Preprints
- MaizeEar-SAM: Zero-shot maize ear phenotyping. arXiv doi: 10.48550/arXiv.2502.13399 Preprint (2025)
- Scalable methods for quantifying the stay green ability of corn for yield prediction by using satellite images. doi: 10.31220/agriRxiv.2025.00339 agriRxiv doi: 10.31220/agriRxiv.2025.00339 Preprint (2025)
- Models trained to predict differential expression across plant organs identify distal and proximal regulatory regions. doi: 10.1101/2024.06.04.597477 bioRxiv doi: 10.1101/2024.06.04.597477 Preprint (2024)
- Phenotypic variation in maize can be largely explained by genetic variation at transcription factor binding sites. doi: 10.1101/2023.08.08.551183 bioRxiv doi: 10.1101/2023.08.08.551183 Preprint (2023)
2025
- Off-the-shelf image analysis models outperform human visual assessment in identifying genes controlling seed color variation in sorghum. The Plant Phenome Journal doi: 10.1002/ppj2.70013 bioRxiv doi: 10.1101/2024.07.22.604683 (2025)
- Quantitative genetics of photosynthetic trait variation in maize. Journal of Experimental Botany doi: 10.1093/jxb/eraf198 bioRxiv doi: 10.1101/2024.11.25.625283 (2025)
- Genes and pathways determining flowering time variation in temperate adapted sorghum. The Plant Journal doi: 10.1111/tpj.70250 bioRxiv doi: 10.1101/2024.12.12.628249 (2025)
- Heritability, heterosis, and hybrid/inbred classification ability of maize leaf hyperspectral signals under changing soil nitrogen. Crop Science doi: 10.1002/csc2.70073 (2025)
- Plot-level satellite imagery can substitute for UAVs in assessing maize phenotypes across multistate field trials. Plants Planet People doi: 10.1002/ppp3.10613 agriRxiv doi: 10.31220/agriRxiv.2024.00251 (2025)
- Assessing the impact of yield plasticity on hybrid performance in maize. Physiologia Plantarum doi: 10.1111/ppl.70278 bioRxiv doi: 10.1101/2025.01.21.634104 (2025)
- Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions. BMC Genomics doi: 10.1186/s12864-025-11580-3 bioRxiv doi: 10.1101/2024.08.26.609532 (2025)
- 3D reconstruction enables high-throughput phenotyping and quantitative genetic analysis of phyllotaxy. Plant Phenomics doi: 10.1016/j.plaphe.2025.100023 bioRxiv doi: 10.1101/2024.10.03.616344 (2025)
- Nighttime fluorescence phenotyping reduces environmental variability for photosynthetic traits and enables the identification of candidate loci in maize. Frontiers in Plant Science doi: 10.3389/fpls.2025.1595339 (2025)
- Evolving best practices for transcriptome-wide association studies accelerate discovery of gene-phenotype links. Current Opinion in Plant Biology doi: 10.1016/j.pbi.2024.102670 (2025)
- Nitrogen response and growth trajectory of sorghum CRISPR-Cas9 mutants using high-throughput phenotyping. Genomics Communications doi: 10.48130/gcomm-0025-0011 bioRxiv doi: 10.1101/2024.12.13.624727 (2025)
- Enhancing yield prediction from plot-level satellite imagery through genotype and environment feature disentanglement. Frontiers in Plant Science doi: 10.3389/fpls.2025.1617831 (2025)
- Designing a nitrogen efficient cold tolerant maize for modern agricultural systems. The Plant Cell doi: 10.1093/plcell/koaf139 (Schnable JC is 48 of 56 authors) (2025)
- Employing spectral features to accelerate sorghum phenotyping against sap-feeding aphids. Plant Direct doi: 10.1002/pld3.70092 (2025)
- In context promoter bashing of the Sorghum bicolor gene models functionally annotated as bundle sheath cell preferred expressing phosphoenolpyruvate carboxykinase and alanine aminotransferase. Sorghum bicolor doi: 10.1002/csc2.70039 (2025)
- Phenotypic plasticity in maize grain yield: genetic and environmental insights of response to environmental gradients. The Plant Genome doi: 10.1002/tpg2.70078 (Schnable JC is 11 of 16 authors) (2025)
- Positioning accuracy of RTK-GNSS-enabled drones and their performance in agricultural crop sensing. Journal of the ASABE doi: 10.13031/ja.16306 (2025)
- Unveiling shared genetic regulators for plant architectural and biomass yield traits in sorghum. Journal of Experimental Botany doi: 10.1093/jxb/eraf012 bioRxiv doi: 10.1101/2024.03.13.584802 (2025)
2024
- Population level gene expression can repeatedly link genes to functions in maize. The Plant Journal doi: 10.1101/2023.10.31.565032 bioRxiv doi: 10.1101/2023.10.31.565032 (2024)
- Data driven discovery and quantification of hyperspectral leaf reflectance phenotypes across a maize diversity panel. The Plant Phenome Journal doi: 10.1002/ppj2.20106 bioRxiv doi: 10.1101/2023.12.15.571950 (2024)
- Genomic co-localization of variation affecting agronomic and human gut microbiome traits in a meta-analysis of diverse sorghum. doi: 10.1093/g3journal/jkae145 bioRxiv doi: 10.1101/2023.09.20.558616 (2024)
- Imitating the "breeder’s eye": predicting grain yield from measurements of non-yield traits. The Plant Phenome Journal doi: 10.1002/ppj2.20102 bioRxiv doi: 10.1101/2023.11.29.568906 (2024)
- Rhythmic lipid and gene expression responses to chilling in panicoid grasses. Journal of Experimental Botany doi: 10.1093/jxb/erae247 bioRxiv doi: 10.1101/2023.09.29.560160 (2024)
- THI1 gene evolutionary trends: A comprehensive plant-focused Assessment via data Mining and large-scale analysis. Genome Biology and Evolution doi: 10.1093/gbe/evae212 (2024)
- Variation in leaf chlorophyll concentration in response to nitrogen application across maize hybrids in contrasting environments. microPublication Biology doi: 10.17912/micropub.biology.001115 (2024)
- TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean. Plant Communications doi: 10.1016/j.xplc.2024.101010 bioRxiv doi: 10.1101/2023.07.03.545230 (2024)
- Nonphotochemical quenching kinetics GWAS in sorghum identifies genes that may play conserved roles in maize and Arabidopsis thaliana photoprotection. The Plant Journal doi: 10.1111/tpj.16967 bioRxiv doi: 10.1101/2023.08.29.555201 (2024)
- Sorghum segmentation and leaf counting using an in silico trained deep neural model. in silico doi: 10.1002/ppj2.70002 (2024)
- Disentangling genotype and environment specific latent features for improved trait prediction using a compositional autoencoder. Frontiers in Plant Science doi: 10.3389/fpls.2024.1476070 (2024)
- Genotype-specific nonphotochemical quenching responses to nitrogen deficit are linked to chlorophyll a to b ratios. Journal of Plant Physiology doi: 10.1016/j.jplph.2024.154261 (2024)
- Dissecting the genetic architecture of sunflower disc diameter using genome-wide association study. Plant Direct doi: 10.1002/pld3.70010 (2024)
- Genetic and environmental patterns underlying phenotypic plasticity in flowering time and plant height in sorghum. Plant, Cell and Environment doi: 10.1111/pce.15213 (2024)
- Genome-wide association study reveals marker-trait associations for major agronomic traits in proso millet (Panicum miliaceum L.). Panicum miliaceum doi: 10.1007/s00425-024-04465-4 (2024)
- GWAS analysis for plant height and stem diameter in sorghum using multiple phenotyping approaches. The Plant Phenome Journal doi: 10.1002/ppj2.70008 (2024)
- High-throughput physiological phenotyping of crop evapotranspiration at the plot scale. Field Crop Research doi: 10.1016/j.fcr.2024.109507 (2024)
- Image filtering to improve maize tassel detection accuracy using machine learning algorithms. Sensors doi: 10.3390/s24072172 (2024)
- Optimizing feature selection with gradient boosting machines in PLS regression for predicting moisture and protein in multi-Country corn kernels via NIR spectroscopy. Food Chemistry doi: 10.1016/j.foodchem.2024.140062 (2024)
- PlantSegNet: 3D point cloud instance segmentation of nearby plant organs with identical semantics. Computers and Electronics in Agriculture doi: 10.1016/j.compag.2024.108922 (2024)
2023
- A role for heritable transcriptomic variation in maize adaptation to temperate environments. Genome Biology doi: 10.1186/s13059-023-02891-3 bioRxiv doi: 10.1101/2022.01.28.478212 (2023)
- A common resequencing-based genetic marker dataset for global maize diversity. The Plant Journal doi: 10.1111/tpj.16123 (2023)
- Genetic control of photoprotection and photosystem II operating efficiency in plants. New Phytologist doi: 10.1111/nph.18980 (2023)
- Multi-view triangulation without correspondences. Computers and Electronics in Agriculture doi: 10.1016/j.compag.2023.107688 (2023)
- 2018–2019 field seasons of the Maize Genomes to Fields (G2F) G x E project. BMC Genomic Data doi: 10.1186/s12863-023-01129-2 (Schnable JC is 26 of 37 authors) (2023)
- 2020-2021 field seasons of Maize GxE project within the Genomes to Fields Initiative. doi: 10.1186/s13104-023-06430-y (Schnable JC is 24 of 35 authors) (2023)
- A complete telomere-to-telomere assembly of the maize genome. Nature Genetics doi: 10.1038/s41588-023-01419-6 (2023)
- A leaf-level spectral library to support high throughput plant phenotyping: Predictive accuracy and model transfer. Journal of Experimental Botany doi: 10.1093/jxb/erad129 (2023)
- Localization of crop damage utilizing a wake up gas sensor network. Transducers 2023 (2023)
- Multiple highly expressed phosphoenolpyruvate carboxylase genes have divergent enzyme kinetic properties in two C4 grasses. Annals Of Botany doi: 10.1093/aob/mcad116 (2023)
- Oligogalactolipid production during cold challenge is conserved in early diverging lineages. Journal of Experimental Botany doi: 10.1093/jxb/erad241 (2023)
- Role of the genomics–phenomics–agronomy paradigm in plant breeding. Plant Breeding Reviews doi: 10.1002/9781119874157.ch10 (2023)
- Yield prediction through integration of genetic, environment, and management data through deep learning. doi: 10.1093/g3journal/jkad006 bioRxiv doi: 10.1101/2022.07.29.502051 (2023)
2022
- Association mapping across a multitude of traits collected in diverse environments identifies pleiotropic loci in maize. Gigascience doi: 10.1093/gigascience/giac080 bioRxiv doi: 10.1101/2022.02.25.480753 (2022)
- Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass. Paspalum vaginatum doi: 10.1038/s41467-022-35507-8 (Foltz A is 17 of 26 authors) bioRxiv doi: 10.1101/2021.08.18.456832 (2022)
- Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel. BMC Plant Biology doi: 10.1101/2022.06.08.495271 bioRxiv doi: 10.1101/2022.06.08.495271 (2022)
- Can the grains offer each other helping hands? Convergent molecular mechanisms associated with domestication and crop improvement in rice and maize. Molecular Plant doi: 10.1016/j.molp.2022.04.003 (2022)
- The unique seed protein composition of quality protein popcorn promotes growth of beneficial bacteria from the human gut microbiome. Frontiers in Microbiology doi: 10.3389/fmicb.2022.921456 (2022)
- SNP Discovery in Proso millet (Panicum miliaceum L.) using low-pass genome sequencing. Panicum miliaceum doi: 10.1002/pld3.447 (2022)
- Maize root-associated microbes likely under adaptive selection by the host to enhance phenotypic performance. eLife doi: 10.7554/eLife.75790 bioRxiv doi: 10.1101/2021.11.01.466815 (2022)
- Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants. Nature Communications doi: 10.1038/s41467-022-28449-8 (2022)
- Sorghum association panel whole-genome sequencing establishes pivotal resource for dissecting genomic diversity. The Plant Journal doi: 10.1111/tpj.15853 (2022)
- A UAV-based high-throughput phenotyping approach to assess time-series nitrogen responses and identify traits associated genetic components in maize. The Plant Phenome Journal doi: 10.1002/ppj2.20030 bioRxiv doi: 10.1101/2021.05.24.445447 (2022)
- Field deployment of a nanogap gas sensor for crop damage detection. MEMS 2022 doi: 10.1109/MEMS51670.2022.9699614 (2022)
- Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome. Nature Communications doi: 10.1038/s41467-022-33419-1 (2022)
- The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceae polyploidization and its distinct traits. Orychophragmus violaceus doi: 10.1016/j.xplc.2022.100431 (2022)
- Time series canopy phenotyping enables the identification of genetic variants controlling dynamic phenotypes in soybean. Journal of Integrative Plant Biology doi: 10.1111/jipb.13380 (2022)
2021
- Predicting transcriptional responses to cold stress across plant species. Proceedings of the National Academy of Sciences doi: 10.1073/pnas.2026330118 bioRxiv doi: 10.1101/2020.08.25.266635 (2021)
- 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves. PeerJ doi: 10.7717/peerj.12628 bioRxiv doi: 10.1101/2021.06.15.448566 (2021)
- Meta-analysis identifies pleiotropic loci controlling phenotypic trade-offs in sorghum. Genetics doi: 10.1093/genetics/iyab087 bioRxiv doi: 10.1101/2020.10.27.355495 (2021)
- Quantitative resistance loci to southern rust mapped in a temperate maize diversity panel. Phytopathology doi: 10.1101/2021.04.02.438220 bioRxiv doi: 10.1101/2021.04.02.438220 (2021)
- 72-hour diurnal RNA-seq analysis of fully expanded third leaves from maize, sorghum, and foxtail millet at 3-hour resolution. BMC Research Notes doi: 10.1186/s13104-020-05431-5 (2021)
- Automation of leaf counting in maize and sorghum using deep learning. The Plant Phenome Journal doi: 10.1002/ppj2.20022 bioRxiv doi: 10.1101/2020.12.19.423626 (2021)
- Hyperspectral reflectance-based phenotyping for quantitative genetics in crops: progress and challenges. Plant Communications doi: 10.1016/j.xplc.2021.100209 (2021)
- Comparative transcriptome analysis reveals genetic mechanisms of sugarcane aphid resistance in grain sorghum. International Journal of Molecular Sciences doi: 10.3390/ijms22137129 (2021)
- A co-opted steroid synthesis gene, maintained in sorghum but not maize, is associated with a divergence in leaf wax chemistry. Proceedings of the National Academy of Sciences of the United States of America doi: 10.1073/pnas.2022982118 (2021)
- Can high resolution satellite imagery be used in high-throughput field phenotyping. Transactions of the ASABE doi: 10.13031/trans.14197 (2021)
- Continuous in situ soil nitrate sensors: a comparison with conventional measurements and the value of high temporal resolution measurements. in situ doi: 10.1002/saj2.20226 (2021)
- DCT4 - a new member of the dicarboxylate transporter family in C4 grasses. Genome Biology and Evolution doi: 10.1093/gbe/evaa251 bioRxiv doi: 10.1101/762724 (2021)
- Development of a gas sensor for green leaf volatile detection. Transducers 2021 doi: 10.1109/Transducers50396.2021.9495597 (2021)
- Genome-wide DNA polymorphism analysis and molecular marker development for the Setaria italica variety ‘SSR41’ and positional cloning of the Setaria white leaf sheath gene SiWLS1. Setaria italica doi: 10.3389/fpls.2021.743782 (2021)
- Genomic resources in plant breeding for sustainable agriculture. Journal of Plant Physiology doi: 10.1016/j.jplph.2020.153351 (2021)
- Identification and utilization of genetic determinants of trait measurement errors in image-based, high-throughput phenotyping. The Plant Cell doi: 10.1093/plcell/koab134 (2021)
- Maize tassel detection from UAV imagery using deep learning. Frontiers in Robotics and AI doi: 10.3389/frobt.2021.600410 (2021)
- Phosphoenolpyruvate carboxylase kinetic variation provides opportunity to enhance C4 photosynthetic efficiency. enol doi: 10.1111/tpj.15141 (2021)
- Rhizosphere microbiomes in a historical maize/soybean rotation system respond to host species and nitrogen fertilization at genus and sub-genus levels. Applied and Environmental Microbiology doi: 10.1128/AEM.03132-20 (2021)
- The importance of dominance and genotype-by-environment interactions on grain yield variation in a large-scale public cooperative maize experiment. G3:Genes\|Genomes\|Genetics doi: 10.1093/g3journal/jkaa050 (Schnable JC is 24 of 39 authors) (2021)
- Utility of climatic information via combining ability models to improve genomic prediction for yield within the Genomes to Fields maize project. Frontiers in Genetics doi: 10.3389/fgene.2020.592769 (Schnable JC is 24 of 33 authors) (2021)
- qTeller: A tool for comparative multi-genomic gene expression analysis. Bioinformatics doi: 10.1093/bioinformatics/btab604 (2021)
- Robotic technologies for high-throughput plant phenotyping: reviews and perspectives. Frontiers in Plant Science doi: 10.3389/fpls.2021.611940 (2021)
2020
- Interspecific analysis of diurnal gene regulation in panicoid grasses identifies known and novel regulatory motifs. BMC Genomics doi: 10.1186/s12864-020-06824-3 (2020)
- IsoSeq transcriptome assembly of C3 panicoid grasses provides tools to study evolutionary change in the Panicoideae. Plant Direct doi: 10.1002/pld3.203 bioRxiv doi: 10.1101/689356 (2020)
- Leaf Angle eXtractor - A high throughput image processing framework for leaf angle measurement in maize and sorghum. Applications in Plant Sciences doi: 10.1002/aps3.11385 (2020)
- Semantic segmentation of sorghum using hyperspectral data identifies genetic associations. Plant Phenomics doi: 10.34133/2020/4216373 (2020)
- Genome-phenome wide association in maize and arabidopsis identifies a common molecular and evolutionary signature. Molecular Plant doi: 10.1016/j.molp.2020.03.003 bioRxiv doi: 10.1101/534503 (2020)
- Increased power and accuracy of causal locus identification in time-series genome-wide association in sorghum.
Plant Physiology
doi: 10.1104/pp.20.00277
bioRxiv doi: 10.1101/2020.02.16.951467
[First
(2020)
- Non-homology-based prediction of gene functions. The Plant Genome doi: 10.1002/tpg2.20015 bioRxiv doi: 10.1101/730473 (2020)
- Shared genetic control of root system architecture between Zea mays and Sorghum bicolor. Zea mays doi: 10.1104/pp.19.00752 (2020)
- Voxel carving based 3D reconstruction of sorghum identifies genetic determinants of radiation interception efficiency. Plant Direct doi: 10.1002/pld3.255 bioRxiv doi: 10.1101/2020.04.06.028605 (2020)
- A high-throughput phenotyping pipeline for image processing and functional growth curve analysis. Plant Phenomics doi: 10.34133/2020/7481687 (2020)
- Advancing multi-scale crop modeling for agricultural climate change adaptation assessment. Nature Plants doi: 10.1038/s41477-020-0625-3 (2020)
- Enhancing hybrid prediction in pearl millet using genomic and/or multi-environment phenotypic information of inbreds. Frontiers in Genetics doi: 10.3389/fgene.2019.01294 (2020)
- Genome-wide characterization of DNase I-hypersensitive sites and cold response regulatory landscapes in grasses. The Plant Cell doi: 10.1105/tpc.19.00716 (2020)
- Investigating the potential of satellite imagery for high-throughput field phenotyping applications. SPIE Defense + Commercial Sensing doi: 10.1117/12.2558729 (2020)
- Multiscale computational models can guide experimentation and targeted measurements for crop improvement. The Plant Journal doi: 10.1111/tpj.14722 (2020)
- RGPDB: Database of root-associated genes and promoters in maize, soybean, and sorghum. Database doi: 10.1093/database/baaa038 (2020)
- Sorghum Segmentation by Skeleton Extraction. CVPPP 2020 (2020)
- Advances in plant phenomics: From data and algorithms to biological insights. Applications in Plant Sciences doi: 10.1002/aps3.11386 (2020)
- Faster-R-CNN based deep learning for locating corn tassels in UAV imagery. SPIE Defense + Commercial Sensing doi: 10.1117/12.2560596 (2020)
- Maize Genomes to Fields (G2F): 2014 –2017 field seasons’ genotype, phenotype, climatic, soil and inbred ear image datasets. BMC Research Notes doi: 10.1186/s13104-020-4922-8 (Schnable JC is 34 of 51 authors) (2020)
- Plant segmentation by supervised machine learning methods. The Plant Phenome Journal doi: 10.1002/ppj2.20001 (2020)
- Robotic detection and grasp of maize and sorghum: stem measurement with contact. Robotics doi: 10.3390/robotics9030058 (2020)
2019
- Parallel natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize. Tripsacum dactyloides doi: 10.1111/tpj.14376 bioRxiv doi: 10.1101/187575 (2019)
- Continuous Monitoring of Soil Nitrate Using a Miniature Sensor with Poly(3-octyl-thiophene) and Molybdenum Disulfide Nanocomposite. ACS Applied Materials & Interfaces doi: 10.1021/acsami.9b07120 (2019)
- High density genetic maps of seashore paspalum using genotyping-by-sequencing and their relationship to the Sorghum bicolor genome. Sorghum bicolor doi: 10.1038/s41598-019-48257-3 (2019)
- High-throughput analysis of leaf physiological and chemical traits with VIS-NIR-SWIR spectroscopy: A case study with a maize diversity panel. Plant Methods doi: 10.1186/s13007-019-0450-8 (2019)
- Identification of Loci Controlling Adaptation in Chinese Soybean Landraces via a Combination of Conventional and Bioclimatic GWAS. Plant Biotechnology Journal doi: 10.1111/pbi.13206 (2019)
- In-planta nitrate detection using insertable plant microsensor. 20th International Conference on Solid-State Sensors, Actuators and Microsystems doi: 10.1109/TRANSDUCERS.2019.8808527 (2019)
- Novel all-solid-state soil nutrient sensor using nanocomposite of poly(3-octyl-thiophene) and molybdenum sulfate. 20th International Conference on Solid-State Sensors, Actuators and Microsystems doi: 10.1109/TRANSDUCERS.2019.8808341 (2019)
- NU-Spidercam: A large-scale, cable-driven, integrated sensing and robotic system for precision phenotyping, remote sensing, and agronomic research. Computers and Electronics in Agriculture doi: 10.1016/j.compag.2019.03.009 (2019)
- QTL identification and epistatic effect analysis of seed size- and weight-related traits in Zea mays L. Zea mays doi: 10.1007/s11032-019-0981-8 (2019)
- The genome of broomcorn millet. Nature Communications doi: 10.1038/s41467-019-08409-5 (2019)
- Genes and Gene Models, an Important Distinction. New Phytologist doi: 10.1111/nph.16011 (2019)
- In vivo human-like robotic phenotyping of leaf traits in maize and sorghum. In vivo doi: 10.1016/j.compag.2019.104854 (2019)
2018
- Phenotypic data from inbred parents can improve genomic prediction in pearl millet hybrids. G3: Genes Genomes Genetics doi: 10.1534/g3.118.200242 (2018)
- Genotype-Corrector: improved genotype calls for genetic mapping. Scientific Reports doi: 10.1038/s41598-018-28294-0 (2018)
- Integrating phylogenetic and network approaches to study gene family evolution: the case of the AGAMOUS family of floral genes. Evolutionary Bioinformatics doi: 10.1177/1176934318764683 (2018)
- Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum. The Plant Journal doi: 10.1111/tpj.13806 (2018)
- Optimizing the identification of causal variants across varying genetic architectures in crops. Plant Biotechnology Journal doi: 10.1111/pbi.13023 (2018)
- Functional Divergence Between Subgenomes and Gene Pairs After Whole Genome Duplications. Molecular Plant doi: 10.1016/j.molp.2017.12.010 (2018)
- Low-temperature tolerance in land plants: Are transcript and membrane responses conserved?. Plant Science doi: 10.1016/j.plantsci.2018.08.002 (2018)
- Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels. Molecular Biology and Evolution doi: 10.1093/molbev/msy174 (2018)
- Linked read technology for assembling large complex and polyploid genomes. BMC Genomics doi: 10.1186/s12864-018-5040-z (2018)
- Location of low copy genes in chromosomes of Brachiaria spp. Molecular Biology Reports doi: 10.1007/s11033-018-4144-5 (2018)
- Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets. BMC Research Notes (Schnable JC is 31 of 44 authors) (2018)
- Functional Modeling of Plant Growth Dynamics. The Plant Phenome Journal doi: 10.2135/tppj2017.09.0007 (2018)
2017
- Differentially regulated orthologs in sorghum and the subgenomes of maize. The Plant Cell doi: 10.1105/tpc.17.00354 (2017)
- Genome-Wide Characterization of Non-Reference Transposable Elements Insertion Polymorphisms Reveals Genetic Diversity in Tropical and Temperate Maize. BMC Genomics doi: 10.1186/s12864-017-4103-x (2017)
- Conventional and hyperspectral time-series imaging of maize lines widely used in field trials. GigaScience doi: 10.1093/gigascience/gix117 (2017)
- Harnessing the potential of the tea tree genome. Molecular Plant doi: 10.1016/j.molp.2017.05.009 (2017)
- Genome-Guided Phylo-Transcriptomics. Scientific Reports doi: 10.1038/s41598-017-13236-z (2017)
- A comprehensive analysis of alternative splicing in paleopolyploid maize. Frontiers in Plant Science doi: 10.3389/fpls.2017.00694 (2017)
- DiCE: Discovery of Conserved Noncoding Sequences Efficiently. IEEE BIBM doi: 10.1109/BIBM.2017.8217628 (2017)
- Evolutionarily conserved alternative splicing across monocots. Genetics doi: 10.1534/genetics.117.300189 (2017)
- High throughput in vivo analysis of plant leaf chemical properties using hyperspectral imaging. Frontiers in Plant Science doi: 10.3389/fpls.2017.01348 (2017)
- STAG-CNS: An order-aware conserved noncoding sequence discovery tool for arbitrary numbers of species. Molecular Plant doi: 10.1016/j.molp.2017.05.010 (2017)
- The effect of artificial selection on phenotypic plasticity in maize. Nature Communications doi: 10.1038/s41467-017-01450-2 (Schnable JC is 29 of 40 authors) (2017)
- Tunable Genotyping-By-Sequencing (tGBS) enables reliable genotyping of heterozygous loci. Nucleic Acids Research doi: 10.1093/nar/gkx853 (2017)
2016
- RNA-seq based analysis of population structure within the maize inbred B73. PLoS One doi: 10.1371/journal.pone.0157942 (2016)
- Automated vegetative stage phenotyping analysis of maize plants using visible light images. KDD: Data Science for Food, Energy, and Water (2016)
- Cross species selection scans identify components of C4 photosynthesis in the grasses. Journal of Experimental Botany doi: 10.1093/jxb/erw256 (2016)
- Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa. New Phytologist doi: 10.1111/nph.13884 (2016)
- FractBias: a graphical tool for assessing fractionation bias after whole genome duplications. Bioinformatics doi: 10.1093/bioinformatics/btw666 (2016)
- Integration of omic networks in a developmental atlas of maize. Science doi: 10.1126/science.aag1125 (2016)
- 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]. Journal of Experimental Botany doi: 10.1093/jxb/erw135 (2016)
- Mapping QTLs for morpho-agronomic traits in proso millet (Panicum miliaceum L.). Molecular Breeding doi: 10.1007/s11032-016-0460-4 (2016)
- Temporal dynamics of maize plant growth, water use, and plant water content using automated high throughput RGB and hyperspectral imaging. Computers and Electronics in Agriculture doi: 10.1016/j.compag.2016.07.028 (2016)
- The draft genome of Dichanthelium oligosanthes: A C3 panicoid grass species. Genome Biology doi: 10.1186/s13059-016-1080-3 (2016)
2015
- ALLMAPS: robust scaffold ordering based on multiple maps. Genome Biology doi: 10.1186/s13059-014-0573-1 (2015)
- Impacts of Whole Genome Triplication on MIRNA Evolution in Brassica rapa. Genome Biology and Evolution doi: 10.1093/gbe/evv206 (2015)
- Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China. PLoS One doi: 10.1371/journal.pone.0125688 (2015)
- Phylogeny and photosynthesis of the grass tribe Paniceae. American Journal of Botany doi: 10.3732/ajb.1500222 (2015)
- SynFind: compiling syntenic regions across any set of genomes on demand. Genome Biology and Evolution doi: 10.1093/gbe/evv219 (2015)
- Genome evolution in maize: from genomes back to genes. Annual Review of Plant Biology doi: 10.1146/annurev-arplant-043014-115604 (2015)
2014
- A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing. Scientific Reports doi: 10.1038/srep04519 (2014)
- Co-option of the polarity gene network shapes filament morphology in angiosperms. Scientific Reports doi: 10.1038/srep06194 (2014)
- Initiation of Setaria as a model plant. Frontiers of Agricultural Science and Engineering doi: 10.15302/J-FASE-2014011 (2014)
- Mapping of Quantitative Trait Locus (QTLs) that Contribute to Germination and Early Seedling Drought Tolerance in the Interspecific Cross Setaria italica x Setaria viridis. PLoS One doi: 10.1371/journal.pone.0101868 (2014)
- Nonsyntenic Genes Drive Highly Dynamic Complementation of Gene Expression in Maize Hybrids. Plant Cell doi: 10.1105/tpc.114.130948 (2014)
2013
- Automated conserved noncoding sequence (CNS) discovery reveals differences in gene content and promoter evolution among the grasses. Frontiers in Plant Sciences doi: 10.3389/fpls.2013.00170 (2013)
- Two Evolutionarily Distinct Classes of Paleopolyploidy. Molecular Biology and Evolution doi: 10.1093/molbev/mst230 (2013)
2012
- Escape from preferential retention following repeated whole genome duplication in plants. Frontiers in Plant Science doi: 10.3389/fpls.2012.00094 (2012)
- Genome-wide analysis of syntenic gene deletion in the grasses. Genome Biology and Evolution doi: 10.1093/gbe/evs009 (2012)
- Altered patterns of fractionation and exon deletions in Brassica rapa support a two-step model of paleohexaploidy. Genetics doi: 10.1534/genetics.111.137349 (2012)
- High-resolution mapping of open chromatin in the rice genome. Genome Research doi: 10.1101/gr.131342.111 (2012)
- Fractionation mutagenesis and similar consequences of mechanisms removing dispensable or less-expressed DNA in plants. Current Opinion in Plant Biology doi: 10.1016/j.pbi.2012.01.015 (2012)
2011
- Comparative genomics with maize and other grasses: from genes to genomes. Maydica (2011)
- Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss. PNAS doi: 10.1073/pnas.1101368108 (2011)
- Dose-sensitivity, conserved noncoding sequences and duplicate gene retention through multiple tetraploidies in the grasses. Frontiers in Plant Science doi: 10.3389/fpls.2011.00002 (2011)
- Genes identified by visible mutant phenotypes show increased bias towards one of two maize subgenomes. PLoS One doi: 10.1371/journal.pone.0017855 (2011)
- Screening synteny blocks in pairwise genome comparisons through integer programming. BMC Bioinformatics doi: 10.1186/1471-2105-12-102 (2011)
- Heritable epigenetic variation among maize inbreds. PLoS Genetics doi: 10.1371/journal.pgen.1002372 (2011)