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Author Details

Doreen Ware
USDA ARS NAA Robert W. Holley Center for Agriculture and Health
1989
149
66
Christopher Churas (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
37992296Expression Atlas update: insights from sequencing data at both bulk and single cell level.Nucleic Acids Res2024
37953337Ensembl 2024.Nucleic Acids Res2024
36200899Toward a data infrastructure for the Plant Cell Atlas.Plant Physiol2023
37965006Two related families of metal transferases, ZNG1 and ZNG2, are involved in acclimation to poor Zn nutrition in Arabidopsis.Front Plant Sci2023
37530518Engineering homoeologs provide a fine scale for quantitative traits in polyploid.Plant Biotechnol J2023
37213686The complete reference genome for grapevine (<i>Vitis vinifera</i> L.) genetics and breeding.Hortic Res2023
36944612Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice.Nat Commun2023
36966465An improved reference of the grapevine genome reasserts the origin of the PN40024 highly homozygous genotype.G3 (Bethesda)2023
36684744Ten new high-quality genome assemblies for diverse bioenergy sorghum genotypes.Front Plant Sci2023
36640454Era of gapless plant genomes: innovations in sequencing and mapping technologies revolutionize genomics and breeding.Curr Opin Biotechnol2023
34791415Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.Nucleic Acids Res2022
35440059Experimental demonstration and pan-structurome prediction of climate-associated riboSNitches in Arabidopsis.Genome Biol2022
35600998Sorghum root epigenetic landscape during limiting phosphorus conditions.Plant Direct2022
35955798Role of a ZF-HD Transcription Factor in miR157-Mediated Feed-Forward Regulatory Module That Determines Plant Architecture in <i>Arabidopsis</i>.Int J Mol Sci2022
35015132SorghumBase: a web-based portal for sorghum genetic information and community advancement.Planta2022
35037207SciApps: An Automated Platform for Processing and Distribution of Plant Genomics Data.Methods Mol Biol2022
35037202Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways.Methods Mol Biol2022
34850121Expression Atlas update: gene and protein expression in multiple species.Nucleic Acids Res2022
35260190Author Correction: Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline.Genome Biol2022
32777814BSAseq: an interactive and integrated web-based workflow for identification of causal mutations in bulked F2 populations.Bioinformatics2021
34353948De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes.Science2021
34297055Ranked choice voting for representative transcripts with TRaCE.Bioinformatics2021
33170273Gramene 2021: harnessing the power of comparative genomics and pathways for plant research.Nucleic Acids Res2021
33400914Single-cell RNA sequencing of developing maize ears facilitates functional analysis and trait candidate gene discovery.Dev Cell2021
32296450Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud.Front Plant Sci2020
31964885Haplotyping the Vitis collinear core genome with rhAmpSeq improves marker transferability in a diverse genus.Nat Commun2020
32071408Variant phasing and haplotypic expression from long-read sequencing in maize.Commun Biol2020
31680153Plant Reactome: a knowledgebase and resource for comparative pathway analysis.Nucleic Acids Res2020
33266228Amino Acid and Carbohydrate Metabolism Are Coordinated to Maintain Energetic Balance during Drought in Sugarcane.Int J Mol Sci2020
33203859Highly accurate long-read HiFi sequencing data for five complex genomes.Sci Data2020
32385271Effect of sequence depth and length in long-read assembly of the maize inbred NC358.Nat Commun2020
32434565Gapless assembly of maize chromosomes using long-read technologies.Genome Biol2020
31105749Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing.Front Genet2019
31843001Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline.Genome Biol2019
31744902A high-resolution gene expression atlas links dedicated meristem genes to key architectural traits.Genome Res2019
31661847Sorghum <i>MSD3</i> Encodes an Ï¿-3 Fatty Acid Desaturase that Increases Grain Number by Reducing Jasmonic Acid Levels.Int J Mol Sci2019
31658277Double triage to identify poorly annotated genes in maize: The missing link in community curation.PLoS One2019
33016577Identification of the First Nuclear Male Sterility Gene (Male-sterile 9) in Sorghum.Plant Genome2019
31597271Fertility of Pedicellate Spikelets in Sorghum Is Controlled by a Jasmonic Acid Regulatory Module.Int J Mol Sci2019
29092050Ensembl Genomes 2018: an integrated omics infrastructure for non-vertebrate species.Nucleic Acids Res2018
30239679AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture.Database (Oxford)2018
30061736The maize W22 genome provides a foundation for functional genomics and transposon biology.Nat Genet2018
30061735Extensive intraspecific gene order and gene structural variations between Mo17 and other maize genomes.Nat Genet2018
29979655KBase: The United States Department of Energy Systems Biology Knowledgebase.Nat Biotechnol2018
29897418SciApps: a cloud-based platform for reproducible bioinformatics workflows.Bioinformatics2018
30168903Improved RNA-seq Workflows Using CyVerse Cyberinfrastructure.Curr Protoc Bioinformatics2018
30291357Publisher Correction: Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza.Nat Genet2018
30563848The Dominant and Poorly Penetrant Phenotypes of Maize <i>Unstable factor for orange1</i> Are Caused by DNA Methylation Changes at a Linked Transposon.Plant Cell2018
30356219Transcriptional regulation of nitrogen-associated metabolism and growth.Nature2018
29701825Predicting gene structure changes resulting from genetic variants via exon definition features.Bioinformatics2018
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Collaborators

Lincoln Stein
Ontario Institute for Cancer Research, University Avenue
Co-authored papers 30
Pankaj Jaiswal
Oregon State University
Co-authored papers 23
Marcela K Tello-Ruiz
State University of New York at Old Westbury
Co-authored papers 17
Sunita Kumari
Manav Rachna International Institute of Research and Studies
Co-authored papers 15
Rod A Wing
Arizona Genomics Institute, University of Arizona
Co-authored papers 12
Liya Wang
Henan Eye Hospital and Henan Eye Institute, People's Hospital of Zhengzhou University
Co-authored papers 11
Jer-Ming Chia
The Genome Institute of Singapore
Co-authored papers 10
Paul Kersey
European Bioinformatics Institute
Co-authored papers 10
Sushma Naithani
Oregon State University
Co-authored papers 10
Justin Preece
Oregon State University
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Shiran Pasternak
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James Thomason
USDA-ARS Laboratory at Cold Spring Harbor Laboratory
Co-authored papers 7
Peter D'Eustachio
NYU Grossman School of Medicine
Co-authored papers 7
William Spooner
Eagle Genomics Ltd.
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Bonnie L Hurwitz
The University of Arizona
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Vivek Kumar
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Justin Elser
Oregon State University
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Irene Papatheodorou
Co-authored papers 6
Daniel M Staines
European Bioinformatics Institute
Co-authored papers 6
Seung Y Rhee
Carnegie Institution for Science
Co-authored papers 5
Mary L Schaeffer
University of Missouri
Co-authored papers 5
Margaret R Woodhouse
USDA-ARS, Corn Insects and Crop Genetics Research Unit
Co-authored papers 5
Christopher A Maher
Washington University in St Louis
Co-authored papers 5
Antonio Fabregat
Co-authored papers 5
Leonore Reiser
Carnegie Institution for Science
Co-authored papers 5
Mark Yandell
University of Utah
Co-authored papers 4
Shiguo Zhou
Sage Science Inc.
Co-authored papers 4
Matthew W Vaughn
Co-authored papers 4
David C Schwartz
University of Wisconsin-Madison
Co-authored papers 4
Carson M Andorf
USDA-ARS, Corn Insects and Crop Genetics Research Unit
Co-authored papers 4
Release 1.2