Damien Farrell
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View article: SNiPgenie: a tool for microbial SNP site detection from whole-genome sequencing data
SNiPgenie: a tool for microbial SNP site detection from whole-genome sequencing data Open
Whole-genome sequencing (WGS) of microbial pathogens provides a high-resolution approach to antibiotic resistance profiling, lineage classification and outbreak surveillance. Identification of SNPs across the genome by alignment against a …
View article: Transcriptional comparison between the PhoPR system of Mycobacterium tuberculosis and Mycobacterium bovis on an M. bovis AF2122/97 genetic background
Transcriptional comparison between the PhoPR system of Mycobacterium tuberculosis and Mycobacterium bovis on an M. bovis AF2122/97 genetic background Open
Tuberculosis (TB) is an infectious disease that affects humans and animals. The pathogens that cause TB belong to the Mycobacterium tuberculosis Complex (MTBC), with Mycobacterium tuberculosis and Mycobacterium bovis as the main representa…
View article: SNiPgenie: A tool for microbial SNP site detection from whole genome sequencing data
SNiPgenie: A tool for microbial SNP site detection from whole genome sequencing data Open
Whole-genome sequencing (WGS) of microbial pathogens provides a high-resolution approach to antibiotic resistance profiling, lineage classification, and outbreak surveillance. Identification of single nucleotide polymorphisms (SNPs) across…
View article: SNiPgenie: A tool for microbial SNP site detection from whole genome sequencing data
SNiPgenie: A tool for microbial SNP site detection from whole genome sequencing data Open
Whole-genome sequencing (WGS) of microbial pathogens provides a high-resolution approach to antibiotic resistance profiling, lineage classification, and outbreak surveillance. Identification of single nucleotide polymorphisms (SNPs) across…
View article: Isolation and genetic analysis of mycobacteria from suspect tuberculous lesions in slaughtered cattle from Wolaita, Ethiopia
Isolation and genetic analysis of mycobacteria from suspect tuberculous lesions in slaughtered cattle from Wolaita, Ethiopia Open
Bovine tuberculosis (bTB), caused by Mycobacterium bovis and other members of the Mycobacterium tuberculosis complex (MTBC), is a significant concern for livestock and public health in Ethiopia. This study aimed to isolate and genetically …
View article: Isolation and genetic analysis of mycobacteria from suspect tuberculous lesions in slaughtered cattle from Wolaita, Ethiopia
Isolation and genetic analysis of mycobacteria from suspect tuberculous lesions in slaughtered cattle from Wolaita, Ethiopia Open
Bovine tuberculosis (bTB), caused by Mycobacterium bovis and other members of the Mycobacterium tuberculosis complex (MTBC), is a significant concern for livestock and public health in Ethiopia. This study aimed to isolate and genetically …
View article: Isolation and genetic analysis of mycobacteria from suspect tuberculous lesions in slaughtered cattle from Wolaita, Ethiopia
Isolation and genetic analysis of mycobacteria from suspect tuberculous lesions in slaughtered cattle from Wolaita, Ethiopia Open
Bovine tuberculosis (bTB), caused by Mycobacterium bovis and other members of the Mycobacterium tuberculosis complex (MTBC), is a significant concern for livestock and public health in Ethiopia. This study aimed to isolate and genetically …
View article: Whole-Genome sequencing in routine Mycobacterium bovis epidemiology – scoping the potential
Whole-Genome sequencing in routine Mycobacterium bovis epidemiology – scoping the potential Open
Mycobacterium bovis the main agent of bovine tuberculosis (bTB), presents as a series of spatially-localised micro-epidemics across landscapes. Classical molecular typing methods applied to these micro-epidemics, based on genotyping a few …
View article: Burkitt Lymphoma With Aberrant Expression of Cytoplasmic Terminal Deoxynucleotidyl Transferase: A Case Report
Burkitt Lymphoma With Aberrant Expression of Cytoplasmic Terminal Deoxynucleotidyl Transferase: A Case Report Open
This study describes a rare case of Burkitt lymphoma with aberrant expression of cytoplasmic terminal deoxynucleotidyl transferase (TdT). Flow cytometry demonstrated a predominantly mature B cell immunophenotype as expected for Burkitt lym…
View article: Corrigendum: The TbD1 Locus Mediates a Hypoxia-Induced Copper Response in Mycobacterium bovis
Corrigendum: The TbD1 Locus Mediates a Hypoxia-Induced Copper Response in Mycobacterium bovis Open
[This corrects the article DOI: 10.3389/fmicb.2022.817952.].
View article: Defining the pknH Transcriptional Network in the Animal Tuberculosis bacillus, Mycobacterium bovis
Defining the pknH Transcriptional Network in the Animal Tuberculosis bacillus, Mycobacterium bovis Open
The Mycobacterium tuberculosiscomplex (MTBC) is a group of bacteria that show more than 99% genetic identity, yet they diverge in their host preference and the severity of associated disease. Mycobacterium bovis causes the disease in cattl…
View article: The TbD1 Locus Mediates a Hypoxia-Induced Copper Response in Mycobacterium bovis
The TbD1 Locus Mediates a Hypoxia-Induced Copper Response in Mycobacterium bovis Open
The Mycobacterium tuberculosis complex (MTBC) contains the causative agents of tuberculosis (TB) in mammals. The archetypal members of the MTBC, Mycobacterium tuberculosis and Mycobacterium bovis , cause human tuberculosis and bovine tuber…
View article: Evidence for local and international spread of Mycobacterium avium subspecies paratuberculosis through whole genome sequencing of isolates from the island of Ireland
Evidence for local and international spread of Mycobacterium avium subspecies paratuberculosis through whole genome sequencing of isolates from the island of Ireland Open
We describe application of whole genome sequencing (WGS) to a collection of 197 Mycobacterium avium subsp paratuberculosis (MAP) isolates gathered from 122 cattle herds across 27 counties of the island of Ireland. We compare WGS to MAP div…
View article: Performance and Agreement Between WGS Variant Calling Pipelines Used for Bovine Tuberculosis Control: Toward International Standardization
Performance and Agreement Between WGS Variant Calling Pipelines Used for Bovine Tuberculosis Control: Toward International Standardization Open
Whole genome sequencing (WGS) and allied variant calling pipelines are a valuable tool for the control and eradication of infectious diseases, since they allow the assessment of the genetic relatedness of strains of animal pathogens. In th…
View article: Performance and agreement between WGS variant calling pipelines used for bovine tuberculosis control: towards international standardisation
Performance and agreement between WGS variant calling pipelines used for bovine tuberculosis control: towards international standardisation Open
This repository contains the simulated genomes and FASTQ files used for the analyses reported in the publication: Performance and agreement between WGS variant calling pipelines used for bovine tuberculosis control: towards international s…
View article: Performance and agreement between WGS variant calling pipelines used for bovine tuberculosis control: towards international standardisation
Performance and agreement between WGS variant calling pipelines used for bovine tuberculosis control: towards international standardisation Open
This repository contains the simulated genomes and FASTQ files used for the analyses reported in the publication: Performance and agreement between WGS variant calling pipelines used for bovine tuberculosis control: towards international s…
View article: epitopepredict: a tool for integrated MHC binding prediction
epitopepredict: a tool for integrated MHC binding prediction Open
A key step in the cellular adaptive immune response is the presentation of antigens to T cells. Computational prediction of T cell epitopes has many applications in vaccine design and immuno-diagnostics. This is the basis of immunoinformat…
View article: epitopepredict: A tool for integrated MHC binding prediction
epitopepredict: A tool for integrated MHC binding prediction Open
A key step in the cellular adaptive immune response is the presentation of antigen to T cells. During this process short peptides processed from self or foreign proteins may be presented on the surface bound to MHC molecules for binding to…
View article: Independent genomic polymorphisms in the PknH serine threonine kinase locus during evolution of the Mycobacterium tuberculosis Complex affect virulence and host preference
Independent genomic polymorphisms in the PknH serine threonine kinase locus during evolution of the Mycobacterium tuberculosis Complex affect virulence and host preference Open
Species belonging to the Mycobacterium tuberculosis Complex (MTBC) show more than 99% genetic identity but exhibit distinct host preference and virulence. The molecular genetic changes that underly host specificity and infection phenotype …
View article: Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome
Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome Open
Mycobacterium bovis AF2122/97 is the reference strain for the bovine tuberculosis bacillus. Here we report an update to the M. bovis AF2122/97 genome annotation to reflect 616 new protein identifications that replace many of the old hypoth…
View article: Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome - datasets
Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome - datasets Open
This is an archive of the repository held under https://github.com/dmnfarrell/gordon-group/tree/master/mbovis_annotation It contains a notebook and required input files for updating the MTB/Mbovis AF2122/97 genomes with new protein product…
View article: Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome - datasets
Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome - datasets Open
This is an archive of the repository held under https://github.com/dmnfarrell/gordon-group/tree/master/mbovis_annotation It contains a notebook and required input files for updating the MTB/Mbovis AF2122/97 genomes with new protein product…
View article: Draft Genome Sequences of Three Novel Acinetobacter Isolates from an Irish Commercial Pig Farm
Draft Genome Sequences of Three Novel Acinetobacter Isolates from an Irish Commercial Pig Farm Open
Acinetobacter species are important in the emergence and spread of antimicrobial resistance (AMR), which threatens human and animal health worldwide. Here, we present the draft genome sequences of three Acinetobacter species strains (RF14B…
View article: Updated functional annotation of the <i>Mycobacterium bovis</i> AF2122/97 reference genome
Updated functional annotation of the <i>Mycobacterium bovis</i> AF2122/97 reference genome Open
Mycobacterium bovis AF2122/97 is the reference strain for the bovine tuberculosis bacillus. We here report an update to the M. bovis AF2122/97 genome annotation to reflect 616 new protein identifications which replace many of the old hypot…