Publications

2024 | 2023 | 2022 | 2021 | 2020 | 2019 | 2018 | 2017 | 2016 | 2015 | 2014 | 2013 | 2012 | 2011 | 2010 | 2009 | 2008 | 2007

2024 | back to top

  • Trans-species mobility of RNA interference between plants and associated organisms. Ya-Chi Nien, Allison Vanek, Michael J Axtell. Plant and Cell Physiology https://doi.org/10.1093/pcp/pcae012

2023 | back to top

  • Trans-species microRNA loci in the parasitic plant Cuscuta campestris have a U6-like snRNA promoter. Collin Hudzik, Sean Maguire, Shengxi Guan, Jeremy Held, Michael J. Axtell. The Plant Cell https://doi.org/10.1093/plcell/koad076

2022 | back to top

  • Quality control and evaluation of plant epigenomics data. Robert J Schmitz, Alexandre P Marand, Xuan Zhang, Rebecca A Mosher, Franziska Turck, Xuemei Chen, Michael J Axtell, Xuehua Zhong, Siobhan M Brady, Molly Megraw, Blake C Meyers. The Plant Cell https://doi.org/10.1093/plcell/koab255

2021 | back to top

  • Expression and processing of polycistronic artificial microRNAs and trans‐acting siRNAs from transiently introduced transgenes in Solanum lycopersicum and Nicotiana benthamiana Lunardon A, Kariuki SM, Axtell MJ. The Plant Journal https://doi.org/10.1111/tpj.15221

2020 | back to top

  • Mechanisms of Resistance and Virulence in Parasitic Plant–Host Interactions. Albert M, Axtell MJ, Timko MP. Plant Physiology. https://doi.org/10.1093/plphys/kiaa064
  • MSH1-induced heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants. Kundariya H, Yang X, Morton K, Sanchez R, Axtell MJ, Hutton SF, Fromm M, Mackenzie SA. Nature Communications https://doi.org/10.1038/s41467-020-19140-x
  • Segregation of an MSH1 RNAi transgene produces heritable non-genetic memory in association with methylome reprogramming. Yang X, Sanchez R, Kundariya H, Maher T, Dopp I, Schwegel R, Virdi K, Axtell MJ, Mackenzie SA. Nature Communications https://doi.org/10.1038/s41467-020-16036-8
  • Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants. Lunardon A, Johnson NR, Hagerott E, Phifer T, Polydore S, Coruh C, Axtell MJ. Genome Research https://doi.org/10.1101/gr.256750.119

2019 | back to top

  • Compensatory sequence variation between trans-species small RNAs and their target sites. Johnson NR, dePamphilis CW, Axtell MJ. eLife 8:e49750. https://doi.org/10.7554/eLife.49750
  • Exchange of small regulatory RNAs between plants and their pests. Hudzik C, Hou Y, Ma W, Axtell MJ. Plant Physiology https://doi.org/10.1104/pp.19.00931
  • Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants. Yang Z, Wafula EK, Kim G, Shahid S, McNeal JR, Ralph PE, Timilsena PR, Yu W-B, Kelly EA, Zhang H, Person TN, Altman NS, Axtell MJ, Westwood JH, dePamphilis CW. Nature Plants https://doi.org/10.1038/s41477-019-0458-0
  • Molecular Dialog Between Parasitic Plants and Their Hosts. Clarke CR, Timko MP, Yoder JI, Axtell MJ, Westwood JH. Annual Review of Phytopathology https://doi.org/10.1146/annurev-phyto-082718-100043
  • MicroRNAs in Plants: Key Findings from the Early Years. Meyers BC, Axtell MJ. The Plant Cell (non-peer reviewed commentary). https://doi.org/10.1105/tpc.19.00310
  • Small RNA warfare: exploring origins and function of trans-species microRNAs from the parasitic plant Cuscuta. Johnson NR, Axtell MJ. Current Opinion in Plant Biology. https://doi.org/10.1016/j.pbi.2019.03.014
  • Second to none: Plant secondary siRNAs as defensive agents against Phytophthora. Axtell MJ.  Cell Host & Microbe. (non-peer reviewed commentary) https://doi.org/10.1016/j.chom.2018.12.007
  • Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future. International Arabidopsis Informatics Consortium. Plant Direct. https://doi.org/10.1002/pld3.109

2018 | back to top

  • Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA-dominated PHAS loci. Polydore S, Lunardon A, Axtell MJ. Plant Direct. doi: 10.1002/pld3.101
  • Analysis of RDR1/RDR2/RDR6-independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals novel siRNA loci. Polydore S, Axtell MJ. The Plant Journal. 94: 1051-1063. doi: 10.1111/tpj.13919 PMID: 29654642
  • Revisiting criteria for plant miRNA annotation in the era of big data. Axtell MJ, Meyers BC. The Plant Cell. 30: 272-284 doi: 10.1105/tpc.17.00851  PMID: 29343505 PDF
  • 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 J, Axtell MJ. Nature 553:82-85. doi: 10.1038/nature25027 PMID: 29300014   PDF

2017 | back to top

2016 | back to top

  • AGO4 is specifically required for heterochromatic siRNA accumulation at Pol V-dependent loci in Arabidopsis thaliana. Wang F and Axtell MJ. The Plant Journal. doi: 10.1111/tpj.13463 PMID: 28002617  PDF
  • Genome-Wide Analysis of Single Non-Tempated Nucleotides in Plant Endogenous siRNAs and miRNAs. Wang F, Johnson NR, Coruh C, Axtell MJ. Nucleic Acids Research doi: 10.1093/nar/gkw457 PMID: 27207877 PDF
  • Improved placement of multi-mapping small RNAs. Johnson NR, Yeoh JM, Coruh C, Axtell MJ.  G3  doi: 10.1534/g3.116.028100 PMID: 27175019  PDF

  • 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 Physiology. doi: 10.1104/pp.15.01205 PMID: 26747286 PDF

2015 | back to top

  • 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. doi: 10.1016/j.virusres.2015.09.019 PMID: 26432447 PDF
  • 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. doi: 10.1016/j.pbi.2015.06.012 PMID: 26246393 PDF
  • 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 doi: ​10.​1105/​tpc.​15.​00228 PMID: 26209555 PDF
  • 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. doi: 10.1016/j.virusres.2015.05.021 PMID: 26047586 PDF
  • Non-coding RNAs: The small mysteries of males. Axtell MJ. Nature Plants doi: 10.1038/nplants.2015.55 PDF [Commentary on Zhai et al. 2015]
  • Quantitating plant microRNA-mediated target repression using a dual-luciferase transient expression system. Liu Q, Axtell MJ. Methods Mol Biol. doi: 10.1007/978-1-4939-2444-8_14 PMID: 25757778  PDF

2014 | back to top

  • Identification of apple miRNAs and their potential role in fire blight resistance.  Kaja E, Szcześniak MW, Jensen PJ, Axtell MJ, McNellis T, and Makałowska I. Tree Genetics and Genomes  doi: 10.1007/s11295-014-0812-3 PDF
  • Seeing the forest for the trees: annotating small RNA producing genes in plants. Coruh C, Shahid S, Axtell MJ. Curr Opin Plant Biol. doi: 10.1016/j.pbi.2014.02.008 PMID: 24632306 PDF
  • [Manuscript preprint – NOT peer reviewed] Butter: High-precision genomic alignment of small RNA-seq data. Axtell MJ. BioRXiv doi: 10.1101/007427 PDF
  • A non-canonical plant microRNA target site. Brousse C, Liu Q, Beauclair L, Deremetz A, Axtell MJ, Bouché N. Nucleic Acids Res. doi: 10.1093/nar/gku157 PMID: 24561804 PDF
  • Analysis of complementarity requirements for plant microRNA targeting using a Nicotiana benthamiana quantitative transient assay. Liu Q, Wang F, Axtell MJ. Plant Cell.  doi: 10.1105/tpc.113.120972 PMID: 24510721  PDF

2013 | back to top

2012 | back to top

  • miR156 and miR390 regulate tasiRNA accumulation and developmental timing in Physcomitrella patens. Cho SH, Coruh C, Axtell MJ. Plant Cell. doi: 10.1105/tpc.112.103176  PMID: 23263766  PDF
  • 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. doi: 10.1093/mp/sss036  PMID: 22511605  PDF
  • The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during microRNA biogenesis.
    Liu C, Axtell MJ, Fedoroff NV. Plant Physiol.  doi: 10.1104/pp.112.193508  PMID: 22474216 PDF

2011 | back to top

  • Vive la différence: biogenesis and evolution of microRNAs in plants and animals. Axtell MJ, Westholm JO, Lai EC. Genome Biol. doi: 10.1186/gb-2011-12-4-221  PMID: 21554756
  • 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.  doi: 10.1126/science.1203810  PMID: 21551031  PDF
  • 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. doi: 10.1038/ng.736  PMID: 21186351  PDF

2010 | back to top

  • Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. Ma Z, Coruh C, Axtell MJ. Plant Cell.  doi: 10.1105/tpc.110.073882  PMID: 20407023  PDF
  • 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. doi: 10.1111/j.1365-313X.2010.04187.x  PMID: 20202174  PDF
  • RNA secondary structural determinants of miRNA precursor processing in Arabidopsis. Song L, Axtell MJ, Fedoroff NV.
    Curr Biol. 2010  doi: 10.1016/j.cub.2009.10.076  PMID: 20015653  PDF
  • A method to discover phased siRNA loci. Axtell MJ. Methods Mol Biol. doi: 10.1007/978-1-60327-005-2_5  PMID: 19802589

2009 | back to top

  • 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 doi: 10.1261/rna.1774909  PMID: 19850910  PDF

2008 | back to top

  • 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.  doi: 10.1371/journal.pgen.1000314.  PMID: 19096705  PDF
  • 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. doi: 10.1105/tpc.108.064311  PMID: 19074682  PDF
  • CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Addo-Quaye C, Miller W, Axtell MJ.
    Bioinformatics  doi: 10.1093/bioinformatics/btn604  PMID: 19017659  PDF
  • Evolution of plant microRNAs and their targets. Axtell MJ, Bowman JL. Trends Plant Sci.  doi: 10.1016/j.tplants.2008.03.009  PMID: 18502167  PDF
  • Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ. Curr Biol.  doi: 10.1016/j.cub.2008.04.042  PMID: 18472421  PDF
  • Evolution of microRNAs and their targets: are all microRNAs biologically relevant? Axtell MJ. Biochim Biophys Acta  doi: 10.1016/j.bbagrm.2008.02.007  PMID: 18342023  PDF

2007 | back to top