Monitoring the interplay between transposable element families and DNA methylation in maize
Noshay, Jaclyn M, Anderson, Sarah N, Zhou, Peng, Ji, Lexiang, Ricci, William, Lu, Zefu, Stitzer, Michelle C, Crisp, Peter A, Hirsch, Candice N, Zhang, Xiaoyu, Schmitz, Robert J, Springer, Nathan M
Published in PLoS genetics (09.09.2019)
Published in PLoS genetics (09.09.2019)
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Journal Article
Stable unmethylated DNA demarcates expressed genes and their cis-regulatory space in plant genomes
Crisp, Peter A., Marand, Alexandre P., Noshay, Jaclyn M., Zhou, Peng, Lu, Zefu, Schmitz, Robert J., Springer, Nathan M.
Published in Proceedings of the National Academy of Sciences - PNAS (22.09.2020)
Published in Proceedings of the National Academy of Sciences - PNAS (22.09.2020)
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Journal Article
Quantum biological insights into CRISPR-Cas9 sgRNA efficiency from explainable-AI driven feature engineering
Noshay, Jaclyn M, Walker, Tyler, Alexander, William G, Klingeman, Dawn M, Romero, Jonathon, Walker, Angelica M, Prates, Erica, Eckert, Carrie, Irle, Stephan, Kainer, David, Jacobson, Daniel A
Published in Nucleic acids research (27.10.2023)
Published in Nucleic acids research (27.10.2023)
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Journal Article
Prediction of conserved and variable heat and cold stress response in maize using cis-regulatory information
Zhou, Peng, Enders, Tara A, Myers, Zachary A, Magnusson, Erika, Crisp, Peter A, Noshay, Jaclyn M, Gomez-Cano, Fabio, Liang, Zhikai, Grotewold, Erich, Greenham, Kathleen, Springer, Nathan M
Published in The Plant cell (20.01.2022)
Published in The Plant cell (20.01.2022)
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Journal Article
Transposable elements contribute to dynamic genome content in maize
Anderson, Sarah N., Stitzer, Michelle C., Brohammer, Alex B., Zhou, Peng, Noshay, Jaclyn M., O'Connor, Christine H., Hirsch, Cory D., Ross‐Ibarra, Jeffrey, Hirsch, Candice N., Springer, Nathan M.
Published in The Plant journal : for cell and molecular biology (01.12.2019)
Published in The Plant journal : for cell and molecular biology (01.12.2019)
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Journal Article
Meta Gene Regulatory Networks in Maize Highlight Functionally Relevant Regulatory Interactions[OPEN]
Zhou, Peng, Li, Zhi, Magnusson, Erika, Gomez Cano, Fabio, Crisp, Peter A., Noshay, Jaclyn M., Grotewold, Erich, Hirsch, Candice N., Briggs, Steven P., Springer, Nathan M.
Published in The Plant cell (01.05.2020)
Published in The Plant cell (01.05.2020)
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Journal Article
Widespread long-range cis-regulatory elements in the maize genome
Ricci, William A., Lu, Zefu, Ji, Lexiang, Marand, Alexandre P., Ethridge, Christina L., Murphy, Nathalie G., Noshay, Jaclyn M., Galli, Mary, Mejía-Guerra, María Katherine, Colomé-Tatché, Maria, Johannes, Frank, Rowley, M. Jordan, Corces, Victor G., Zhai, Jixian, Scanlon, Michael J., Buckler, Edward S., Gallavotti, Andrea, Springer, Nathan M., Schmitz, Robert J., Zhang, Xiaoyu
Published in Nature plants (01.12.2019)
Published in Nature plants (01.12.2019)
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Journal Article
Natural variation for gene expression responses to abiotic stress in maize
Waters, Amanda J., Makarevitch, Irina, Noshay, Jaclyn, Burghardt, Liana T., Hirsch, Candice N., Hirsch, Cory D., Springer, Nathan M.
Published in The Plant journal : for cell and molecular biology (01.02.2017)
Published in The Plant journal : for cell and molecular biology (01.02.2017)
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Journal Article
The maize W22 genome provides a foundation for functional genomics and transposon biology
Springer, Nathan M., Anderson, Sarah N., Andorf, Carson M., Ahern, Kevin R., Bai, Fang, Barad, Omer, Barbazuk, W. Brad, Bass, Hank W., Baruch, Kobi, Ben-Zvi, Gil, Buckler, Edward S., Bukowski, Robert, Campbell, Michael S., Cannon, Ethalinda K. S., Chomet, Paul, Dawe, R. Kelly, Davenport, Ruth, Dooner, Hugo K., Du, Limei He, Du, Chunguang, Easterling, Katherine A., Gault, Christine, Guan, Jiahn-Chou, Hunter, Charles T., Jander, Georg, Jiao, Yinping, Koch, Karen E., Kol, Guy, Köllner, Tobias G., Kudo, Toru, Li, Qing, Lu, Fei, Mayfield-Jones, Dustin, Mei, Wenbin, McCarty, Donald R., Noshay, Jaclyn M., Portwood, John L., Ronen, Gil, Settles, A. Mark, Shem-Tov, Doron, Shi, Jinghua, Soifer, Ilya, Stein, Joshua C., Stitzer, Michelle C., Suzuki, Masaharu, Vera, Daniel L., Vollbrecht, Erik, Vrebalov, Julia T., Ware, Doreen, Wei, Sharon, Wimalanathan, Kokulapalan, Woodhouse, Margaret R., Xiong, Wenwei, Brutnell, Thomas P.
Published in Nature genetics (01.09.2018)
Published in Nature genetics (01.09.2018)
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Journal Article
Assessing the regulatory potential of transposable elements using chromatin accessibility profiles of maize transposons
Noshay, Jaclyn M, Marand, Alexandre P, Anderson, Sarah N, Zhou, Peng, Mejia Guerra, Maria Katherine, Lu, Zefu, O’Connor, Christine H, Crisp, Peter A, Hirsch, Candice N, Schmitz, Robert J, Springer, Nathan M
Published in Genetics (Austin) (03.03.2021)
Published in Genetics (Austin) (03.03.2021)
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Journal Article
A capture-based assay for detection and characterization of transposon polymorphisms in maize
Li, Minqi, Noshay, Jaclyn M, Dong, Xiaoxiao, Springer, Nathan M, Li, Qing
Published in G3 : genes - genomes - genetics (01.07.2021)
Published in G3 : genes - genomes - genetics (01.07.2021)
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Journal Article
Opportunities to Use DNA Methylation to Distil Functional Elements in Large Crop Genomes
Crisp, Peter A., Noshay, Jaclyn M., Anderson, Sarah N., Springer, Nathan M.
Published in Molecular plant (04.03.2019)
Published in Molecular plant (04.03.2019)
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Journal Article
Whole-genome variation of transposable element insertions in a maize diversity panel
Qiu, Yinjie, O'Connor, Christine H, Della Coletta, Rafael, Renk, Jonathan S, Monnahan, Patrick J, Noshay, Jaclyn M, Liang, Zhikai, Gilbert, Amanda, Anderson, Sarah N, McGaugh, Suzanne E, Springer, Nathan M, Hirsch, Candice N
Published in G3 : genes - genomes - genetics (01.10.2021)
Published in G3 : genes - genomes - genetics (01.10.2021)
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Journal Article
Stability of DNA methylation and chromatin accessibility in structurally diverse maize genomes
Noshay, Jaclyn M, Liang, Zhikai, Zhou, Peng, Crisp, Peter A, Marand, Alexandre P, Hirsch, Candice N, Schmitz, Robert J, Springer, Nathan M
Published in G3 : genes - genomes - genetics (07.08.2021)
Published in G3 : genes - genomes - genetics (07.08.2021)
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Journal Article
Author Correction: Widespread long-range cis-regulatory elements in the maize genome
Ricci, William A., Lu, Zefu, Ji, Lexiang, Marand, Alexandre P., Ethridge, Christina L., Murphy, Nathalie G., Noshay, Jaclyn M., Galli, Mary, Mejía-Guerra, María Katherine, Colomé-Tatché, Maria, Johannes, Frank, Rowley, M. Jordan, Corces, Victor G., Zhai, Jixian, Scanlon, Michael J., Buckler, Edward S., Gallavotti, Andrea, Springer, Nathan M., Schmitz, Robert J., Zhang, Xiaoyu
Published in Nature plants (01.03.2020)
Published in Nature plants (01.03.2020)
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Journal Article
Identification of the expressome by machine learning on omics data
Sartor, Ryan C., Noshay, Jaclyn, Springer, Nathan M., Briggs, Steven P.
Published in Proceedings of the National Academy of Sciences - PNAS (03.09.2019)
Published in Proceedings of the National Academy of Sciences - PNAS (03.09.2019)
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Journal Article
Genome‐wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE (DRM) mutants
Read, Andrew, Weiss, Trevor, Crisp, Peter A., Liang, Zhikai, Noshay, Jaclyn, Menard, Claire C., Wang, Chunfang, Song, Meredith, Hirsch, Candice N., Springer, Nathan M., Zhang, Feng
Published in The Plant journal : for cell and molecular biology (01.07.2022)
Published in The Plant journal : for cell and molecular biology (01.07.2022)
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Journal Article
Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize
Xue, Wei, Anderson, Sarah N, Wang, Xufeng, Yang, Liyan, Crisp, Peter A, Li, Qing, Noshay, Jaclyn, Albert, Patrice S, Birchler, James A, Bilinski, Paul, Stitzer, Michelle C, Ross-Ibarra, Jeffrey, Flint-Garcia, Sherry, Chen, Xuemei, Springer, Nathan M, Doebley, John F
Published in Genetics (Austin) (01.09.2019)
Published in Genetics (Austin) (01.09.2019)
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Journal Article