Publications

2017

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. (in press).

Brohammer, A., T. Kono, N. Springer, S. McGaugh, C. Hirsch. 2017. Limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines. bioRxiv doi:10.1101/179119.

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. bioRxiv doi:10.1101/131342. 

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. 28:2700-2714.

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.

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. 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.

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. 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 (www.springerreference.com). 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.

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. 193:1073-1081.

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.

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-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.

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., 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.