A5023964599- Genomics and Phylogenetic Studies
- Genetic Mapping and Diversity in Plants and Animals
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Genetic diversity and population structure
- CRISPR and Genetic Engineering
- Chromosomal and Genetic Variations
- Agriculture and Rural Development Research
- Genetics, Bioinformatics, and Biomedical Research
- Turtle Biology and Conservation
- Molecular Biology Techniques and Applications
- RNA and protein synthesis mechanisms
- Plant Molecular Biology Research
- Plant Gene Expression Analysis
- Genomics and Chromatin Dynamics
- Cell Image Analysis Techniques
- Yeasts and Rust Fungi Studies
- Viral Infectious Diseases and Gene Expression in Insects
- Forest Insect Ecology and Management
- Microbial Metabolic Engineering and Bioproduction
- Evolution and Paleontology Studies
- Plant Reproductive Biology
- ATP Synthase and ATPases Research
- Plant Virus Research Studies
- Insect Resistance and Genetics
Iowa State University
2015-2024
University of Maine
2021
Miami University
2011-2014
The maize W22 inbred has served as a platform for genetics since the mid twentieth century. To streamline genome analyses, we have sequenced and de novo assembled reference using short-read sequencing technologies. We show that significant structural heterogeneity exists in comparison to B73 at multiple scales, from transposon composition copy number variation single-nucleotide polymorphisms. generation of this enables accurate placement thousands Mutator (Mu) Dissociation (Ds) transposable...
MaizeGDB is a highly curated, community-oriented database and informatics service to researchers focused on the crop plant model organism Zea mays ssp. mays. Although some form of maize community has existed over last 25 years, there have only been two major releases. In 1991, original genetics MaizeDB was created. 2003, combined contents sequence data from ZmDB were made accessible as single resource named MaizeGDB. Over next decade, became more driven while still maintaining traditional...
Colorado potato beetle (CPB,
We created a new high-coverage, robust, and reproducible functional annotation of maize protein-coding genes based on Gene Ontology (GO) term assignments. Whereas the existing Phytozome Gramene GO sets only cover 41% 56% genes, respectively, this study provides annotations for 100% genes. also compared quality our newly derived with by comparing all three to manually annotated gold standard set 1,619 where were primarily inferred from direct assay or mutant phenotype. Evaluations indicate...
Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only few SSRs (simple sequence repeats), also known simple tandem repeats or microsatellites, mapped in P. taeda. The objective this study was to integrate large set SSR markers from sources published cDNA into composite map constructed two reference mapping pedigrees. A dense that incorporates loci will benefit complete genome...
The shoot apical meristem (SAM) orchestrates the balance between stem cell proliferation and organ initiation essential for postembryonic growth. Meristems show a striking diversity in shape size. How this morphological relates to variation plant architecture molecular circuitries driving it are unclear. By generating high-resolution gene expression atlas of vegetative maize apex, we here that distinct sets genes govern regulation identity cells versus Arabidopsis. Cell identities SAM...
Abstract Annotating gene structures and functions to genome assemblies is necessary make assembly resources useful for biological inference. Gene Ontology (GO) term assignment the most used functional annotation system, new methods GO have improved quality of GO-based function predictions. The Meta Annotator Plants (GOMAP) an optimized, high-throughput, reproducible pipeline genome-scale plants. We containerized GOMAP increase portability reproducibility also optimized its performance HPC...
Diversification of the turtle's shell comprises remarkable phenotypic transformations. For instance, two divergent species convergently evolved shell‐closing systems with shoulder blade (scapula) segments that enable coordinated movements shell. We expected these unusual structures to originate via similar changes in underlying gene networks, as skeletal segment formation is an evolutionarily conserved developmental process. tested this hypothesis by comparing transcriptomes scapula tissue...
Abstract Background Genome-wide gene function annotations are useful for hypothesis generation and prioritizing candidate genes potentially responsible phenotypes of interest. We functionally annotated the 18 crop plant genomes across 14 species using GOMAP pipeline. Results By comparison to existing GO annotation datasets, GOMAP-generated datasets cover more genes, contain terms, similar in quality (based on precision recall metrics gold standards as basis comparison). From there, we sought...
Abstract Annotating gene structures and functions to genome assemblies is necessary make assembly resources useful for biological inference. Gene Ontology (GO) term assignment the most used functional annotation system, new methods GO have improved quality of GO-based function predictions. The Meta Annotator Plants (GOMAP) an optimized, high-throughput, reproducible pipeline genome-scale plants. We containerized GOMAP increase portability reproducibility also optimized its performance HPC...
1 Summary We created a new high-coverage, robust, and reproducible functional annotation of maize protein coding genes based on Gene Ontology (GO) term assignments. Whereas the existing Phytozome Gramene GO sets only cover 41% 56% genes, respectively, this study provides annotations for 100% genes. also compared quality our newly-derived with by comparing all three to manually annotated gold standard set 1,619 where were primarily inferred from direct assay or mutant phenotype. Evaluations...
Abstract Objectives We annotated the latest published sequences of 26 Zea mays Nested Association Mapping (NAM) founder lines using GOMAP, Gene Ontology Meta Annotator for Plants. The maize NAM panel enables researchers to understand and identify genetic basis complex traits. Annotations predicted functions genes can help investigate gene-phenotype associations, prioritize candidate phenotypes interest, formulate testable hypotheses about gene function/phenotype associations. creation...
Comparative genetic maps are used in examination of genome organization, detection conserved gene order, and exploration marker order variations. YouGenMap is an open-source web tool that offers dynamic comparative mapping capability users’ own between 2 or more map sets. Users’ data optional annotations uploaded, either publically privately, as long they follow our template which available several standard file formats. Data parsed loaded into MySQL relational database to be displayed...
Polymerase Chain Reaction (PCR) is one of the most important inventions 20th century in molecular biology. PCR a technique to amplify or make test tube many copies specific DNA region. Miniscule amounts genetic material from any organism can now be amplified identify individuals, manipulate DNA, detect infectious organisms including viruses that cause AIDS, hepatitis, and tuberculosis, variations mutations genes, numerous other tasks. primers are short, single-stranded DNAs define section...
Most gene expression analysis methods discover groups of genes that are co-expressed, rather than testing whether a specified group behaves in concerted manner.We implemented novel statistical method designed to assess significance differences RNA levels among genes.Our Shiny web application C-REx (Comparison Expression) enables researchers readily test hypotheses about specific share profiles and those differ from other genes.We data transformation, normality visualizer, both parametric...
Background Genome-wide gene function annotations are useful for hypothesis generation and prioritizing candidate genes potentially responsible phenotypes of interest. We functionally annotated the 18 crop plant genomes across 14 species using GOMAP pipeline. Results By comparison to existing GO annotation datasets, GOMAP-generated datasets cover more genes, contain terms, produce similar in quality (based on precision recall metrics gold standards as basis comparison). From there, we sought...