Preprints
Schulz, A. J., Bohn, M. O., Bradbury, P., Lima, D. C., De Leon, N., Flint-Garcia, S., Holland, J. B., Lepak, N., Lorenz, A. J., Romay, M. C., Hirsch, C. N., Buckler, E. S., & Robbins, K. R. (2026). Inter-variety competition dynamics in US inbred and hybrid maize. bioRxiv. 10.64898/2026.02.26.708322
Li, H., Griffis, H. K., Edwards, J., Flint-Garcia, S., Hirsch, C. N., Holland, J. B., Knoll, J. E., Lima, D. C., de Leon, N., Murray, S. C., Singh, M. P., Schnable, J. C., Sekhon, R. S., Thomison, P., Thompson, A., & Wallace, J. G. (2025). Gene-by-environment interaction significantly drives bacterial endophyte communities in maize stalks. bioRxiv. 10.64898/2025.12.23.696053
Liu, B., Munasinghe, M., Fairbanks, R. A., Hirsch, C. N., & Ross-Ibarra, J. (2025). Genome-wide selection on transposable elements in maize. bioRxiv. 10.1101/2025.09.16.676665
Menard, C., N. Catlin, A. Platts, Y. Qiu, E. Roback, M. Munasinghe, N. Springer, E. Josephs, C. Hirsch. 2025. SWIF-TE: identifying novel transposable element insertions from short read data. bioRxiv. 10.1101/2025.07.30.667279.
Cooper, J., D. Sweet, S. Tirado, N. Springer, C.N. Hirsch, C.D. Hirsch. 2024. Dissecting the temporal phenomics and genomics of maize canopy cover using UAV mediated image capture. bioRxiv. 10.1101/2024.06.25.600603.
2026
Adak, A., A.S. DeSalvio. Murray, N. de Leon, M. Bohn, J. Edwards, D. Ertl, C. Hirsch, J. Holland, S. Kaeppler, J. Knoll, D. Lima, R. Minyo, J. Schnable, R. Sekhon, M. Singh, E. Sparks, A. Thompson, M. Tuinstra, J. Washburn, T. Weldekidan. 2026. Pheomics-derived Temporal Maize Health Signals and Enviromics Enhance Physiology-Informed Prediction of Yield Across Environments. Plant Physiology. (in press).
Burns, M., S. Berry, A. Gilbert, P. Hermanson, C. Hirsch. 2026. Maize kernel composition and morphology influences pericarp retention during nixtamalization. Cereal Chemistry.
Chen, Q., Washburn, J. D., Lima, D. C., Romay, M. C., Gage, J. L., Holland, J. B., Xavier, A., Murray, S. C., Ertl, D., Lopez-Cruz, M., de Los Campos, G., Aguate, F. M., Beissinger, T. M., Bohn, M. O., Buckler, E. S., Edwards, J., Flint-Garcia, S. A., Gore, M. A., Hirsch, C. N., … de Leon, N. (2026). Genomes to fields 2024 maize genotype by environment prediction competition. BMC Research Notes.
Burns, M., R. Della Coletta, S. Fernanades, M. Bohn, A. Lipka, C. Hirsch. 2026. Optimizing population simulations to accurately parallel empirical data for digital breeding. Crop Science. 66(1).
2025
Burns, M., S. Berry, M. Loftus, A. Gilbert, C. Hirsch. 2025. Genomic insights and breeding strategies for nixtamalization moisture content in hybrid maize. Crop Science. 65:e70174.
Burns, M., S. Berry, M. Loftus, A. Gilbert, C. Hirsch. 2025. CHIP-NMC: an application for Corn Hybrid and Inbred Prediction of Nixtamalization Moisture Content. Cereal Chemistry. 102:573-585.
Catlin, N., H. Agha, A. Platts, M. Munasinghe, C. Hirsch, E. Josephs. 2025. Structural variants contribute to phenotypic variation in maize. Molecular Ecology. e17662.
Ojeda-Rivera, J., A. Barnes, E. Ainsworth, R. Angelovici, B. Basso, L. Brindisi, M. Brooks, W. Bush, G. Buttelmann, M. Castellano, J. Chen, D. Costich, N. de Leon, B. Emmett, D. Ertl, S. Fitzsimmons, S. Flint-Garcia, M. Gore, K. Guan, C. O’Hale, S. Herr, C. Hirsch, D. Holding, J. Holland, S. Hsu, J. Hua, M. Hufford, S. Kaeppler, E. Leary, Z. Liu, A. Mahama, T. McCubbin, C. Messina, T. Michael, S. Miller, S. Murray, S. Okumoto, E. Oren, A. Park, M. Pineros, N. Pugh, V. Raboy, R. Rellan-Alvarez, M.C. Romay, R. Rooney, R. Roston, R. Sawers, J. Schnable, A. Schulz, M.P. Scott, N. Springer, J. Washburn, M. Zambrano, J. Zhai, J. Zou, E. Buckler. 2025. Designing a nitrogen efficient cold tolerant maize for modern agricultural systems. The Plant Cell. https://doi.org/10.1093/plcell/koaf139.
Ozair, F., A. Adak, S. Murray, R. Alpers, D. Lima, J. Edwards, D. Ertl, M. Gore, C. Hirsch, J. Knoll, J. Schnable, M. Singh, E. Sparks, A. Thompson, T. Weldekidan, W. Xu. 2025. Phenotypic Plasticity in Maize Grain Yield: Genetic and Environmental Insights of Response to Environmental Gradients. The Plant Genome. 18(3):1-15.
Sweet, D., J. Cooper, C.D. Hirsch, C.N. Hirsch. 2025. Plant height defined growth curves during vegetative development have the potential to predict end of season maize yield and assist with mid-season management decisions. TPPJ. 8:e70025.
2024
Ellison, E., P. Zhou, Y. Chu, P. Hermanson, L. Gomez-Cano, Z. Myers, A. Abnave, J. Gray, C. Hirsch, E. Grotewold, N. Springer. 2024. Transcriptome profiling of maize transcription factor mutants to probe gene regulatory network predictions. Genes Genomes Genetics | G3. 15(1):jkae274.
Kusmec, A., C. Yeh, The Genomes to Fields Initiative, P. Schnable. 2024. Data-driven identification of environmental variables influencing phenotypic plasticity to facilitate breeding for future climates. New Phytologist. 244(2):618-634.
Ou, S., N. Jiang, C. Hirsch**, M. Hufford**. 2024. Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies . Genome Biology. 25(6):1-4. ** co-corresponding authors
Ou, S., A. Scheben, T. Collins, Y. Qiu, A. Seetharam, C. Menard, N. Manchanda, J. Gent, M. Schatz, S. Anderson, M. Hufford**, C. Hirsch**. 2024. Differences in activity and stability drive transposable element variation in tropical and temperate maize. Genome Research. 10.1101/gr.278131.123. **co-corresponding authors.
Schoemaker, D., Y. Qiu, N. de Leon, C. Hirsch, S. Kappler. 2024. Genetic analysis of pericarp pigmentation variation in Corn Belt dent maize. Genes Genomes and Genetics | G3. 14(1):jkad256.
Sweet, D., S. Tirado, J. Cooper, N. Springer, C.D. Hirsch, C.N. Hirsch. 2024. Temporally resolved growth patterns reveal novel information about the polygenic nature of complex quantitative traits. The Plant Journal. 120:1969-1986.
2023
Barreto Ortiz, J., C. Hirsch, N. Ehlke, E. Watkins. 2023. SpykProps: An Imaging Pipeline to Quantify Architecture in Unilateral Grass Inflorescences . Plant Methods. 19:125.
Della Coletta, R., S. Fernandes, P. Monnahan, M. Mikel, M. Bohn, A. Lipka, C. Hirsch. 2023. Importance of genetic architecture in marker selection decisions for genomic prediction. Theoretical and Applied Genetics. 136:220.
Della Coletta, R., S. Liese, S. Fernandes, M. Mikel, M. Bohn, A. Lipka, C. Hirsch. 2023. Linking genetic and environmental factors through marker effect networks to understand trait plasticity. Genetics. 224(4):iyad103.
Ellison, E., P. Zhou, P. Hermanson, Y. Chu, A. Read, C. Hirsch, E. Grotewold, N. Springer. 2023. Mutator transposon insertions within maize genes often provide a novel outward reading promoter . Genetics. 225(3):iyad171.
Kick, D., J. Wallace, J. Schnable, J. Kolkman, B. Alaca, T. Beissinger, J. Edwards, D. Ertl, S. Flint-Garcia, J. Gage, C. Hirsch, J. Knoll, N. de Leon, D. Lima, D. Moreta, M. Singh, A. Thompson, T. Weldekidan, J. Washburn. 2023. Yield Prediction Through Integration of Genetic, Environment, and Management Data Through Deep Learning. Genes Genomes and Genetics | G3. 13(4):jkad006.
Lima, D., A. Aviles, R. Alpers, A. Perkins, D. Schoemaker, M. Costa, K. Michel, S. Kaeppler, D. Ertl, M.C. Romay, J. Gage, J. Holland, T. Beissinger, M. Bohn, E. Buckler, J. Edwards, S. Flint-Garcia, M. Gore, C. Hirsch, J. Knoll, J. McKay, R. Minyo, S. Murray, J. Schnable, R. Sekhon, M. Singh, E. Sparks, P. Thomison, A. Thompson, M. Tuinstra, J. Wallace, J. Washburn, T. Weldekidan, W. Xu, N. de Leon. 2023. 2020-2021 Field Seasons of Maize GxE Project within Maize Genomes to Fields Initiative . BMC Research Notes. 16:219.
Lima, D., A. Alviles, R. Alpers, B. McFarland, S. Kaeppler, D. Ertl, M.C. Romay, J. Gage, J. Holland, T. Beissinger, M. Bohn, E. Buckler, J. Edwards, S. Flint-Garcia, C. Hirsch, E. Hood, D. Hooker, J. Knoll, J. Kolkman, S. Liu, J. McKay, R. Minyo, D. Moreta, S. Murray, R. Nelson, J. Schnable, R. Sekhon, M. Singh, P. Thomison, A. Thompson, M. Tuinstra, J. Wallace, J. Washburn, T. Weldekidan, R. Wisser, W. Xu, N. de Leon. 2023. 2018-2019 field seasons of the Maize Genomes to Fields (G2F) GxE project. BMC Genomic Data. 24:29.
Lima, D., J. Washburn, J. Varela, Q. Chen, J. Gage, M.C. Romay, J. Holland, D. Ertl, M. Lopez-Cruz, F. Aguate, G. de los Campos, S. Kaeppler, T. Beissinger, M. Bohn, E. Buckler, J. Edwards, S. Flint-Garcia, M. Gore, C. Hirsch, J. Knoll, J. McKay, R. Minyo, S. Murray, O. Ortez, J. Schnable, R. Sekhon, M. Singh, E. Sparks, A. Thompson, M. Tuinstra, J. Wallace, T. Weldekidan, W. Xu, N. de Leon. 2023. Genomes to Fields 2022 Maize Genotype by Environment Prediction Competition. BMC Research Notes. 16:148.
Munasinghe, M., A. Read, M. Stitzer, B. Song, C. Menard, K. Ma, Y. Brandvain, C. Hirsch, N. Springer. 2023. Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion . PLoS Genetics. 19(12): e1011086.
2022
Li, Z., J. Sun, C. Hirsch. 2022. Understanding environmental modulation of heterosis. Plant Breeding Reviews. 46:219-237.
Read, A., T. Weiss, P. Crisp, Z. Liang, J. Noshay, C. Menard, C. Wang, M. Song, C. Hirsch, N. Springer, F. Zhang. 2022. Genome-wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants . The Plant Journal. 111(1):103-116.
Renk, J., M. Burns, A. Gilbert, N. Anderson, A. Waters, D. Eickholt, S. Kalambur, G. Annor, C. Hirsch. 2022. Variability in changes of acrylamide precursors during nixtamalization for masa production. Lebensmittel-Wissenschaft & Technologie (LWT) Food Science and Technology. 161:113400.
Sweet, D, S. Tirado, N. Springer, C.N. Hirsch, C.D. Hirsch. 2022. Opportunities and challenges in phenotyping row crops using drone-based RGB imaging. The Plant Phenome Journal. 5(1):e20044.
2021
Bornowski, N., K. Michel, J. Hamilton, S. Ou, A. Somwarpet-Seetharam, J. Jenkins, J. Grimwood, C. Plott, S. Shu, J. Talag, M. Kennedy, H. Hundley, V. Singan, K. Barry, C. Daum, Y. Yoshinga, J. Schmutz, C. Hirsch, M. Hufford, N. de Leon, S. Kaeppler, C.R. Buell. 2021. Genomic variation within the maize Stiff Stalk heterotic germplasm pool. The Plant Genome. 14(3):e20114.
Burns, M., J. Renk, D. Eickholt, A. Gilbert, T. Hattery, M. Holmes, N. Anderson, A. Waters, S. Kalambur, S. Flint-Garcia, M. Yandeau-Nelson, G. Annor, C. Hirsch. 2021. Predicting Moisture Content During Maize Nixtamalization Using Machine Learning with NIR Spectroscopy. Theoretical and Applied Genetics. 134:3743-3757.
Della Coletta, R., Y. Qiu, S. Ou, M. Hufford**, C. Hirsch**. 2021. How the pan-genome is changing crop genomics and improvement. Genome Biology. 22(3):1-19. **co-corresponding authors
Haas, M., T. Kono, M. Macchietto, R. Millas, L. McGilp, M. Shao, J. Duquette, C. Hirsch, J. Kimball. 2021. Whole Genome Assembly and Annotation of Northern Wild Rice, Zizania palustris L., Supports a Whole Genome Duplication in the Zizania Genus. The Plant Journal. 107(6):1802-1818.
Hufford, M., A. Seetharam, M. Woodhouse, K. Chougule, S. Ou, J. Liu, W. Ricci, T. Guo, A. Olson, Y. Qiu, R. Della Coletta, S. Tittes, A. Hudson, A. Marand, S. Wei, Z. Lu, B. Wang, M. Tello-Ruiz, R. Piri, N. Wang, D. Kim, Y. Zeng, C. O’Connor, X. Li, A. Gilbert, E. Baggs, K. Krasileva, J. Portwood II, E. Cannon, C. Andorf, N. Manchanda, S. Snodgrass, D. Hufnagel, Q. Jiang, S. Pedersen, M. Syring, D. Kudrna, V. Llaca, K. Fengler, R. Schmitz, J. Ross-Ibarra, J. Yu, J. Gent, C. Hirsch, D. Ware, R.K. Dawe. 2021. De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science. 373(6555):655-662.
Jarquin, D. N. de Leon, C. Romay, M. Bohn, E. Buckler, I. Ciampitti, J. Edwards, D. Ertl, S. Flint-Garcia, M. Gore, C. Graham, C. Hirsch, J. Holland, D. Hooker, S. Kaeppler, J. Knoll, E. Lee, C. Lawrence-Dill, J. Lynch, S. Moose, S. Murray, R. Nelson, T. Rocheford, J. Schnable, P. Schnable, M. Smith, N. Springer, P. Thomison, M. Tuinstra, R. Wisser, W. Xu, J. Yu, A. Lorenz. 2021. Utility of Climate Information via Combining Ability Models to Improve Genomic Prediction for Yield within the Genomes to Fields Maize Project. Frontiers in Genetics. 11:592769.
Noshay, J., A. Marand, S. Anderson, P. Zhou, M. Guerra, Z. Lu, C. O’Connor, P. Crisp, C. Hirsch, R. Schmitz, N. Springer. 2021. Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons. Genetics. 217(1):1-13.
Noshay, J., Z. Liang, P. Zhou, P. Crisp, A. Marand, C. Hirsch, R. Schmitz, N. Springer. 2021. Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. G3 Genes|Genomes|Genetics. 11(8):jkab190.
Qiu, Y.**, C. O’Connor**, R. Della Coletta, J. Renk, P. Monnahan, J. Noshay, A. Gilbert, S. Anderson, S. McGaugh, N. Springer, C. Hirsch. 2021. Whole-Genome Variation of Transposable Element Insertions in a Maize Diversity Panel. G3 Genes|Genomes|Genetics. 11(10):jkab238. **These authors contributed equally to this work.
Renk, J., A. Gilbert, T. Hattery, C. O’Connor, P. Monnahan, N. Anderson, A. Waters, D. Eickholt, S. Flint-Garcia, M. Yandeau-Nelson, C. Hirsch. 2021. Genetic control of kernel compositional variation in a maize diversity panel. The Plant Genome. 14(3):e20115.
Rogers, A., J. Dunne, C. Romay, M. Bohn, E. Buckler, I. Ciampitti, J. Edwards, D. Ertl, S. Flint-Garcia, M. Gore, C. Graham, C. Hirsch, E. Hood, D. Hooker, J. Knoll, E. Lee, A. Lorenz, J. Lynch, J. McKay, S. Moose, S. Murray, R. Nelson, T. Rocheford, J. Schnable, P. Schnable, R. Sekhon, M. Singh, M. Smith, N. Springer, K. Thelen, P. Thomison, A. Thompson, M. Tuinstra, J. Wallace, R. Wisser, W. Xu, S. Kaeppler, N. de Leon, J. Holland. 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. 11(2):jkaa050.
Tirado, S. C. Hirsch, N. Springer. 2021. Utilizing Temporal Measurements from UAVs to Assess Root Lodging in Maize and its Impact on Productivity. Field Crops Research. 262:108014.
2020
Crisp, P., R. Hammond, P. Zhou, B. Vaillancourt, A. Lipzen, C. Daum, K. Barry, N. de Leon, C.R. Buell, S. Kaeppler, B. Meyers, C. Hirsch, N. Springer. 2020. Variation and inheritance of small RNAs in maize inbreds and F1 hybrids. Plant Physiology. 182(1):318-331.
Falcon, C., S. Kaeppler, E. Spalding, N. Miller, N. Haase, N. AlKalifah, M. Bohn, E. Buckler, D. Campbell, I. Ciampitti, L. Coffey, J. Edwards, D. Ertl, S. Flint-Garcia, M. Gore, C. Graham, C. Hirsch, J. Holland, D. Jarquin, J. Knoll, N. Lauter, C. Lawrence-Dill, E. Lee, A. Lorenz, J. Lynch, S. Murray, R. Nelson, M.C. Romay, T. Rocheford, P. Schnable, B. Scully, M. Smith, N. Springer, M. Tuinstra, R. Walton, T. Weldekidan, R. Wisser, W. Xu, N. de Leon. 2020. Relative Utility of Agronomic, Phenological, and Morphological Traits for Assessing Genotype-by-Environment Interaction in Maize Inbreds. Crop Science. 60:62-81.
Li, Z., P. Zhou, R. Della Coletta, T. Zhang, A. Brohammer, C. O'Connor, B. Vaillancourt, A. Lipzen, C. Daum, K. Barry, N. de Leon, C.D. Hirsch, C.R. Buell, S. Kaeppler, N. Springer, C.N. Hirsch. 2020. Single-parent expression drives dynamic gene expression complementation in maize hybrids. The Plant Journal. 105(1):93-107.
Li, Z., S. Tirado, D. Kadam, L. Coffey, N. Miller, E. Spalding, A. Lorenz, N. de Leon, S. Kaeppler, P. Schnable, N. Springer, C. Hirsch. 2020. Characterizing introgression-by-environment interactions using maize near isogenic lines. Theoretical and Applied Genetics. 133(10): 2761-2773.
Liu, J., A. Seetharam, K. Chougule, S. Ou, K. Swentowsky, J. Gent, V. Llaca, M. Woodhouse, N. Manchanda, G. Presting, D. Kudrna, M. Alabady, C. Hirsch, K. Fengler, D. Ware, T. Michael, M. Hufford, R.K. Dawe. 2020. Gapless assembly of maize chromosomes using long read technologies. Genome Biology. 21:121.
McFarland, B., N. AlKhalifah, M. Bohn, J. Bubert, E. S. Buckler, I. Ciampitti, J. Edwards, D. Ertl, J. Gage, C. Falcon, S. Flint-Garcia, M. Gore, C. Graham, C. Hirsch, J. Holland, E. Hood, D. Hooker, D. Jarquin, S. M. Kaeppler, J. Knoll, G. Kruger, N. Lauter, E. Lee, D. Lima, A. Lorenz, J. Lynch, J. McKay, N. Miller, S. Moose, S. Murray, R. Nelson, C. Poudyal, T. Rocheford, O. Rodriguez, M. Romay, J. Schnable, P. Schnable, B. Scully, R. Sekhon, K. Silverstein, M. Singh, M. Smith, E. Spalding, N. Springer, K. Thelen, P. Thomison, M. Tuinstra, J. Wallace, R. Walls, D. Wills, R. Wisser, W. Xu, C. Yeh, N. de Leon. 2020. Maize Genomes to Fields (G2F): 2014-2017 field season’s genotype, phenotype, climatic, soil, and inbred ear images datasets. BMC Research Notes. 13:71.
Monnahan, P., J. Michno, C. O'Connor, A. Brohammer, N. Springer, S. McGaugh, C. Hirsch. 2020. Using multiple reference genomes to identify and resolve annotation inconsistencies. BMC Genomics. 21(281):1-13.
Ou, S., J. Liu, K. Chougule, A. Fungtammasan, A. Seetharam, J. Stein, V. Llaca, N. Manchanda, A. Gilbert, X. Wei, C. Chin, D. Hufnagel, S. Pedersen, S. Snodgrass, K. Fengler, M. Woodhouse, B. Walenz, S. Koren, A. Phillippy, B. Hannigan, R.K. Dawe**, C. Hirsch**, M. Hufford**, D. Ware**. 2020. Effect of Sequence Depth and Length in Long-read Assembly of the Maize Inbred NC358. Nature Communications. 11:2288. **co-corresponding authors
Tirado, S., C. Hirsch, N. Springer. 2020. UAV-based imaging platform for monitoring maize growth throughout development. Plant Direct. 4(6):e00230.
Zhou, P., Z. Li, E. Magnusson, F. Cano, P. Crisp, J. Noshay, E. Grotewold, C. Hirsch, S. Briggs, N. Springer. 2020. Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions. The Plant Cell. 32(5):1377-1396.
2019
Anderson, S.**, M. Stitzer**, A. Brohammer**, P. Zhou, J. Noshay, C. O'Connor, C.D. Hirsch, J. Ross-Ibarra, C.N. Hirsch, N. Springer. 2019. Transposable elements contribute to dynamic genome content in maize. The Plant Journal. 100(5):1052-1065 **These authors contributed equally to this work.
Della Coletta, R., C. Hirsch, M. Rouse, A. Lorenz, D. Garvin. 2019. Genetic Dissection of Nonhost Resistance to Wheat Stem Rust in Brachypodium distachyon. Molecular Plant-Microbe Interactions. 32(4):392-400.
Hemshrot, A., A. Poets, P. Tyagi, L. Lei, C. Carter, C. Hirsch, L. Li, G. Brown-Guedira, P. Morrell, G. Muehlbauer, K. Smith. 2019. Development of a Multiparent Population for Genetic Mapping and Allele Discovery in Six-Row Barley. Genetics. 213(2):595-613.
Holmes, M., J. Renk, P. Coaldrake, S. Kalambur, C. Schmitz, N. Anderson, G. Gusmini, G. Annor, C. Hirsch. 2019. Food Grade Maize Composition, Evaluation, and Genetics for Masa-Based Products. Crop Science. 59(4):1392-1405.
Mazaheri, M., M. Heckwolf, B. Vaillancourt, J. Gage, B. Burdo, S. Heckwolf, K. Barry, A. Lipzen, C. Ribeiro, T. Kono, H. Kaeppler, E. Spalding, C. Hirsch, C.R. Buell, N. de Leon, S. Kaeppler. 2019. Genome-wide association analysis of stalk biomass and anatomical traits in maize. BMC Plant Biology. 19:45.
Noshay, J. S. Anderson, P. Zhou, L. Ji, W. Ricci, Z. Lu, M. Stitzer, P. Crisp, C. Hirsch, Z. Zhang, R. Schmitz, N. Springer. 2019. Monitoring the interplay between transposable element families and DNA methylation in maize. Plos Genetics. 15(9):e1008291.
Ou, S., W. Su, Y. Liao, K. Chougule, J. Agda, A. Hellinga, C. Santiago Blanco Lugo, T. Elliot, D. Ware, T. Peterson, N. Jiang**, C. Hirsch**, M. Hufford**. 2019. Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline. Genome Biology. 20:275. **co-corresponding authors
Singh, A., G. Li, A. Brohammer, D. Jarquin, C. Hirsch, J. Alfano, A. Lorenz. 2019. Genome-Wide Association and Gene Co-Expression Network Analysis Reveals Complex Genetics of Resistance to Goss’s Wilt of Maize. G3 Genes|Genomes|Genetics. 9(10):3139-3152.
Zhang, X., J. Pang, Z. Ma, Z. Zhang, Y. He, C. Hirsch, J. Zhao. 2019. Multivariate analyses of root phenotype and dynamic transcriptome underscore valuable root traits and water-deficit responsive gene networks in maize. Plant Direct. 3(3):e00130.
Zhang, X., K. Haro von Mogel, V. Lor, C. Hirsch, B. De Vries, H. Kaeppler, W. Tracy, S. Kaeppler. 2019. Maize sugary enhancner1 (se1) is a novel gene affecting starch metabolism. PNAS. 116(41):20776-20785.
Zhou, P., C. Hirsch, S. Briggs, N. Springer. 2019. Dynamic Patterns of Gene Expression Additivity and Regulatory Variation Throughout Maize Development. Molecular Plant. 12(3):410-425.
2018
AlKhalifah, N., D. Campbell, C. Falcon, J. Gardiner, N. Miller, M.C. Romay, R. Walls, R. Walton, C. Yeh, M. Bohn, J. Bubert, E. Buckler, I. Ciampitti, S. Flint-Garcia, M. Gore, C. Graham, C. Hirsch, J. Holland, D. Hooker, S. Kaeppler, J. Knoll, N. Lauter, E. Lee, A. Lorenz, J. Lynch, S. Moose, S. Murray, R. Nelson, T. Rocheford, O. Rodriguez, J. Schnable, B. Scully, M. Smith, N. Springer, P. Thomison, M. Tuinstra, R. Wisser, W. Xu, D. Ertl, P. Schnable, N. de leon, E. Spalding, J. Edwards, C. Lawrence-Dill. 2018. Maize Genomes to Fields: 2014 and 2015 Field Season Genotype, Phenotype, Environment, and Inbred Ear Image Datasets. BMC Research Notes. 11:452.
Brohammer, A., T. Kono, N. Springer, S. McGaugh, C. Hirsch. 2018. Limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines. The Plant Journal. 93(1):131-141.
Brohammer, A., T. Kono, C. Hirsch. 2018. The Maize Pan-Genome. In: J. Bennetzen, S. Flint-Garcia, C. Hirsch, R. Tuberosa. (Ed.) The Maize Genome. Compendium of Plant Genomes. Springer, Cham.
Hirsch, C. and N. Springer. 2018. Weeding out bad alleles. Nature Plants. 4:193-194.
Kono, T., A. Brohammer, S. McGaugh, C. Hirsch. 2018. Tandem Duplicate Genes in Maize are Abundant and Date to Two Distinct Periods of Time. G3 Genes|Genomes|Genetics. 8(9):3049-3058.
Li, Z., L. Coffey, J. Garfin, N. Miller, M. White, E. Spalding, N. de Leon, S. Kaeppler, P. Schnable, N. Springer, C. Hirsch. 2017. Genotype-by-envrionment interactions affecting heterosis in maize. PLoSOne. 13(1):e0191321.
Salvo, St., J. Cook, A. Carlson, C. Hirsch, S. Kaeppler, H. Kaeppler. 2018. Genetic Fine-Mapping of a Quantitative Trait Locus (QTL) Associated with Embryogenic Tissue Culture Response and Plant Regeneration Ability in Maize. The Plant Genome. 11(2):170111.
2017
Gage, J., D. Jarquin, C. Romay, A. Lorenz, E. Buckler, S. Kaeppler, N. Alkhalifah, M. Bohn, D. Campbell, J. Edwards, D. Ertl, S. Flint-Garcia, J. Gardiner, B. Good, C. Hirsch, J. Holland, D. Hooker, J. Knoll, J. Kolkman, G. Kruger, N. Lauter, C. Lawrence-Dill, E. Lee, J. Lynch, S. Murray, R. Nelson, J. Petzoldt, T. Rocheford, J. Schnable, P. Schnable, B. Scully, M. Smith, N. Springer, S. Srinivasan, R. Walton, T. Weldekidan, R. Wisser, W. Xu, J. Yu, N. de Leon. 2017. The effect of artificial selection on phenotypic plasticity in maize. Nature Communications. 8(1):1348.
Waters, A., I. Makarevitch, J. Noshay, L. Burghardt, C.N. Hirsch, C.D. Hirsch, N. Springer. 2017. Natural variation for gene expression responses to abiotic stress in maize. The Plant Journal. 89(4):706-717.
2016
Hirsch, C.N., C.D. Hirsch, A. Brohammer, M. Bowman, I. Soifer, O. Barad, S. Doron, K. Baruch, F. Lu, A. Hernandez, C. Fields, C. Wright, K. Koehler, N. Springer, E. Buckler, C.R. Buell, N. de Leon, S. Kaeppler, K. Childs, M. Mikel. 2016. Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. The Plant Cell. 28(11):2700-2714.
Hirsch, C.D., C.R. Buell, C.N. Hirsch. 2016. A Toolbox of Potato Genetic and Genomic Resources. American Journal of Potato Research. 93(1):21-32.
Stelpflug, S., R. Sekhon, B. Vaillancourt, C. Hirsch, C.R. Buell, N. de Leon, S. Kaeppler. 2016. An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development. The Plant Genome. 9(1):1-16.
Zhang, X., C. Hirsch, R. Sekhon, N. de Leon, S. Kaeppler. 2016. Evidence for maternal control of seed size in maize from phenotypic and transcriptional analysis. Journal of Experimental Botany. 67(6):1907-1917.
2015
Haase, N., T. Beissinger, C. Hirsch, B. Vaillancourt, S. Deshpande, K. Barry, C.R. Buell, S. Kaeppler, N. de Leon. 2015. Shared Genomic Regions Between Derivatives of Large Segregating Population of Maize Identified Using Bulked Segregant Analysis Sequencing and Traditional Linkage Analysis. G3 Genes|Genomes|Genetics. 5(8):1593-1602.
Hirsch, C.D., N. Springer, C.N. Hirsch. 2015. Genomic limitations to RNA sequencing expression profiling. The Plant Journal. 84(3):491-503.
Li, Q, J. Gent, G. Zynda, J. Song, I. Makarevitch, C.D. Hirsch, C.N. Hirsch, R.K. Dawe, T. Madzima, K. McGinnis, D. Lisch, R. Schmitz, M. Vaughn, N. Springer. 2015. RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome. PNAS. 112(47):14728-14733.
Makarevitch, I., A. Waters, P. West, M. Stitzer, C. Hirsch, J. Ross-Ibarra, N. Springer. 2015. Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress. PLoS Genetics. 11(10):e1005566.
2014
Beissinger, T., C. Hirsch, B. Vaillancourt, S. Deshpande, K. Barry, C.R. Buell, S. Kaeppler, D. Gianola, N. de Leon. 2014. A Genome-Wide Scan for Evidence of Selection in a Maize Population Under Long-Term Artificial Selection for Ear Number. Genetics. 196(3):829-840
Burton, A., J. Johnson, J. Foerster, C. Hirsch, C.R. Buell, M. Hanlon, S. Kaeppler, K. Brown, J. Lynch. 2014. QTL mapping and phenotypic variation for root architectural traits in maize (Zea mays L.). Theoretical and Applied Genetics. 127:2293-2311.
Childs, K., A. Nandety, C. Hirsch, E. Góngora-Castillo, J. Schmutz, S. Kaeppler, M. Casler, C.R. Buell. 2014. Generation of Transcript Assemblies and Identification of Single Nucleotide Polymorphisms from Seven Lowland and Upland Cultivars of Switchgrass. The Plant Genome. 7(2):-.
Douches, D., C. Hirsch, N. Manrique-Carpintero, A. N. Massa, J. Coombs, M. Hardigan, D. Bisognin, W. De Jong, C. R. Buell. 2014. The Contribution of the Solanaceae Coordinated Agricultural Project to Potato Breeding. Potato Research. 57:215-224.
Hirsch, C. 2014. Genomic Sequence and Structural Diversity in Plants. In: Bell E., Bond J., Klinman J., Masters B., Wells R. (Ed.) Molecular Life Sciences. Springer, New York, NY.
Hirsch, C.D., J. Evans, C.R. Buell, C.N. Hirsch. 2014. Reduced representation approaches to interrogate genome diversity in large, repetitive plant genomes. Briefings in Functional Genomics. 13(4):257-267.
Hirsch, C.D, J. Hamilton, K. Childs, J. Cepela, E. Crisovan, B. Vaillancourt, C.N. Hirsch, M. Habermann, B. Neal, C.R. Buell. 2014. Spud DB: A Resource for Mining Sequences, Genotypes, and Phenotypes to Accelerate Potato Breeding. The Plant Genome. 7:-.
Hirsch, C., J. Foerster, J. Johnson, R. Sekhon, G. Muttoni, B. Vaillancourt, F. Peñagaricano, E. Lindquist, K. Barry, N. de Leon, S. Kaeppler, C.R. Buell. 2014. Insights into the Maize Pan-Genome and Pan-Transcriptome. The Plant Cell. 26(1):121-135.
Hirsch, C., S. Flint-Garcia, T. Beissinger, S. Eichten, S. Deshpande, K. Barry, M. McMullen, J. Holland, E. Buckler, N. Springer, C.R. Buell, N. de Leon, S. Kaeppler. 2014. Insights into the Effects of Long-Term Artificial Selection on Seed Size in Maize. Genetics. 198(1):409-421.
Salvo, S., C. Hirsch, C.R. Buell, S. Kaeppler, H. Kaeppler. 2014. Whole Transcriptome Profiling of Maize During Early Somatic Embryogenesis Reveals Altered Expression of Stress Factors and Embryogenesis-Related Genes. PLoSOne. 9(10):e111407.
Sekhon, R., C. Hirsch, K. Childs, M. Breitzman, P. Kell, S. Duvick, E. Spalding, C.R. Buell, N. de Leon, S. Kaeppler. 2014. Phenotypic and Transcriptional Analysis of Divergently Selected Maize Populations Reveals the Role of Developmental Timing in Seed Size Determination. Plant Physiology. 165(2):658-669.
2013
Beissinger, T., C. Hirsch, R. Sekhon, J. Foerster, J. Johnson, G. Muttoni, B. Vaillancourt, C.R. Buell, S. Kaeppler, N. de Leon. 2013. Marker Density and Read Depth for Genotyping Populations Using Genotyping-by-Sequencing. Genetics. 193(4):1073-1081.
Hirsch, C.N., C.D. Hirsch, K. Felcher, J. Coombs, D. Zarka, A. Van Deynze, W. De Jong, R. Veilleux, S. Jansky, P. Bethke, D. Douches, C.R. Buell. 2013. Retrospective View of North American Potato (Solanum tuberosum L.) Breeding in the 20th and 21st centuries. G3 Genes|Genomes|Genetics. 3(6):1003-1013.
Hirsch, C., C.R. Buell. 2013. Tapping the Promise of Genomics in Species with Complex, Nonmodel Genomes. Annual Review of Plant Biology. 64:89-110.
Jansen, C., N. de Leon, N. Lauter, C. Hirsch, L. Ruff, T. Lübberstedt. 2013. Genetic and Morphometric Analysis of Cob Architecture and Biomass-Related Traits in the Intermated B73 x Mo17 Recombinant Inbred Lines of Maize. BioEnergy Research. 6:903-916.
Sekhon, R., R. Briskine, C. Hirsch, C. Myers, N. Springer, C.R. Buell, N. de Leon, S. Kaeppler. 2013. Maize Gene Atlas Developed by RNA Sequencing and Comparative Evaluation of Transcriptomes Based on RNA Sequencing and Microarrays. PLoSOne. 8(4):e61005.
2012
Felcher, K., J. Coombs, A. Massa, C. Hansey, J. Hamilton, R. Veilleux, C.R. Buell, D. Douches. 2012. Integration of Two Diploid Potato Linkage Maps with the Potato Genome Sequence. PLoSOne. 7(4):e36347.
Hansey, C., B. Vaillancourt, R. Sekhon, N. de Leon, S. Kaeppler, C.R. Buell. 2012. Maize (Zea mays L.) Genome Diversity as Revealed by RNA-Sequencing. PLoSOne. 7(3):e33071.
Smith, A., C. Hansey, S. Kaeppler. 2012. TCUP: a novel hAT transposon active in maize tissue culture. Frontiers in Plant Science. 3:6.
2011
Davidson, R.**, C. Hansey**, M. Gowda, K. Childs, H. Lin, B. Vaillancourt, R. Sekhon, N. de Leon, S. Kaeppler, N. Jiang, C.R. Buell. 2011. Utility of RNA Sequencing for Analysis of Maize Reproductive Transcriptomes. The Plant Genome. 4(3):191-203. **These authors contributed equally to this work.
Hamilton, J., C. Hansey, B. Whitty, K. Stoffel, A. Massa, A. Van Deynze, W. De Jong, D. Douches, C.R. Buell. 2011. Single nucleotide polymorphism discovery in elite north american potato germplasm. BMC Genomics. 12:302.
Hansey, C., J. Johnson, R. Sekhon, S. Kaeppler, N. de Leon. 2011. Genetic Diversity of a Maize Association Population with Restricted Phenology. Crop Sci. 51:704-715.
Hansey, C. and N. de Leon. 2011. Biomass Yield and Cell Wall Composition of Corn with Alternative Morphologies Planted at Variable Densities. Crop Sci. 51:1005-1015.
Sekhon, R., H. Lin, K. Childs, C. Hansey, C.R. Buell, N. de Leon, S. Kaeppler. 2011. Genome-wide atlas of transcription through maize development. The Plant Journal. 66(4):553-563.
2010
Hansey, C., A. Lorenz and N. de Leon. 2010. Cell Wall Composition and Ruminant Digestibility of Various Maize Tissues Across Development. BioEnergy Research. 3(1):28-37.
Lorenz, A.J., G. Coors, C. Hansey, N. de Leon, and S.M. Kaeppler. 2010. Genetic Analysis of Cell Wall Traits Relevant to Cellulosic Ethanol Production in Maize (Zea mays L.). Crop Sci. 50:842-852.