Michael J. Axtell, Ph.D. - Publications

2003 University of California, Berkeley, Berkeley, CA 
Plant Pathology Agriculture, Molecular Biology, Genetics

54 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2021 Lunardon A, Kariuki SM, Axtell MJ. Expression and processing of polycistronic artificial microRNAs and trans-acting siRNAs from transiently introduced transgenes in Solanum lycopersicum and Nicotiana benthamiana. The Plant Journal : For Cell and Molecular Biology. PMID 33655542 DOI: 10.1111/tpj.15221  1
2020 Lunardon A, Johnson NR, Hagerott E, Phifer T, Polydore S, Coruh C, Axtell MJ. Integrated annotations and analyses of small RNA-producing loci from 47 diverse plants. Genome Research. PMID 32179590 DOI: 10.1101/gr.256750.119  1
2019 Johnson NR, dePamphilis CW, Axtell MJ. Compensatory sequence variation between -species small RNAs and their target sites. Elife. 8. PMID 31845648 DOI: 10.7554/eLife.49750  1
2019 Yang Z, Wafula EK, Kim G, Shahid S, McNeal JR, Ralph PE, Timilsena PR, Yu WB, Kelly EA, Zhang H, Person TN, Altman NS, Axtell MJ, Westwood JH, dePamphilis CW. Convergent horizontal gene transfer and cross-talk of mobile nucleic acids in parasitic plants. Nature Plants. PMID 31332314 DOI: 10.1038/s41477-019-0458-0  1
2019 Johnson NR, Axtell MJ. Small RNA warfare: exploring origins and function of trans-species microRNAs from the parasitic plant Cuscuta. Current Opinion in Plant Biology. 50: 76-81. PMID 31029811 DOI: 10.1016/j.pbi.2019.03.014  1
2018 Polydore S, Lunardon A, Axtell MJ. Several phased siRNA annotation methods can frequently misidentify 24 nucleotide siRNA-dominated loci. Plant Direct. 2: e00101. PMID 31245701 DOI: 10.1002/pld3.101  1
2018 Polydore S, Axtell MJ. Analysis of RDR1/RDR2/RDR6-independent small RNAs in Arabidopsis thaliana improves MIRNA annotations and reveals unexplained types of siRNA loci. The Plant Journal : For Cell and Molecular Biology. PMID 29654642 DOI: 10.1111/tpj.13919  1
2018 Shahid S, Kim G, Johnson NR, Wafula E, Wang F, Coruh C, Bernal-Galeano V, Phifer T, dePamphilis CW, Westwood JH, Axtell MJ. MicroRNAs from the parasitic plant Cuscuta campestris target host messenger RNAs. Nature. 553: 82-85. PMID 29300014 DOI: 10.1038/nature25027  1
2016 Wang F, Axtell MJ. AGO4 is specifically required for heterochromatic siRNA accumulation at Pol V-dependent loci in Arabidopsis thaliana. The Plant Journal : For Cell and Molecular Biology. PMID 28002617 DOI: 10.1111/tpj.13463  1
2016 Wang F, Johnson NR, Coruh C, Axtell MJ. Genome-wide analysis of single non-templated nucleotides in plant endogenous siRNAs and miRNAs. Nucleic Acids Research. PMID 27207877 DOI: 10.1093/nar/gkw457  1
2016 Johnson NR, Yeoh JM, Coruh C, Axtell MJ. Improved Placement of Multi-Mapping Small RNAs. G3 (Bethesda, Md.). PMID 27175019 DOI: 10.1534/g3.116.030452  1
2016 Lunardon A, Forestan C, Farinati S, Axtell MJ, Varotto S. 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. Plant Physiology. 170: 1535-48. PMID 26747286 DOI: 10.1104/pp.15.01205  1
2016 Margaria P, Miozzi L, Ciuffo M, Rosa C, Axtell MJ, Pappu HR, Turina M. Comparison of small RNA profiles in Nicotiana benthamiana and Solanum lycopersicum infected by polygonum ringspot tospovirus reveals host-specific responses to viral infection. Virus Research. 211: 38-45. PMID 26432447 DOI: 10.1016/j.virusres.2015.09.019  1
2015 Wang F, Polydore S, Axtell MJ. More than meets the eye? Factors that affect target selection by plant miRNAs and heterochromatic siRNAs. Current Opinion in Plant Biology. 27: 118-124. PMID 26246393 DOI: 10.1016/j.pbi.2015.06.012  1
2015 Coruh C, Cho SH, Shahid S, Liu Q, Wierzbicki A, Axtell MJ. Comprehensive Annotation of Physcomitrella patens Small RNA Loci Reveals That the Heterochromatic Short Interfering RNA Pathway Is Largely Conserved in Land Plants. The Plant Cell. PMID 26209555 DOI: 10.1105/tpc.15.00228  1
2015 Margaria P, Miozzi L, Rosa C, Axtell MJ, Pappu HR, Turina M. Small RNA profiles of wild-type and silencing suppressor-deficient tomato spotted wilt virus infected Nicotiana benthamiana. Virus Research. 208: 30-8. PMID 26047586 DOI: 10.1016/j.virusres.2015.05.021  1
2015 Liu Q, Axtell MJ. Quantitating plant microRNA-mediated target repression using a dual-luciferase transient expression system. Methods in Molecular Biology (Clifton, N.J.). 1284: 287-303. PMID 25757778 DOI: 10.1007/978-1-4939-2444-8_14  1
2015 Kaja E, Szcześniak MW, Jensen PJ, Axtell MJ, McNellis T, Makałowska I. Identification of apple miRNAs and their potential role in fire blight resistance Tree Genetics and Genomes. 11. DOI: 10.1007/s11295-014-0812-3  1
2014 Coruh C, Shahid S, Axtell MJ. Seeing the forest for the trees: annotating small RNA producing genes in plants. Current Opinion in Plant Biology. 18: 87-95. PMID 24632306 DOI: 10.1016/j.pbi.2014.02.008  1
2014 Brousse C, Liu Q, Beauclair L, Deremetz A, Axtell MJ, Bouché N. A non-canonical plant microRNA target site. Nucleic Acids Research. 42: 5270-9. PMID 24561804 DOI: 10.1093/nar/gku157  1
2014 Liu Q, Wang F, Axtell MJ. Analysis of complementarity requirements for plant microRNA targeting using a Nicotiana benthamiana quantitative transient assay. The Plant Cell. 26: 741-53. PMID 24510721 DOI: 10.1105/tpc.113.120972  1
2014 Shahid S, Axtell MJ. Identification and annotation of small RNA genes using ShortStack. Methods (San Diego, Calif.). 67: 20-7. PMID 24139974 DOI: 10.1016/j.ymeth.2013.10.004  1
2013 Ma Z, Axtell MJ. Long-range genomic enrichment, sequencing, and assembly to determine unknown sequences flanking a known microRNA. Plos One. 8: e83721. PMID 24376739 DOI: 10.1371/journal.pone.0083721  1
2013 Zhu H, Zhou Y, Castillo-González C, Lu A, Ge C, Zhao YT, Duan L, Li Z, Axtell MJ, Wang XJ, Zhang X. Bidirectional processing of pri-miRNAs with branched terminal loops by Arabidopsis Dicer-like1. Nature Structural & Molecular Biology. 20: 1106-15. PMID 23934148 DOI: 10.1038/nsmb.2646  1
2013 Axtell MJ. ShortStack: comprehensive annotation and quantification of small RNA genes. Rna (New York, N.Y.). 19: 740-51. PMID 23610128 DOI: 10.1261/rna.035279.112  1
2013 Axtell MJ. Classification and comparison of small RNAs from plants. Annual Review of Plant Biology. 64: 137-59. PMID 23330790 DOI: 10.1146/annurev-arplant-050312-120043  1
2013 DePamphilis CW, Palmer JD, Rounsley S, Sankoff D, Schuster SC, Ammiraju JSS, Barbazuk WB, Chamala S, Chanderbali AS, Determann R, Hong M, Ralph P, Talag J, Tomsho L, Walts B, ... ... Axtell MJ, et al. The Amborella genome and the evolution of flowering plants Science. 342. DOI: 10.1126/science.1241089  1
2012 Cho SH, Coruh C, Axtell MJ. miR156 and miR390 regulate tasiRNA accumulation and developmental timing in Physcomitrella patens. The Plant Cell. 24: 4837-49. PMID 23263766 DOI: 10.1105/tpc.112.103176  1
2012 Arif MA, Fattash I, Ma Z, Cho SH, Beike AK, Reski R, Axtell MJ, Frank W. DICER-LIKE3 activity in Physcomitrella patens DICER-LIKE4 mutants causes severe developmental dysfunction and sterility. Molecular Plant. 5: 1281-94. PMID 22511605 DOI: 10.1093/mp/sss036  1
2012 Liu C, Axtell MJ, Fedoroff NV. The helicase and RNaseIIIa domains of Arabidopsis Dicer-Like1 modulate catalytic parameters during microRNA biogenesis. Plant Physiology. 159: 748-58. PMID 22474216 DOI: 10.1104/pp.112.193508  1
2012 Puzey JR, Karger A, Axtell M, Kramer EM. Deep annotation of Populus trichocarpa microRNAs from diverse tissue sets. Plos One. 7: e33034. PMID 22442676 DOI: 10.1371/journal.pone.0033034  1
2011 Axtell MJ, Westholm JO, Lai EC. Vive la différence: biogenesis and evolution of microRNAs in plants and animals. Genome Biology. 12: 221. PMID 21554756 DOI: 10.1186/gb-2011-12-4-221  1
2011 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, et al. The Selaginella genome identifies genetic changes associated with the evolution of vascular plants. Science (New York, N.Y.). 332: 960-3. PMID 21551031 DOI: 10.1126/science.1203810  1
2011 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, ... ... Axtell MJ, et al. The genome of Theobroma cacao Nature Genetics. 43: 101-108. PMID 21186351 DOI: 10.1038/ng.736  1
2010 Ma Z, Coruh C, Axtell MJ. Arabidopsis lyrata small RNAs: transient MIRNA and small interfering RNA loci within the Arabidopsis genus. The Plant Cell. 22: 1090-103. PMID 20407023 DOI: 10.1105/tpc.110.073882  1
2010 Li YF, Zheng Y, Addo-Quaye C, Zhang L, Saini A, Jagadeeswaran G, Axtell MJ, Zhang W, Sunkar R. Transcriptome-wide identification of microRNA targets in rice. The Plant Journal : For Cell and Molecular Biology. 62: 742-59. PMID 20202174 DOI: 10.1111/j.1365-313X.2010.04187.x  1
2010 Song L, Axtell MJ, Fedoroff NV. RNA secondary structural determinants of miRNA precursor processing in Arabidopsis. Current Biology : Cb. 20: 37-41. PMID 20015653 DOI: 10.1016/j.cub.2009.10.076  1
2010 Axtell MJ. A method to discover phased siRNA loci. Methods in Molecular Biology (Clifton, N.J.). 592: 59-70. PMID 19802589 DOI: 10.1007/978-1-60327-005-2_5  1
2009 Addo-Quaye C, Snyder JA, Park YB, Li YF, Sunkar R, Axtell MJ. Sliced microRNA targets and precise loop-first processing of MIR319 hairpins revealed by analysis of the Physcomitrella patens degradome. Rna (New York, N.Y.). 15: 2112-21. PMID 19850910 DOI: 10.1261/rna.1774909  1
2009 Addo-Quaye C, Miller W, Axtell MJ. CleaveLand: a pipeline for using degradome data to find cleaved small RNA targets. Bioinformatics (Oxford, England). 25: 130-1. PMID 19017659 DOI: 10.1093/bioinformatics/btn604  1
2008 Cho SH, Addo-Quaye C, Coruh C, Arif MA, Ma Z, Frank W, Axtell MJ. Physcomitrella patens DCL3 is required for 22-24 nt siRNA accumulation, suppression of retrotransposon-derived transcripts, and normal development. Plos Genetics. 4: e1000314. PMID 19096705 DOI: 10.1371/journal.pgen.1000314  1
2008 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, et al. Criteria for annotation of plant MicroRNAs. The Plant Cell. 20: 3186-90. PMID 19074682 DOI: 10.1105/tpc.108.064311  0.92
2008 Axtell MJ, Bowman JL. Evolution of plant microRNAs and their targets. Trends in Plant Science. 13: 343-9. PMID 18502167 DOI: 10.1016/j.tplants.2008.03.009  1
2008 Addo-Quaye C, Eshoo TW, Bartel DP, Axtell MJ. Endogenous siRNA and miRNA targets identified by sequencing of the Arabidopsis degradome. Current Biology : Cb. 18: 758-62. PMID 18472421 DOI: 10.1016/j.cub.2008.04.042  1
2008 Axtell MJ. Evolution of microRNAs and their targets: are all microRNAs biologically relevant? Biochimica Et Biophysica Acta. 1779: 725-34. PMID 18342023 DOI: 10.1016/j.bbagrm.2008.02.007  1
2007 Axtell MJ, Snyder JA, Bartel DP. Common functions for diverse small RNAs of land plants. The Plant Cell. 19: 1750-69. PMID 17601824 DOI: 10.1105/tpc.107.051706  1
2006 Ruby JG, Jan C, Player C, Axtell MJ, Lee W, Nusbaum C, Ge H, Bartel DP. Large-scale sequencing reveals 21U-RNAs and additional microRNAs and endogenous siRNAs in C. elegans. Cell. 127: 1193-207. PMID 17174894 DOI: 10.1016/j.cell.2006.10.040  1
2006 Axtell MJ, Jan C, Rajagopalan R, Bartel DP. A two-hit trigger for siRNA biogenesis in plants. Cell. 127: 565-77. PMID 17081978 DOI: 10.1016/j.cell.2006.09.032  1
2005 Axtell MJ, Bartel DP. Antiquity of microRNAs and their targets in land plants. The Plant Cell. 17: 1658-73. PMID 15849273 DOI: 10.1105/tpc.105.032185  1
2003 Axtell MJ, Chisholm ST, Dahlbeck D, Staskawicz BJ. Genetic and molecular evidence that the Pseudomonas syringae type III effector protein AvrRpt2 is a cysteine protease. Molecular Microbiology. 49: 1537-46. PMID 12950919 DOI: 10.1046/j.1365-2958.2003.03666.x  1
2003 Axtell MJ, Staskawicz BJ. Initiation of RPS2-specified disease resistance in Arabidopsis is coupled to the AvrRpt2-directed elimination of RIN4. Cell. 112: 369-77. PMID 12581526 DOI: 10.1016/S0092-8674(03)00036-9  1
2002 Jin H, Axtell MJ, Dahlbeck D, Ekwenna O, Zhang S, Staskawicz B, Baker B. NPK1, an MEKK1-like mitogen-activated protein kinase kinase kinase, regulates innate immunity and development in plants. Developmental Cell. 3: 291-7. PMID 12194859 DOI: 10.1016/S1534-5807(02)00205-8  1
2001 Axtell MJ, McNellis TW, Mudgett MB, Hsu CS, Staskawicz BJ. Mutational analysis of the Arabidopsis RPS2 disease resistance gene and the corresponding pseudomonas syringae avrRpt2 avirulence gene. Molecular Plant-Microbe Interactions : Mpmi. 14: 181-8. PMID 11204781 DOI: 10.1094/MPMI.2001.14.2.181  1
1999 Kunz TH, Bicer E, Hood WR, Axtell MJ, Harrington WR, Silvia BA, Widmaier EP. Plasma leptin decreases during lactation in insectivorous bats. Journal of Comparative Physiology. B, Biochemical, Systemic, and Environmental Physiology. 169: 61-6. PMID 10093906 DOI: 10.1007/s003600050194  1
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