Candice N Hirsch

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 40

Top Topics

Dna Methylation

Top Venues

The Plant journal : for cell and molecular biology

G3 (Bethesda, Md.)

This page only lists publications with an associated author ORCID identifier.

Publications

Shujun Ou, Ning Jiang, Candice N Hirsch, Matthew B Hufford
Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome biology 25 (1) (2024)
Shujun Ou, Ning Jiang, Candice N Hirsch, Matthew B Hufford
Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome biology 25 (1) (2024)
Shujun Ou, Ning Jiang, Candice N Hirsch, Matthew B Hufford
Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome biology 25 (1) (2024)
Shujun Ou, Ning Jiang, Candice N Hirsch, Matthew B Hufford
Response to Commentary: Accounting for diverse transposable element landscapes is key to developing and evaluating accurate de novo annotation strategies. Genome biology 25 (1) (2024)
Daniel R Kick, Mitchell Tuinstra, Osler A Ortez, Judith M Kolkman, Barış Alaca, Timothy M Beissinger, Jode W Edwards, Maria Cinta Romay, Sherry A Flint-Garcia, Joseph L Gage, Candice N Hirsch, Joseph E Knoll, Natalia de Leon, Dayane Cristina Lima, Danilo E Moreta, Rajandeep S Sekhon, Addie M Thompson, Teclemariam Weldekidan, Jacob D Washburn
Yield Prediction Through Integration of Genetic, Environment, and Management Data Through Deep Learning. G3 (Bethesda, Md.) (2023)
Dylan L Schoemaker, Yinjie Qiu, Natalia de Leon, Candice N Hirsch, Shawn M Kaeppler
Genetic analysis of pericarp pigmentation variation in Corn Belt dent maize. G3 (Bethesda, Md.) (2023)
Manisha Munasinghe, Andrew Read, Michelle C Stitzer, Baoxing Song, Claire C Menard, Kristy Yubo Ma, Yaniv Brandvain, Candice N Hirsch, Nathan Springer
Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. PLoS genetics 19 (12) (2023)
Dayane Cristina Lima, Alejandro Castro Aviles, Ryan Timothy Alpers, Alden C Perkins, Dylan L Schoemaker, Martin Costa, Kathryn J Michel, Shawn M Kaeppler, Maria Cinta Romay, Maria Cinta Romay, Joseph L Gage, James B Holland, Timothy M Beissinger, Martin O Bohn, Edward S Buckler, Jode W Edwards, Sherry A Flint-Garcia, Michael A Gore, Candice N Hirsch, Joseph E Knoll, John K McKay, Richard Minyo, Richard Minyo, Osler A Ortez, Rajandeep S Sekhon, Rajandeep S Sekhon, Maninder P Singh, Peter Thomison, Addie M Thompson, Mitchell R Tuinstra, Mitchell Tuinstra, Jacob D Washburn, Teclemariam Weldekidan, Wenwei Xu, Natalia de Leon
2020-2021 field seasons of Maize GxE project within the Genomes to Fields Initiative. BMC research notes 16 (1) (2023)
Manisha Munasinghe, Andrew Read, Michelle C Stitzer, Baoxing Song, Claire C Menard, Kristy Yubo Ma, Yaniv Brandvain, Candice N Hirsch, Nathan Springer
Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. PLoS genetics 19 (12) (2023)
Rafael Della Coletta, Samuel B Fernandes, Patrick J Monnahan, Mark A Mikel, Martin O Bohn, Alexander E Lipka, Candice N Hirsch
Importance of genetic architecture in marker selection decisions for genomic prediction. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 136 (11) (2023)
Dayane Cristina Lima, Jacob D Washburn, José Ignacio Varela, Qiuyue Chen, Joseph L Gage, Maria Cinta Romay, James B Holland, Maria Cinta Romay, Marco Lopez-Cruz, Fernando M Aguate, Gustavo de Los Campos, Shawn M Kaeppler, Timothy M Beissinger, Martin O Bohn, Edward S Buckler, Jode W Edwards, Sherry A Flint-Garcia, Michael A Gore, Candice N Hirsch, Joseph E Knoll, John K McKay, Richard Minyo, Seth C Murray, Osler A Ortez, Rajandeep S Sekhon, Rajandeep S Sekhon, Maninder P Singh, Addie M Thompson, Mitchell R Tuinstra, Mitchell Tuinstra, Teclemariam Weldekidan, Teclemariam Weldekidan, Natalia de Leon, Natalia de Leon
Genomes to Fields 2022 Maize genotype by Environment Prediction Competition. BMC research notes 16 (1) (2023)
Manisha Munasinghe, Andrew Read, Michelle C Stitzer, Baoxing Song, Claire C Menard, Kristy Yubo Ma, Yaniv Brandvain, Candice N Hirsch, Nathan Springer
Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. PLoS genetics 19 (12) (2023)
Rafael Della Coletta, Sharon E Liese, Samuel B Fernandes, Mark A Mikel, Martin O Bohn, Alexander E Lipka, Candice N Hirsch
Linking genetic and environmental factors through marker effect networks to understand trait plasticity. Genetics (2023)
Dayane Cristina Lima, Alejandro Castro Aviles, Ryan Timothy Alpers, Bridget A McFarland, Shawn M Kaeppler, Maria Cinta Romay, Maria Cinta Romay, Joseph L Gage, James B Holland, Timothy Beissinger, Martin Bohn, Edward Buckler, Jode W Edwards, Sherry A Flint-Garcia, Candice N Hirsch, Elizabeth E Hood, David C Hooker, Joseph E Knoll, Judith M Kolkman, Sanzhen Liu, John K McKay, Richard Minyo, Danilo E Moreta, Richard Minyo, Rebecca Nelson, Osler A Ortez, Rajandeep S Sekhon, Rajandeep S Sekhon, Peter Thomison, Addie M Thompson, Mitchell R Tuinstra, Mitchell Tuinstra, Jacob D Washburn, Teclemariam Weldekidan, Randall J Wisser, Wenwei Xu, Natalia de Leon
2018-2019 field seasons of the Maize Genomes to Fields (G2F) G x E project. BMC genomic data 24 (1) (2023)
Manisha Munasinghe, Andrew Read, Michelle C Stitzer, Baoxing Song, Claire C Menard, Kristy Yubo Ma, Yaniv Brandvain, Candice N Hirsch, Nathan Springer
Combined analysis of transposable elements and structural variation in maize genomes reveals genome contraction outpaces expansion. PLoS genetics 19 (12) (2023)
Erika L Ellison, Peng Zhou, Peter Hermanson, Yi-Hsuan Chu, Andrew Read, Candice N Hirsch, Erich Grotewold, Springer M Nathan
Mutator transposon insertions within maize genes often provide a novel outward reading promoter. Genetics (2023)
Andrew Read, Trevor Weiss, Peter A Crisp, Zhikai Liang, Jaclyn M Noshay, Claire C Menard, Chunfang Wang, Meredith Song, Candice N Hirsch, Springer M Nathan, Feng Zhang
Genome-wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants. The Plant journal : for cell and molecular biology 111 (1) (2022)
Jaclyn M Noshay, Zhikai Liang, Peng Zhou, Peter A Crisp, Alexandre P Marand, Candice N Hirsch, Robert J Schmitz, Springer M Nathan
Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes. G3 (Bethesda, Md.) 11 (8) (2022)
Jonathan S Renk, Amanda M Gilbert, Travis J Hattery, Christine H O'Connor, Patrick J Monnahan, Nickolas Anderson, Amanda J Waters, David P Eickholt, Sherry A Flint-Garcia, Marna D Yandeau-Nelson, Candice N Hirsch
Genetic control of kernel compositional variation in a maize diversity panel. The plant genome 14 (3) (2021)
Matthew B Hufford, Arun S Seetharam, Margaret R Woodhouse, Kapeel M Chougule, Shujun Ou, Jianing Liu, William A Ricci, Tingting Guo, Andrew Olson, Yinjie Qiu, Rafael Della Coletta, Silas B Tittes, Asher I Hudson, Alexandre P Marand, Sharon Wei, Zhenyuan Lu, Bo Wang, Marcela Karey Tello-Ruiz, Rebecca D Piri, Na Wang, Dong Won Kim, Yibing Zeng, Christine H O'Connor, Xianran Li, Amanda M Gilbert, Erin L Baggs, Ksenia V Krasileva, John L Portwood, Ethalinda K S Cannon, Carson M Andorf, Nancy Manchanda, Samantha J Snodgrass, David E Hufnagel, Qiuhan Jiang, Sarah Pedersen, Michael L Syring, David A Kudrna, Victor Llaca, Kevin Fengler, Robert J Schmitz, Jeffrey Ross-Ibarra, Jianming Yu, Jonathan I Gent, Candice N Hirsch, Doreen H Ware, R Kelly Dawe
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Science (New York, N.Y.) 373 (6555) (2021)
Nolan Bornowski, Kathryn J Michel, John P Hamilton, Shujun Ou, Arun S Seetharam, Jerry Jenkins, Jane Grimwood, Chris Plott, Shengqiang Shu, Jayson Talag, Megan Kennedy, Hope Hundley, Vasanth R Singan, Kerrie Barry, Chris Daum, Yuko Yoshinaga, Jeremy Schmutz, Candice N Hirsch, Matthew B Hufford, Natalia de Leon, Shawn M Kaeppler, Carol Robin Buell
Genomic variation within the maize stiff-stalk heterotic germplasm pool. The plant genome 14 (3) (2021)
Rafael Della Coletta, Yinjie Qiu, Shujun Ou, Matthew B Hufford, Candice N Hirsch
How the pan-genome is changing crop genomics and improvement. Genome biology 22 (1) (2021)
Michael J Burns, Jonathan S Renk, David P Eickholt, Amanda M Gilbert, Travis J Hattery, Mark Holmes, Nickolas Anderson, Amanda J Waters, Sathya Kalambur, Sherry A Flint-Garcia, Marna D Yandeau-Nelson, George A Annor, Candice N Hirsch
Predicting moisture content during maize nixtamalization using machine learning with NIR spectroscopy. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 134 (11) (2021)
Matthew Haas, Thomas J Y Kono, Marissa G Macchietto, Reneth Millas, Lillian McGilp, Mingqin Shao, Jacques Duquette, Yinjie Qiu, Candice N Hirsch, Jennifer Kimball
Whole-genome assembly and annotation of northern wild rice, Zizania palustris L., supports a whole-genome duplication in the Zizania genus. The Plant journal : for cell and molecular biology 107 (6) (2021)
Yinjie Qiu, Christine H O'Connor, Rafael Della Coletta, Jonathan S Renk, Patrick J Monnahan, Jaclyn M Noshay, Zhikai Liang, Amanda Gilbert, Sarah N Anderson, Suzanne E McGaugh, Springer M Nathan, Candice N Hirsch
Whole-genome variation of transposable element insertions in a maize diversity panel. G3 (Bethesda, Md.) 11 (10) (2021)
Shujun Ou, Jianing Liu, Kapeel M Chougule, Arkarachai Fungtammasan, Arun S Seetharam, Joshua C Stein, Victor Llaca, Nancy Manchanda, Amanda M Gilbert, Sharon Wei, Chen-Shan Chin, David E Hufnagel, Sarah Pedersen, Samantha J Snodgrass, Kevin Fengler, Margaret R Woodhouse, Brian P Walenz, Sergey Koren, Adam M Phillippy, Brett T Hannigan, R Kelly Dawe, Candice N Hirsch, Matthew B Hufford, Doreen H Ware
Effect of sequence depth and length in long-read assembly of the maize inbred NC358. Nature communications 11 (1) (2020)
Peng Zhou, Zhi Li, Erika L Ellison, Fabio Gomez Cano, Peter A Crisp, Jaclyn M Noshay, Erich Grotewold, Candice N Hirsch, Steven P Briggs, Springer M Nathan
Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions. The Plant cell 32 (5) (2020)
Sara B Tirado, Candice N Hirsch, Springer M Nathan
UAV-based imaging platform for monitoring maize growth throughout development. Plant direct 4 (6) (2020)
Zhi Li, Peng Zhou, Rafael Della Coletta, Tifu Zhang, Alex B Brohammer, Christine H O'Connor, Brieanne Vaillancourt, Anna Lipzen, Chris Daum, Kerrie Barry, Natalia de Leon, Cory D Hirsch, Carol Robin Buell, Shawn M Kaeppler, Springer M Nathan, Candice N Hirsch
Single-parent expression drives dynamic gene expression complementation in maize hybrids. The Plant journal : for cell and molecular biology 105 (1) (2020)
Zhi Li, Sara B Tirado, Dnyaneshwar C Kadam, Lisa Coffey, Nathan D Miller, Edgar P Spalding, Aaron J Lorenz, Natalia de Leon, Shawn M Kaeppler, Patrick S Schnable, Nathan M Springer, Candice N Hirsch
Characterizing introgression-by-environment interactions using maize near isogenic lines. TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik 133 (10) (2020)
Patrick J Monnahan, Jean-Michel Michno, Christine O'Connor, Alex B Brohammer, Nathan M Springer, Suzanne E McGaugh, Candice N Hirsch
Using multiple reference genomes to identify and resolve annotation inconsistencies. BMC genomics 21 (1) (2020)
Peter A Crisp, Reza K Hammond, Peng Zhou, Brieanne Vaillancourt, Anna Lipzen, Chris Daum, Kerrie W Barry, Natalia de Leon, Carol Robin Buell, Shawn M Kaeppler, Blake C Meyers, Candice N Hirsch, Springer M Nathan
Variation and Inheritance of Small RNAs in Maize Inbreds and F1 Hybrids. Plant physiology 182 (1) (2019)
Jaclyn M Noshay, Sarah N Anderson, Peng Zhou, Lexiang Ji, William Ricci, Zefu Lu, Michelle C Stitzer, Peter A Crisp, Candice N Hirsch, Xiaoyu Zhang, Robert J Schmitz, Springer M Nathan
Monitoring the interplay between transposable element families and DNA methylation in maize. PLoS genetics 15 (9) (2019)
Alex Hemshrot, Ana M Poets, Priyanka Tyagi, Li Lei, Corey K Carter, Candice N Hirsch, Lin Li, Gina Brown-Guedira, Peter Laurent Morrell, Gary J Muehlbauer, Kevin P Smith
Development of a Multiparent Population for Genetic Mapping and Allele Discovery in Six-Row Barley. Genetics 213 (2) (2019)
Xia Zhang, Karl J Haro von Mogel, Vai S Lor, Candice N Hirsch, Brian De Vries, Heidi F Kaeppler, William F Tracy, Shawn M Kaeppler
Maize sugary enhancer1 (se1) is a gene affecting endosperm starch metabolism. Proceedings of the National Academy of Sciences of the United States of America 116 (41) (2019)
Sarah N Anderson, Michelle C Stitzer, Alex B Brohammer, Peng Zhou, Jaclyn M Noshay, Christine H O'Connor, Cory D Hirsch, Jeffrey Ross-Ibarra, Candice N Hirsch, Springer M Nathan
Transposable elements contribute to dynamic genome content in maize. The Plant journal : for cell and molecular biology 100 (5) (2019)
Thomas J Y Kono, Alex B Brohammer, Suzanne E McGaugh, Candice N Hirsch
Tandem Duplicate Genes in Maize Are Abundant and Date to Two Distinct Periods of Time. G3 (Bethesda, Md.) 8 (9) (2018)
Zhi Li, Lisa Coffey, Jacob Garfin, Nathan D Miller, Michael R White, Edgar P Spalding, Natalia de Leon, Shawn M Kaeppler, Patrick S Schnable, Nathan M Springer, Candice N Hirsch
Genotype-by-environment interactions affecting heterosis in maize. PloS one 13 (1) (2018)
Alex B Brohammer, Thomas J Y Kono, Springer M Nathan, Suzanne E McGaugh, Candice N Hirsch
The limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines. The Plant journal : for cell and molecular biology 93 (1) (2017)
Candice N Hirsch, Cory D Hirsch, Alex B Brohammer, Megan J Bowman, Ilya Soifer, Omer Barad, Doron Shem-Tov, Kobi Baruch, Fei Lu, Alvaro G Hernandez, Christopher J Fields, Chris L Wright, Klaus Koehler, Springer M Nathan, Edward S Buckler, C Robin Buell, Natalia de Leon, Shawn M Kaeppler, Kevin L Childs, Mark A Mikel
Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize. The Plant cell 28 (11) (2016)