Fiona M. McCarthy
A5089552380- Genomics and Phylogenetic Studies
- Bioinformatics and Genomic Networks
- Gene expression and cancer classification
- Biomedical Text Mining and Ontologies
- Genetic Mapping and Diversity in Plants and Animals
- Animal Genetics and Reproduction
- Advanced Proteomics Techniques and Applications
- Genetic and phenotypic traits in livestock
- Chromosomal and Genetic Variations
- Animal Disease Management and Epidemiology
- Pancreatic function and diabetes
- Vector-Borne Animal Diseases
- RNA and protein synthesis mechanisms
- Viral gastroenteritis research and epidemiology
- Machine Learning in Bioinformatics
- Animal Nutrition and Physiology
- Molecular Biology Techniques and Applications
- CRISPR and Genetic Engineering
- Identification and Quantification in Food
- Cytomegalovirus and herpesvirus research
- Microbial Metabolic Engineering and Bioproduction
- Herpesvirus Infections and Treatments
- Mass Spectrometry Techniques and Applications
- Livestock and Poultry Management
- Lipid metabolism and biosynthesis
University of Arizona
2015-2025
Flatiron Health (United States)
2024
Flatiron Institute
2024
Institute of Mathematical Sciences
2024
University of Cambridge
2024
Mississippi State University
2005-2021
St. Paul's Hospital
2018
Trinity College Dublin
2017
BIO5 Institute
2013
University of Delaware
2012
The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over past year, GOC has implemented several processes to increase quantity, quality and specificity GO annotations. First, number manual, literature-based annotations grown at an increasing rate. Second, as result new 'phylogenetic annotation' process, manually reviewed, homology-based...
To provide context for the diversification of archosaurs--the group that includes crocodilians, dinosaurs, and birds--we generated draft genomes three crocodilians: Alligator mississippiensis (the American alligator), Crocodylus porosus saltwater crocodile), Gavialis gangeticus Indian gharial). We observed an exceptionally slow rate genome evolution within crocodilians at all levels, including nucleotide substitutions, indels, transposable element content movement, gene family evolution,...
Abstract We describe the organization of a nascent international effort, Functional Annotation Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps functional elements in genomes domesticated animal species.
Identification and analysis of host–pathogen interactions (HPI) is essential to study infectious diseases. However, HPI data are sparse in existing molecular interaction databases, especially for agricultural systems. Therefore, resources that annotate, predict display the underpin diseases critical developing novel intervention strategies. HPIDB 2.0 ( http://www.agbase.msstate.edu/hpi/main.html ) a resource data, contains 45, 238 manually curated entries current release. Since first...
Observations of the millimeter sky contain valuable information on a number signals, including blackbody cosmic microwave background (CMB), Galactic emissions, and Compton-y distortion due to thermal Sunyaev-Zel'dovich (tSZ) effect. Extracting new insight into cosmological astrophysical questions often requires combining multiwavelength observations spectrally isolate one component. In this work, we present arc-minute-resolution map, which traces out line-of-sight-integrated electron...
Many agricultural species and their pathogens have sequenced genomes more are in progress. Agricultural provide food, fiber, xenotransplant tissues, biopharmaceuticals biomedical models. Moreover, many microorganisms human zoonoses. However, systems biology from functional genomics data is hindered because genome sequences relatively poor structural annotation research communities smaller with limited funding compared to model organism communities.To facilitate these traditionally we...
The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. number GO annotations products has increased due to curation efforts among Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. ontologies continue expand improve as result targeted ontology development, introduction computable logical definitions...
The Gene Ontology (GO) is a collaborative effort that provides structured vocabularies for annotating the molecular function, biological role, and cellular location of gene products in highly systematic way species-neutral manner with aim unifying representation function across different organisms. Each contributing member GO Consortium independently associates terms to from organism(s) they are annotating. Here we introduce Reference Genome project, which brings together those independent...
The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) Indian gharial (Gavialis gangeticus) genomes. status of these projects our planned analyses are described.
Mature mammalian sperm contain a complex population of RNAs some which might regulate spermatogenesis while others probably play role in fertilization and early development. Due to this limited knowledge, the biological functions remain enigmatic. Here we report first characterization global transcriptome fertile stallions. The findings improved understanding significance turn will allow discovery sperm-based biomarkers for stallion fertility. was interrogated by analyzing testes RNA on...
Abstract Dramatic improvements in measuring genetic variation across agriculturally relevant populations (genomics) must be matched by identifying and trait such many environments (phenomics). Identifying the most critical opportunities challenges genome to phenome (G2P) research is focus of this paper. Previously (Genome Biol, 23(1):1–11, 2022), we laid out how Agricultural Genome Phenome Initiative (AG2PI) will coordinate activities with USA federal government agencies expand...
Editorial on the Research Topic Food safety in low-and middle-income countriesThis is first special edition food informal markets low-and-middle income countries (LMICs).Despite their important public health and socio-economic impacts, foodborne diseases have only recently gained attention of development institutes initiatives (Grace, 2023).The result growing appreciation enormous burden disease LMICs: comparable to that malaria, HIV/AIDs or tuberculosis economic cost more than 100 billion...
Heat stress triggers an evolutionarily conserved set of responses in cells. The transcriptome responds to hyperthermia by altering expression genes adapt the cell or organism survive heat challenge. RNA-seq technology allows rapid identification environmentally responsive on a large scale. In this study, we have used identify chicken male white leghorn hepatocellular (LMH) line. transcripts 812 were (p < 0.01) with 235 upregulated and 577 downregulated following 2.5 h stress. Among whose...
Background Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor cultivated hexaploid wheat, and therefore useful model for study components regulating photomorphogenesis in diploid wheat. In order to develop genetic genomic resources such study, we constructed genome-wide transcriptomes two subspecies, wild winter wheat ssp. aegilopoides (accession G3116) domesticated spring DV92) by generating de novo assemblies RNA-Seq data derived from both etiolated green...
The future of agricultural research depends on data. sheer volume biological data being produced today makes excellent management essential. Governmental agencies, publishers and science funders require plans for publicly funded research. Furthermore, the value increases exponentially when they are properly stored, described, integrated shared, so that can be easily utilized in analyses. AgBioData (https://www.agbiodata.org) is a consortium people working at databases, archives knowledgbases...
Analysis of functional genomics (transcriptomics and proteomics) datasets is hindered in agricultural species because genome sequences have relatively poor structural annotation. To facilitate systems biology these we established the curated, web-accessible, public resource 'AgBase' (www.agbase.msstate.edu). We improved annotation agriculturally important genomes by experimentally confirming vivo expression electronically predicted proteins proteogenomic mapping. Proteogenomic data are...
When proteins are subjected to proteolytic digestion and analyzed by mass spectrometry using a method such as 2D LC MS/MS, only portion of the proteotypic peptides associated with each protein will be observed. The ability predict which can cannot potentially observed for particular experimental dataset has several important applications in proteomics research including calculation peptide coverage terms detectable peptides, systems biology analysis data sets, quantification. We have...
Abstract Background The hypothalamus plays a central role in regulating appetite and metabolism. However, the gene networks within that regulate feed intake metabolism, effects of fasting on those pathways are not completely understood any species. present experiment evaluated global hypothalamic expression newly hatched chicks using microarray analysis to elucidate genes regulated by feeding, fasting, delayed feeding. Ten groups were sampled over four days post-hatch, including fed, fasted,...
AgBase (http://www.agbase.msstate.edu/)provides resources to facilitate modeling of functional genomics data and structural annotation agriculturally important animal, plant, microbe parasite genomes.The website is redesigned improve accessibility ease use, including improved search capabilities.Expanded capabilities include new dedicated pages for horse, cat, dog, cotton, rice soybean.We currently provide 590 240 Gene Ontology (GO) annotations 105 454 gene products in 64 different species,...
Summary Transgenic soya bean ( Glycine max ) plants overexpressing a seed‐specific bacterial phytoene synthase gene from Pantoea ananatis modified to target plastids accumulated 845 μg β carotene g −1 dry seed weight with desirable 12:1 ratio of α. The accumulating seeds exhibited shift in oil composition increasing oleic acid concomitant decrease linoleic and an increase protein content by at least 4% (w/w). Elevated β‐carotene cotyledons contain 40% the amount abscisic compared...
Differential detergent fractionation (DDF), which relies on detergents to sequentially extract proteins from eukaryotic cells, has been used increase proteome coverage of 2D-PAGE. Here, we DDF extraction in conjunction with the nonelectrophoretic proteomics method liquid chromatography and electrospray ionization tandem mass spectrometry. We demonstrate that can be 2D-LC ESI MS2 for comprehensive cellular proteomics, including a large proportion membrane proteins. Compared some published...
The major histocompatibility complex (MHC) is a dynamic genome region with an essential role in the adaptive immunity of vertebrates, especially antigen presentation. MHC generally divided into subregions (classes I, II and III) containing genes similar function across species, but different gene number organisation. Crocodylia (crocodilians) are widely distributed represent evolutionary distinct group among higher genomic organisation within this lineage has been largely unexplored. Here,...