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Research Output

2020

Author Correction: Widespread long-range cis-regulatory elements in the maize genome (Nature Plants, (2019), 5, 12, (1237-1249), 10.1038/s41477-019-0547-0)

Ricci, W. A., Lu, Z., Ji, L., Marand, A. P., Ethridge, C. L., Murphy, N. G., Noshay, J. M., Galli, M., Mejía-Guerra, M. K., Colomé-Tatché, M., Johannes, F., Rowley, M. J., Corces, V. G., Zhai, J., Scanlon, M. J., Buckler, E. S., Gallavotti, A., Springer, N. M., Schmitz, R. J. & Zhang, X., Mar 1 2020, In : Nature plants. 6, 3, 1 p.

Research output: Contribution to journalComment/debate

Open Access

Variation and Inheritance of Small RNAs in Maize Inbreds and F1 Hybrids

Crisp, P. A., Hammond, R., Zhou, P., Vaillancourt, B., Lipzen, A., Daum, C., Barry, K., de Leon, N., Buell, C. R., Kaeppler, S. M., Meyers, B. C., Hirsch, C. N. & Springer, N. M., Jan 1 2020, In : Plant physiology. 182, 1, p. 318-331 14 p.

Research output: Contribution to journalArticle

Open Access
2019

Challenges of Translating Gene Regulatory Information into Agronomic Improvements

Springer, N., de León, N. & Grotewold, E., Dec 2019, In : Trends in Plant Science. 24, 12, p. 1075-1082 8 p.

Research output: Contribution to journalReview article

Classifying cold-stress responses of inbred maize seedlings using RGB imaging

Enders, T. A., St. Dennis, S., Oakland, J., Callen, S. T., Gehan, M. A., Miller, N. D., Spalding, E. P., Springer, N. M. & Hirsch, C. D., Jan 2019, In : Plant Direct. 3, 1, e00104.

Research output: Contribution to journalArticle

Open Access

Correction: Genotype-by-environment interactions affecting heterosis in maize (PLoS ONE (2018) 13:1 (e0191321) DOI: 10.1371/journal.pone)

Li, Z., Coffey, L., Garfin, J., Miller, N. D., White, M. R., Spalding, E. P., de Leon, N., Kaeppler, S. M., Schnable, P. S., Springer, N. M. & Hirsch, C. N., Jan 1 2019, In : PloS one. 14, 8, e0219528.

Research output: Contribution to journalComment/debate

Open Access

Dynamic Patterns of Gene Expression Additivity and Regulatory Variation throughout Maize Development

Zhou, P., Hirsch, C. N., Briggs, S. P. & Springer, N. M., Mar 4 2019, In : Molecular Plant. 12, 3, p. 410-425 16 p.

Research output: Contribution to journalArticle

Open Access
3 Scopus citations

Dynamic patterns of transcript abundance of transposable element families in maize

Anderson, S. N., Stitzer, M. C., Zhou, P., Ross-Ibarra, J., Hirsch, C. D. & Springer, N. M., Nov 1 2019, In : G3: Genes, Genomes, Genetics. 9, 11, p. 3673-3682 10 p.

Research output: Contribution to journalArticle

Open Access

Genome-wide nucleotide patterns and potential mechanisms of genome divergence following domestication in maize and soybean

Wang, J., Li, X., Do Kim, K., Scanlon, M. J., Jackson, S. A., Springer, N. M. & Yu, J., Apr 25 2019, In : Genome biology. 20, 1, 74.

Research output: Contribution to journalArticle

Open Access

Hybrid decay: A transgenerational epigenetic decline in vigor and viability triggered in backcross populations of teosinte with maize

Xue, W., Anderson, S. N., Wang, X., Yang, L., Crisp, P. A., Li, Q., Noshay, J., Albert, P. S., Birchler, J. A., Bilinski, P., Stitzer, M. C., Ross-Ibarra, J., Flint-Garcia, S., Chen, X., Springer, N. M. & Doebley, J. F., Jan 1 2019, In : Genetics. 213, 1, p. 143-160 18 p.

Research output: Contribution to journalArticle

Open Access

Idea factory: The maize genomes to fields initiative

Lawrence-Dill, C. J., Schnable, P. S. & Springer, N. M., Jul 1 2019, In : Crop Science. 59, 4, p. 1406-1410 5 p.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Identification of the expressome by machine learning on omics data

Sartor, R. C., Noshay, J., Springer, N. M. & Briggs, S. P., Sep 3 2019, In : Proceedings of the National Academy of Sciences of the United States of America. 116, 36, p. 18119-18125 7 p.

Research output: Contribution to journalArticle

Open Access

Maize Carbohydrate Partitioning Defective33 Encodes an MCTP Protein and Functions in Sucrose Export from Leaves

Tran, T. M., McCubbin, T. J., Bihmidine, S., Julius, B. T., Baker, R. F., Schauflinger, M., Weil, C., Springer, N., Chomet, P., Wagner, R., Woessner, J., Grote, K., Peevers, J., Slewinski, T. L. & Braun, D. M., Sep 2 2019, In : Molecular Plant. 12, 9, p. 1278-1293 16 p.

Research output: Contribution to journalArticle

2 Scopus citations

Monitoring the interplay between transposable element families and DNA methylation in maize

Noshay, J. M., Anderson, S. N., Zhou, P., Ji, L., Ricci, W., Lu, Z., Stitzer, M. C., Crisp, P. A., Hirsch, C. N., Zhang, X., Schmitz, R. J. & Springer, N. M., Jan 1 2019, In : PLoS genetics. 15, 9, e1008291.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Opportunities to Use DNA Methylation to Distil Functional Elements in Large Crop Genomes

Crisp, P. A., Noshay, J. M., Anderson, S. N. & Springer, N. M., Mar 4 2019, In : Molecular Plant. 12, 3, p. 282-284 3 p.

Research output: Contribution to journalComment/debate

Open Access
1 Scopus citations

Population-level analysis reveals the widespread occurrence and phenotypic consequence of DNA methylation variation not tagged by genetic variation in maize

Xu, J., Chen, G., Hermanson, P. J., Xu, Q., Sun, C., Chen, W., Kan, Q., Li, M., Crisp, P. A., Yan, J., Li, L., Springer, N. M. & Li, Q., Nov 19 2019, In : Genome biology. 20, 1, 243.

Research output: Contribution to journalArticle

Open Access
1 Scopus citations

Transposable elements contribute to dynamic genome content in maize

Anderson, S. N., Stitzer, M. C., Brohammer, A. B., Zhou, P., Noshay, J. M., O'Connor, C. H., Hirsch, C. D., Ross-Ibarra, J., Hirsch, C. N. & Springer, N. M., Dec 1 2019, In : Plant Journal. 100, 5, p. 1052-1065 14 p.

Research output: Contribution to journalArticle

4 Scopus citations

Widespread long-range cis-regulatory elements in the maize genome

Ricci, W. A., Lu, Z., Ji, L., Marand, A. P., Ethridge, C. L., Murphy, N. G., Noshay, J. M., Galli, M., Mejía-Guerra, M. K., Colomé-Tatché, M., Johannes, F., Rowley, M. J., Corces, V. G., Zhai, J., Scanlon, M. J., Buckler, E. S., Gallavotti, A., Springer, N. M., Schmitz, R. J. & Zhang, X., Dec 1 2019, In : Nature plants. 5, 12, p. 1237-1249 13 p.

Research output: Contribution to journalArticle

5 Scopus citations
2018

Correction: Genome-wide discovery and characterization of maize long non-coding RNAs [Genome Biol., 15, (2014) (R40)] DOI: 10.1186/gb-2014-15-2-r40

Li, L., Eichten, S. R., Shimizu, R., Petsch, K., Yeh, C. T., Wu, W., Chettoor, A. M., Givan, S. A., Cole, R. A., Fowler, J. E., Evans, M. M. S., Scanlon, M. J., Yu, J., Schnable, P. S., Timmermans, M. C. P., Springer, N. M. & Muehlbauer, G. J., Aug 23 2018, In : Genome biology. 19, 1, 122.

Research output: Contribution to journalComment/debate

Detection of DNA methylation by whole-genome bisulfite sequencing

Li, Q., Hermanson, P. J. & Springer, N. M., Jan 1 2018, Methods in Molecular Biology. Humana Press Inc., p. 185-196 12 p. (Methods in Molecular Biology; vol. 1676).

Research output: Chapter in Book/Report/Conference proceedingChapter

5 Scopus citations

Erratum: Correction: Mendelian and Non-Mendelian Regulation of Gene Expression in Maize (PLoS genetics (2013) 9 1 (e1003202))

Li, L., Petsch, K., Shimizu, R., Liu, S., Xu, W. W., Ying, K., Yu, J., Scanlon, M. J., Schnable, P. S., Timmermans, M. C. P., Springer, N. M. & Muehlbauer, G. J., Feb 1 2018, In : PLoS genetics. 14, 2, p. e1007234

Research output: Contribution to journalComment/debate

Open Access
2 Scopus citations

Genotype-by-environment interactions affecting heterosis in maize

Li, Z., Coffey, L., Garfin, J., Miller, N. D., White, M. R., Spalding, E. P., De Leon, N., Kaeppler, S. M., Schnable, P. S., Springer, N. M. & Hirsch, C. N., Jan 2018, In : PloS one. 13, 1, e0191321.

Research output: Contribution to journalArticle

10 Scopus citations

Heritable epigenomic changes to the maize methylome resulting from tissue culture

Han, Z., Crisp, P. A., Stelpflug, S., Kaeppler, S. M., Li, Q. & Springer, N. M., Aug 2018, In : Genetics. 209, 4, p. 983-995 13 p.

Research output: Contribution to journalArticle

11 Scopus citations

Intragenic meiotic crossovers generate novel alleles with transgressive expression levels

Liu, S., Schnable, J. C., Ott, A., Yeh, C. T. E., Springer, N. M., Yu, J., Muehlbauer, G., Timmermans, M. C. P., Scanlon, M. J. & Schnable, P. S., Jan 1 2018, In : Molecular biology and evolution. 35, 11, p. 2762-2772 11 p.

Research output: Contribution to journalArticle

2 Scopus citations

Maize Genomes to Fields: 2014 and 2015 field season genotype, phenotype, environment, and inbred ear image datasets

Alkhalifah, N., Campbell, D. A., Falcon, C. M., Gardiner, J. M., Miller, N. D., Romay, M. C., Walls, R., Walton, R., Yeh, C. T., Bohn, M., Bubert, J., Buckler, E. S., Ciampitti, I., Flint-Garcia, S., Gore, M. A., Graham, C., Hirsch, C., Holland, J. B., Hooker, D., Kaeppler, S. & 24 others, Knoll, J., Lauter, N., Lee, E. C., Lorenz, A., Lynch, J. P., Moose, S. P., Murray, S. C., Nelson, R., Rocheford, T., Rodriguez, O., Schnable, J. C., Scully, B., Smith, M., Springer, N., Thomison, P., Tuinstra, M., Wisser, R. J., Xu, W., Ertl, D., Schnable, P. S., De Leon, N., Spalding, E. P., Edwards, J. & Lawrence-Dill, C. J., Jul 9 2018, In : BMC Research Notes. 11, 1, 452.

Research output: Contribution to journalArticle

5 Scopus citations

Potential roles for transposable elements in creating imprinted expression

Anderson, S. N. & Springer, N. M., Apr 2018, In : Current Opinion in Genetics and Development. 49, p. 8-14 7 p.

Research output: Contribution to journalReview article

4 Scopus citations

Subtle perturbations of the maize methylome reveal genes and transposons silenced by chromomethylase or RNA-directed DNA methylation pathways

Anderson, S. N., Zynda, G. J., Song, J., Han, Z., Vaughn, M. W., Li, Q. & Springer, N. M., Jun 1 2018, In : G3: Genes, Genomes, Genetics. 8, 6, p. 1921-1932 12 p.

Research output: Contribution to journalArticle

7 Scopus citations

The limited role of differential fractionation in genome content variation and function in maize (Zea mays L.) inbred lines

Brohammer, A. B., Kono, T., Springer, N. M., McGaugh, S. E. & Hirsch, C. N., Jan 2018, In : Plant Journal. 93, 1, p. 131-141 11 p.

Research output: Contribution to journalArticle

11 Scopus citations

The maize w22 genome provides a foundation for functional genomics and transposon biology

Springer, N. M., Anderson, S. N., Andorf, C. M., Ahern, K. R., Bai, F., Barad, O., Barbazuk, W. B., Bass, H. W., Baruch, K., Ben-Zvi, G., Buckler, E. S., Bukowski, R., Campbell, M. S., Cannon, E. K. S., Chomet, P., Kelly Dawe, R., Davenport, R., Dooner, H. K., Du, L. H., Du, C. & 34 others, Easterling, K. A., Gault, C., Guan, J. C., Hunter, C. T., Jander, G., Jiao, Y., Koch, K. E., Kol, G., Köllner, T. G., Kudo, T., Li, Q., Lu, F., Mayfield-Jones, D., Mei, W., McCarty, D. R., Noshay, J. M., Portwood, J. L., Ronen, G., Settles, A. M., Shem-Tov, D., Shi, J., Soifer, I., Stein, J. C., Stitzer, M. C., Suzuki, M., Vera, D. L., Vollbrecht, E., Vrebalov, J. T., Ware, D., Wei, S., Wimalanathan, K., Woodhouse, M. R., Xiong, W. & Brutnell, T. P., Sep 1 2018, In : Nature Genetics. 50, 9

Research output: Contribution to journalArticle

33 Scopus citations

Weeding out bad alleles

Hirsch, C. N. & Springer, N. M., Apr 1 2018, In : Nature plants. 4, 4, p. 193-194 2 p.

Research output: Contribution to journalShort survey

1 Scopus citations
2017

A comparative genomic hybridization approach to study gene copy number variations among chinese hamster cell lines

Vishwanathan, N., Bandyopadhyay, A., Fu, H. Y., Johnson, K. C., Springer, N. M. & Hu, W. S., Aug 2017, In : Biotechnology and bioengineering. 114, 8, p. 1903-1908 6 p.

Research output: Contribution to journalArticle

2 Scopus citations

A comprehensive analysis of alternative splicing in paleopolyploid maize

Mei, W., Liu, S., Schnable, J. C., Yeh, C. T., Springer, N. M., Schnable, P. S. & Barbazuk, W. B., May 10 2017, In : Frontiers in Plant Science. 8, 694.

Research output: Contribution to journalArticle

24 Scopus citations

Exploiting induced and natural epigenetic variation for crop improvement

Springer, N. M. & Schmitz, R. J., Sep 1 2017, In : Nature Reviews Genetics. 18, 9, p. 563-575 13 p.

Research output: Contribution to journalReview article

49 Scopus citations

Genome-wide mapping of transcriptional enhancer candidates using DNA and chromatin features in maize

Oka, R., Zicola, J., Weber, B., Anderson, S. N., Hodgman, C., Gent, J. I., Wesselink, J. J., Springer, N. M., Hoefsloot, H. C. J., Turck, F. & Stam, M., Jul 21 2017, In : Genome biology. 18, 1, 137.

Research output: Contribution to journalArticle

26 Scopus citations

Genomic features shaping the landscape of meiotic double-strand-break hotspots in maize

He, Y., Wang, M., Dukowic-Schulze, S., Zhou, A., Tiang, C. L., Shilo, S., Sidhu, G. K., Eichten, S., Bradbury, P., Springer, N. M., Buckler, E. S., Levy, A. A., Sun, Q., Pillardy, J., Kianian, P. M. A., Kianian, S. F., Chen, C. & Pawlowski, W. P., Nov 14 2017, In : Proceedings of the National Academy of Sciences of the United States of America. 114, 46, p. 12231-12236 6 p.

Research output: Contribution to journalArticle

18 Scopus citations

Improved maize reference genome with single-molecule technologies

Jiao, Y., Peluso, P., Shi, J., Liang, T., Stitzer, M. C., Wang, B., Campbell, M. S., Stein, J. C., Wei, X., Chin, C. S., Guill, K., Regulski, M., Kumari, S., Olson, A., Gent, J., Schneider, K. L., Wolfgruber, T. K., May, M. R., Springer, N. M., Antoniou, E. & 8 others, McCombie, W. R., Presting, G. G., McMullen, M., Ross-Ibarra, J., Dawe, R. K., Hastie, A., Rank, D. R. & Ware, D., Jun 22 2017, In : Nature. 546, 7659, p. 524-527 4 p.

Research output: Contribution to journalArticle

226 Scopus citations

Natural variation for gene expression responses to abiotic stress in maize

Waters, A. J., Makarevitch, I., Noshay, J., Burghardt, L. T., Hirsch, C. N., Hirsch, C. D. & Springer, N. M., Feb 1 2017, In : Plant Journal. 89, 4, p. 706-717 12 p.

Research output: Contribution to journalArticle

21 Scopus citations

News from the plant world: Listening to transcription

Grotewold, E. & Springer, N. M., Jan 1 2017, In : Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1860, 1, p. 1-2 2 p.

Research output: Contribution to journalEditorial

1 Scopus citations

Plant epigenomics-deciphering the mechanisms of epigenetic inheritance and plasticity in plants

Köhler, C. & Springer, N., Jul 6 2017, In : Genome biology. 18, 1, 132.

Research output: Contribution to journalEditorial

3 Scopus citations

The effect of artificial selection on phenotypic plasticity in maize

Gage, J. L., Jarquin, D., Romay, C., Lorenz, A., Buckler, E. S., Kaeppler, S., Alkhalifah, N., Bohn, M., Campbell, D. A., Edwards, J., Ertl, D., Flint-Garcia, S., Gardiner, J., Good, B., Hirsch, C. N., Holland, J., Hooker, D. C., Knoll, J., Kolkman, J., Kruger, G. & 20 others, Lauter, N., Lawrence-Dill, C. J., Lee, E., Lynch, J., Murray, S. C., Nelson, R., Petzoldt, J., Rocheford, T., Schnable, J., Schnable, P. S., Scully, B., Smith, M., Springer, N. M., Srinivasan, S., Walton, R., Weldekidan, T., Wisser, R. J., Xu, W., Yu, J. & De Leon, N., Dec 1 2017, In : Nature communications. 8, 1, 1348.

Research output: Contribution to journalArticle

17 Scopus citations

The repetitive landscape of the 5100 Mbp barley genome

Wicker, T., Schulman, A. H., Tanskanen, J., Spannagl, M., Twardziok, S., Mascher, M., Springer, N. M., Li, Q., Waugh, R., Li, C., Zhang, G., Stein, N., Mayer, K. F. X. & Gundlach, H., Dec 20 2017, In : Mobile DNA. 8, 1, 22.

Research output: Contribution to journalArticle

14 Scopus citations

Transposable element influences on gene expression in plants

Hirsch, C. D. & Springer, N. M., Jan 1 2017, In : Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1860, 1, p. 157-165 9 p.

Research output: Contribution to journalArticle

Open Access
52 Scopus citations
2016

Advancing crop transformation in the era of genome editing

Altpeter, F., Springer, N. M., Bartley, L. E., Blechl, A. E., Brutnell, T. P., Citovsky, V., Conrad, L. J., Gelvin, S. B., Jackson, D. P., Kausch, A. P., Lemaux, P. G., Medford, J. I., Orozco-Cárdenas, M. L., Tricoli, D. M., Van Eck, J., Voytas, D. F., Walbot, V., Wang, K., Zhang, Z. J. & Neal Stewart, C., Jul 2016, In : Plant Cell. 28, 7, p. 1510-1520 11 p.

Research output: Contribution to journalArticle

130 Scopus citations

Co-expression network analysis of duplicate genes in maize (Zea mays L.) reveals no subgenome bias

Li, L., Briskine, R., Schaefer, R., Schnable, P. S., Myers, C. L., Flagel, L. E., Springer, N. M. & Muehlbauer, G. J., Nov 4 2016, In : BMC Genomics. 17, 1, 875.

Research output: Contribution to journalArticle

11 Scopus citations

Draft assembly of elite inbred line PH207 provides insights into genomic and transcriptome diversity in maize

Hirsch, C. N., Hirsch, C. D., Brohammer, A. B., Bowman, M. J., Soifer, I., Barad, O., Shem-Tov, D., Baruch, K., Lu, F., Hernandez, A. G., Fields, C. J., Wright, C. L., Koehler, K., Springer, N. M., Buckler, E., Buell, C. R., de Leon, N., Kaeppler, S. M., Childs, K. L. & Mikel, M. A., Nov 2016, In : Plant Cell. 28, 11, p. 2700-2714 15 p.

Research output: Contribution to journalArticle

64 Scopus citations

Widespread natural variation of DNA methylation within angiosperms

Niederhuth, C. E., Bewick, A. J., Ji, L., Alabady, M. S., Kim, K. D., Li, Q., Rohr, N. A., Rambani, A., Burke, J. M., Udall, J. A., Egesi, C., Schmutz, J., Grimwood, J., Jackson, S. A., Springer, N. M. & Schmitz, R. J., Sep 27 2016, In : Genome biology. 17, 1, 194.

Research output: Contribution to journalArticle

116 Scopus citations
2015

Correction: Discovering functional modules across diverse maize transcriptomes using COB, the Co-expression Browser

Schaefer, R. J., Briskine, R., Springer, N. M. & Myers, C. L., Mar 13 2015, In : PloS one. 10, 3, e0120222.

Research output: Contribution to journalComment/debate

Correction To: Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress (PLoS Genet, 11, 10)

Makarevitch, I., Waters, A. J., West, P. T., Stitzer, M., Hirsch, C. N., Ross-Ibarra, J. & Springer, N. M., Oct 9 2015, In : PLoS genetics. 11, 10, e1005566.

Research output: Contribution to journalComment/debate

20 Scopus citations

Creating order from chaos: Epigenome dynamics in plants with complex genomes

Springer, N. M., Lisch, D. & Li, Q., Feb 2015, In : Plant Cell. 28, 2, p. 314-325 12 p.

Research output: Contribution to journalReview article

35 Scopus citations

Examining the causes and consequences of context-specific differential DNA methylation in maize

Li, Q., Song, J., West, P. T., Zynda, G., Eichten, S. R., Vaughn, M. W. & Springer, N. M., Aug 1 2015, In : Plant physiology. 168, 4, p. 1262-1274 13 p.

Research output: Contribution to journalArticle

31 Scopus citations

Genomic limitations to RNA sequencing expression profiling

Hirsch, C. D., Springer, N. M. & Hirsch, C. N., Nov 2015, In : Plant Journal. 84, 3, p. 491-503 13 p.

Research output: Contribution to journalArticle

12 Scopus citations