Format
Sort by
Items per page

Send to

Choose Destination

Search results

Items: 1 to 50 of 104

1.

Dynamic Patterns of Transcript Abundance of Transposable Element Families in Maize.

Anderson SN, Stitzer MC, Zhou P, Ross-Ibarra J, Hirsch CD, Springer NM.

G3 (Bethesda). 2019 Sep 10. pii: g3.400431.2019. doi: 10.1534/g3.119.400431. [Epub ahead of print]

2.

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

Noshay JM, Anderson SN, Zhou P, Ji L, Ricci W, Lu Z, Stitzer MC, Crisp PA, Hirsch CN, Zhang X, Schmitz RJ, Springer NM.

PLoS Genet. 2019 Sep 9;15(9):e1008291. doi: 10.1371/journal.pgen.1008291. eCollection 2019 Sep.

3.

Identification of the expressome by machine learning on omics data.

Sartor RC, Noshay J, Springer NM, Briggs SP.

Proc Natl Acad Sci U S A. 2019 Sep 3;116(36):18119-18125. doi: 10.1073/pnas.1813645116. Epub 2019 Aug 16.

4.

Correction: Genotype-by-environment interactions affecting heterosis in maize.

Li Z, Coffey L, Garfin J, Miller ND, White MR, Spalding EP, Leon N, Kaeppler SM, Schnable PS, Springer NM, Hirsch CN.

PLoS One. 2019 Aug 5;14(8):e0219528. doi: 10.1371/journal.pone.0219528. eCollection 2019.

5.

Transposable elements contribute to dynamic genome content in maize.

Anderson SN, Stitzer MC, Brohammer AB, Zhou P, Noshay JM, O'Connor CH, Hirsch CD, Ross-Ibarra J, Hirsch CN, Springer NM.

Plant J. 2019 Aug 5. doi: 10.1111/tpj.14489. [Epub ahead of print]

PMID:
31381222
6.

Hybrid Decay: A Transgenerational Epigenetic Decline in Vigor and Viability Triggered in Backcross Populations of Teosinte with Maize.

Xue W, Anderson SN, Wang X, Yang L, Crisp PA, Li Q, Noshay J, Albert PS, Birchler JA, Bilinski P, Stitzer MC, Ross-Ibarra J, Flint-Garcia S, Chen X, Springer NM, Doebley JF.

Genetics. 2019 Sep;213(1):143-160. doi: 10.1534/genetics.119.302378. Epub 2019 Jul 18.

7.

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

Enders TA, St Dennis S, Oakland J, Callen ST, Gehan MA, Miller ND, Spalding EP, Springer NM, Hirsch CD.

Plant Direct. 2019 Jan 2;3(1):e00104. doi: 10.1002/pld3.104. eCollection 2019 Jan.

8.

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

Wang J, Li X, Do Kim K, Scanlon MJ, Jackson SA, Springer NM, Yu J.

Genome Biol. 2019 Apr 25;20(1):74. doi: 10.1186/s13059-019-1683-6.

9.

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

Crisp PA, Noshay JM, Anderson SN, Springer NM.

Mol Plant. 2019 Mar 4;12(3):282-284. doi: 10.1016/j.molp.2019.02.006. Epub 2019 Feb 22. No abstract available.

PMID:
30797889
10.

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

Zhou P, Hirsch CN, Briggs SP, Springer NM.

Mol Plant. 2019 Mar 4;12(3):410-425. doi: 10.1016/j.molp.2018.12.015. Epub 2018 Dec 27.

PMID:
30593858
11.

Intragenic Meiotic Crossovers Generate Novel Alleles with Transgressive Expression Levels.

Liu S, Schnable JC, Ott A, Yeh CE, Springer NM, Yu J, Muehlbauer G, Timmermans MCP, Scanlon MJ, Schnable PS.

Mol Biol Evol. 2018 Nov 1;35(11):2762-2772. doi: 10.1093/molbev/msy174.

12.

Correction to: Genome-wide discovery and characterization of maize long non-coding RNAs.

Li L, Eichten SR, Shimizu R, Petsch K, Yeh CT, Wu W, Chettoor AM, Givan SA, Cole RA, Fowler JE, Evans MMS, Scanlon MJ, Yu J, Schnable PS, Timmermans MCP, Springer NM, Muehlbauer GJ.

Genome Biol. 2018 Aug 23;19(1):122. doi: 10.1186/s13059-018-1508-z.

13.

The maize W22 genome provides a foundation for functional genomics and transposon biology.

Springer NM, Anderson SN, Andorf CM, Ahern KR, Bai F, Barad O, Barbazuk WB, Bass HW, Baruch K, Ben-Zvi G, Buckler ES, Bukowski R, Campbell MS, Cannon EKS, Chomet P, Dawe RK, Davenport R, Dooner HK, Du LH, Du C, Easterling KA, Gault C, Guan JC, Hunter CT, Jander G, Jiao Y, Koch KE, Kol G, Köllner TG, Kudo T, Li Q, Lu F, Mayfield-Jones D, Mei W, McCarty DR, Noshay JM, Portwood JL 2nd, Ronen G, Settles AM, Shem-Tov D, Shi J, Soifer I, Stein JC, Stitzer MC, Suzuki M, Vera DL, Vollbrecht E, Vrebalov JT, Ware D, Wei S, Wimalanathan K, Woodhouse MR, Xiong W, Brutnell TP.

Nat Genet. 2018 Sep;50(9):1282-1288. doi: 10.1038/s41588-018-0158-0. Epub 2018 Jul 30.

PMID:
30061736
14.

Heritable Epigenomic Changes to the Maize Methylome Resulting from Tissue Culture.

Han Z, Crisp PA, Stelpflug S, Kaeppler SM, Li Q, Springer NM.

Genetics. 2018 Aug;209(4):983-995. doi: 10.1534/genetics.118.300987. Epub 2018 May 30.

15.

Subtle Perturbations of the Maize Methylome Reveal Genes and Transposons Silenced by Chromomethylase or RNA-Directed DNA Methylation Pathways.

Anderson SN, Zynda GJ, Song J, Han Z, Vaughn MW, Li Q, Springer NM.

G3 (Bethesda). 2018 May 31;8(6):1921-1932. doi: 10.1534/g3.118.200284.

16.

Weeding out bad alleles.

Hirsch CN, Springer NM.

Nat Plants. 2018 Apr;4(4):193-194. doi: 10.1038/s41477-018-0133-x. No abstract available.

PMID:
29556084
17.

Potential roles for transposable elements in creating imprinted expression.

Anderson SN, Springer NM.

Curr Opin Genet Dev. 2018 Apr;49:8-14. doi: 10.1016/j.gde.2018.01.008. Epub 2018 Feb 13. Review.

PMID:
29453082
18.

Correction: Mendelian and Non-Mendelian Regulation of Gene Expression in Maize.

Li L, Petsch K, Shimizu R, Liu S, Xu WW, Ying K, Yu J, Scanlon MJ, Schnable PS, Timmermans MCP, Springer NM, Muehlbauer GJ.

PLoS Genet. 2018 Feb 14;14(2):e1007234. doi: 10.1371/journal.pgen.1007234. eCollection 2018 Feb.

19.

Genotype-by-environment interactions affecting heterosis in maize.

Li Z, Coffey L, Garfin J, Miller ND, White MR, Spalding EP, de Leon N, Kaeppler SM, Schnable PS, Springer NM, Hirsch CN.

PLoS One. 2018 Jan 17;13(1):e0191321. doi: 10.1371/journal.pone.0191321. eCollection 2018. Erratum in: PLoS One. 2019 Aug 5;14(8):e0219528.

20.

The repetitive landscape of the 5100 Mbp barley genome.

Wicker T, Schulman AH, Tanskanen J, Spannagl M, Twardziok S, Mascher M, Springer NM, Li Q, Waugh R, Li C, Zhang G, Stein N, Mayer KFX, Gundlach H.

Mob DNA. 2017 Dec 20;8:22. doi: 10.1186/s13100-017-0102-3. eCollection 2017.

21.

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

Brohammer AB, Kono TJY, Springer NM, McGaugh SE, Hirsch CN.

Plant J. 2018 Jan;93(1):131-141. doi: 10.1111/tpj.13765. Epub 2017 Dec 2.

22.

The effect of artificial selection on phenotypic plasticity in maize.

Gage JL, Jarquin D, Romay C, Lorenz A, Buckler ES, Kaeppler S, Alkhalifah N, Bohn M, Campbell DA, Edwards J, Ertl D, Flint-Garcia S, Gardiner J, Good B, Hirsch CN, Holland J, Hooker DC, Knoll J, Kolkman J, Kruger G, Lauter N, Lawrence-Dill CJ, Lee E, Lynch J, Murray SC, Nelson R, Petzoldt J, Rocheford T, Schnable J, Schnable PS, Scully B, Smith M, Springer NM, Srinivasan S, Walton R, Weldekidan T, Wisser RJ, Xu W, Yu J, de Leon N.

Nat Commun. 2017 Nov 7;8(1):1348. doi: 10.1038/s41467-017-01450-2.

23.

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

He Y, Wang M, Dukowic-Schulze S, Zhou A, Tiang CL, Shilo S, Sidhu GK, Eichten S, Bradbury P, Springer NM, Buckler ES, Levy AA, Sun Q, Pillardy J, Kianian PMA, Kianian SF, Chen C, Pawlowski WP.

Proc Natl Acad Sci U S A. 2017 Nov 14;114(46):12231-12236. doi: 10.1073/pnas.1713225114. Epub 2017 Oct 30.

24.

Detection of DNA Methylation by Whole-Genome Bisulfite Sequencing.

Li Q, Hermanson PJ, Springer NM.

Methods Mol Biol. 2018;1676:185-196. doi: 10.1007/978-1-4939-7315-6_11.

PMID:
28986911
25.

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

Oka R, Zicola J, Weber B, Anderson SN, Hodgman C, Gent JI, Wesselink JJ, Springer NM, Hoefsloot HCJ, Turck F, Stam M.

Genome Biol. 2017 Jul 21;18(1):137. doi: 10.1186/s13059-017-1273-4.

26.

Exploiting induced and natural epigenetic variation for crop improvement.

Springer NM, Schmitz RJ.

Nat Rev Genet. 2017 Sep;18(9):563-575. doi: 10.1038/nrg.2017.45. Epub 2017 Jul 3. Review.

PMID:
28669983
27.

Improved maize reference genome with single-molecule technologies.

Jiao Y, Peluso P, Shi J, Liang T, Stitzer MC, Wang B, Campbell MS, Stein JC, Wei X, Chin CS, Guill K, Regulski M, Kumari S, Olson A, Gent J, Schneider KL, Wolfgruber TK, May MR, Springer NM, Antoniou E, McCombie WR, Presting GG, McMullen M, Ross-Ibarra J, Dawe RK, Hastie A, Rank DR, Ware D.

Nature. 2017 Jun 22;546(7659):524-527. doi: 10.1038/nature22971. Epub 2017 Jun 12.

PMID:
28605751
28.

A Comprehensive Analysis of Alternative Splicing in Paleopolyploid Maize.

Mei W, Liu S, Schnable JC, Yeh CT, Springer NM, Schnable PS, Barbazuk WB.

Front Plant Sci. 2017 May 10;8:694. doi: 10.3389/fpls.2017.00694. eCollection 2017.

29.

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

Vishwanathan N, Bandyopadhyay A, Fu HY, Johnson KC, Springer NM, Hu WS.

Biotechnol Bioeng. 2017 Aug;114(8):1903-1908. doi: 10.1002/bit.26311. Epub 2017 May 12.

PMID:
28409824
30.

Natural variation for gene expression responses to abiotic stress in maize.

Waters AJ, Makarevitch I, Noshay J, Burghardt LT, Hirsch CN, Hirsch CD, Springer NM.

Plant J. 2017 Feb;89(4):706-717. doi: 10.1111/tpj.13414. Epub 2017 Feb 11.

31.

News from the plant world: Listening to transcription.

Grotewold E, Springer NM.

Biochim Biophys Acta Gene Regul Mech. 2017 Jan;1860(1):1-2. doi: 10.1016/j.bbagrm.2016.11.004. Epub 2016 Nov 16. No abstract available.

PMID:
27866003
32.

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

Li L, Briskine R, Schaefer R, Schnable PS, Myers CL, Flagel LE, Springer NM, Muehlbauer GJ.

BMC Genomics. 2016 Nov 4;17(1):875.

33.

Draft Assembly of Elite Inbred Line PH207 Provides Insights into Genomic and Transcriptome Diversity in Maize.

Hirsch CN, Hirsch CD, Brohammer AB, Bowman MJ, Soifer I, Barad O, Shem-Tov D, Baruch K, Lu F, Hernandez AG, Fields CJ, Wright CL, Koehler K, Springer NM, Buckler E, Buell CR, de Leon N, Kaeppler SM, Childs KL, Mikel MA.

Plant Cell. 2016 Nov;28(11):2700-2714. Epub 2016 Nov 1.

34.

Widespread natural variation of DNA methylation within angiosperms.

Niederhuth CE, Bewick AJ, Ji L, Alabady MS, Kim KD, Li Q, Rohr NA, Rambani A, Burke JM, Udall JA, Egesi C, Schmutz J, Grimwood J, Jackson SA, Springer NM, Schmitz RJ.

Genome Biol. 2016 Sep 27;17(1):194.

35.

Advancing Crop Transformation in the Era of Genome Editing.

Altpeter F, Springer NM, Bartley LE, Blechl AE, Brutnell TP, Citovsky V, Conrad LJ, Gelvin SB, Jackson DP, Kausch AP, Lemaux PG, Medford JI, Orozco-Cárdenas ML, Tricoli DM, Van Eck J, Voytas DF, Walbot V, Wang K, Zhang ZJ, Stewart CN Jr.

Plant Cell. 2016 Jul;28(7):1510-20. doi: 10.1105/tpc.16.00196. Epub 2016 Jun 22. Review.

36.

Transposable element influences on gene expression in plants.

Hirsch CD, Springer NM.

Biochim Biophys Acta Gene Regul Mech. 2017 Jan;1860(1):157-165. doi: 10.1016/j.bbagrm.2016.05.010. Epub 2016 May 25. Review.

PMID:
27235540
37.

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes.

Springer NM, Lisch D, Li Q.

Plant Cell. 2016 Feb;28(2):314-25. doi: 10.1105/tpc.15.00911. Epub 2016 Feb 11. Review.

38.

RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome.

Li Q, Gent JI, Zynda G, Song J, Makarevitch I, Hirsch CD, Hirsch CN, Dawe RK, Madzima TF, McGinnis KM, Lisch D, Schmitz RJ, Vaughn MW, Springer NM.

Proc Natl Acad Sci U S A. 2015 Nov 24;112(47):14728-33. doi: 10.1073/pnas.1514680112. Epub 2015 Nov 9.

39.

Correction: Transposable Elements Contribute to Activation of Maize Genes in Response to Abiotic Stress.

Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN, Ross-Ibarra J, Springer NM.

PLoS Genet. 2015 Oct 9;11(10):e1005566. doi: 10.1371/journal.pgen.1005566. eCollection 2015 Oct. No abstract available.

40.

Genomic limitations to RNA sequencing expression profiling.

Hirsch CD, Springer NM, Hirsch CN.

Plant J. 2015 Nov;84(3):491-503. doi: 10.1111/tpj.13014. Epub 2015 Oct 6.

41.

Paramutation in evolution, population genetics and breeding.

Springer NM, McGinnis KM.

Semin Cell Dev Biol. 2015 Aug;44:33-8. doi: 10.1016/j.semcdb.2015.08.010. Epub 2015 Sep 11. Review.

PMID:
26325077
42.

Reassess the t Test: Interact with All Your Data via ANOVA.

Brady SM, Burow M, Busch W, Carlborg Ö, Denby KJ, Glazebrook J, Hamilton ES, Harmer SL, Haswell ES, Maloof JN, Springer NM, Kliebenstein DJ.

Plant Cell. 2015 Aug;27(8):2088-94. doi: 10.1105/tpc.15.00238. Epub 2015 Jul 28.

43.

Minimal evidence for consistent changes in maize DNA methylation patterns following environmental stress.

Eichten SR, Springer NM.

Front Plant Sci. 2015 May 6;6:308. doi: 10.3389/fpls.2015.00308. eCollection 2015.

44.

Examining the Causes and Consequences of Context-Specific Differential DNA Methylation in Maize.

Li Q, Song J, West PT, Zynda G, Eichten SR, Vaughn MW, Springer NM.

Plant Physiol. 2015 Aug;168(4):1262-74. doi: 10.1104/pp.15.00052. Epub 2015 Apr 13.

45.

Post-conversion targeted capture of modified cytosines in mammalian and plant genomes.

Li Q, Suzuki M, Wendt J, Patterson N, Eichten SR, Hermanson PJ, Green D, Jeddeloh J, Richmond T, Rosenbaum H, Burgess D, Springer NM, Greally JM.

Nucleic Acids Res. 2015 Jul 13;43(12):e81. doi: 10.1093/nar/gkv244. Epub 2015 Mar 26.

46.

Transposable elements contribute to activation of maize genes in response to abiotic stress.

Makarevitch I, Waters AJ, West PT, Stitzer M, Hirsch CN, Ross-Ibarra J, Springer NM.

PLoS Genet. 2015 Jan 8;11(1):e1004915. doi: 10.1371/journal.pgen.1004915. eCollection 2015 Jan. Erratum in: PLoS Genet. 2015 Oct;11(10):e1005566.

47.

Transposable elements: Microbiomes in the genomes.

Springer NM.

Nat Plants. 2015 Feb 3;1:15004. doi: 10.1038/nplants.2015.4. No abstract available.

PMID:
27251779
48.

Genetic perturbation of the maize methylome.

Li Q, Eichten SR, Hermanson PJ, Zaunbrecher VM, Song J, Wendt J, Rosenbaum H, Madzima TF, Sloan AE, Huang J, Burgess DL, Richmond TA, McGinnis KM, Meeley RB, Danilevskaya ON, Vaughn MW, Kaeppler SM, Jeddeloh JA, Springer NM.

Plant Cell. 2014 Dec;26(12):4602-16. doi: 10.1105/tpc.114.133140. Epub 2014 Dec 19.

49.

Utilization of deletion bins to anchor and order sequences along the wheat 7B chromosome.

Belova T, Grønvold L, Kumar A, Kianian S, He X, Lillemo M, Springer NM, Lien S, Olsen OA, Sandve SR.

Theor Appl Genet. 2014 Sep;127(9):2029-40. doi: 10.1007/s00122-014-2358-z. Epub 2014 Aug 19.

PMID:
25134516
50.

Genomic distribution of H3K9me2 and DNA methylation in a maize genome.

West PT, Li Q, Ji L, Eichten SR, Song J, Vaughn MW, Schmitz RJ, Springer NM.

PLoS One. 2014 Aug 14;9(8):e105267. doi: 10.1371/journal.pone.0105267. eCollection 2014.

Supplemental Content

Loading ...
Support Center