C. Hirsch

发表

How the pan-genome is changing crop genomics and improvement

Rafael Della Coletta, Y. Qiu, Shujun Ou, 2021, Genome Biology.

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

Michelle C. Stitzer, N. Springer, C. Hirsch, 2014, bioRxiv.

An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development

R. Sekhon, C. Buell, N. Leon, 2016, The plant genome.

Generation of Transcript Assemblies and Identification of Single Nucleotide Polymorphisms from Seven Lowland and Upland Cultivars of Switchgrass

J. Schmutz, C. Buell, S. Kaeppler, 2014 .

Insights into the Maize Pan-Genome and Pan-Transcriptome[W][OPEN]

M. A. Pedraza, R. Sekhon, F. Peñagaricano, 2014, Plant Cell.

Spud DB: A Resource for Mining Sequences, Genotypes, and Phenotypes to Accelerate Potato Breeding

C. Buell, K. Childs, C. Hirsch, 2014 .

Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions[OPEN]

Peter A. Crisp, Nathan M. Springer, S. Briggs, 2020, Plant Cell.

UAV‐based imaging platform for monitoring maize growth throughout development

N. Springer, C. Hirsch, Sara B. Tirado, 2020, Plant direct.

UAV‐based imaging platform for monitoring maize growth throughout development

Nathan M. Springer, N. Springer, C. Hirsch, 2019, bioRxiv.

Genome-wide association analysis of stalk biomass and anatomical traits in maize

Joseph L. Gage, K. Barry, S. Kaeppler, 2019, BMC Plant Biology.

Limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines

Alex B. Brohammer, Nathan M. Springer, N. Springer, 2017, bioRxiv.

The effect of artificial selection on phenotypic plasticity in maize

Joseph L. Gage, Darwin A. Campbell, James C. Schnable, 2017, Nature Communications.

Opportunities and challenges in phenotyping row crops using drone‐based RGB imaging

Nathan M. Springer, N. Springer, C. Hirsch, 2022, The Plant Phenome Journal.

De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Carson M. Andorf, Ethalinda K. S. Cannon, Robert J. Schmitz, 2021, Science.

Population Level Variation of Transposable Elements in a Maize Diversity Panel

Christine H. O’Connor, Nathan M. Springer, Amanda M. Gilbert, 2020, bioRxiv.

Transposable elements contribute to dynamic genome content in maize

Alex B. Brohammer, Nathan M. Springer, Michelle C. Stitzer, 2019, bioRxiv.

Shared Genomic Regions Between Derivatives of a Large Segregating Population of Maize Identified Using Bulked Segregant Analysis Sequencing and Traditional Linkage Analysis

Timothy M. Beissinger, K. Barry, C. Buell, 2015, G3: Genes, Genomes, Genetics.

Yield Prediction Through Integration of Genetic, Environment, and Management Data Through Deep Learning

Joseph L. Gage, James C. Schnable, Timothy M. Beissinger, 2022, bioRxiv.

Variation and Inheritance of Small RNAs in Maize Inbreds and F1 Hybrids1[OPEN]

Peter A. Crisp, Nathan M. Springer, B. Meyers, 2019, Plant Physiology.

Short Small RNAs and heterosis in maize Variation and inheritance of small RNAs in maize inbreds and F 1 hybrids

Peter A. Crisp, Nathan M. Springer, K. Barry, 2019 .

Correction: Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

Nathan M. Springer, Michelle C. Stitzer, N. Springer, 2015, PLoS genetics.

Dynamic Patterns of Gene Expression Additivity and Regulatory Variation throughout Maize Development.

Nathan M. Springer, S. Briggs, N. Springer, 2019, Molecular plant.

Genome-wide scan for selection following thirty generations of artificial selection for increased number of ears per plant in the Golden Glow maize population

Timothy M. Beissinger, D. Gianola, K. Barry, 2013 .

Highly Genotype- and Tissue-specific Single-Parent Expression Drives Dynamic Gene Expression Complementation in Maize Hybrids

Alex B. Brohammer, Nathan M. Springer, K. Barry, 2019, bioRxiv.

Genome-Wide Association and Gene Co-expression Network Analyses Reveal Complex Genetics of Resistance to Goss’s Wilt of Maize

Alex B. Brohammer, D. Jarquín, Amritpal S. Singh, 2019, G3: Genes, Genomes, Genetics.

Food‐Grade Maize Composition, Evaluation, and Genetics for Masa‐Based Products

Peter D. Coaldrake, Nickolas A. Anderson, C. Hirsch, 2019, Crop Science.

Weeding out bad alleles

N. Springer, C. Hirsch, 2018, Nature Plants.

Differences in activity and stability drive transposable element variation in tropical and temperate maize

Arun S. Seetharam, M. Schatz, Y. Qiu, 2022, bioRxiv.

Utility of Climatic Information via Combining Ability Models to Improve Genomic Prediction for Yield Within the Genomes to Fields Maize Project

James C. Schnable, Carolyn J. Lawrence-Dill, Nathan M. Springer, 2021, Frontiers in Genetics.

Relative utility of agronomic, phenological, and morphological traits for assessing genotype‐by‐environment interaction in maize inbreds

Darwin A. Campbell, Carolyn J. Lawrence-Dill, Nathan D. Miller, 2020, Crop Science.

Correction: Genotype-by-environment interactions affecting heterosis in maize

Nathan D. Miller, P. Schnable, N. Springer, 2019, PloS one.

Gapless assembly of maize chromosomes using long-read technologies

Arun S. Seetharam, Magdy S. Alabady, G. Presting, 2020, Genome Biology.

A Genome-Wide Scan for Evidence of Selection in a Maize Population Under Long-Term Artificial Selection for Ear Number

D. Gianola, K. Barry, C. Buell, 2013, Genetics.

The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment.

Nathan M. Springer, Jason G. Wallace, P. Schnable, 2021, G3.

Development of a Multiparent Population for Genetic Mapping and Allele Discovery in Six-Row Barley.

Kevin P. Smith, Lin Li, P. Morrell, 2019, Genetics.

Correction: Maize Gene Atlas Developed by RNA Sequencing and Comparative Evaluation of Transcriptomes Based on RNA Sequencing and Microarrays

C. Myers, R. Sekhon, C. Buell, 2014, PLoS ONE.

Maize Gene Atlas Developed by RNA Sequencing and Comparative Evaluation of Transcriptomes Based on RNA Sequencing and Microarrays

C. Robin Buell, Chad L. Myers, Shawn M. Kaeppler, 2013, PloS one.

Tapping the promise of genomics in species with complex, nonmodel genomes.

C. Buell, C. Hirsch, C. R. Buell, 2013, Annual review of plant biology.

Marker Density and Read Depth for Genotyping Populations Using Genotyping-by-Sequencing

C. Robin Buell, Brieanne Vaillancourt, Shawn M. Kaeppler, 2013, Genetics.

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome

Robert J. Schmitz, Gregory J. Zynda, Nathan M. Springer, 2015, Proceedings of the National Academy of Sciences.

Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

C. Buell, C. Hirsch, C. Hirsch, 2014, Briefings in functional genomics.

Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes

Robert J. Schmitz, Peter A. Crisp, Nathan M. Springer, 2021, bioRxiv.

A Toolbox of Potato Genetic and Genomic Resources

C. Buell, C. Hirsch, C. Hirsch, 2016, American Journal of Potato Research.

QTL mapping and phenotypic variation for root architectural traits in maize (Zea mays L.)

J. Lynch, C. Buell, S. Kaeppler, 2014, Theoretical and Applied Genetics.

Monitoring the interplay between transposable element families and DNA methylation in maize

Robert J. Schmitz, Peter A. Crisp, Nathan M. Springer, 2019, PLoS genetics.

Whole Transcriptome Profiling of Maize during Early Somatic Embryogenesis Reveals Altered Expression of Stress Factors and Embryogenesis-Related Genes

C. Buell, S. Kaeppler, C. Hirsch, 2014, PloS one.

Natural variation for gene expression responses to abiotic stress in maize

Nathan M. Springer, N. Springer, C. Hirsch, 2017, The Plant journal : for cell and molecular biology.

The Contribution of the Solanaceae Coordinated Agricultural Project to Potato Breeding

D. Bisognin, M. Hardigan, C. Buell, 2014, Potato Research.

Genetic Fine‐Mapping of a Quantitative Trait Locus (QTL) Associated with Embryogenic Tissue Culture Response and Plant Regeneration Ability in Maize (Zea mays L.)

S. Kaeppler, C. Hirsch, H. Kaeppler, 2018, The plant genome.

Retrospective View of North American Potato (Solanum tuberosum L.) Breeding in the 20th and 21st Centuries

R. Veilleux, C. Buell, C. Hirsch, 2013, G3: Genes, Genomes, Genetics.

Genotype-by-environment interactions affecting heterosis in maize

Nathan D. Miller, Nathan M. Springer, P. Schnable, 2017, bioRxiv.

Gapless assembly of maize chromosomes using long-read technologies

Arun S. Seetharam, Magdy S. Alabady, G. Presting, 2020, Genome Biology.

Gapless assembly of maize chromosomes using long-read technologies

Doreen Ware, Todd P. Michael, Arun S. Seetharam, 2020, Genome Biology.

Importance of genetic architecture in marker selection decisions for genomic prediction

Samuel B. Fernandes, M. Bohn, M. Mikel, 2023, bioRxiv.

Linking genetic and environmental factors through marker effect networks to understand trait plasticity

Samuel B. Fernandes, M. Bohn, M. Mikel, 2023, bioRxiv.

Whole-genome variation of transposable element insertions in a maize diversity panel

Christine H. O’Connor, Nathan M. Springer, Amanda M. Gilbert, 2021, G3.

Genome-wide association analysis of stalk biomass and anatomical traits in maize

Joseph L. Gage, K. Barry, S. Kaeppler, 2019, BMC Plant Biology.

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

Arun S. Seetharam, David E. Hufnagel, Amanda M. Gilbert, 2019, bioRxiv.

Variation and Inheritance of Small RNAs in Maize Inbreds and F1 Hybrids1[OPEN]

Peter A. Crisp, B. Meyers, K. Barry, 2019, Plant Physiology.

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

Thomas Peterson, Yi Liao, Doreen Ware, 2019, Genome Biology.

Using multiple reference genomes to identify and resolve annotation inconsistencies

Candice N. Hirsch, Patrick J. Monnahan, Jean-Michel Michno, 2019, BMC Genomics.

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize[OPEN]

Kevin L. Childs, C. Robin Buell, Christopher J. Fields, 2016, Plant Cell.

Limited consequences for loss of RNA-directed DNA methylation in Setaria viridis domains rearranged methyltransferase (DRM) mutants

Peter A. Crisp, Nathan M. Springer, N. Springer, 2022, bioRxiv.

Title: Limited consequences for loss of RNA-directed DNA methylation in Setaria viridis

Peter A. Crisp, N. Springer, Zhikai Liang, 2022 .

Whole Genome Assembly and Annotation of Northern Wild Rice, Zizania palustris L., Supports a Whole Genome Duplication in the Zizania Genus.

Y. Qiu, C. Hirsch, Jennifer A. Kimball, 2021, The Plant journal : for cell and molecular biology.

Whole Genome Assembly and Annotation of Northern Wild Rice, Zizania palustris L., Supports a Whole Genome Duplication in the Zizania Genus

C. Hirsch, Jennifer A. Kimball, Thomas J. Y. Kono, 2021, bioRxiv.

Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination1[W][OPEN]

Matthew W. Breitzman, R. Sekhon, C. Buell, 2014, Plant Physiology.

The Maize Pan-Genome

Candice N. Hirsch, Alex B. Brohammer, C. Hirsch, 2018 .

Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons.

Robert J. Schmitz, Peter A. Crisp, Christine H. O’Connor, 2020, Genetics.

Maize sugary enhancer1 (se1) is a gene affecting endosperm starch metabolism

Vai S. Lor, S. Kaeppler, C. Hirsch, 2019, Proceedings of the National Academy of Sciences.

Insights into the Effects of Long-Term Artificial Selection on Seed Size in Maize

Timothy M. Beissinger, Nathan M. Springer, Steven R. Eichten, 2014, Genetics.

Genomic limitations to RNA sequencing expression profiling.

Nathan M. Springer, N. Springer, C. Hirsch, 2015, The Plant journal : for cell and molecular biology.

Evidence for maternal control of seed size in maize from phenotypic and transcriptional analysis

R. Sekhon, S. Kaeppler, N. de Leon, 2016, Journal of experimental botany.

Development of a Multiparent Population for Genetic Mapping and Allele Discovery in Six-Row Barley

Kevin P. Smith, P. Morrell, G. Brown-Guedira, 2019, Genetics.

Genomic Sequence and Structural Diversity in Plants

C. Hirsch, 2014 .

Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion

Nathan M. Springer, Michelle C. Stitzer, Y. Brandvain, 2023, bioRxiv.

Cis-regulatory elements within TEs can influence expression of nearby maize genes

Robert J. Schmitz, Peter A. Crisp, Christine H. O’Connor, 2020, bioRxiv.

Genomic variation within the maize stiff‐stalk heterotic germplasm pool

Arun S. Seetharam, S. Shu, Y. Yoshinaga, 2021, The plant genome.

Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time

Alex B. Brohammer, C. Hirsch, S. McGaugh, 2017, G3: Genes, Genomes, Genetics.

QTL mapping and phenotypic variation for root architectural traits in maize (Zea mays L.)

J. Lynch, C. Buell, S. Kaeppler, 2014, Theoretical and Applied Genetics.

Limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines

Alex B. Brohammer, N. Springer, C. Hirsch, 2017, bioRxiv.

Utilizing Temporal Measurements from UAVs to Assess Root Lodging in Maize and its Impact on Productivity

N. Springer, C. Hirsch, Sara B. Tirado, 2020, bioRxiv.

Multivariate analyses of root phenotype and dynamic transcriptome underscore valuable root traits and water-deficit responsive gene networks in maize

C. Hirsch, Yuting He, Jun Zhao, 2019, Plant Direct.

Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets

Patrick S. Schnable, Seth C. Murray, Michael A. Gore, 2018, BMC Research Notes.

Predicting moisture content during maize nixtamalization using machine learning with NIR spectroscopy

Amanda M. Gilbert, Nickolas A. Anderson, C. Hirsch, 2021, Theoretical and Applied Genetics.

The Maize Genome

J. Bennetzen, C. Kole, C. Hirsch, 2018, Compendium of Plant Genomes.

Genetic and Morphometric Analysis of Cob Architecture and Biomass-Related Traits in the Intermated B73 × Mo17 Recombinant Inbred Lines of Maize

N. Leon, C. Hirsch, T. Lübberstedt, 2013, BioEnergy Research.

Single-parent expression drives dynamic gene expression complementation in maize hybrids.

Christine H. O’Connor, Alex B. Brohammer, Nathan M. Springer, 2020, The Plant journal : for cell and molecular biology.

Characterizing introgression-by-environment interactions using maize near isogenic lines

Nathan D. Miller, Nathan M. Springer, P. Schnable, 2020, Theoretical and Applied Genetics.

Genetic control of kernel compositional variation in a maize diversity panel

Christine H. O’Connor, Amanda M. Gilbert, Nickolas A. Anderson, 2021, The plant genome.

Genetic Architecture of Kernel Compositional Variation in a Maize Diversity Panel

Christine H. O’Connor, Amanda M. Gilbert, Nickolas A. Anderson, 2021, bioRxiv.

Mutator transposon insertions within maize genes often provide a novel outward reading promoter

Nathan M. Springer, E. Grotewold, N. Springer, 2023, bioRxiv.

Maize genomes to fields (G2F): 2014–2017 field seasons: genotype, phenotype, climatic, soil, and inbred ear image datasets

Patrick S. Schnable, Seth C. Murray, Joseph L. Gage, 2020, BMC Research Notes.

Variability in changes of acrylamide precursors during nixtamalization for masa production

Amanda M. Gilbert, Nickolas A. Anderson, C. Hirsch, 2022, LWT.

Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress

Nathan M. Springer, Michelle C. Stitzer, N. Springer, 2015, PLoS genetics.

Genomes to Fields 2022 Maize genotype by Environment Prediction Competition

Joseph L. Gage, Jacob D. Washburn, Jason G. Wallace, 2023, BMC Research Notes.

A Genome-Wide Scan for Evidence of Selection in a Maize Population Under Long-Term Artificial Selection for Ear Number

Timothy M. Beissinger, D. Gianola, K. Barry, 2013, Genetics.

Short Small RNAs and heterosis in maize Variation and inheritance of small RNAs in maize inbreds and F 1 hybrids

Peter A. Crisp, Nathan M. Springer, K. Barry, 2019 .

Transposable elements contribute to dynamic genome content in maize 1

Alex B. Brohammer, Nathan M. Springer, Michelle C. Stitzer, 2022 .

Tapping the promise of genomics in species with complex, nonmodel genomes.

C. Hirsch, C. R. Buell, 2013, Annual review of plant biology.

Genetic analysis of pericarp pigmentation variation in Corn Belt dent maize

S. Kaeppler, Y. Qiu, C. Hirsch, 2023, G3.

Characterizing allele-by-environment interactions using maize introgression lines

Nathan D. Miller, Nathan M. Springer, P. Schnable, 2019, bioRxiv.

SpykProps: an imaging pipeline to quantify architecture in unilateral grass inflorescences

C. Hirsch, N. Ehlke, Eric Watkins, 2023, Plant Methods.

Correction: Genotype-by-environment interactions affecting heterosis in maize

Nathan D. Miller, Nathan M. Springer, P. Schnable, 2019, PloS one.

Plant height defined growth curves during vegetative development have the potential to predict end of season maize yield and assist with mid-season management decisions

C. Hirsch, C. Hirsch, Dorothy D. Sweet, 2024, bioRxiv.

Broader Impacts of the Proposed Work

Nathan M. Springer, Michelle C. Stitzer, I. Ruczinski, 2015 .