Research Projects
At the very beginning of any research project, it's important to choose datasets that are relevant to the questions at hand. The Field Crop FAIR Data Demonstrator enables those who are unfamiliar with a group of field trials across many environments and years to browse what's available. Here, the demonstrator is populated with the first three field seasons' data from the maize Genomes to Fields (G2F) GxE project. Efforts to make the data Findable, Accessible, Interoperable, and Reusable (FAIR) are supported through the use of BrAPI for data access. See AlKhalifah et al., 2018 for details. Additional G2F datasets can be found here.
C-REx: A shiny web application to compare RNA expression
C-REx implements a novel statistical method that was designed to assess significance of differences in RNA expression levels among specified groups of genes. This Shiny web application called C-REx (Comparison of RNA Expression) enables researchers to readily test hypotheses about whether specific gene groups share expression profiles and whether those profiles differ from those of other groups of genes. The method implemented via C-REx is more sensitive than GO enrichment when fold change between conditions is small.
GOMAP
Gene Ontology Meta Annotator for Plants (GOMAP) is a high-throughput pipeline to annotate GO terms to plant protein sequences in a high-confidence and reproducible manner. It combines sequence-similarity, domain-presence and mixed-method based approaches and we are currently applying it to the reference genomes of several agriculturally important plants (maize, wheat, rice, cotton, soybean). All generated annotation datasets as well as the source code are publicly available.
An accelerator for climate change research: Enviratron
The ENVIRATRON project is a phenomics platform that enables researchers to monitor the performance of plants throughout their lifespan when subject to a variety of environmental conditions, including anticipated future environments. The ENVIRATRON will permit researchers to incrementally alter critical variables to better simulate changing conditions that we face in the future.
CRISPR Genome Analysis Tool: CGAT
CRISPR Genome Analysis Tool works in two steps: 1) Identify potential target sites for CRISPR gene editing in DNA sequences. 2) Optionally, use identified target sequences from step 1 to search a genome of interest for potential off-target matches.
Maize model organism database: MaizeGDB
MaizeGDB is a community-oriented, long-term, federally funded informatics service to researchers focused on the crop plant and model organism Zea mays.
Find Mu TIRs in maize: MuTAlyzer
MuTAlyzer takes as its input one or more FASTA format DNA sequences and locates within them the MuTIR sequences, Adapter sequences, and Insertion sequences.
Resample phylogenetic treespace: LumberJack
LumberJack is a Heuristic Tool for Sequence Alignment Exploration and Phylogenetic Inference.
