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Items: 1 to 50 of 177

1.

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 PJ, Xu Q, Sun C, Chen W, Kan Q, Li M, Crisp PA, Yan J, Li L, Springer NM, Li Q.

Genome Biol. 2019 Nov 19;20(1):243. doi: 10.1186/s13059-019-1859-0.

2.

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

Ricci WA, Lu Z, Ji L, Marand AP, Ethridge CL, Murphy NG, Noshay JM, Galli M, Mejía-Guerra MK, Colomé-Tatché M, Johannes F, Rowley MJ, Corces VG, Zhai J, Scanlon MJ, Buckler ES, Gallavotti A, Springer NM, Schmitz RJ, Zhang X.

Nat Plants. 2019 Dec;5(12):1237-1249. doi: 10.1038/s41477-019-0547-0. Epub 2019 Nov 18.

PMID:
31740773
3.

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

Crisp PA, Hammond R, Zhou P, Vaillancourt B, Lipzen A, Daum C, Barry K, de Leon N, Buell CR, Kaeppler SM, Meyers BC, Hirsch CN, Springer NM.

Plant Physiol. 2020 Jan;182(1):318-331. doi: 10.1104/pp.19.00817. Epub 2019 Oct 1.

4.

Hydroxyapatite mineral enhances malignant potential in a tissue-engineered model of ductal carcinoma in situ (DCIS).

He F, Springer NL, Whitman MA, Pathi SP, Lee Y, Mohanan S, Marcott S, Chiou AE, Blank BS, Iyengar N, Morris PG, Jochelson M, Hudis CA, Shah P, Kunitake JAMR, Estroff LA, Lammerding J, Fischbach C.

Biomaterials. 2019 Dec;224:119489. doi: 10.1016/j.biomaterials.2019.119489. Epub 2019 Sep 11.

PMID:
31546097
5.

Regulation of proteoglycan production by varying glucose concentrations controls fiber formation in tissue engineered menisci.

McCorry MC, Kim J, Springer NL, Sandy J, Plaas A, Bonassar LJ.

Acta Biomater. 2019 Dec;100:173-183. doi: 10.1016/j.actbio.2019.09.026. Epub 2019 Sep 20.

PMID:
31546030
6.

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 Nov 5;9(11):3673-3682. doi: 10.1534/g3.119.400431.

7.

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.

8.

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.

9.

Fields on fire: Alternatives to crop residue burning in India.

Shyamsundar P, Springer NP, Tallis H, Polasky S, Jat ML, Sidhu HS, Krishnapriya PP, Skiba N, Ginn W, Ahuja V, Cummins J, Datta I, Dholakia HH, Dixon J, Gerard B, Gupta R, Hellmann J, Jadhav A, Jat HS, Keil A, Ladha JK, Lopez-Ridaura S, Nandrajog SP, Paul S, Ritter A, Sharma PC, Singh R, Singh D, Somanathan R.

Science. 2019 Aug 9;365(6453):536-538. doi: 10.1126/science.aaw4085. No abstract available.

PMID:
31395767
10.

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.

11.

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 Dec;100(5):1052-1065. doi: 10.1111/tpj.14489. Epub 2019 Sep 18.

PMID:
31381222
12.

Challenges of Translating Gene Regulatory Information into Agronomic Improvements.

Springer N, de León N, Grotewold E.

Trends Plant Sci. 2019 Dec;24(12):1075-1082. doi: 10.1016/j.tplants.2019.07.004. Epub 2019 Jul 31. Review.

PMID:
31377174
13.

Obesity-Associated Extracellular Matrix Remodeling Promotes a Macrophage Phenotype Similar to Tumor-Associated Macrophages.

Springer NL, Iyengar NM, Bareja R, Verma A, Jochelson MS, Giri DD, Zhou XK, Elemento O, Dannenberg AJ, Fischbach C.

Am J Pathol. 2019 Oct;189(10):2019-2035. doi: 10.1016/j.ajpath.2019.06.005. Epub 2019 Jul 16.

PMID:
31323189
14.

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.

15.

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.

16.

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

Tran TM, McCubbin TJ, Bihmidine S, Julius BT, Baker RF, Schauflinger M, Weil C, Springer N, Chomet P, Wagner R, Woessner J, Grote K, Peevers J, Slewinski TL, Braun DM.

Mol Plant. 2019 Sep 2;12(9):1278-1293. doi: 10.1016/j.molp.2019.05.001. Epub 2019 May 16.

PMID:
31102785
17.

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.

18.

Inequity in consumption of goods and services adds to racial-ethnic disparities in air pollution exposure.

Tessum CW, Apte JS, Goodkind AL, Muller NZ, Mullins KA, Paolella DA, Polasky S, Springer NP, Thakrar SK, Marshall JD, Hill JD.

Proc Natl Acad Sci U S A. 2019 Mar 26;116(13):6001-6006. doi: 10.1073/pnas.1818859116. Epub 2019 Mar 11.

19.

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
20.

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
21.

Five financial incentives to revive the Gulf of Mexico dead zone and Mississippi basin soils.

Tallis H, Polasky S, Hellmann J, Springer NP, Biske R, DeGeus D, Dell R, Doane M, Downes L, Goldstein J, Hodgman T, Johnson K, Luby I, Pennington D, Reuter M, Segerson K, Stark I, Stark J, Vollmer-Sanders C, Weaver SK.

J Environ Manage. 2019 Mar 1;233:30-38. doi: 10.1016/j.jenvman.2018.11.140. Epub 2018 Dec 14.

PMID:
30554022
22.

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.

23.

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.

24.

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
25.

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

AlKhalifah N, Campbell DA, Falcon CM, Gardiner JM, Miller ND, Romay MC, Walls R, Walton R, Yeh CT, Bohn M, Bubert J, Buckler ES, Ciampitti I, Flint-Garcia S, Gore MA, Graham C, Hirsch C, Holland JB, Hooker D, Kaeppler S, Knoll J, Lauter N, Lee EC, Lorenz A, Lynch JP, Moose SP, Murray SC, Nelson R, Rocheford T, Rodriguez O, Schnable JC, Scully B, Smith M, Springer N, Thomison P, Tuinstra M, Wisser RJ, Xu W, Ertl D, Schnable PS, De Leon N, Spalding EP, Edwards J, Lawrence-Dill CJ.

BMC Res Notes. 2018 Jul 9;11(1):452. doi: 10.1186/s13104-018-3508-1.

26.

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.

27.

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.

28.

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
29.

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
30.

CD44v6 increases gastric cancer malignant phenotype by modulating adipose stromal cell-mediated ECM remodeling.

Lourenço BN, Springer NL, Ferreira D, Oliveira C, Granja PL, Fischbach C.

Integr Biol (Camb). 2018 Mar 1;10(3):145-158. doi: 10.1039/c7ib00179g. Epub 2018 Feb 16.

31.

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.

32.

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.

33.

Socio-environmental consideration of phosphorus flows in the urban sanitation chain of contrasting cities.

Metson GS, Powers SM, Hale RL, Sayles JS, Öberg G, MacDonald GK, Kuwayama Y, Springer NP, Weatherley AJ, Hondula KL, Jones K, Chowdhury RB, Beusen AHW, Bouwman AF.

Reg Environ Change. 2018;18(5):1387-1401. doi: 10.1007/s10113-017-1257-7. Epub 2017 Dec 19.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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
39.

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.

40.

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

Köhler C, Springer N.

Genome Biol. 2017 Jul 6;18(1):132. doi: 10.1186/s13059-017-1260-9. No abstract available.

41.

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
42.

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
43.

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.

44.

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
45.

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.

46.

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
47.

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.

48.

Physical, technical, and economic accessibility of resources and reserves need to be distinguished by grade: Application to the case of phosphorus.

Springer NP.

Sci Total Environ. 2017 Jan 15;577:319-328. doi: 10.1016/j.scitotenv.2016.10.190. Epub 2016 Oct 31.

PMID:
27810306
49.

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.

50.

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.

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