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Items: 46

1.

Revisiting criteria for plant miRNA annotation in the era of big data.

Axtell MJ, Meyers BC.

Plant Cell. 2018 Jan 17. pii: tpc.00851.2017. doi: 10.1105/tpc.17.00851. [Epub ahead of print] No abstract available.

2.

MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs.

Shahid S, Kim G, Johnson NR, Wafula E, Wang F, Coruh C, Bernal-Galeano V, Phifer T, dePamphilis CW, Westwood JH, Axtell MJ.

Nature. 2018 Jan 3;553(7686):82-85. doi: 10.1038/nature25027.

PMID:
29300014
3.

Lost in translation? microRNAs at the rough ER.

Axtell MJ.

Trends Plant Sci. 2017 Apr;22(4):273-274. doi: 10.1016/j.tplants.2017.03.002. Epub 2017 Mar 17. Review.

PMID:
28320581
4.

AGO4 is specifically required for heterochromatic siRNA accumulation at Pol V-dependent loci in Arabidopsis thaliana.

Wang F, Axtell MJ.

Plant J. 2017 Apr;90(1):37-47. doi: 10.1111/tpj.13463. Epub 2017 Feb 11.

PMID:
28002617
5.

Genome-wide analysis of single non-templated nucleotides in plant endogenous siRNAs and miRNAs.

Wang F, Johnson NR, Coruh C, Axtell MJ.

Nucleic Acids Res. 2016 Sep 6;44(15):7395-405. doi: 10.1093/nar/gkw457. Epub 2016 May 20.

6.

Improved Placement of Multi-mapping Small RNAs.

Johnson NR, Yeoh JM, Coruh C, Axtell MJ.

G3 (Bethesda). 2016 Jul 7;6(7):2103-11. doi: 10.1534/g3.116.030452.

7.

Genome-Wide Characterization of Maize Small RNA Loci and Their Regulation in the required to maintain repression6-1 (rmr6-1) Mutant and Long-Term Abiotic Stresses.

Lunardon A, Forestan C, Farinati S, Axtell MJ, Varotto S.

Plant Physiol. 2016 Mar;170(3):1535-48. doi: 10.1104/pp.15.01205. Epub 2016 Jan 8.

8.

Comparison of small RNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot tospovirus reveals host-specific responses to viral infection.

Margaria P, Miozzi L, Ciuffo M, Rosa C, Axtell MJ, Pappu HR, Turina M.

Virus Res. 2016 Jan 4;211:38-45. doi: 10.1016/j.virusres.2015.09.019. Epub 2015 Sep 30.

PMID:
26432447
9.

More than meets the eye? Factors that affect target selection by plant miRNAs and heterochromatic siRNAs.

Wang F, Polydore S, Axtell MJ.

Curr Opin Plant Biol. 2015 Oct;27:118-24. doi: 10.1016/j.pbi.2015.06.012. Epub 2015 Jul 31. Review.

10.

Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants.

Coruh C, Cho SH, Shahid S, Liu Q, Wierzbicki A, Axtell MJ.

Plant Cell. 2015 Aug;27(8):2148-62. doi: 10.1105/tpc.15.00228. Epub 2015 Jul 24.

11.

Small RNA profiles of wild-type and silencing suppressor-deficient tomato spotted wilt virus infected Nicotiana benthamiana.

Margaria P, Miozzi L, Rosa C, Axtell MJ, Pappu HR, Turina M.

Virus Res. 2015 Oct 2;208:30-8. doi: 10.1016/j.virusres.2015.05.021. Epub 2015 Jun 3.

PMID:
26047586
12.

Quantitating plant microRNA-mediated target repression using a dual-luciferase transient expression system.

Liu Q, Axtell MJ.

Methods Mol Biol. 2015;1284:287-303. doi: 10.1007/978-1-4939-2444-8_14.

PMID:
25757778
13.

Seeing the forest for the trees: annotating small RNA producing genes in plants.

Coruh C, Shahid S, Axtell MJ.

Curr Opin Plant Biol. 2014 Apr;18:87-95. doi: 10.1016/j.pbi.2014.02.008. Epub 2014 Mar 15. Review.

14.

A non-canonical plant microRNA target site.

Brousse C, Liu Q, Beauclair L, Deremetz A, Axtell MJ, Bouché N.

Nucleic Acids Res. 2014 Apr;42(8):5270-9. doi: 10.1093/nar/gku157. Epub 2014 Feb 21.

15.

Analysis of complementarity requirements for plant microRNA targeting using a Nicotiana benthamiana quantitative transient assay.

Liu Q, Wang F, Axtell MJ.

Plant Cell. 2014 Feb;26(2):741-53. doi: 10.1105/tpc.113.120972. Epub 2014 Feb 7.

16.

Long-range genomic enrichment, sequencing, and assembly to determine unknown sequences flanking a known microRNA.

Ma Z, Axtell MJ.

PLoS One. 2013 Dec 20;8(12):e83721. doi: 10.1371/journal.pone.0083721. eCollection 2013.

17.

Identification and annotation of small RNA genes using ShortStack.

Shahid S, Axtell MJ.

Methods. 2014 May 1;67(1):20-7. doi: 10.1016/j.ymeth.2013.10.004. Epub 2013 Oct 16.

18.

Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1.

Zhu H, Zhou Y, Castillo-González C, Lu A, Ge C, Zhao YT, Duan L, Li Z, Axtell MJ, Wang XJ, Zhang X.

Nat Struct Mol Biol. 2013 Sep;20(9):1106-15. doi: 10.1038/nsmb.2646. Epub 2013 Aug 11.

19.

ShortStack: comprehensive annotation and quantification of small RNA genes.

Axtell MJ.

RNA. 2013 Jun;19(6):740-51. doi: 10.1261/rna.035279.112. Epub 2013 Apr 22.

20.

Classification and comparison of small RNAs from plants.

Axtell MJ.

Annu Rev Plant Biol. 2013;64:137-59. doi: 10.1146/annurev-arplant-050312-120043. Epub 2013 Jan 16. Review.

PMID:
23330790
21.

miR156 and miR390 regulate tasiRNA accumulation and developmental timing in Physcomitrella patens.

Cho SH, Coruh C, Axtell MJ.

Plant Cell. 2012 Dec;24(12):4837-49. doi: 10.1105/tpc.112.103176. Epub 2012 Dec 21.

22.

DICER-LIKE3 activity in Physcomitrella patens DICER-LIKE4 mutants causes severe developmental dysfunction and sterility.

Arif MA, Fattash I, Ma Z, Cho SH, Beike AK, Reski R, Axtell MJ, Frank W.

Mol Plant. 2012 Nov;5(6):1281-94. doi: 10.1093/mp/sss036. Epub 2012 Apr 17.

23.

The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during microRNA biogenesis.

Liu C, Axtell MJ, Fedoroff NV.

Plant Physiol. 2012 Jun;159(2):748-58. doi: 10.1104/pp.112.193508. Epub 2012 Apr 3.

24.

Vive la différence: biogenesis and evolution of microRNAs in plants and animals.

Axtell MJ, Westholm JO, Lai EC.

Genome Biol. 2011;12(4):221. doi: 10.1186/gb-2011-12-4-221. Epub 2011 Apr 28. Review.

25.

The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.

Banks JA, Nishiyama T, Hasebe M, Bowman JL, Gribskov M, dePamphilis C, Albert VA, Aono N, Aoyama T, Ambrose BA, Ashton NW, Axtell MJ, Barker E, Barker MS, Bennetzen JL, Bonawitz ND, Chapple C, Cheng C, Correa LG, Dacre M, DeBarry J, Dreyer I, Elias M, Engstrom EM, Estelle M, Feng L, Finet C, Floyd SK, Frommer WB, Fujita T, Gramzow L, Gutensohn M, Harholt J, Hattori M, Heyl A, Hirai T, Hiwatashi Y, Ishikawa M, Iwata M, Karol KG, Koehler B, Kolukisaoglu U, Kubo M, Kurata T, Lalonde S, Li K, Li Y, Litt A, Lyons E, Manning G, Maruyama T, Michael TP, Mikami K, Miyazaki S, Morinaga S, Murata T, Mueller-Roeber B, Nelson DR, Obara M, Oguri Y, Olmstead RG, Onodera N, Petersen BL, Pils B, Prigge M, Rensing SA, Riaño-Pachón DM, Roberts AW, Sato Y, Scheller HV, Schulz B, Schulz C, Shakirov EV, Shibagaki N, Shinohara N, Shippen DE, Sørensen I, Sotooka R, Sugimoto N, Sugita M, Sumikawa N, Tanurdzic M, Theissen G, Ulvskov P, Wakazuki S, Weng JK, Willats WW, Wipf D, Wolf PG, Yang L, Zimmer AD, Zhu Q, Mitros T, Hellsten U, Loqué D, Otillar R, Salamov A, Schmutz J, Shapiro H, Lindquist E, Lucas S, Rokhsar D, Grigoriev IV.

Science. 2011 May 20;332(6032):960-3. doi: 10.1126/science.1203810. Epub 2011 May 5.

26.

The genome of Theobroma cacao.

Argout X, Salse J, Aury JM, Guiltinan MJ, Droc G, Gouzy J, Allegre M, Chaparro C, Legavre T, Maximova SN, Abrouk M, Murat F, Fouet O, Poulain J, Ruiz M, Roguet Y, Rodier-Goud M, Barbosa-Neto JF, Sabot F, Kudrna D, Ammiraju JS, Schuster SC, Carlson JE, Sallet E, Schiex T, Dievart A, Kramer M, Gelley L, Shi Z, Bérard A, Viot C, Boccara M, Risterucci AM, Guignon V, Sabau X, Axtell MJ, Ma Z, Zhang Y, Brown S, Bourge M, Golser W, Song X, Clement D, Rivallan R, Tahi M, Akaza JM, Pitollat B, Gramacho K, D'Hont A, Brunel D, Infante D, Kebe I, Costet P, Wing R, McCombie WR, Guiderdoni E, Quetier F, Panaud O, Wincker P, Bocs S, Lanaud C.

Nat Genet. 2011 Feb;43(2):101-8. doi: 10.1038/ng.736. Epub 2010 Dec 26.

PMID:
21186351
27.

Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus.

Ma Z, Coruh C, Axtell MJ.

Plant Cell. 2010 Apr;22(4):1090-103. doi: 10.1105/tpc.110.073882. Epub 2010 Apr 20.

28.

Transcriptome-wide identification of microRNA targets in rice.

Li YF, Zheng Y, Addo-Quaye C, Zhang L, Saini A, Jagadeeswaran G, Axtell MJ, Zhang W, Sunkar R.

Plant J. 2010 Jun 1;62(5):742-59. doi: 10.1111/j.1365-313X.2010.04187.x. Epub 2010 Feb 26.

29.

RNA secondary structural determinants of miRNA precursor processing in Arabidopsis.

Song L, Axtell MJ, Fedoroff NV.

Curr Biol. 2010 Jan 12;20(1):37-41. doi: 10.1016/j.cub.2009.10.076.

30.

Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome.

Addo-Quaye C, Snyder JA, Park YB, Li YF, Sunkar R, Axtell MJ.

RNA. 2009 Dec;15(12):2112-21. doi: 10.1261/rna.1774909. Epub 2009 Oct 22.

31.

A method to discover phased siRNA loci.

Axtell MJ.

Methods Mol Biol. 2010;592:59-70. doi: 10.1007/978-1-60327-005-2_5.

PMID:
19802589
32.

Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development.

Cho SH, Addo-Quaye C, Coruh C, Arif MA, Ma Z, Frank W, Axtell MJ.

PLoS Genet. 2008 Dec;4(12):e1000314. doi: 10.1371/journal.pgen.1000314. Epub 2008 Dec 19.

33.

Criteria for annotation of plant MicroRNAs.

Meyers BC, Axtell MJ, Bartel B, Bartel DP, Baulcombe D, Bowman JL, Cao X, Carrington JC, Chen X, Green PJ, Griffiths-Jones S, Jacobsen SE, Mallory AC, Martienssen RA, Poethig RS, Qi Y, Vaucheret H, Voinnet O, Watanabe Y, Weigel D, Zhu JK.

Plant Cell. 2008 Dec;20(12):3186-90. doi: 10.1105/tpc.108.064311. Epub 2008 Dec 12.

34.

CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets.

Addo-Quaye C, Miller W, Axtell MJ.

Bioinformatics. 2009 Jan 1;25(1):130-1. doi: 10.1093/bioinformatics/btn604. Epub 2008 Nov 18.

35.

Evolution of plant microRNAs and their targets.

Axtell MJ, Bowman JL.

Trends Plant Sci. 2008 Jul;13(7):343-9. doi: 10.1016/j.tplants.2008.03.009. Epub 2008 May 22. Review.

PMID:
18502167
36.

Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome.

Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ.

Curr Biol. 2008 May 20;18(10):758-762. doi: 10.1016/j.cub.2008.04.042. Epub 2008 May 8.

37.

Evolution of microRNAs and their targets: are all microRNAs biologically relevant?

Axtell MJ.

Biochim Biophys Acta. 2008 Nov;1779(11):725-34. doi: 10.1016/j.bbagrm.2008.02.007. Epub 2008 Mar 10. Review.

PMID:
18342023
38.

Common functions for diverse small RNAs of land plants.

Axtell MJ, Snyder JA, Bartel DP.

Plant Cell. 2007 Jun;19(6):1750-69. Epub 2007 Jun 29.

39.

Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans.

Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP.

Cell. 2006 Dec 15;127(6):1193-207.

40.

A two-hit trigger for siRNA biogenesis in plants.

Axtell MJ, Jan C, Rajagopalan R, Bartel DP.

Cell. 2006 Nov 3;127(3):565-77.

41.

Antiquity of microRNAs and their targets in land plants.

Axtell MJ, Bartel DP.

Plant Cell. 2005 Jun;17(6):1658-73. Epub 2005 Apr 22.

42.

Genetic and molecular evidence that the Pseudomonas syringae type III effector protein AvrRpt2 is a cysteine protease.

Axtell MJ, Chisholm ST, Dahlbeck D, Staskawicz BJ.

Mol Microbiol. 2003 Sep;49(6):1537-46.

44.

NPK1, an MEKK1-like mitogen-activated protein kinase kinase kinase, regulates innate immunity and development in plants.

Jin H, Axtell MJ, Dahlbeck D, Ekwenna O, Zhang S, Staskawicz B, Baker B.

Dev Cell. 2002 Aug;3(2):291-7.

45.

Mutational analysis of the Arabidopsis RPS2 disease resistance gene and the corresponding pseudomonas syringae avrRpt2 avirulence gene.

Axtell MJ, McNellis TW, Mudgett MB, Hsu CS, Staskawicz BJ.

Mol Plant Microbe Interact. 2001 Feb;14(2):181-8.

46.

Plasma leptin decreases during lactation in insectivorous bats.

Kunz TH, Bicer E, Hood WR, Axtell MJ, Harrington WR, Silvia BA, Widmaier EP.

J Comp Physiol B. 1999 Feb;169(1):61-6.

PMID:
10093906

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