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. 2019. Variation and inheritance of small RNAs in maize inbreds an F1 hybrids.

Li, Z., P. Zhou, R. Della Coletta, T. Zhang, A. Brohammer, B. Vaillancourt, A. Lipzen, C. Daum, K. Barry, N. de Leon, C.D. Hirsch, C.R. Buell, S. Kaeppler, N. Springer, C.N. Hirsch. 2019. Highly Genotype- and Tissue-specific Single Parent Expression Drives Dynamic Gene Expression Complementaion in Maize Hybrids. bioRxiv. 

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. 2019. Characterizing allele-by-environment interactions using maize introgression lines. bioRxiv.

Monnahan, P., J. Michno, C. O'Connor, A. Brohammer, N. Springer, S. McGaugh, C. Hirsch. 2019. Using multiple reference genomes to identify and resolve annotation inconsistencies.

Ou, S., W. Su, Y. Liao, K. Chougule, D. Ware, T. Peterson, N. Jiang**, C. Hirsch**, M. Hufford**. 2019. Benchmarking Transposable Element Annotation Methods for Creation of a Streamlined, Comprehensive Pipeline. bioRxiv. **co-corresponding authors


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. **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 multi-parent population for genetic mapping and allele discovery in six row barley. Genetics. DOI:10.1534/genetics.119.302046.

Holmes, M., P. Coaldrake, S. Kalambur, C. Schmitz, N. Anderson, G. Gusmini, G. Annor, C. Hirsch. 2019. Food grade corn 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. DOI:10.1371/journal.pgen.1008291.

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. Genes Genomes and Genetics. DOI:10.1534/g3.119.400347.

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. DOI:10.1002/pld3.130

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.


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. Genes Genomes and Genetics. 8(9):3049-3058.

Li, Z., L. Coffey, J. G arfin, 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. 11:170111.


Gage, J., D. Jarquin, M. 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.


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. 28:2700-2714.

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. 9:1-16

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.


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. Genes Genomes and Genetics. 5:1593-1602.

Hirsch, C.D., N. Springer, C.N. Hirsch. 2015. Genomic Limitations to RNAseq 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(1):e1004915.


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. Gongora-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:–.

Douches, D., C. Hirsch, N.Manrique-Carpintero, A. Massa, J. Coombs, M. Hardigan, D. Bisognin, W. De Jong, C.R. Buell. 2014. The Contributions 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: An Encyclopedic Reference: SpringerReference ( Springer-Verlag Berlin Heidelberg.

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, N. de Leon, S. Kaeppler, C.R. Buell. 2014.Insights into the Maize Pan-Genome and Pan-Transcriptome. The Plant Cell. 26:121-135.

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. Phenotypic and transcriptional analysis of divergently selected maize populations reveals the role of developmental timing in seed size determination. 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. 165:658-669.


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. 193:1073-1081.

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 20thand 21st centuries. Genes Genomes and Genetics. 3:1003-1013.

Hirsch, C., C.R. Buell. 2013. Tapping the promise of genomics in species with complex, non-model 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 B73xMo17 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 microarray.PLoSOne. 8(4):e61005.


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.


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-seq for Analysis of Maize Reproductive Transcriptomes. The Plant Genome. 4:191-203. **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. Plant Journal. 66(4):553-563.


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., N. de Leon, C. Hansey, J. Coors and S. Kaeppler. 2010. Genetic Analysis of Agronomic and Cell Wall Traits Relevant to Cellulosic Ethanol Production in Maize (Zea mays L.). Crop Sci. 50: 1-11.