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List of works by Doreen Ware

A 4-gigabase physical map unlocks the structure and evolution of the complex genome of Aegilops tauschii, the wheat D-genome progenitor

scientific article published on 22 April 2013

A Sorghum Mutant Resource as an Efficient Platform for Gene Discovery in Grasses.

scientific article published on 27 June 2016

A comparative transcriptional landscape of maize and sorghum obtained by single-molecule sequencing

scientific article published on 30 April 2018

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

scientific article (publication date: 29 May 2013)

A genome-wide characterization of microRNA genes in maize

scientific article

A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes

scientific article

A single molecule scaffold for the maize genome

scientific article

A stele-enriched gene regulatory network in the Arabidopsis root

scientific article

AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture

article

Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane

scientific article published on 30 November 2020

An ultra-high-density map as a community resource for discerning the genetic basis of quantitative traits in maize

scientific article

Applications and methods utilizing the Simple Semantic Web Architecture and Protocol (SSWAP) for bioinformatics resource discovery and disparate data and service integration

scientific article

BSAseq: an interactive and integrated web-based workflow for identification of causal mutations in bulked F2 populations

scientific article published on 10 August 2020

Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline

scientific article published on 16 December 2019

CMap 1.01: a comparative mapping application for the Internet

scientific article published on 30 July 2009

Characterization of miRNAs in Response to Short-Term Waterlogging in Three Inbred Lines of Zea mays ⬇️

scientific article published on June 29, 2012

Comparative population genomics of maize domestication and improvement

scientific article published on 3 June 2012

Comparison of genes among cereals

scientific article

Construction of the third generation Zea mays haplotype map.

scientific article published on 30 December 2017

Construction, alignment and analysis of twelve framework physical maps that represent the ten genome types of the genus Oryza

scientific article published on 28 February 2008

DNA methylation and gene expression regulation associated with vascularization in Sorghum bicolor

scientific article

Detailed analysis of a contiguous 22-Mb region of the maize genome

scientific article

Development and Mapping of 2240 New SSR Markers for Rice (Oryza sativa L.) (Supplement)

article

Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.).

scientific article

Digital gene expression signatures for maize development.

scientific article

Disentangling methodological and biological sources of gene tree discordance on Oryza (Poaceae) chromosome 3.

scientific article

Double triage to identify poorly annotated genes in maize: The missing link in community curation

scientific article published in 2019

Dynamic Oryza Genomes: Repetitive DNA Sequences as Genome Modeling Agents

Effect of sequence depth and length in long-read assembly of the maize inbred NC358

scientific article published on 08 May 2020

Efficient Identification of Causal Mutations through Sequencing of Bulked F 2 from Two Allelic Bloomless Mutants of Sorghum bicolor.

scientific article published in January 2017

Enhanced Y1H assays for Arabidopsis.

scientific article published on 30 October 2011

Ensembl 2024

scientific article published on 11 November 2023

Ensembl Genomes 2013: scaling up access to genome-wide data

scientific article

Ensembl Genomes 2016: more genomes, more complexity

scientific article

Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.

scientific article published on 30 October 2017

Ensembl Genomes 2020-enabling non-vertebrate genomic research

scientific article published on 01 January 2020

Evidence-based gene predictions in plant genomes

scientific article published on 18 June 2009

Evolution of Arabidopsis microRNA families through duplication events

scientific article

Expression Atlas update: gene and protein expression in multiple species

scientific article published on 19 November 2021

Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes

scientific article published on 30 July 2018

Fertility of Pedicellate Spikelets in Sorghum Is Controlled by a Jasmonic Acid Regulatory Module

scientific article published on 08 October 2019

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid ⬇️

scientific article published on October 18, 2011

Gapless assembly of maize chromosomes using long-read technologies

scientific article published on 20 May 2020

Gene disruption by structural mutations drives selection in US rice breeding over the last century

scientific article published on 18 March 2021

Genetic properties of the maize nested association mapping population

scientific article

Genetic structure and domestication history of the grape

scientific article

Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs).

scientific article

Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population

scientific article published on 9 January 2011

Genome-wide computational prediction and analysis of core promoter elements across plant monocots and dicots

scientific article

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.

scientific article

Gramene 2013: comparative plant genomics resources.

scientific article

Gramene 2016: comparative plant genomics and pathway resources

scientific article

Gramene 2018: unifying comparative genomics and pathway resources for plant research

scientific article

Gramene 2021: harnessing the power of comparative genomics and pathways for plant research

scientific article published on 10 November 2020

Gramene Database: Navigating Plant Comparative Genomics Resources

scientific article

Gramene QTL database: development, content and applications

scientific article published on 08 May 2009

Gramene database in 2010: updates and extensions

scientific article (publication date: 2011)

Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways

scientific article published on January 2016

Gramene: a bird's eye view of cereal genomes

scientific article

Gramene: a growing plant comparative genomics resource

scientific article

Gramene: a resource for comparative grass genomics ⬇️

scientific article published on January 1, 2002

Gramene: development and integration of trait and gene ontologies for rice

scientific article published on January 2002

GrameneMart: the BioMart data portal for the Gramene project

scientific article

Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus

scientific article published on 21 January 2020

High-throughput comparison, functional annotation, and metabolic modeling of plant genomes using the PlantSEED resource

scientific article

Highly accurate long-read HiFi sequencing data for five complex genomes

scientific article published on 17 November 2020

Identification of the First Nuclear Male Sterility Gene (Male-sterile 9) in Sorghum

scientific article published on 01 November 2019

Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure

scientific article published on 31 August 2018

Improved maize reference genome with single-molecule technologies

scientific article published on 12 June 2017

Integration of hybridization-based markers (overgos) into physical maps for comparative and evolutionary explorations in the genus Oryza and in Sorghum

scientific article published on 8 August 2006

KBase: The United States Department of Energy Systems Biology Knowledgebase

article

Large-scale atlas of microarray data reveals the distinct expression landscape of different tissues in Arabidopsis.

scientific article

Look-Align: an interactive web-based multiple sequence alignment viewer with polymorphism analysis support

scientific article published on 10 February 2006

Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats

scientific article

MSD1 regulates pedicellate spikelet fertility in sorghum through the jasmonic acid pathway.

scientific article published on 26 February 2018

Maize HapMap2 identifies extant variation from a genome in flux.

scientific article

Maize Metabolic Network Construction and Transcriptome Analysis

Microdissection of shoot meristem functional domains

scientific article

Panzea: a database and resource for molecular and functional diversity in the maize genome

scientific article

Panzea: an update on new content and features

scientific article

Pervasive gene content variation and copy number variation in maize and its undomesticated progenitor

scientific article

Phylogenomic Analysis of BAC-end Sequence Libraries in Oryza (Poaceae)

scholarly article by Karen Cranston et al published 1 September 2010 in Systematic Botany

Plant Ontology (PO): a Controlled Vocabulary of Plant Structures and Growth Stages

scientific article

Plant Reactome: a knowledgebase and resource for comparative pathway analysis

scientific article published on 01 January 2020

Plant Reactome: a resource for plant pathways and comparative analysis

scientific article published on 30 October 2016

Predicting gene structure changes resulting from genetic variants via exon definition features

scientific article published on 01 November 2018

Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

scholarly article published in Nature Genetics

Rapid genomic characterization of the genus vitis

scientific article

Registration of 252 sequenced sorghum mutants as a community reverse genetic resource

scientific article published in 2023

Regulatory modules controlling maize inflorescence architecture.

scientific article

Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing

scholarly article by Bo Wang et al published 2019 in Frontiers in Genetics

Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza

scientific article

SciApps: A cloud-based platform for reproducible bioinformatics workflows

scientific article published on 01 November 2018

Single-Cell RNA Sequencing of Developing Ears Facilitates Functional Analysis and Trait Candidate Gene Discovery in Maize

scientific article published in 2020

Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery

scientific article published on 30 December 2020

Sorghum MSD3 Encodes an ω-3 Fatty Acid Desaturase that Increases Grain Number by Reducing Jasmonic Acid Levels

scientific article published on 28 October 2019

Sorghum root epigenetic landscape during limiting phosphorus conditions

scientific article published on 14 May 2022

Species trees from highly incongruent gene trees in rice

scientific article published on 21 September 2009

The B73 Maize Genome: Complexity, Diversity, and Dynamics

scientific article

The BioMart community portal: an innovative alternative to large, centralized data repositories

scientific article (publication date: July 2015)

The Dominant and Poorly Penetrant Phenotypes of Maize Unstable factor for orange1 Are Caused by DNA Methylation Changes at a Linked Transposon

scientific article published on 18 December 2018

The Gramene Genetic Diversity Module: a resource for genotype-phenotype association analysis in grass species

scientific article published on 18 July 2019

The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology.

scientific article published in December 2017

The Oryza BAC resource: a genus-wide and genome scale tool for exploring rice genome evolution and leveraging useful genetic diversity from wild relatives

scientific article published in 2010

The Plant Ontology Database: a community resource for plant structure and developmental stages controlled vocabulary and annotations

scientific article

The Plastid and Mitochondrial Peptidase Network in Arabidopsis thaliana: A Foundation for Testing Genetic Interactions and Functions in Organellar Proteostasis

scientific article

The Sorghum bicolor genome and the diversification of grasses

scientific article

The genetic architecture of maize flowering time.

scientific article

The iPlant Collaborative: Cyberinfrastructure for Enabling Data to Discovery for the Life Sciences

scientific article

The iPlant Collaborative: Cyberinfrastructure for Plant Biology

scientific article published in 2011

The maize W22 genome provides a foundation for functional genomics and transposon biology

scientific article published on 30 July 2018

The maize methylome influences mRNA splice sites and reveals widespread paramutation-like switches guided by small RNA.

scientific article

The physical and genetic framework of the maize B73 genome

scientific article

Toward a data infrastructure for the Plant Cell Atlas

scientific article published on 6 October 2022

Transcriptional regulation of nitrogen-associated metabolism and growth

scientific article published in Nature

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

scientific article published on 24 June 2016

Variant phasing and haplotypic expression from long-read sequencing in maize

scientific article published on 18 February 2020

Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa, document novel gene space of aus and indica

scientific article

Whole-plant growth stage ontology for angiosperms and its application in plant biology

scientific article

ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize

scientific article

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