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever

Linkage mapping of the locus for inherited ovine arthrogryposis (IOA) to sheep Chromosome 5

Messenger RNA sequence rather than protein sequence determines the level of self-synthesis and antigen presentation of the EBV-encoded antigen, EBNA1.

MicroRNA profiling of the bovine alveolar macrophage response to Mycobacterium bovis infection suggests pathogen survival is enhanced by microRNA regulation of endocytosis and lysosome trafficking.

MicroRNA regulation of bovine monocyte inflammatory and metabolic networks in an in vivo infection model

Modification of chicken avian beta-defensin-8 at positively selected amino acid sites enhances specific antimicrobial activity.

Network Visualization and Analysis of Spatially Aware Gene Expression Data with InsituNet

Next generation sequencing reveals the expression of a unique miRNA profile in response to a gram-positive bacterial infection

PSICQUIC and PSISCORE: accessing and scoring molecular interactions

Pathway-GPS and SIGORA: identifying relevant pathways based on the over-representation of their gene-pair signatures.

Profiling microRNA expression in bovine alveolar macrophages using RNA-seq

Protein interaction data curation: the International Molecular Exchange (IMEx) consortium

RNA-seq analysis of differential gene expression in liver from lactating dairy cows divergent in negative energy balance

Retinal Pigment Epithelial Cells are a Potential Reservoir for Ebola Virus in the Human Eye.

The bovine lactation genome: insights into the evolution of mammalian milk

The early whole-blood transcriptional signature of dengue virus and features associated with progression to dengue shock syndrome in Vietnamese children and young adults

The genome sequence of taurine cattle: a window to ruminant biology and evolution

The human transcriptome during nontyphoid Salmonella and HIV coinfection reveals attenuated NFkappaB-mediated inflammation and persistent cell cycle disruption

The imprinted retrotransposon-like gene PEG11 (RTL1) is expressed as a full-length protein in skeletal muscle from Callipyge sheep

The miRNAome of the postpartum dairy cow liver in negative energy balance

The non-specific and sex-differential effects of vaccines

The potential of the microbiota to influence vaccine responses.

The synthetic form of a novel chicken beta-defensin identified in silico is predominantly active against intestinal pathogens

Towards a unified open access dataset of molecular interactions

Transcriptional response in the peripheral blood of patients infected with Salmonella enterica serovar Typhi

Transcriptomic analysis of the stress response to weaning at housing in bovine leukocytes using RNA-seq technology

Using biological networks to integrate, visualize and analyze genomics data

Using the Contextual Hub Analysis Tool (CHAT) in Cytoscape to Identify Contextually Relevant Network Hubs

Whole blood gene expression profiling of neonates with confirmed bacterial sepsis

Whole exome sequencing implicates eye development, the unfolded protein response and plasma membrane homeostasis in primary open-angle glaucoma.

Zika Virus Infection of Human Iris Pigment Epithelial Cells