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Research Output 2000 2019

2 Citations (Scopus)

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 1 2017, In : Biotechnology and Bioengineering. 114, 8, p. 1903-1908 6 p.

Research output: Contribution to journalArticle

Comparative Genomic Hybridization
Gene Dosage
Cricetulus
Genes
Cells
22 Citations (Scopus)

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

alternative splicing
corn
genes
inbred lines
introns
121 Citations (Scopus)

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 1 2016, In : Plant Cell. 28, 7, p. 1510-1520 11 p.

Research output: Contribution to journalArticle

genome
crops
Ensifer
synthetic biology
Regeneration
88 Citations (Scopus)

Allele-specific expression patterns reveal biases and embryo-specific parent-of-origin effects in hybrid maize

Springer, N. M. & Stupar, R. M., Aug 1 2007, In : Plant Cell. 19, 8, p. 2391-2402 12 p.

Research output: Contribution to journalArticle

Zea mays
Embryonic Structures
Alleles
alleles
Seedlings
222 Citations (Scopus)

Allelic variation and heterosis in maize: How do two halves make more than a whole?

Springer, N. M. & Stupar, R. M., Mar 1 2007, In : Genome Research. 17, 3, p. 264-275 12 p.

Research output: Contribution to journalReview article

Hybrid Vigor
Zea mays
Alleles
Phenotype
Gene Expression
32 Citations (Scopus)

A recommendation for naming transcription factor proteins in the grasses

Gray, J., Bevan, M., Brutnell, T., Buell, C. R., Cone, K., Hake, S., Jackson, D., Kellogg, E., Lawrence, C., McCouch, S., Mockler, T., Moose, S., Paterson, A., Peterson, T., Rokshar, D., Souza, G. M., Springer, N., Stein, N., Timmermans, M., Wang, G. L. & 1 others, Grotewold, E., Jan 1 2009, In : Plant physiology. 149, 1, p. 4-6 3 p.

Research output: Contribution to journalLetter

Plant Proteins
plant proteins
Poaceae
Transcription Factors
transcription factors
46 Citations (Scopus)

Assessing the efficiency of RNA interference for maize functional genomics

McGinnis, K., Murphy, N., Carlson, A. R., Akula, A., Akula, C., Basinger, H., Carlson, M., Hermanson, P., Kovacevic, N., McGill, M. A., Seshadri, V., Yoyokie, J., Cone, K., Kaeppler, H. F., Kaeppler, S. M. & Springer, N. M., Apr 1 2007, In : Plant physiology. 143, 4, p. 1441-1451 11 p.

Research output: Contribution to journalArticle

Genomics
RNA Interference
RNA interference
Zea mays
genomics
47 Citations (Scopus)

B73-Mo17 near-isogenic lines demonstrate dispersed structural variation in maize

Eichten, S. R., Foerster, J. M., de Leon, N., Kai, Y., Yeh, C. T., Liu, S., Jeddeloh, J. A., Schnable, P. S., Kaeppler, S. M. & Springer, N. M., Aug 1 2011, In : Plant physiology. 156, 4, p. 1679-1690 12 p.

Research output: Contribution to journalArticle

isogenic lines
Zea mays
Quantitative Trait Loci
corn
Genome
53 Citations (Scopus)

Brd1 gene in maize encodes a brassinosteroid C-6 oxidase

Makarevitch, I., Thompson, A., Muehlbauer, G. J. & Springer, N. M., Jan 26 2012, In : PloS one. 7, 1, e30798.

Research output: Contribution to journalArticle

Brassinosteroids
brassinosteroids
Zea mays
Oxidoreductases
Genes

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

regulator genes
regulatory sequences
genome
quantitative traits
agronomic traits
14 Citations (Scopus)

Changes in genome content generated via segregation of non-allelic homologs

Liu, S., Ying, K., Yeh, C. T., Yang, J., Swanson-Wagner, R., Wu, W., Richmond, T., Gerhardt, D. J., Lai, J., Springer, N., Nettleton, D., Jeddeloh, J. A. & Schnable, P. S., Nov 1 2012, In : Plant Journal. 72, 3, p. 390-399 10 p.

Research output: Contribution to journalArticle

Exome
Quantitative Trait Loci
Sequence Homology
inbred lines
Zea mays
1 Citation (Scopus)

Chapter 3 Epigenetics. The Second Genetic Code

Springer, N. M. & Kaeppler, S. M., Jan 1 2008, In : Advances in Agronomy. 100, C, p. 59-80 22 p.

Research output: Contribution to journalReview article

genetic code
epigenetics
gene expression
cultivar
DNA
2 Citations (Scopus)

Characterization of a novel maize retrotransposon family sprite that shows high levels of variability among maize inbred lines

Springer, N. M., Eichten, S., Smith, A., Papa, C. M., Steinway, S. & Kaeppler, S. M., Dec 1 2009, In : Maydica. 54, 4, p. 417-428 12 p.

Research output: Contribution to journalArticle

Retroelements
decitabine
retrotransposons
inbred lines
Zea mays
182 Citations (Scopus)
Zea mays
Genes
Gene Expression
Microarray Analysis
Seedlings

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
Cold-Shock Response
Seedlings
Zea mays
genotype
cold stress
11 Citations (Scopus)

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

Duplicate Genes
Gene Duplication
Zea mays
Genome
Genes
113 Citations (Scopus)

Comparative analysis of SET domain proteins in maize and Arabidopsis reveals multiple duplications preceding the divergence of monocots and dicots

Springer, N. M., Napoli, C. A., Selinger, D. A., Pandey, R., Cone, K. C., Chandler, V. L., Kaeppler, H. F. & Kaeppler, S. M., Jun 1 2003, In : Plant physiology. 132, 2, p. 907-925 19 p.

Research output: Contribution to journalArticle

Magnoliopsida
Liliopsida
Arabidopsis
Zea mays
Plant Proteins
396 Citations (Scopus)

Comparative population genomics of maize domestication and improvement

Hufford, M. B., Xu, X., Van Heerwaarden, J., Pyhäjärvi, T., Chia, J. M., Cartwright, R. A., Elshire, R. J., Glaubitz, J. C., Guill, K. E., Kaeppler, S. M., Lai, J., Morrell, P. L., Shannon, L. M., Song, C., Springer, N. M., Swanson-Wagner, R. A., Tiffin, P. L., Wang, J., Zhang, G., Doebley, J. & 5 others, McMullen, M. D., Ware, D., Buckler, E. S., Yang, S. & Ross-Ibarra, J., Jul 1 2012, In : Nature Genetics. 44, 7, p. 808-811 4 p.

Research output: Contribution to journalArticle

Metagenomics
Zea mays
Genes
Gene Expression Profiling
Breeding
61 Citations (Scopus)

Comprehensive analysis of imprinted genes in maize reveals allelic variation for imprinting and limited conservation with other species

Waters, A. J., Bilinski, P., Eichten, S. R., Vaughn, M. W., Ross-Ibarra, J., Gehring, M. & Springer, N. M., Nov 26 2013, In : Proceedings of the National Academy of Sciences of the United States of America. 110, 48, p. 19639-19644 6 p.

Research output: Contribution to journalArticle

Zea mays
Genes
Endosperm
Alleles
Mothers
172 Citations (Scopus)

Conserved plant genes with similarity to mammalian de novo DNA methyltransferases

Cao, X., Springer, N. M., Muszynski, M. G., Phillips, R. L., Kaeppler, S. & Jacobsen, S. E., Apr 25 2000, In : Proceedings of the National Academy of Sciences of the United States of America. 97, 9, p. 4979-4984 6 p.

Research output: Contribution to journalArticle

Plant Genes
Methyltransferases
Ubiquitin
DNA
DNA Methylation
29 Citations (Scopus)

Consistent and heritable alterations of DNA methylation are induced by tissue culture in maize

Stelpflug, S. C., Eichten, S. R., Hermanson, P. J., Springer, N. M. & Kaeppler, S. M., Apr 11 2014, In : Genetics. 198, 1, p. 209-218 10 p.

Research output: Contribution to journalArticle

DNA Methylation
Zea mays
Epigenomics
Methylation
Genome

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

Allura Red AC Dye
Long Noncoding RNA
additive effect
Zea mays
Single Nucleotide Polymorphism

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
Hybrid Vigor
heterosis
Zea mays
Ear
ears

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

2 Citations (Scopus)

Correction: Maize gene atlas developed by RNA sequencing and comparative evaluation of transcriptomes based on RNA sequencing and microarrays (PLoS ONE)

Sekhon, R. S., Briskine, R., Hirsch, C. N., Myers, C. L., Springer, N. M., Buell, C. R., De Leon, N. & Kaeppler, S. M., Jan 3 2014, In : PloS one. 9, 1

Research output: Contribution to journalComment/debate

Microarrays
Genes
RNA
20 Citations (Scopus)

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

Viverridae
genet
DNA Transposable Elements
transposons
Transcriptional Activation
35 Citations (Scopus)

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

DNA Transposable Elements
transposons
Chromatin
Genome
chromatin
4 Citations (Scopus)

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

DNA Methylation
Genome
Gene Expression Regulation
Hordeum
Zea mays
8 Citations (Scopus)

Developmental origins of cancer

Johnson, K. J., Springer, N. M., Bielinsky, A. K., Largaespada, D. A. & Ross, J. A., Aug 15 2009, In : Cancer Research. 69, 16, p. 6375-6377 3 p.

Research output: Contribution to journalArticle

Developmental Gene Expression Regulation
Genetic Epigenesis
Developmental Genes
Animal Disease Models
Neoplasms
308 Citations (Scopus)

Differentiation of the maize subgenomes by genome dominance and both ancient and ongoing gene loss

Schnable, J. C., Springer, N. M. & Freeling, M., Mar 8 2011, In : Proceedings of the National Academy of Sciences of the United States of America. 108, 10, p. 4069-4074 6 p.

Research output: Contribution to journalArticle

Tetraploidy
Zea mays
Genome
Duplicate Genes
Genes
18 Citations (Scopus)

Discovering functional modules across diverse maize transcriptomes using COB, the co-expression browser

Schaefer, R. J., Briskine, R., Springer, N. M. & Myers, C. L., Jun 12 2014, In : PloS one. 9, 6, e99193.

Research output: Contribution to journalArticle

Atlases
Transcriptome
transcriptome
Zea mays
Genes
265 Citations (Scopus)

Discovery of induced point mutations in maize genes by TILLING

Till, B. J., Reynolds, S. H., Weil, C., Springer, N., Burtner, C., Young, K., Bowers, E., Codomo, C. A., Enns, L. C., Odden, A. R., Greene, E. A., Comai, L. & Henikoff, S., Jul 28 2004, In : BMC plant biology. 4, 12.

Research output: Contribution to journalArticle

lesions (plant)
point mutation
mutagenesis
genome
corn
11 Citations (Scopus)

Disruption of imprinting by Mutator transposon insertions in the 5′ proximal regions of the Zea mays Mez1 locus

Haun, W. J., Danilevskaya, O. N., Meeley, R. B. & Springer, N. M., Apr 1 2009, In : Genetics. 181, 4, p. 1229-1237 9 p.

Research output: Contribution to journalArticle

Zea mays
Alleles
Endosperm
Mothers
Epigenomics
60 Citations (Scopus)

Distribution, functional impact, and origin mechanisms of copy number variation in the barley genome

Muñoz-Amatriaín, M., Eichten, S. R., Wicker, T., Richmond, T. A., Mascher, M., Steuernagel, B., Scholz, U., Ariyadasa, R., Spannagl, M., Nussbaumer, T., Mayer, K. F. X., Taudien, S., Platzer, M., Jeddeloh, J. A., Springer, N. M., Muehlbauer, G. J. & Stein, N., Jun 12 2013, In : Genome biology. 14, 6, R58.

Research output: Contribution to journalArticle

Hordeum
barley
genome
Genome
comparative genomic hybridization
63 Citations (Scopus)

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

Transcriptome
transcriptome
inbred lines
Zea mays
genome assembly
3 Citations (Scopus)

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

Zea mays
Gene Expression
gene expression
corn
Genes

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
DNA Transposable Elements
Zea mays
Genotype
Transcriptome
Transcriptional Silencer Elements
118 Citations (Scopus)

Epigenetic and Genetic Influences on DNA Methylation Variation in Maize Populations

Eichten, S. R., Briskine, R., Song, J., Li, Q., Swanson-Wagner, R., Hermanson, P. J., Waters, A. J., Starr, E., West, P. T., Tiffin, P., Myers, C. L., Vaughn, M. W. & Springer, N. M., Aug 1 2013, In : Plant Cell. 25, 8, p. 2783-2797 15 p.

Research output: Contribution to journalArticle

DNA methylation
DNA Methylation
Epigenomics
epigenetics
Zea mays
2 Citations (Scopus)

Epigenetic phenomena and epigenomics in maize

Hollick, J. B. & Springer, N., Jan 1 2009, Epigenomics. Springer Netherlands, p. 119-147 29 p.

Research output: Chapter in Book/Report/Conference proceedingChapter

Epigenomics
Zea mays
Genome
Research
DNA Transposable Elements
63 Citations (Scopus)

Epigenetics: Beyond chromatin modifications and complex genetic regulation

Eichten, S. R., Schmitz, R. J. & Springer, N. M., Jul 2014, In : Plant physiology. 165, 3, p. 933-947 15 p.

Research output: Contribution to journalArticle

Epigenomics
epigenetics
Chromatin
chromatin
histones
61 Citations (Scopus)

Epigenetics and crop improvement

Springer, N. M., Apr 1 2013, In : Trends in Genetics. 29, 4, p. 241-247 7 p.

Research output: Contribution to journalReview article

Epigenomics
Developmental Genes
Transgenes
Gene Expression
43 Citations (Scopus)

Evolutionary divergence of monocot and dicot methyl-CpG-binding domain proteins

Springer, N. M. & Kaeppler, S. M., Dec 1 2005, In : Plant Physiology. 138, 1, p. 92-104 13 p.

Research output: Contribution to journalArticle

divergent evolution
Magnoliopsida
Liliopsida
Carrier Proteins
DNA Methylation
30 Citations (Scopus)

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

DNA methylation
DNA Methylation
Zea mays
corn
Genes
45 Citations (Scopus)

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

Epigenomics
Alleles
101 Citations (Scopus)

Gene expression analyses in maize inbreds and hybrids with varying levels of heterosis

Stupar, R. M., Gardiner, J. M., Oldre, A. G., Haun, W. J., Chandler, V. L. & Springer, N. M., May 14 2008, In : BMC plant biology. 8, 33.

Research output: Contribution to journalArticle

heterosis
gene expression
corn
genetic variation
genes
8 Citations (Scopus)

Genetic control of maize shoot apical meristem architecture

Thompson, A. M., Crants, J., Schnable, P. S., Yu, J., Timmermans, M. C. P., Springer, N. M., Scanlon, M. J. & Muehlbauer, G. J., Jan 1 2014, In : G3: Genes, Genomes, Genetics. 4, 7, p. 1327-1337 11 p.

Research output: Contribution to journalArticle

Meristem
Zea mays
Growth
Population
Chromosomes, Human, Pair 8
30 Citations (Scopus)

Genetic Determinants for Enzymatic Digestion of Lignocellulosic Biomass are Independent of Those for Lignin abundance in a maize Recombinant Inbred population

Penning, B. W., Sykes, R. W., Babcock, N. C., Dugard, C. K., Held, M. A., Klimek, J. F., Shreve, J. T., Fowler, M., Ziebell, A., Davis, M. F., Decker, S. R., Turner, G. B., Mosier, N. S., Springer, N. M., Thimmapuram, J., Weil, C. F., Mccann, M. C. & Carpita, N. C., Aug 2014, In : Plant physiology. 165, 4, p. 1475-1487 13 p.

Research output: Contribution to journalArticle

Lignin
Biomass
Quantitative Trait Loci
Zea mays
Digestion
68 Citations (Scopus)

Genetic perturbation of the maize methylome

Li, Q., Eichten, S. R., Hermanson, P. J., Zaunbrecher, V. M., Song, J., Wendt, J., Rosenbaum, H., Madzima, T. F., Sloan, A. E., Huang, J., Burgess, D. L., Richmond, T. A., McGinnis, K. M., Meeley, R. B., Danilevskaya, O. N., Vaughn, M. W., Kaeppler, S. M., Jeddeloh, J. A. & Springer, N. M., Jan 1 2014, In : Plant Cell. 26, 12, p. 4602-4616 15 p.

Research output: Contribution to journalArticle

DNA Methylation
Zea mays
DNA methylation
Methylation
methylation
198 Citations (Scopus)

Genome-wide discovery and characterization of maize long non-coding RNAs

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., Feb 27 2014, In : Genome biology. 15, 2, R40.

Research output: Contribution to journalArticle

Long Noncoding RNA
Zea mays
RNA
genome
maize
22 Citations (Scopus)

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

Chromosome Mapping
Zea mays
Chromatin
chromatin
genome