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List of works by James Schnable

A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize

scientific article

A High-Throughput Phenotyping Pipeline for Image Processing and Functional Growth Curve Analysis

scientific article published on 14 July 2020

A UAV‐based high‐throughput phenotyping approach to assess time‐series nitrogen responses and identify trait‐associated genetic components in maize

scientific article published in 2022

A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.

scientific article published on 31 March 2014

A role for heritable transcriptomic variation in maize adaptation to temperate environments

scientific article published in 2023

ALLMAPS: robust scaffold ordering based on multiple maps.

scientific article

Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy

scientific article published on 2 February 2012

Association mapping across a multitude of traits collected in diverse environments in maize

scientific article published in 2022

Author Correction: Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogenetic Tree of the Paniceae Grasses

scientific article published in Scientific Reports

Automated conserved non-coding sequence (CNS) discovery reveals differences in gene content and promoter evolution among grasses

scientific article published on 02 July 2013

Co-option of the polarity gene network shapes filament morphology in angiosperms

scientific article

Continuous Monitoring of Soil Nitrate Using a Miniature Sensor with Poly(3-octyl-thiophene) and Molybdenum Disulfide Nanocomposite

scientific article published on 31 July 2019

Conventional and hyperspectral time-series imaging of maize lines widely used in field trials

scientific article published on 24 November 2017

Cross species selection scans identify components of C4 photosynthesis in the grasses.

scientific article

Differentially Regulated Orthologs in Sorghum and the Subgenomes of Maize.

scientific article

Differentially regulated orthologs in sorghum and the subgenomes of maize

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

scientific article

Dose-sensitivity, conserved non-coding sequences, and duplicate gene retention through multiple tetraploidies in the grasses

scientific article

Early History of the Angiosperms

scientific article published in 2014

Enhancing Hybrid Prediction in Pearl Millet Using Genomic and/or Multi-Environment Phenotypic Information of Inbreds

scientific article published on 01 January 2019

Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa.

scientific article published on 12 February 2016

Escape from preferential retention following repeated whole genome duplications in plants

scientific article published on 15 May 2012

Evolutionarily Conserved Alternative Splicing Across Monocots.

scientific article published on 24 August 2017

Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homologs.

scientific article

FractBias: a graphical tool for assessing fractionation bias following polyploidy.

scientific article

Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants

scientific article

Functional Divergence Between Subgenomes and Gene Pairs After Whole Genome Duplications

scientific article published on 21 December 2017

Genes and gene models, an important distinction

scientific article published on 26 June 2019

Genes identified by visible mutant phenotypes show increased bias toward one of two subgenomes of maize

scientific article

Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome

scientific article published in 2022

Genome evolution in maize: from genomes back to genes

scientific article published on December 2014

Genome sequencing and analysis of the model grass Brachypodium distachyon

scientific article

Genome-Guided Phylo-Transcriptomic Methods and the Nuclear Phylogentic Tree of the Paniceae Grasses

scientific article published on 19 October 2017

Genome-phenome wide association in maize and Arabidopsis identifies a common molecular and evolutionary signature

scientific article published on 11 March 2020

Genome-wide Characterization of DNase I-hypersensitive Sites and Cold Response Regulatory Landscapes in Grasses

scientific article published on 29 May 2020

Genome-wide analysis of syntenic gene deletion in the grasses

scientific article (publication date: 2012)

Genome-wide characterization of non-reference transposable element insertion polymorphisms reveals genetic diversity in tropical and temperate maize

scientific article published on 6 September 2017

Genotype-Corrector: improved genotype calls for genetic mapping in F2 and RIL populations

scientific article published on 04 July 2018

Harnessing the Potential of the Tea Tree Genome.

scientific article published on 29 May 2017

Heritable epigenetic variation among maize inbreds

scientific article

High Density Genetic Maps of Seashore Paspalum Using Genotyping-By-Sequencing and Their Relationship to The Sorghum Bicolor Genome

scientific article published on 21 August 2019

High Throughput In vivo Analysis of Plant Leaf Chemical Properties Using Hyperspectral Imaging

scientific article

High-resolution mapping of open chromatin in the rice genome

scientific article published on 22 November 2011

High-throughput analysis of leaf physiological and chemical traits with VIS-NIR-SWIR spectroscopy: a case study with a maize diversity panel

scientific article published on 26 June 2019

Hyperspectral reflectance-based phenotyping for quantitative genetics in crops: Progress and challenges

scientific article published on 12 July 2021

Identification and utilization of genetic determinants of trait measurement errors in image-based, high-throughput phenotyping

scientific article published in 2021

Identification of loci controlling adaptation in Chinese soya bean landraces via a combination of conventional and bioclimatic GWAS

scientific article published on 24 July 2019

Impacts of Whole-Genome Triplication on MIRNA Evolution in Brassica rapa.

scientific article published on November 2015

Increased power and accuracy of causal locus identification in time-series genome-wide association in sorghum

scientific article published on 27 May 2020

Integrating Phylogenetic and Network Approaches to Study Gene Family Evolution: The Case of the AGAMOUS Family of Floral Genes.

scientific article published on 23 April 2018

Integration of omic networks in a developmental atlas of maize.

scientific article published on August 2016

Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs

scientific article published on 25 June 2020

Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels

scientific article published on 01 November 2018

IsoSeq transcriptome assembly of C3 panicoid grasses provides tools to study evolutionary change in the Panicoideae

scientific article published on 28 February 2020

Kinetic variation in grass phosphoenolpyruvate carboxylases provides opportunity to enhance C<sub>4</sub> photosynthetic efficiency

scientific article published on 20 December 2020

Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum.

scientific article published on 19 December 2017

Leaf Angle eXtractor: A high-throughput image processing framework for leaf angle measurements in maize and sorghum

scientific article published on 01 August 2020

Linked read technology for assembling large complex and polyploid genomes

Location of low copy genes in chromosomes of Brachiaria spp.

scientific article published on 12 January 2018

Low-temperature tolerance in land plants: Are transcript and membrane responses conserved?

scientific article published in 2018

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

article

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

scientific article published on 12 February 2020

Mapping of quantitative trait locus (QTLs) that contribute to germination and early seedling drought tolerance in the interspecific cross Setaria italica×Setaria viridis

scientific article

Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China

scientific article published on May 2015

Multiscale computational models can guide experimentation and targeted measurements for crop improvement

scientific article published on 13 February 2020

NU-Spidercam: A large-scale, cable-driven, integrated sensing and robotic system for advanced phenotyping, remote sensing, and agronomic research

scientific article published in 2019

Non-homology-based prediction of gene functions in maize (Zea mays ssp. mays)

scientific article published on 29 April 2020

Nonsyntenic genes drive highly dynamic complementation of gene expression in maize hybrids.

scientific article published on 14 October 2014

Optimizing the identification of causal variants across varying genetic architectures in crops

scientific article published on 09 November 2018

Parallels between natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize

scientific article published on 26 June 2019

Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants

scientific article published on 10 February 2022

Phenotypic Data from Inbred Parents Can Improve Genomic Prediction in Pearl Millet Hybrids.

scientific article

Phylogeny and photosynthesis of the grass tribe Paniceae

scientific article published on 15 September 2015

RGPDB: database of root-associated genes and promoters in maize, soybean, and sorghum

scientific article published on 01 January 2020

RNA-Seq Based Analysis of Population Structure within the Maize Inbred B73.

scientific article

Rhythmic lipid and gene expression responses to chilling in panicoid grasses

scientific article published in 2024

STAG-CNS: An Order-Aware Conserved Noncoding Sequences Discovery Tool for Arbitrary Numbers of Species

scientific article published on 05 June 2017

Screening synteny blocks in pairwise genome comparisons through integer programming

scientific article

Semantic Segmentation of Sorghum Using Hyperspectral Data Identifies Genetic Associations

scientific article published on 04 February 2020

Shared Genetic Control of Root System Architecture between Zea mays and Sorghum bicolor

scientific article published on 18 November 2019

SynFind: Compiling Syntenic Regions across Any Set of Genomes on Demand

scientific article

The C-terminal motif of SiAGO1b is required for the regulation of growth, development and stress responses in foxtail millet (Setaria italica (L.) P. Beauv)

scientific article published on 04 April 2016

The draft genome of the C3 panicoid grass species Dichanthelium oligosanthes

scientific article

The effect of artificial selection on phenotypic plasticity in maize.

scientific article published on 7 November 2017

The genome of broomcorn millet

scientific article published in Nature Communications

Time Series Canopy Phenotyping Enables the Identification of Genetic Variants Controlling Dynamic Phenotypes in Soybean

scientific article published in 2022

Towards a multiscale crop modelling framework for climate change adaptation assessment

scientific article published on 15 April 2020

Two evolutionarily distinct classes of paleopolyploidy

scientific article published in December 2013

Voxel carving-based 3D reconstruction of sorghum identifies genetic determinants of light interception efficiency

scientific article published on 07 October 2020

tGBS® genotyping-by-sequencing enables reliable genotyping of heterozygous loci

scientific article published on 25 September 2017

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