18 Result(s)

Article

Current challenges and future of agricultural genomes to phenomes in the USA

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 populati...

Christopher K. Tuggle, Jennifer L. Clarke, Brenda M. Murdoch, Eric Lyons… in Genome Biology (2024)

Article

The case for standardizing gene nomenclature in vertebrates

Fiona M. McCarthy, Tamsin E. M. Jones, Anne E. Kwitek, Cynthia L. Smith… in Nature (2023)

Article

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of ...

Leif Andersson, Alan L Archibald, Cynthia D Bottema, Rudiger Brauning… in Genome Biology (2015)

Article

Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes

The International Crocodilian Genomes Working Group (ICGWG) will sequence and assemble the American alligator (Alligator mississippiensis), saltwater crocodile (Crocodylus porosus) and Indian gharial (Gavialis ga...

John A St John, Edward L Braun, Sally R Isberg, Lee G Miles… in Genome Biology (2012)

Article

The Proteogenomic Map** Tool

High-throughput mass spectrometry (MS) proteomics data is increasingly being used to complement traditional structural genome annotation methods. To keep pace with the high speed of experimental data generatio...

William S Sanders, Nan Wang, Susan M Bridges, Brandon M Malone… in BMC Bioinformatics (2011)

Article

Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences

Bovine Viral Diarrhea Virus (BVDV) infection is widespread in cattle worldwide, causing important economic losses. Pathogenesis of the disease caused by BVDV is complex, as each BVDV strain has two biotypes: n...

Mais Ammari, Fiona M McCarthy, Bindu Nanduri, Lesya M Pinchuk in BMC Bioinformatics (2010)

Article

GOModeler- A tool for hypothesis-testing of functional genomics datasets

Functional genomics technologies that measure genome expression at a global scale are accelerating biological knowledge discovery. Generating these high throughput datasets is relatively easy compared to the d...

Prashanti Manda, McKinley G Freeman, Susan M Bridges, TJ Jankun-Kelly… in BMC Bioinformatics (2010)

Article

Facilitating functional annotation of chicken microarray data

Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest...

Teresia J Buza, Ranjit Kumar, Cathy R Gresham, Shane C Burgess… in BMC Bioinformatics (2009)

Article

Structural and functional-annotation of an equine whole genome oligoarray

The horse genome is sequenced, allowing equine researchers to use high-throughput functional genomics platforms such as microarrays; next-generation sequencing for gene expression and proteomics. However, for ...

Lauren A Bright, Shane C Burgess, Bhanu Chowdhary… in BMC Bioinformatics (2009)

Article

Introduction to the Proceedings of the Avian Genomics and Gene Ontology Annotation Workshop

The Avian Genomics Conference and Gene Ontology Annotation Workshop brought together researchers and students from around the world to present their latest research addressing the delivery of value from the bi...

Susan M Bridges, Shane C Burgess, Fiona M McCarthy in BMC Genomics (2009)

Article

The chicken gene nomenclature committee report

Comparative genomics is an essential component of the post-genomic era. The chicken genome is the first avian genome to be sequenced and it will serve as a model for other avian species. Moreover, due to its u...

David W Burt, Wilfrid Carrë, Mark Fell, Andy S Law, Parker B Antin… in BMC Genomics (2009)

Article

ArrayIDer: automated structural re-annotation pipeline for DNA microarrays

Systems biology modeling from microarray data requires the most contemporary structural and functional array annotation. However, microarray annotations, especially for non-commercial, non-traditional biomedic...

Bart HJ van den Berg, Jay H Konieczka, Fiona M McCarthy… in BMC Bioinformatics (2009)

Article

Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome

The chicken genome was sequenced because of its phylogenetic position as a non-mammalian vertebrate, its use as a biomedical model especially to study embryology and development, its role as a source of human ...

Teresia J Buza, Fiona M McCarthy, Shane C Burgess in BMC Genomics (2007)

Article

Prediction of peptides observable by mass spectrometry applied at the experimental set level

When proteins are subjected to proteolytic digestion and analyzed by mass spectrometry using a method such as 2D LC MS/MS, only a portion of the proteotypic peptides associated with each protein will be observ...

William S Sanders, Susan M Bridges, Fiona M McCarthy, Bindu Nanduri… in BMC Bioinformatics (2007)

Article

AgBase: a functional genomics resource for agriculture

Many agricultural species and their pathogens have sequenced genomes and more are in progress. Agricultural species provide food, fiber, xenotransplant tissues, biopharmaceuticals and biomedical models. Moreov...

Fiona M McCarthy, Nan Wang, G Bryce Magee, Bindu Nanduri, Mark L Lawrence… in BMC Genomics (2006)