Fiona McCarthy
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View article: Emerging technologies in poultry genomics: Unlocking innovation for the future of sustainable production
Emerging technologies in poultry genomics: Unlocking innovation for the future of sustainable production Open
Over the past decade, poultry genomics has undergone a transformative shift from genome assembly to functional annotation, mechanistic discovery, and integrative applications that advance sustainable poultry production. This symposium high…
View article: CLASS_SZ II: Notes and Examples of Fast and Accurate Calculations of Halo Model, Large Scale Structure and Cosmic Microwave Background Observables
CLASS_SZ II: Notes and Examples of Fast and Accurate Calculations of Halo Model, Large Scale Structure and Cosmic Microwave Background Observables Open
These notes are very much work-in-progress and simply intended to showcase, in various degrees of details (and rigour), some of the cosmology calculations that class_sz can do. We describe the class_sz code in C, Python and Jax. Based on t…
View article: Providing Standardized Gene Nomenclature for Domestic Ungulate Scavenger Receptor Genes
Providing Standardized Gene Nomenclature for Domestic Ungulate Scavenger Receptor Genes Open
Scavenger Receptor (SCAR) genes are a heterogeneous group involved in innate immunity and immunomodulation. While standardized gene nomenclature is provided for model organism SCAR genes, ungulates have novel SCAR genes which have not been…
View article: Standardized Gene Nomenclature for Chicken Scavenger Receptors
Standardized Gene Nomenclature for Chicken Scavenger Receptors Open
Scavenger Receptors (SCARs) are a heterogeneous group involved in innate immunity and immunomodulation. We provided standardized nomenclature for chicken SCAR genes in line with other vertebrate nomenclatures. Chicken SCAR genes orthologou…
View article: Atacama Cosmology Telescope: High-resolution component-separated maps across one third of the sky
Atacama Cosmology Telescope: High-resolution component-separated maps across one third of the sky Open
Observations of the millimeter sky contain valuable information on a number of signals, including the blackbody cosmic microwave background (CMB), Galactic emissions, and the Compton-y distortion due to the thermal Sunyaev-Zel’dovich (tSZ)…
View article: class_sz I: Overview
class_sz I: Overview Open
class_sz is a versatile, robust and efficient code, in C and Python, optimized to compute theoretical predictions for a wide range of observables relevant to cross-survey science in the Stage IV era. The code is public at https://github.co…
View article: class_sz I: Overview
class_sz I: Overview Open
class_sz is a versatile and robust code in C and Python that can compute theoretical predictions for a wide range of observables relevant to cross-survey science in the Stage IV era. The code is public at https://github.com/CLASS-SZ/class_…
View article: Comparative proteomic analysis of tail regeneration in the green anole lizard, <i>Anolis carolinensis</i>
Comparative proteomic analysis of tail regeneration in the green anole lizard, <i>Anolis carolinensis</i> Open
As amniote vertebrates, lizards are the most closely related organisms to humans capable of appendage regeneration. Lizards can autotomize, or release their tails as a means of predator evasion, and subsequently regenerate a functional rep…
View article: Proteomic insight into human directed selection of the domesticated chicken Gallus gallus.
Proteomic insight into human directed selection of the domesticated chicken Gallus gallus. Open
Chicken domestication began at least 3,500 years ago for purposes of divination, cockfighting, and food. Prior to industrial scale chicken production, domestication selected larger birds with increased egg production. In the mid-20 th cent…
View article: Current Challenges and Future of Agricultural Genomes to Phenomes in the U.S.
Current Challenges and Future of Agricultural Genomes to Phenomes in the U.S. Open
Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by improvements in identifying and measuring relevant trait variation in such populations across many environments (…
View article: Proteomic insight into human directed evolution of the domesticated chicken<i>Gallus gallus</i>
Proteomic insight into human directed evolution of the domesticated chicken<i>Gallus gallus</i> Open
Chicken domestication began at least 3,500 years ago for purposes of divination, cockfighting, and food. Prior to industrial scale chicken production, domestication selected larger birds with increased egg production. In the mid-20 th cent…
View article: Constraints on primordial non-Gaussianity from halo bias measured through CMB lensing cross-correlations
Constraints on primordial non-Gaussianity from halo bias measured through CMB lensing cross-correlations Open
Local non-Gaussianities in the initial conditions of the Universe, parameterized by $f_{\rm NL}$, induce a scale-dependence in the large-scale bias of halos in the late Universe. This effect is a promising path to constrain multi-field inf…
View article: Genome-scale host-pathogen prediction for non-medical microbes
Genome-scale host-pathogen prediction for non-medical microbes Open
Background Network studies of host-pathogen interactions (HPI) are critical in understanding the mechanisms of pathogenesis. However, accessible HPI data for agriculturally important pathogens are limited. This lack of HPI data impedes net…
View article: The Case for Standardising Gene Nomenclature Across Vertebrates
The Case for Standardising Gene Nomenclature Across Vertebrates Open
Standardized gene nomenclature supports unambiguous communication and identification of the scientific literature associated with genes. To support the increasing number of annotated genomes that are now available for comparative studies, …
View article: Fourth Report on Chicken Genes and Chromosomes 2022
Fourth Report on Chicken Genes and Chromosomes 2022 Open
View article: Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO)
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO) Open
Experimental data about gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resource fo…
View article: The Case for Standardising Gene Nomenclature Across Vertebrates
The Case for Standardising Gene Nomenclature Across Vertebrates Open
Standardized gene nomenclature supports unambiguous communication and identification of the scientific literature associated with genes. To support the increasing number of annotated genomes that are now available for comparative studies, …
View article: Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes
Workflows for Rapid Functional Annotation of Diverse Arthropod Genomes Open
Genome sequencing of a diverse array of arthropod genomes is already underway, and these genomes will be used to study human health, agriculture, biodiversity, and ecology. These new genomes are intended to serve as community resources and…
View article: Workflows for rapid functional annotation of diverse arthropod genomes
Workflows for rapid functional annotation of diverse arthropod genomes Open
Genome sequencing of a diverse array of arthropod genomes is already underway and these genomes will be used to study human health, agriculture, biodiversity and ecology. These new genomes are intended to serve as community resources and p…
View article: Crowdsourcing biocuration: the Community Assessment of Community Annotation with Ontologies (CACAO)
Crowdsourcing biocuration: the Community Assessment of Community Annotation with Ontologies (CACAO) Open
Experimental data about known gene functions curated from the primary literature have enormous value for research scientists in understanding biology. Using the Gene Ontology (GO), manual curation by experts has provided an important resou…
View article: <p>Modeling the pasture-associated severe equine asthma bronchoalveolar lavage fluid proteome identifies molecular events mediating neutrophilic airway inflammation</p>
Modeling the pasture-associated severe equine asthma bronchoalveolar lavage fluid proteome identifies molecular events mediating neutrophilic airway inflammation Open
Background: Pasture-associated severe equine asthma is a warm season, environmentally-induced respiratory disease characterized by reversible airway obstruction, persistent and non-specific airway hyper-responsiveness, and chronic neutroph…
View article: Comparison of the Transcriptomes and Proteomes of Serum Exosomes from Marek’s Disease Virus-Vaccinated and Protected and Lymphoma-Bearing Chickens
Comparison of the Transcriptomes and Proteomes of Serum Exosomes from Marek’s Disease Virus-Vaccinated and Protected and Lymphoma-Bearing Chickens Open
Marek’s disease virus (MDV) is the causative agent of Marek’s disease (MD), a complex pathology of chickens characterized by paralysis, immunosuppression, and T-cell lymphomagenesis. MD is controlled in poultry production via vaccines admi…
View article: Chickspress: a resource for chicken gene expression
Chickspress: a resource for chicken gene expression Open
This FAIRsharing record describes: Chickspress is a gene expression database for chicken tissues. Chickspress incorporates both NCBI and Ensembl gene models and links these gene sets with experimental gene expression data and QTL informati…