Preprints

• Davis JM, Gaillard M, Tross MC, Shrestha N, Ostermann I, Grove RJ, Li B, Benes B, Schnable JC 3D reconstruction enables high-throughput phenotyping and quantitative genetic analysis of phyllotaxy. bioRxiv doi: 10.1101/2024.10.03.616344

• Tross MC, Duggan G, Shrestha N, Schnable JC Models trained to predict differential expression across plant organs identify distal and proximal regulatory regions. bioRxiv doi: 10.1101/2024.06.04.597477

• Shrestha N, Mangal H, Torres-Rodriguez JV, Tross MC, Lopez-Corona L, Linders K, Sun G, Mural RV, Schnable JC Off-the-shelf image analysis models outperform human visual assessment in identifying genes controlling seed color variation in sorghum. bioRxiv doi: 10.1101/2024.07.22.604683

• Mathivanan RK, Pedersen C, Turkus J, Shrestha N, Torres-Rodriguez JV, Mural RV, Obata T, Schnable JC Transcripts and genomic intervals associated with variation in metabolite abundance in maize leaves under field conditions. bioRxiv doi: 10.1101/2024.08.26.609532

• Singh S, Newton L, Schnable JC, Thompson AM Unveiling shared genetic regulators for plant architectural and biomass yield traits in sorghum. bioRxiv doi: 10.1101/2024.03.13.584802

• Engelhorn J, Snodgrass S, Kok A, Seetharam A, Schneider M, Kiwit T, Singh A, Banf M, Khaipho-Burch M, Runcie D, Camargo V, Torres-Rodriguez JV, Sun G, Stam M, Fiorani F, Schnable JC, Bass H, Hufford M, Stich B, Frommer W, Ross-Ibarra J, Hartwig T Phenotypic variation in maize can be largely explained by genetic variation at transcription factor binding sites. bioRxiv doi:10.1101/2023.08.08.551183

2024

• Torres-Rodriguez JV, Li D, Schnable JC (2024) Evolving best practices for transcriptome-wide association studies accelerate discovery of gene-phenotype links. Current Opinion in Plant Biology (Accepted)

• Shrestha N, Powadi A, Davis J, Ayanlade TT, Liu H, Tross MC, Mathivanan RK, Bares J, Lopez-Corona L, Turkus J, Coffey L, Tubery TZ, Ge Y, Sarkar S, Schnable JC, Ganapathysubramanian B, Schnable PS (2024) Plot-level satellite imagery can substitute for UAVs in assessing maize phenotypes across multistate field trials. Plants Planet People (Accepted) agriRxiv doi: 10.31220/agriRxiv.2024.00251

• Boatwright L, Thudi M, Sangiredday MKR, Coffin AW, Tadesse HK, Vutla S, Harris-Shultz K, Knoll JE, Cuevas H, Kumar N, Soman C, Schnable JC, Punnuri SM (2024) GWAS analysis for plant height and stem diameter in sorghum using multiple phenotyping approaches. The Plant Phenome Journal (Accepted)

• Wei J, Guo T, Mu Q, Alladassi M, Mural RV, Boyles RE, Hoffman L, Hayes CM, Sigmon B, Thompson AM, Salas-Fernandez M, Rooney WL, Kresovich S, Schnable JC, Li X, Yu J (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

• Moura Dias H, de Teledo NA, Mural RV, Schnable JC, Van Sluys MA (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

• Delen Y, Mural RV, Xu G, Delen SP, Schnable JC, Dweikat I, Yang J (2024) Dissecting the genetic architecture of sunflower disc diameter using genome-wide association study. Plant Direct doi: 10.1002/pld3.70010

• Ostermann I, Benes B, Gaillard M, Li B, Davis J, Grove RJ, Shrestha N, Tross MC, Schnable JC (2024) Sorghum segmentation and leaf counting using an in silico trained deep neural model. The Plant Phenome Journal doi: 10.1002/ppj2.70002

• Sahay S, Shrestha N, Moura Dias H, Mural RV, Grzybowski M, Schnable JC, Glowacka K (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

• Bai G, Barker B, Scoby D, Irmak S, Luck JD, Neale CMU, Schnable JC, Awada T, Kustas WP, Ge Y (2024) High-throughput physiological phenotyping of crop evapotranspiration at the plot scale. Field Crop Research doi: 10.1016/j.fcr.2024.109507

• Li D, Wang Q, Tian Y, Lyu X, Zhang H, Sun Y, Hong H, Gao H, Li Y, Zhao C, Wang J, Wang R, Yang J, Liu B, Schnable PS, Schnable JC, Li Y, Qiu L (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

• Korth N, Yang Q, Van Haute MJ, Tross MC, Peng B, Shrestha N, Zwiener M, Mural RV, Schnable JC, Benson AK (2024) Genomic co-localization of variation affecting agronomic and human gut microbiome traits in a meta-analysis of diverse sorghum. G3 doi: 10.1093/g3journal/jkae145 bioRxiv doi: 10.1101/2023.09.20.558616

• Khound R, Rajput SG, Schnable JC, Mani V, Dipak SK (2024) Genome-wide association study reveals marker-trait associations for major agronomic traits in proso millet (Panicum miliaceum L.). Planta doi: 10.1007/s00425-024-04465-4

• Zheng R, Jia Y, Ullagaddi C, Allen C, Rausch K, Singh V, Schnable JC, Kamruzzaman M (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

• Raju SKK, Zhang Y, Mahboub S, Ngu DW, Qiu Y, Harmon FG, Schnable JC, Roston RL (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

• Sahay S, Grzybowski M, Schnable JC, Glowacka K (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

• Torres-Rodriguez JV, Li D, Turkus J, Newton L, Davis J, Lopez-Corona L, Ali W, Sun G, Mural RV, Grzybowski M, Zamft B, Thompson AM, Schnable JC (2024) Population level gene expression can repeatedly link genes to functions in maize. The Plant Journal 10.1111/tpj.16801 bioRxiv doi: 10.1101/2023.10.31.565032

• Zarei A, Li B, Schnable JC, Lyons E, Pauli D, Benes B, Barnard K (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

• Tross MC, Grzybowski M, Jubery TZ, Grove RJ, Nishimwe AV, Torres-Rodriguez JV, Sun G, Ganapathysubramanian B, Ge Y, Schnable JC (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

• Jin H, Tross MC, Tan R, Newton L, Mural RV, Yang J, Thompson AM, Schnable JC (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

• Rodene E, Fernando GD, Piyush V, Ge Y, Schnable JC, Ghosh S, Yang J (2024) Image filtering to improve maize tassel detection accuracy using machine learning algorithms. Sensors doi: 10.3390/s24072172

• Linders KM, Santra D, Schnable JC, Sigmon B (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

2023

• Lima DC, Aviles AC, Alpers RT … Schnable JC (24th of 35 authors) … Weldekidan T, Xu W, de Leon N (2023) 2020-2021 field seasons of Maize GxE project within the Genomes to Fields Initiative. BMC Research Notes doi: 10.1186/s13104-023-06430-y

• Noh M, Sium F, Tope S, Khan S, Karkhanis M, Wang L, Deshpande A, Dalapati R, Mural RV, Mastrangelo C, Zang L, Ji M, Schnable JC, Kim H (2023) Localization of crop damage utilizing a wake up gas sensor network. Transducers 2023 Kyoto, Japan (Conference Paper)

• DiMario R, Kophs A, Apalla A, Schnable JS, Cousins A (2023) Multiple highly expressed phosphoenolpyruvate carboxylase genes have divergent enzyme kinetic properties in two C4 grasses. Annals Of Botany doi: 10.1093/aob/mcad116

• Barnes AC, Myers JL, Surber SM, Liang Z, Mower JP, Schnable JC, Roston RL (2023) Oligogalactolipid production during cold challenge is conserved in early diverging lineages. Journal of Experimental Botany doi: 10.1093/jxb/erad241

• Chen J, Wang Z, Tan K, Huang W, Shi J, Li T, Hu KJ, Wang K, Wang C, Xin B, Zhao H, Song W, Hufford MB, Schnable JC, Jin W, Lai J (2023) A complete telomere-to-telomere assembly of the maize genome. Nature Genetics doi: 10.1038/s41588-023-01419-6

• Sahay S, Grzybowski M, Schnable JC, Glowacka K (2023) Genetic control of photoprotection and photosystem II operating efficiency in plants. New Phytologist doi: 10.1111/nph.18980

• Lima DC, Aviles AC, Alphers RT … Schnable JC (26th of 37 authors) … Wisser RJ, Xu W, de Leon N (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

• Kick D, Wallace J, Schnable JC, Kolkman JM, Alaca B, Beissinger TM, Ertl D, Flint-Garcia S, Gage JL, Hirsch CN, Knoll JE, de Leon N, Lima DC, Moreta D, Singh MP, Weldekidan T, Washburn JD (2023) Yield prediction through integration of genetic, environment, and management data through deep learning. G3 doi: 10.1093/g3journal/jkad006 bioRxiv doi: 10.1101/2022.07.29.502051

• Wijewardane NK, Zhang H, Yang J, Schnable JC, Schachtman DP, Ge Y (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

• Sun G, Yu H, Wang P, Lopez-Guerrero MG, Mural RV, Mizero ON, Grzybowski M, Song B, van Dijk K, Schachtman DP, Zhang C, Schnable JC (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

• Gaillard M, Benes B, Tross MC, Schnable JC (2023) Multi-view triangulation without correspondences. Computers and Electronics in Agriculture doi: 10.1016/j.compag.2023.107688

• Grzybowski M, Mural RV, Xu G, Turkus, J, Yang Jinliang, Schnable JC (2023) A common resequencing-based genetic marker dataset for global maize diversity. The Plant Journal doi: 10.1111/tpj.16123 Cover Article, March 2023 Research Highlight in The Plant Journal doi: 10.1111/tpj.16123

• Chen C, Rutkoski J, Schnable JC, Murray S, Wang L, Jin X, Stich B, Crossa J, Hayes B Zhang Z (2023) “Role of the genomics–phenomics–agronomy paradigm in plant breeding” Plant Breeding Reviews doi: 10.1002/9781119874157.ch10 preprints.org doi: 10.20944/preprints202103.0519.v1

2022

• Sun G, Wase N, Su S, Jenkins J, Zhou B, Torres-Rodriguez JT … Foltz A (17th of 26 authors) … Sigmon B, Yu B, Obata T, Schmutz J, Schnable JC “Genome of Paspalum vaginatum and the role of trehalose mediated autophagy in increasing maize biomass” Nature Communications doi: 10.1038/s41467-022-35507-8 bioRxiv doi: 10.1101/2021.08.18.456832 Commentary by Chris Surridge published in Nature Plants. doi: 10.1038/s41477-023-01343-x

• Yang Q, Van Haute M, Korth N, Sattler S, Toy J, Rose D, Schnable JC, Benson A “Genetic analysis of seed traits in Sorghum bicolor that affect the human gut microbiome.” Nature Communications doi: 10.1038/s41467-022-33419-1 Research Square doi: 10.21203/rs.3.rs-1490527/v1

• Li D, Bai D, Tian Y, Li Y, Zhao C, Wang Q, Gou S, Gu Y, Luan X, Wang R, Yang J, Hawkesford MJ, Schnable JC, Jin X, Qiu L (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

• Grzybowski M, Zweiner M, Jin H, Wijewardane NK, Atefi A, Naldrett MJ, Alvarez S, Ge Y, Schnable JC (2022) Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel. BMC Plant Biology 10.1186/s12870-022-03823-2 bioRxiv doi: 10.1101/2022.06.08.495271

• Khound R, Sun G, Mural RV, Schnable JC, Santra D (2022) “SNP Discovery in Proso millet (Panicum miliaceum L.) using low-pass genome sequencing.” Plant Direct doi: 10.1002/pld3.447

• Zhang K, Yang Y, Zhang X, Zhang L, Fu Y, Guo Z, Chen S, Wu J, Schnable JC, Yi K, Wang X, Cheng F (2022) “The genome of Orychophragmus violaceus provides genomic insights into the evolution of Brassicaceae polyploidization and its distinct traits.” Plant Communications doi: 10.1016/j.xplc.2022.100431

• Meier M, Xu G, Lopez-Guerrero, Li G, Smith C, Sigmon B, Herr J, Alfano J, Ge Y, Schnable JC, Yang J (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

• Mural RV, Sun G, Grzybowski M, Tross MC, Jin H, Smith C, Newton L, Andorf CM, Woodhouse MR, Thompson AM, Sigmon B, Schnable JC (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

• Korth N, Parsons L, Van Haute M, Yang Q, Hurst JP, Schnable JC, Holding DR, Benson AK (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

• Boatwright L, Sapkota S, Jin H, Schnable JC, Brenton Z, Boyles R, Kresovich S (2022) Sorghum association panel whole-genome sequencing establishes pivotal resource for dissecting genomic diversity. The Plant Journal doi: 10.1111/tpj.15853 bioRxiv doi: 10.1101/2021.12.22.473950

• Mural RV, Schnable JC (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

• Rodene E, Xu G, Delen SP, Smith C, Ge Y, Schnable JC, Yang J (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

• Yu H, Li M, Sandhu J, Sun G, Schnable JC, Walia H, Xie W, Yu B, Mower JP, Zhang C (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

• Khan SH, Karkhanis M, Hatasaka B, Tope S, Noh S, Dalapati R, Bulbul A, Mural RV, Banerjee A, Kim KH, Schnable JC, Ji M, Mastrangelo CH, Zang L, Kim H (2022) “Field deployment of a nanogap gas sensor for crop damage detection.” MEMS 2022 doi: 10.1109/MEMS51670.2022.9699614

2021

• Tross MC, Gaillard M, Zweiner M, Miao C, Grove RJ, Li B, Benes B, Schnable JC “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

• Diao X, Zhang H, Tang S, Schnable JC, He Q, Gao Y, Luo M, Jia G, Feng B, Zhi H (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.” Frontiers in Plant Science doi: 10.3389/fpls.2021.743782

• Miao C, Guo A, Thompson AM, Yang J, Ge Y, Schnable JC “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

• Woodhouse MR, Sen S, Schott D, Portwood JL, Freeling M, JWalley JW, Andorf CM, Schnable JC (2021) “qTeller: A tool for comparative multi-genomic gene expression analysis.” Bioinformatics doi: 10.1093/bioinformatics/btab604

• Sun G, Mural RV, Turkus JD, Schnable JC (2021) “Quantitative resistance loci to southern rust mapped in a temperate maize diversity panel.” Phytopathology doi: doi.org/10.1094/PHYTO-04-21-0160-R bioRxiv doi: 10.1101/2021.04.02.438220

• Mural RV, Grzybowski M, Miao C, Damke A, Sapkota S, Boyles RE, Salas Fernandez MG, Schnable PS, Sigmon B, Kresovich S, Schnable JC (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

• Grzybowski M, Wijewardane NK, Atefi A, Ge Y, Schnable JC (2021) “Hyperspectral reflectance-based phenotyping for quantitative genetics in crops: progress and challenges.” Plant Communications doi: 10.1016/j.xplc.2021.100209

• Zhou Y, Kusmec A, Mirnezami SV, Srinivasan L, Jubery TZ, Schnable JC, Salas-Fernandez MG, Nettleton D, Ganapathysubramanian B, Schnable PS (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

• Atefi A, Ge Y, Pitla S, Schnable JC (2021) “Robotic technologies for high-throughput plant phenotyping: reviews and perspectives.” Frontiers in Plant Science doi: 10.3389/fpls.2021.611940

• Khan SH, Tope S, Dalpati R, Kim KH, Noh S, Bulbul A, Mural RV, Banerjee A, Schnable JC, Ji M, Mastrangelo C, Zang L, Kim H (2021) “Development of a gas sensor for green leaf volatile detection.” Transducers 2021 doi: 10.1109/Transducers50396.2021.9495597

• Alzadjali A, Veeranampalayam-Sivakumar A, Alali MH, Deogun JS, Scott S, Schnable JC, Shi Y (2021) “Maize tassel detection from UAV imagery using deep learning.” Frontiers in Robotics and AI doi: 10.3389/frobt.2021.600410

• Meier MA, Lopenz-Guerrero MG, Guo M, Schmer MR, Herr JR, Schnable JC, Alfano JR, Yang J (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 bioRxiv doi: 10.1101/2020.08.10.244384

• Serb DD, Meng X, Schnable JC, Bashir E, Michaud JP, Vara Prasad PV, Perumal R (2021) “Comparative transcriptome analysis reveals genetic mechanisms of sugarcane aphid resistance in grain sorghum” International Journal of Molecular Sciences doi: 10.3390/ijms22137129

• Busta L, Schmitz E, Kosma D, Schnable JC, Cahoon EB (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

• Meng X, Liang Z, Dai X, Zhang Y, Mahboub S, Ngu DW, Roston RL, Schnable JC (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

• Sankaran S, Marzougui A, Hurst JP, Zhang C, Schnable JC, Shi Y (2021) “Can high resolution satellite imagery be used in high-throughput field phenotyping?” Transactions of the ASABE doi: 10.13031/trans.14197

• Zhu Y, Chen Y, Ali Md. A, Dong L, Wang X, Archontoulis SV, Schnable JC, Castellano MJ (2021) “Continuous in situ soil nitrate sensors: a comparison with conventional measurements and the value of high temporal resolution measurements.” Soil Science Society of America Journal doi: 10.1002/saj2.20226

• Weissmann S, Huang P, Wiechert M, Furoyama, K Brutnell TP, Taniguchi M, Schnable JC, Mockler TC (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

• Rogers AR, Dunne JC, Romay C … Schnable JC (24th of 39 authors) … Kaeppler S, De Leon N, Holland JB (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

• Lai X, Bendix C, Zhang Y, Schnable JC, Harmon FG (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

• DiMario RJ, Kophs AN, Pathare VS, Schnable JC, Cousins AB (2021) “Phosphoenolpyruvate carboxylase kinetic variation provides opportunity to enhance C4 photosynthetic efficiency.” The Plant Journal doi: 10.1111/tpj.15141

• Jarquin D, de Leon N, Romay C … Schnable JC (24th of 33 authors) … Wisser RJ, Xu W, Lorenz A (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

• Thudi M, Palakurthi R, Schnable JC, Chitikineni A, Dreisigacker S, Mace E, Srivastava RK, Satyavathi CT, Odeny D, Tiwari VK, Lam HM, Hong YB, Singh VK, Li G, Xu Y, Chen X, Nguyen H, Sivasankar S, Close TJ, Stein N, Jackson SA, Shubo W, Varshney RK (2021) “Genomic resources in plant breeding for sustainable agriculture.” Journal of Plant Physiology doi: 10.1016/j.jplph.2020.153351

2020

• Gaillard M, Benes B, Schnable JC, Miao C (2020) “Sorghum Segmentation by Skeleton Extraction.” CVPPP 2020 (Conference Proceedings).

• Gaillard M, Miao C, Schnable JC, Benes B (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

• Raju SKK, Thompson AM, Schnable JC (2020) “Advances in plant phenomics: From data and algorithms to biological insights.” Applications in Plant Sciences doi: 10.1002/aps3.11386

• Raju SKK, Atkins M, Enerson A, Carvalho DS, Studer AJ, Ganapathysubramanian B, Schnable PS, Schnable JC (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

• Atefi A, Ge Y, Pitla S, Schnable JC (2020) “Robotic detection and grasp of maize and sorghum: stem measurement with contact.” Robotics doi: 10.3390/robotics9030058

• Wang R, Qiu Y, Zhou Y, Liang Z, Schnable JC (2020) “A high-throughput phenotyping pipeline for image processing and functional growth curve analysis.” Plant Phenomics doi: 10.34133/2020/7481687

• Lai X, Bendix C, Yan L, Zhang Y, Schnable JC, Harmon F (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

• Moisseyev G, Park K, Cui X, Freitas D, Rajagopa D, Konda A, Martin-Olenski M, Mcham M, Liu K, Du Q, Schnable JC, Moriyama E, Cahoon E, Chi Z (2020) “RGPDB: Database of root-associated genes and promoters in maize, soybean, and sorghum.” Database doi: 10.1093/database/baaa038

• Han J, Wang P, Wang Q, Lin Q, Yu G, Miao C, Dao Y, Wu R, Schnable JC, Tang H, Wang K (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

• Miao C, Xu Y, Liu S, Schnable PS, Schnable JC (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 Author Profile for Chenyong Miao
  Chinese Language Version

• Dai X, Xu Z, Liang Z, Tu X, Zhong S, Schnable JC, Li P (2020) “Non-homology-based prediction of gene functions.” The Plant Genome doi: 10.1002/tpg2.20015 bioRxiv doi: 10.1101/730473

• Sankaran S, Zhang C, Hurst JP, Marzougui A, Sivakumar ANV, Li J, Schnable JC, Shi Y (2020) “Investigating the potential of satellite imagery for high-throughput field phenotyping applications.” SPIE Defense + Commercial Sensing (Conference Preceedings) doi: 10.1117/12.2558729

• Al-Zadjali A, Shi Y, Scott S, Deogun JS, Schnable JC (2020) “Faster-R-CNN based deep learning for locating corn tassels in UAV imagery.” SPIE Defense + Commercial Sensing (Conference Preceedings) doi: 10.1117/12.2560596

• Adams J, Qiu Y, Xu Y, Schnable JC (2020) “Plant segmentation by supervised machine learning methods.” The Plant Phenome Journal doi: 10.1002/ppj2.20001

• Liang Z, Qiu Y, Schnable JC (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

• Peng B, Guan K, Ainsworth EA, Asseng S, Bernacchi CJ, Cooper M, Delucia EH, Elliot JW, Ewert F, Grant RF, Gustafson DI, Hammer GL, Jin Z, Jones JW, Kimm H, Lawrence DM, Li Y, Lombardozzi DL, Marshall-Colon A, Messina CD, Ort DR, Schnable JC, Tang J, Vallejos CE, Wu A, Yin X, Zhou W (2020) “Advancing multi-scale crop modeling for agricultural climate change adaptation assessment” Nature Plants doi: 10.1038/s41477-020-0625-3

• Benes B, Guan K, Lang M, Long S, Lynch J, Marshall-Colon A, Peng B, Schnable JC, Sweetlove L, Turk M (2020) “Multiscale computational models can guide experimentation and targeted measurements for crop improvement.” The Plant Journal doi: 10.1111/tpj.14722

• McFarland BA, AlKhalifah N, Bohn … Schnable JC (34 of 51 authors) .. Xu W, Yeh CT, de Leon N (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

• Miao C, Pages A, Xu Z, Rodene E, Yang J, Schnable JC (2020) “Semantic segmentation of sorghum using hyperspectral data identifies genetic associations.” Plant Phenomics doi: 10.34133/2020/4216373

• Carvalho DS, Nishimwe A, Schnable JC (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

• Jarquin D, Howard R, Liang Z, Gupta SK, Schnable JC, Crossa J (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

• Zheng Z, Hey S, Jubery T, Liu T, Yang Y, Coffey L, Miao C, Sigmon B, Schnable JC, Hochholdinger F, Ganapathysubramanian B, Schnable PS (2020) “Shared genetic control of root system architecture between Zea mays and Sorghum bicolor.” Plant Physiology doi: 10.1104/pp.19.00752

2019

• Jiao Y, Wang X, Chen Y, Castellano MJ, Schnable JC, Schnable PS, Dong L (2019) “In-planta nitrate detection using insertable plant microsensor.” 20th International Conference on Solid-State Sensors, Actuators and Microsystems Berlin, Germany doi: 10.1109/TRANSDUCERS.2019.8808527

• Ali MA, Wang X, Chen Y, Jiao Y, Castellano MJ, Schnable JC, Schnable PS, Dong L (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 Berlin, Germany doi: 10.1109/TRANSDUCERS.2019.8808341

• Qi P, Eudy D, Schnable JC, Schmutz J, Raymer P, Devos KM (2019) “High density genetic maps of seashore paspalum using genotyping-by-sequencing and their relationship to the Sorghum bicolor genome.” Scientific Reports doi: 10.1038/s41598-019-48257-3

• Ali MA, Wang X, Chen Y, Jiao Y, Mahal NK, Satyanarayana M, Castellano MJ, Schnable JC, Schnable PS, Dong L (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

• Li Y, Li D, Jiao Y, Schnable JC, Li Y, Li H, Chen H, Hong H, Zhang T, Liu B, Liu Z, You Q, Tian Y, Gou Y, Guan R, Zhang L, Chang R, Zhang Z, Reif J, Zhou X, Schnable PS, Qiu L (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

• Ge Y, Atefi A, Zhang H, Miao C, Ramamurthy RK, Sigmon B, Yang J, Schnable JC (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

• Schnable JC (2019) “Genes and Gene Models, an Important Distinction.” New Phytologist doi: 10.1111/nph.16011

• Atefi A, Ge Y, Pitla S, Schnable JC (2019) “In vivo human-like robotic phenotyping of leaf traits in maize and sorghum.” Computers and Electronics in Agriculture doi: 10.1016/j.compag.2019.104854

• Yan L, Raju SKK, Lai X, Zhang Y, Dai X, Rodriguez O, Mahboub S, Roston RL, Schnable JC (2019) “Parallel natural selection in the cold-adapted crop-wild relative Tripsacum dactyloides and artificial selection in temperate adapted maize.” The Plant Journal doi: 10.1111/tpj.14376 bioRxiv doi: 10.1101/187575

• Li L, Li X, Li L, Schnable JC, Gu R, J Wang (2019) “QTL identification and epistatic effect analysis of seed size- and weight-related traits in Zea mays L.” Molecular Breeding doi: 10.1007/s11032-019-0981-8

• Bai G, Ge Y, Scoby D, Leavit B, Irmak S, Graef G, Schnable JC, Awada T. (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

• Zou C, Miki D, Li D, Tang Q, Xiao L, Rajput S, Deng P, Peng L, Huang R, Zhang M, Sun Y, Hu J, Fu X, Schnable P, Li F, Zhang H, Feng B, Zhu X, Liu R, Schnable JC, Zhu JK, Zhang H. (2019) “The genome of broomcorn millet.” Nature Communications doi: 10.1038/s41467-019-08409-5

2018

• Miao C, Yang J, Schnable JC (2018) “Optimizing the identification of causal variants across varying genetic architectures in crops.” Plant Biotechnology Journal doi: 10.1111/pbi.13023 bioRxiv doi: 10.1101/310391

• Ott A, Schnable JC, Yeh CT, Wu L, Liu C, Hu HC, Dolgard CL, Sarkar S, Schnable PS. (2018) “Linked read technology for assembling large complex and polyploid genomes.” BMC Genomics doi: 10.1186/s12864-018-5040-z

• Liu S, Schnable JC, Ott A, Yeh CT, Springer NM, Yu J, Meuhbauer G, Timmermans MCP, Scanlon MJ, Schnable PS. (2018) “Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels.” Molecular Biology and Evolution doi: 10.1093/molbev/msy174

• Raju SKK, Barnes A, Schnable JC, Roston RL. (2018) “Low-temperature tolerance in land plants: Are transcript and membrane responses conserved?” Plant Science doi: 10.1016/j.plantsci.2018.08.002

• Liang Z, Gupta SK, Yeh CT, Zhang Y, Ngu DW, Kumar R, Patil HT, Mungra KD, Yadav DV, Rathore A, Srivastava RK, Gupkta R, Yang J, Varshney RK, Schnable PS, Schnable JC. (2018) “Phenotypic data from inbred parents can improve genomic prediction in pearl millet hybrids.” G3: Genes Genomes Genetics doi: 10.1534/g3.118.200242 Chinese Language Summary Selected as the outstanding scientific article of 2018 by ICRISAT’s research program in Asia.

• Miao C, Fang J, Li D, Liang P, Zhang X, Yang J, Schnable JC, Tang H. (2018) “Genotype-Corrector: improved genotype calls for genetic mapping.” Scientific Reports doi: 10.1038/s41598-018-28294-0

• Alkhalifah N, Campbell DA, Falcon CM, … Schnable JC (31 of 44 authors) … Spalding EP, Edwards J, Lawrence-Dill CJ. (2018) “Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets.” BMC Research Notes doi: https://doi.org/10.1186/s13104-018-3508-1

• Xu Y, Qiu Y, Schnable JC. (2018) “Functional Modeling of Plant Growth Dynamics.” The Plant Phenome Journal doi: 10.2135/tppj2017.09.0007 bioRxiv doi: 10.1101/190967 An invited webinar organized by the The Plant Phenome Journal where James Schnable describes the key advances from this paper for a wider audience.

• Carvalho DS, Schnable JC, Almeida AMR. (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 bioRxiv doi: 10.1101/195669

• Liang Z, Schnable JC. (2018) “Functional Divergence Between Subgenomes and Gene Pairs After Whole Genome Duplications.” Molecular Plant doi: 10.1016/j.molp.2017.12.010

• Nani TF, Schnable JC, Washburn JD, Albert P, Pereira WA, Sobrinho FS, Birchler JA, Techia VH. (2018) “Location of low copy genes in chromosomes of Brachiaria spp.” Molecular Biology Reports doi: 10.1007/s11033-018-4144-5

• Lai X, Yan L, Lu Y, Schnable JC. (2018) “Largely unlinked gene sets targeted by selection for domestication syndrome phenotypes in maize and sorghum.” The Plant Journal doi: 10.1111/tpj.13806 bioRxiv doi: 10.1101/184424

2017

• Liang Z, Pandey P, Stoerger V, Xu Y, Qiu Y, Ge Y, Schnable JC. (2017) “Conventional and hyperspectral time-series imaging of maize lines widely used in field trials.” GigaScience doi: 10.1093/gigascience/gix117 bioRxiv doi: 10.1101/169045
  Image data, ground truth measurements, and plant pot weights using in this study are shared on Cyverse: 10.7946/P22K7V.

• Gage J, Jarquin D, Romay M, … Schnable JC (29th of 40 authors) .. Yu J, de Leon N. (2017) “The effect of artificial selection on phenotypic plasticity in maize.” Nature Communications doi: 10.1038/s41467-017-01450-2

• Washburn JD, Schnable JC, Brutnell TP, Shao Y, Zhang Y, Ludwig M, Davidse G, Pires JC. (2017) “Genome-Guided Phylo-Transcriptomics.” Scientific Reports doi: 10.1038/s41598-017-13236-z

• Behera S, Deogun JS, Lai X, Schnable JC. (2017) “DiCE: Discovery of Conserved Noncoding Sequences Efficiently.” IEEE BIBM Kansas City, MO, USA B529 (Conference Preceedings) doi: 10.1109/BIBM.2017.8217628

• Ott A,* Liu S,* Schnable JC, Yeh CT, Wang C, Schnable PS. (2017) “Tunable Genotyping-By-Sequencing (tGBS) enables reliable genotyping of heterozygous loci.” Nucleic Acids Research doi: 10.1093/nar/gkx853 bioRxiv doi: 10.1101/100461

• Lai X, Schnable JC, Liao Z, Xu J, Zhang G, Li C, Hu E, Rong T, Xu Y, Lu Y. (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

• Mei W, Boatwright L, Feng G, Schnable JC, Barbazuk WB. (2017) “Evolutionarily conserved alternative splicing across monocots.” Genetics doi: 10.1534/genetics.117.300189 bioRxiv preprint doi: 10.1101/120469
  (Cover Article October 2017)

• Zhang Y, Ngu DW, Carvalho D, Liang Z, Qiu Y, Roston RL, Schnable JC. (2017) “Differentially regulated orthologs in sorghum and the subgenomes of maize.” The Plant Cell doi: 10.1105/tpc.17.00354 bioRxiv preprint doi: 10.1101/120303

• Pandey P, Ge Y, Stoerger V, Schnable JC. (2017) “High throughput in vivo analysis of plant leaf chemical properties using hyperspectral imaging” Frontiers in Plant Science doi: 10.3389/fpls.2017.01348

• Lai X,* Behera S,* Liang Z, Lu Y, Deogun JS, Schnable JC. (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 bioRxiv preprint doi: 10.1101/120428

• Lai X, Schnable JC. (2017) “Harnessing the potential of the tea tree genome.” Molecular Plant doi: 10.1016/j.molp.2017.05.009

• Mei W, Liu S, Schnable JC, Yeh C, Springer NM, Schnable PS, Barbazuk WB. (2017) “A comprehensive analysis of alternative splicing in paleopolyploid maize.” Frontiers in Plant Science doi: 10.3389/fpls.2017.00694

2016

• Joyce BL, Huag-Baltzell A, Davey S, Bomhoff M, Schnable JC, Lyons E. (2016) “FractBias: a graphical tool for assessing fractionation bias after whole genome duplications.” Bioinformatics doi: 10.1093/bioinformatics/btw666

• Studer AJ,* Schnable JC,* Weissmann S, Kolbe AR, McKain MR, Shao Y, Cousins AB, Kellogg EA, Brutnell TP. (2016) “The draft genome of Dichanthelium oligosanthes: A C3 panicoid grass species.” Genome Biology doi: 10.1186/s13059-016-1080-3

• Walley JW,* Sartor RC,* Shen Z, Schmitz RJ, Wu KJ, Urich MA, Nery JR, Smith LG, Schnable JC, Ecker JR, Briggs SP. (2016) “Integration of omic networks in a developmental atlas of maize.” Science doi: 10.1126/science.aag1125

• Chaudhury SD, Steorger V, Samal A, Schnable JC, Liang Z, Yu J. (2016) “Automated vegetative stage phenotyping analysis of maize plants using visible light images.” KDD: Data Science for Food, Energy, and Water San Francisco, CA, USA (Conference Proceedings)

• Ge Y, Bai G, Stoerger V, Schnable JC. (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

• Huang P, Studer AJ, Schnable JC, Kellog EA, Brutnell TP. (2016) “Cross species selection scans identify components of C4 photosynthesis in the grasses.” Journal of Experimental Botany doi: 10.1093/jxb/erw256

• Liang Z, Schnable JC (2016) “RNA-seq based analysis of population structure within the maize inbred B73.” PLoS One doi: 10.1371/journal.pone.0157942 bioRxiv preprint doi: 10.1101/043513

• Liu X, Tang S, Jia G, Schnable JC, Su X, Tang C, Zhi H, Diao X. (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

• Rajput SG, Santra DK, Schnable JC. (2016) “Mapping QTLs for morpho-agronomic traits in proso millet (Panicum miliaceum L.).” Molecular Breeding doi: 10.1007/s11032-016-0460-4

• Cheng F, Sun C, Wu J, Schnable JC, Woodhouse MR, Liang J, Cai C, Freeling M, Wang X. (2016) “Epigenetic regulation of subgenome dominance following whole genome triplication in Brassica rapa.” New Phytologist doi: 10.1111/nph.13884

2015

• Chao S, Wu J, Schnable JC, Yang W, Cheng F, Wang X. (2015) “Impacts of Whole Genome Triplication on MIRNA Evolution in Brassica rapa.” Genome Biology and Evolution doi: 10.1093/gbe/evv206

• Tang H, Bamhoff MD, Briones E, Schnable JC, Lyons E. (2015) “SynFind: compiling syntenic regions across any set of genomes on demand.” Genome Biology and Evolution doi: 10.1093/gbe/evv219

• Washburn JD, Schnable JC, Davidse G, Pires JC. (2015) “Phylogeny and photosynthesis of the grass tribe Paniceae.” American Journal of Botany doi: 10.3732/ajb.1500222

• Jia G, Liu X, Schnable JC, Niu Z, Wang C, Li Y, Wang Sh, Wang Su, Liu J, Gou E, Diao X. (2015) “Microsatellite Variations of Elite Setaria Varieties Released during Last Six Decades in China.” PLoS One doi: 10.1371/journal.pone.0125688

• Tang H, Zhang X, Miao C, Zhang J, Ming R, Schnable JC, Schnable PS, Lyons E, Lu Jianguo. (2015) “ALLMAPS: robust scaffold ordering based on multiple maps.” Genome Biology doi: 10.1186/s13059-014-0573-1

• Schnable JC. (2015) “Genome evolution in maize: from genomes back to genes.” Annual Review of Plant Biology doi: 10.1146/annurev-arplant-043014-115604

2014

• Paschold A, Larson NB, Marcon C, Schnable JC, Yeh C, Lanz C, Nettleton D, Piepho H, Schnable PS, Hochholdinger F. (2014) “Nonsyntenic Genes Drive Highly Dynamic Complementation of Gene Expression in Maize Hybrids” Plant Cell doi: 10.1105/tpc.114.130948

• Almeida AMR, Yockteng R, Schnable JC, Alvarez-Buylla ER, Freeling M, Specht CD. (2014) “Co-option of the polarity gene network shapes filament morphology in angiosperms” Scientific Reports doi: 10.1038/srep06194

• Qie L, Jia G, Zhang W, Schnable JC, Shang Z, Li W, Liu B, Li M, Chai, Y, Zhi H, Diao X. (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

• Diao X, Schnable JC, Bennetzen JL, Li J. (2014) “Initiation of Setaria as a model plant.” Frontiers of Agricultural Science and Engineering doi: 10.15302/J-FASE-2014011

• Martin JA, Johnson NV, Gross SM, Schnable JC, Meng X, Wang M, Coleman-Derr D, Lindquist E, Wei C, Kaeppler S, Chen F, Wang Z. (2014) “A near complete snapshot of the Zea mays seedling transcriptome revealed from ultra-deep sequencing.” Scientific Reports doi: 10.1038/srep04519

2013

• Garsmeur O,* Schnable JC,* Almeida A, Jourda C, D’Hont A, Freeling M (2013) “Two Evolutionarily Distinct Classes of Paleopolyploidy.” Molecular Biology and Evolution doi: 10.1093/molbev/mst230

• Turco G, Schnable JC, Bedersen B, Freeling M. (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

2012

• Schnable JC, Wang X, Pires JC, Freeling M. (2012) “Escape from preferential retention following repeated whole genome duplication in plants.” Frontiers in Plant Science doi: 10.3389/fpls.2012.00094

• Freeling M, Woodhouse MR, Subramaniam S, Turco G, Lisch D, Schnable JC. (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

• Tang H, Woodhouse MR, Cheng F, Schnable JC, Pedersen BS, Conant GC, Wang X, Freeling M, Pires JC. (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

• Schnable JC, Freeling M, Lyons E. (2012) “Genome-wide analysis of syntenic gene deletion in the grasses” Genome Biology and Evolution doi: 10.1093/gbe/evs009

• Zhang W, Wu Y, Schnable JC, Zeng Z, Freeling M, Crawford GE, and Jiang J. (2012) “High-resolution mapping of open chromatin in the rice genome.” Genome Research doi: 10.1101/gr.131342.111

2011

• Eichten SR,* Swanson-Wagner RA,* Schnable JC, Waters AJ, Hermanson PJ, Liu S, Yeh C, Jia Y, Gendler K, Freeling M, Schnable PS, Vaughn MW, Springer NM. (2011) “Heritable epigenetic variation among maize inbreds.” PLoS Genetics doi: 10.1371/journal.pgen.1002372

• Schnable JC, Lyons E. (2011) “Comparative genomics with maize and other grasses: from genes to genomes” Maydica (Link is directly to PDF)

• Tang H, Lyons E, Pedersen B, Schnable JC, Paterson AH, Freeling M. (2011) “Screening synteny blocks in pairwise genome comparisons through integer programming.” BMC Bioinformatics doi: 10.1186/1471-2105-12-102

• Schnable JC, Pedersen BS, Subramaniam S, Freeling M. (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
  (Commentary on this article by Birchler and Veitia, also published in Frontiers in Plant Science)

• Schnable JC, Freeling M. (2011) “Genes identified by visible mutant phenotypes show increased bias towards one of two maize subgenomes.” PLoS One doi: 10.1371/journal.pone.0017855

• Schnable JC, Springer NM, Freeling M. (2011) “Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss.” PNAS doi: 10.1073/pnas.1101368108 Read for free at PubMed Central
  (Selected as an Editor’s Choice by MaizeGDB May 2011)

2010

• Woodhouse MR,* Schnable JC,* Pedersen BS, Lyons E, Lisch D, Subramaniam S, Freeling M. (2010) “Following tetraploidy in maize, a short deletion mechanism removed genes preferentially from one of the two homeologs.” PLoS Biology doi: 10.1371/journal.pbio.1000409
  (Selected as an Editor’s Choice by MaizeGDB August 2010; an image related to this manuscript was used for the journal cover; “recommended” by Faculty of 1000)

• The International Brachypodium Initiative. (2010) “Genome sequencing and analysis of the model grass Brachypodium distachyon.” Nature doi: 10.1038/nature08747 *Authors Contributed Equally