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My main area of research is providing functional annotations to support modeling of functional genomics data sets for non-model organisms. This includes aspect of biocuration, ontology design, gene identification and functional prediction and functional genomics. I am also interested in integrating different date types and the visualization of these results in a way that enables researchers to turn genomics data into practical knowledge that can be applied to agricultural systems.Show Less
VOSviewer
Research Opportunities
- Undergrad Research Opp Volunteer, For Credit
Grant: Not Listed
bioinformatics, ontologies, genomics, functional genomics Prerequisite Courses: Students with an int...
Courses
- CBComputation in Biomedicine
- MMVMedical and Molecular Virology
- EIDEcology of Infectious Disease
Grants
- NIFA AG2PI Collaborative seed grant: Developing standardized bioinformatics capacity across multiple agricultural species
Principal Investigator (PI)
2023
$250.0K
Active - From Genome to Phenome in Animal Genetics Studies
Key Personnel (KP)
2020
$165.0K
Active - Non-Assistance Cooperative Agreement to Provide Rapid Access to Ag100Pest Functional Annotations and Genome Data
Principal Investigator (PI)
2019
$315.4K
Active - Non-Assistance Cooperative Agreement to Provide Rapid Access to Ag100Pest Functional Annotations and Genome Data
Principal Investigator (PI)
2019
$64.2K
Active - Optimizing 3D Canopy Architecture for Better Crops
Co-Investigator (COI)
2021
$5.1K
- Developing Functional Annotation Workflows For Animal Genomics Research
Principal Investigator (PI)
2018
$490.0K
- Acquisition of Goods and Services
Principal Investigator (PI)
2018
$95.0K
- Enhancing Gut and Physiological Health of Neonates by Enhancing The Functional Properties of Soybean
Co-Investigator (COI)
2015
$500.0K
- Enabling Network Analysis of Host-Pathogen Interactions
Principal Investigator (PI)
2015
$478.2K
- iAnimal: cyberinfrastructure enabling animal breeding genetics and genomics
Co-Investigator (COI)
2013
$499.2K
News
- Parker Antin: Leading Life Science Initiatives
2015
- How Happiness Came Into Beings
2015
- New Genome Research Illuminates Bird, Crocodile Evolution
2014
Publications (72)
Recent
- Comparison of the Transcriptomes and Proteomes of Serum Exosomes from Marek s Disease Virus-Vaccinated and Protected and Lymphoma-Bearing Chickens.
2019
- Chickspress: a resource for chicken gene expression.
2019
- AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture.
2018
- Acute Ischemia Induced by High-Density Culture Increases Cytokine Expression and Diminishes the Function and Viability of Highly Purified Human Islets of Langerhans
2017
- Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved (Non-model) Organisms
2017
- iAnimal: Cyberinfrastructure to Support Data-driven Science
2017
- RNA sequencing exposes adaptive and immune responses to intrauterine growth restriction in fetal sheep islets
2017
- Evaluation of bovine viral diarrhea virus interactions with its host proteome during the course of infection
2017
- Development of avian anatomy ontology annotation
2017
- Transcriptome Changes Associated with Protective Immunity in T and B Cell-Deficient Rag1-/-Mutant Zebrafish
2017
- Transcriptome Expression Profiles Identify Increased Metabolic Capacity in Adipose Tissue from Fetal Sheep with Intrauterine Growth Restriction.
2016
- P1039 Bioinformatics resources for animal genomics using CyVerse cyberinfrastructure.
2016
- Resources and recommendations for using transcriptomics to address grand challenges in comparative biology
2016
- Improved genome assembly of American alligator genome reveals conserved architecture of estrogen signaling
2016
- HPIDB 2.0: a curated database for host--pathogen interactions
2016
- Transcriptome response to heat stress in a chicken hepatocellular carcinoma cell line
2015
- ASSESSMENT OF THE VIABILITY, FUNCTION, AND TRANSCRIPTOME OF HUMAN ISLETS FOLLOWING ACUTE ISCHEMIC EXPOSURE.
2015
- Acute ischemic exposure leads to functional deficits and a transcriptome enriched in inflammatory and hypoxic pathways in human islets
2015
- Identification of dopamine receptors across the extant avian family tree and analysis with other clades uncovers a polyploid expansion among vertebrates
2015
- Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project
2015
- Transgenic soya bean seeds accumulating β-carotene exhibit the collateral enhancements of oleate and protein content traits.
2015
- Third Report on Chicken Genes and Chromosomes 2015
2015
- Comparative genome analyses reveal distinct structure in the saltwater crocodile MHC
2014
- Transgenic soya bean seeds accumulating β-carotene exhibit the collateral enhancements of oleate and protein content traits
2014
- Three crocodilian genomes reveal ancestral patterns of evolution among archosaurs
2014
- De novo transcriptome assembly and analyses of gene expression during photomorphogenesis in diploid wheat Triticum monococcum
2014
- Gene Ontology annotations and resources.
2013
- Functional genomics: applications to production agriculture.
2013
- Interestingness measures and strategies for mining multi-ontology multi-level association rules from gene ontology annotations for the discovery of new GO relationships
2013
- From data to function: functional modeling of poultry genomics data.
2013
- Cross-Ontology Multi-level Association Rule Mining in the Gene Ontology
2012
- Systemic response to Campylobacter jejuni infection by profiling gene transcription in the spleens of two genetic lines of chickens
2012
- Stallion sperm transcriptome comprises functionally coherent coding and regulatory RNAs as revealed by microarray analysis and RNA-seq
2012
- Understanding the Pathogenesis of Cytopathic and Noncytopathic Bovine Viral Diarrhea Virus Infection Using Proteomics
2012
- Sequencing three crocodilian genomes to illuminate the evolution of archosaurs and amniotes
2012
- Developing a biocuration workflow for AgBase, a non-model organism database.
2012
- The proteogenomic mapping tool
2011
- Functional modelling of an equine bronchoalveolar lavage fluid proteome provides experimental confirmation and functional annotation of equine genome sequences.
2011
- AgBase: supporting functional modeling in agricultural organisms
2011
- Tibial dyschondroplasia-associated proteomic changes in chicken growth plate cartilage
2010
- Proteome profile of the developing maize (Zea mays L.) rachis
2010
- Transcriptional and pathway analysis in the hypothalamus of newly hatched chicks during fasting and delayed feeding
2010
- GOModeler--a tool for hypothesis-testing of functional genomics datasets
2010
- Analysis of Bovine Viral Diarrhea Viruses-infected monocytes: identification of cytopathic and non-cytopathic biotype differences
2010
- Re-annotation is an essential step in systems biology modeling of functional genomics data
2010
- The gene ontology's reference genome project: A unified framework for functional annotation across species
2009
- ArrayIDer: automated structural re-annotation pipeline for DNA microarrays.
2009
- Understanding animal viruses using the Gene Ontology
2009
- The Chicken Gene Nomenclature Committee report
2009
- Facilitating functional annotation of chicken microarray data
2009
- Introduction to the proceedings of the Avian Genomics and Gene Ontology Annotation Workshop
2009
- Structural and functional-annotation of an equine whole genome oligoarray
2009
- Gene Ontology annotation quality analysis in model eukaryotes.
2008
- The essential and non-essential genes of Bovine herpesvirus 1
2008
- AgBase: a unified resource for functional analysis in agriculture.
2007
- Experimental-confirmation and functional-annotation of predicted proteins in the chicken genome.
2007
- AgBase: A tool for systems biology in agricultural species
2007
- Bovine germinal vesicle oocyte and cumulus cell proteomics.
2007
- GOing from functional genomics to biological significance.
2007
- Differential detergent fractionation for non-electrophoretic bovine peripheral blood monocyte proteomics reveals proteins involved in professional antigen presentation
2006
- AgBase: a functional genomics resource for agriculture.
2006
- Construction of a gene inactivation library for Bovine herpesvirus 1 using infectious clone technology.
2005
- Differential detergent fractionation for non-electrophoretic eukaryote cell proteomics.
2005
- Genetic analysis of bovine viral diarrhoea viruses from Australia
2005
- Rapid and efficient construction of recombinant bovine herpesvirus 1 genomes
2003
- Construction and manipulation of an infectious clone of the bovine herpesvirus 1 genome maintained as a bacterial artificial chromosome
2002
- Molecular characterisation of Australian bovine enteroviruses
1999
- Genetic analysis of Australian bovine viral diarrhoea viruses and bovine herpesviruses
1999
- Primary cell cultures isolated from Penaeus monodon prawns
1999
- Characterization of 65 bovine microsatellites
1994
- A genetic linkage map of the bovine genome
1994