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Candice N. Hirsch
Researcher at University of Minnesota
Publications - 104
Citations - 4592
Candice N. Hirsch is an academic researcher from University of Minnesota. The author has contributed to research in topics: Genome & Gene. The author has an hindex of 27, co-authored 90 publications receiving 3087 citations. Previous affiliations of Candice N. Hirsch include Great Lakes Bioenergy Research Center & Agricultural Research Service.
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Journal ArticleDOI
Insights into the Maize Pan-Genome and Pan-Transcriptome
Candice N. Hirsch,Candice N. Hirsch,Jillian M. Foerster,James M. Johnson,Rajandeep S. Sekhon,Rajandeep S. Sekhon,German Muttoni,Brieanne Vaillancourt,Brieanne Vaillancourt,Francisco Peñagaricano,Erika Lindquist,Mary Ann Pedraza,Kerrie Barry,Natalia de Leon,Natalia de Leon,Shawn M. Kaeppler,Shawn M. Kaeppler,C. Robin Buell,C. Robin Buell +18 more
TL;DR: The dynamic nature of the maize pan-genome was revealed and it was demonstrated that a substantial portion of variation may lie outside the single reference genome for a species.
Journal ArticleDOI
Benchmarking transposable element annotation methods for creation of a streamlined, comprehensive pipeline
Shujun Ou,Weija Su,Yi Liao,Kapeel Chougule,Jireh Agda,Adam J. Hellinga,Carlos Santiago Blanco Lugo,Tyler A. Elliott,Doreen Ware,Doreen Ware,Thomas Peterson,Ning Jiang,Candice N. Hirsch,Matthew B. Hufford +13 more
TL;DR: A comprehensive pipeline called Extensive de-novo TE Annotator (EDTA) is created that produces a filtered non-redundant TE library for annotation of structurally intact and fragmented elements and will greatly facilitate TE annotation in eukaryotic genomes.
Journal ArticleDOI
Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress
Irina Makarevitch,Amanda J. Waters,Patrick T. West,Michelle C. Stitzer,Candice N. Hirsch,Jeffrey Ross-Ibarra,Nathan M. Springer +6 more
TL;DR: It is suggested that TEs provide an important source of allelic regulatory variation in gene response to abiotic stress in maize and may provide local enhancer activities that stimulate stress-responsive gene expression.
Journal ArticleDOI
An Expanded Maize Gene Expression Atlas based on RNA Sequencing and its Use to Explore Root Development
Scott C. Stelpflug,Rajandeep S. Sekhon,Brieanne Vaillancourt,Candice N. Hirsch,C. Robin Buell,Natalia de Leon,Shawn M. Kaeppler +6 more
TL;DR: This comprehensive transcriptome dataset is a powerful tool toward understanding maize development, physiology, and phenotypic diversity.
Journal ArticleDOI
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes
Matthew B. Hufford,Arun S. Seetharam,Margaret R. Woodhouse,Kapeel Chougule,Shujun Ou,Jianing Liu,William A. Ricci,Tingting Guo,Andrew Olson,Yinjie Qiu,Rafael Della Coletta,Silas Tittes,Asher I. Hudson,Alexandre P. Marand,Sharon Wei,Zhenyuan Lu,Bo Wang,Marcela K. Tello-Ruiz,Rebecca D. Piri,Na Wang,Dong Won Kim,Yibing Zeng,Christine H. O’Connor,Xianran Li,Amanda M. Gilbert,Erin Baggs,Ksenia V. Krasileva,John L. Portwood,Ethalinda K. S. Cannon,Carson M. Andorf,Nancy Manchanda,Samantha J. Snodgrass,David E. Hufnagel,David E. Hufnagel,Qiuhan Jiang,Sarah Pedersen,Michael Syring,David Kudrna,Victor Llaca,Kevin Fengler,Robert J. Schmitz,Jeffrey Ross-Ibarra,Jianming Yu,Jonathan I. Gent,Candice N. Hirsch,Doreen Ware,Doreen Ware,R. Kelly Dawe +47 more
TL;DR: In this article, de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population were reported.