James Schnable Publications

James Schnable 

2022

  • https://patentimages.storage.googleapis.com/b0/8e/9a/0e7401378ea208/US20220174903A1.pdf
  • Mural, R. V., & Schnable, J. C. (2022). Can the grains offer each other helping hands? Convergent molecular mechanisms associated with domestication and crop improvement in rice and maize. Molecular Plant15(5), 793-795.
  • Yang, Q., Van Haute, M., Korth, N., Sattler, S., Toy, J., Rose, D., ... & Benson, A. (2022). Complex Trait Analysis of Human Gut Microbiome-Active Traits in Sorghum bicolor: a new category of human health traits in food crops.
  • Sun, G., Mural, R. V., Turkus, J. D., & Schnable, J. C. (2022). Quantitative resistance loci to southern rust mapped in a temperate maize diversity panel. Phytopathology®112(3), 579-587.
  • Yu, H., Li, M., Sandhu, J., Sun, G., Schnable, J. C., Walia, H., ... & Zhang, C. (2022). Pervasive misannotation of microexons that are evolutionarily conserved and crucial for gene function in plants. Nature communications13(1), 1-15.
  • Khan, S. U. H., Karkhanis, M., Hatasaka, B., Tope, S., Noh, S., Bulbul, A., ... & Kim, K. (2022, January). Field Deployment of A Nanogap Gas Sensor For Crop Damage Detection. In 2022 IEEE 35th International Conference on Micro Electro Mechanical Systems Conference (MEMS) (pp. 720-723). IEEE.
  • Grzybowski MZweiner MJin H, Wijewardane NK, Atefi A, Naldrett MJ, Alvarez S, Ge Y, Schnable JC Variation in morpho-physiological and metabolic responses to low nitrogen stress across the sorghum association panel. bioRxiv doi: 10.1101/2022.06.08.495271
  • Yang Q, Van Haute M, Korth N, Sattler S, Toy J, Rose D, Schnable JC, Benson A “Complex trait analysis of human gut microbiome-active traits in Sorghum bicolor: a new category of human health traits in food crops.” Research Square doi: 10.21203/rs.3.rs-1490527/v1
  • Xu G, Lyu J, Obata T, Liu S, Ge Y, Schnable JC, Yang J “A historically balanced locus under recent directional selection in responding to changed nitrogen conditions during modern maize breeding.” bioRxiv doi: 10.1101/2022.02.09.479784
  • Sun G, Yu H, Wang P, Lopez-Guerrero MG, Mural RVMizero ONGrzybowski M, Song B, van Dijk K, Schachtman DP, Zhang C, Schnable JC A role for heritable transcriptomic variation in maize adaptation to temperate environments. bioRxiv doi: 10.1101/2022.01.28.47821
  • Tross MCGrzybowski MNishimwe AVSun G, Ge Y, Schnable JC “Data driven trait quantification across a maize diversity panel using hyperspectral leaf reflectance.” ESSOAr doi: 10.1002/essoar.10508826.1
  • Meier MA, Xu G, Lopez-Guerrero MG, Li G, Smith CSigmon B, Herr JR, Alfano J, Ge Y, Schnable JC, Yang J “Maize root-associated microbes likely under adaptive selection by the host to enhance phenotypic performance.” bioRxiv doi: 10.1101/2021.11.01.466815
  • Sun G, Wase N, Su S … Foltz A (16th of 25 authors) … Sigmon B, Yu B, Obata T, Schmutz J, Schnable JC “The genome of stress tolerant crop wild relative Paspalum vaginatum leads to increased biomass productivity in the crop Zea mays.” bioRxiv doi: 10.1101/2021.08.18.456832
  • Miao CHoban TPPages A, Xu Z, Rodene E, Ubbens J, Stavness I, Yang J, Schnable JC “Simulated plant images improve maize leaf counting accuracy.” bioRxiv doi: 10.1101/706994
  • Zhang Z, Chen C, Rutkoski J, Schnable JC, Murray S, Wang L, Jin X, Stich B, Crossa J, Hayes B. “Harnessing agronomics through genomics and phenomics in plant breeding: a review” preprints.org doi: 10.20944/preprints202103.0519.v
  • Mural RVSun GGrzybowski MTross MCJin HSmith C, Newton L, Andorf CM, Woodhouse MR, Thompson AM, Sigmon BSchnable JC (2022) “Association mapping across a multitude of traits collected in diverse environments identifies pleiotropic loci in maize.” Gigascience (Accepted) bioRxiv doi: 10.1101/2022.02.25.48075
  • 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 HSchnable 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 RVSchnable 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 GSchnable 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/s41467-022-28449-5
  • 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 MMiao C, 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 CGuo 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 GMural RVTurkus JDSchnable 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 RVGrzybowski MMiao CDamke 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 XSchnable 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 XLiang ZDai XZhang 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 YSchnable 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 JCMiao C (2020) “Sorghum Segmentation by Skeleton Extraction.” CVPPP 2020 (Conference Proceedings).
  • Gaillard M, Miao CSchnable 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 ACarvalho 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 ZSchnable 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 LZhang YSchnable 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 CPages 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 DSNishimwe ASchnable 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 CSigmon BSchnable 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 LRaju SKKLai XZhang YDai 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 CYang JSchnable 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 YNgu 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 JSchnable 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 DSSchnable 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 ZSchnable 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 XYan 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 XSchnable 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 XSchnable 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 YNgu DWCarvalho DLiang 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 XSchnable 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 JCLiang 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 ZSchnable 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