Doreen Ware

The paper develops and validates a mid-density SNP array for sorghum using NGS, showing it performs as well as high-density GBS for trait prediction and breeding applications.

The paper presents high-quality genome assemblies and annotations for two Yarrowia lipolytica strains, using a combination of short-read and long-read sequencing technologies.

The paper develops a pan-gene catalogue for Asian cultivated rice by creating a reference panel of 16 cultivars and identifying core and cultivar-specific genes.

The paper identifies bi-directionally expressed enhancers in maize with domestication signatures using integrated epigenomic and transcriptomic data from multiple tissues and inbred lines.

This paper demonstrates that ONT Duplex sequencing combined with Pore-C data can assemble complete, high-quality human and plant chromosomes with base accuracy over 99.999%.

The paper presents DAP-seq profiles of three GRAS family TFs in three crops, identifying unique and shared gene targets and potential novel GRAS-specific DNA-binding motifs.

The paper presents an HPC-based workflow for genome variant calling using GATK, demonstrating SNP detection in four plant species and identifying novel SNPs in rice.

The paper constructs a pan-genome inversion index for Asian rice using 16 genomes and finds a high inversion rate with functional implications.

The paper presents 10 new high-quality genome assemblies for sorghum genotypes, identifying structural variants and SNPs linked to bioenergy traits.

The paper improves the grapevine genome reference PN40024.v4 using long-read sequencing, enhancing continuity, haplotype resolution, and gene annotation.

A multi-genome analysis of maize reveals previously unknown variation in gene content, genome structure, and methylation.

TRaCE ranks transcripts by election-like voting to select canonical transcripts based on RNA-seq data and other criteria.

The paper generates a large-scale genomic resource of sorghum EMS mutants, identifying disruptive mutations in over 15,500 genes and making data accessible via BSAseq integration and a web tool.

The paper tracks structural mutations in rice over a century of breeding, showing exonic mutations are removed more rapidly than other mutation types during selection.

This study constructs high-quality sorghum genome assemblies and identifies structural variations and resistance genes associated with sugarcane aphid resistance.

The paper provides highly accurate long-read HiFi sequencing datasets for five complex genomes to evaluate and develop bioinformatic tools.

BSAseq identifies causal mutations in bulked F2 populations using a probabilistic model and interactive web tool.

The paper presents a gapless maize genome assembly using long read technologies and optical maps, achieving telomere-to-telomere assemblies for chromosomes 3 and 9.

This study evaluates the impact of sequence depth and read length on long-read assembly quality for the maize genome, finding that lower depths and shorter reads result in fragmented assemblies.

The paper describes the development of a cloud-based platform for managing, analyzing, and distributing MaizeCODE data, enhancing reproducibility and accessibility.

The paper develops a tool for haplotype phasing and expression analysis in maize using single-molecule long-read sequencing, revealing allele-specific and imprinted gene expression.

The paper benchmarks TE annotation methods and develops a pipeline called EDTA to create a comprehensive, condensed TE library for both intact and fragmented elements in rice genomes.

The paper identifies poorly annotated genes in maize using a double triage approach combining quality metrics and gene tree visualization, revealing 4,000 novel annotations.

Open-source KBase platform unites reference genomes and biochemistry, over 70 apps, Jupyter-based Narratives with provenance, and a Docker SDK for reproducible plant and microbial systems biology.

NECorr ranks gene importance in biological processes using molecular networks and transcriptome data, identifying known and new regulators in Arabidopsis flower tissue.

The paper constructs the third generation Zea mays haplotype map using whole genome sequencing data from 1,218 maize lines, identifying 83 million variant sites.

The paper improves the maize reference genome using single molecule technologies, resulting in longer contigs and better annotation of repetitive elements and genes.

The paper proposes a distributed bioinformatics platform using iRODS and iPlant Agave API for genomic analysis, validated with a Genome-Wide Association Study workflow.

The paper presents de novo genome assemblies of three rice strains, revealing novel gene spaces and structural variations not captured by reference-based resequencing.

The paper presents a GWAS platform using iPlant cyber-infrastructure for managing and analyzing large genotype and phenotype datasets with customizable workflows.