My work focuses primarily on the function of plant small RNAs, using a combination of experimental and computational methods. Small RNAs in plants function in post-transcriptional control, but also direct de novo DNA methylation (at CG and non-CG sites) and chromatin modifications, and thus they play a critical role in epigenetics, and my lab has played a significant role in characterizing these roles. The informatics methods developed in my lab and the library construction methods developed in my lab and with collaborators have allowed us to identify novel microRNAs and siRNA pathways, identify tissue-specific expression patterns, study microRNA evolution, determine novel targets of microRNAs, and understand the role of small RNAs in plant epigenetics. My lab has developed a novel genome browser for the visualization of transcriptional and DNA methylation data (https://mpss.danforthcenter.org/), optimized for the added complexity of plant small RNAs and DNA methylation at non-CG sites, and we have a customized and optimized database running behind this viewer, with all of the associated data integration and analysis tools and scripts. We have also developed various “apps” available from our websites for small RNA analysis. We are currently dissecting small RNA functions and biogenesis in Arabidopsis, maize, soybean, rice and numerous other plants using a combination of mutant analysis, comparative genomics, imaging, and a variety of molecular approaches. My lab has expertise in both wet-lab experimental biology and computational biology, and we have both developed and applied these methods to a broad range of experimental systems and questions.

We identified miRNAs in many of the first-sequenced plant genomes, investigating miRNA diversity and biogenesis, and characterizing plant miRNA evolution. We also conducted studies of other small RNA biogenesis pathways in plants, for example, investigating the plant-specific RNA polymerase IV and V-derived siRNAs that direct and maintain DNA methylation. I'm quite interested in the set of plant-specific, phased, secondary siRNAs that are triggered from mRNA targets, mainly by 22-nt miRNAs. The target mRNAs include a variety of long, non-coding RNAs (such as the best-described “tasiRNAs” but also many loci of unknown function) and several families of protein-coding genes (those encoding NB-LRRs, PPRs, MYB transcription factors, and F-box proteins are the largest families of genes generating phasiRNAs, thus far).

Most recently, working in maize and other grasses, we are studying phasiRNAs in grass reproductive organs, possible analogs of animal `piRNAs'. A current project aims to integrate diverse and novel datasets to determine spatiotemporal patterns of mRNA transcription, protein accumulation, and sRNA biogenesis focused on early maize anther development through successful meiosis - the stages at which two genetically separable sets of phasiRNAs are highly enriched. In this case, it appears that the tapetum and sporogenous cells are the sites of accumulation of these phasiRNAs; a key objective is to determine the functions, targets, and modes of action of these unusual and poorly-characterized phasiRNAs. We'd also like to better understand the Argonaute binding partners of these phasiRNAs, and of course their targets - both of which will be a key part of working out their functions.

• First of Four Joint University of Missouri/Donald Danforth Plant Science Center Researchers Hired

• ISI Highly Cited Researcher, 2014 & 2015 (Top 1% most-cited, for subject area)
• Elected Fellow, American Association for the Advancement of Science (AAAS), 2012
• Edward F. and Elizabeth Goodman Rosenberg Professor, Univ. of Delaware; 2010 – 2015
• Elected member, North American Arabidopsis Steering Committee (NAASC), 2009 – 2013
• President of NAASC, 2012 – 2013

B Khatabi, S Arikit, R Xia, S Winter, D Oumar, K Mongomake, BC Meyers, VN Fondong. (2016) High-resolution identification and abundance profiling of cassava (Manihot esculenta Crantz) microRNAs. BMC Genomics 17: 85. DOI: 10.1186/s12864-016-2391-1.

Curtin SJ, Michno JM, Campbell BW, Gil-Humanes J, Mathioni SM, Donohue RC, Kantar MB, Eamens AL, Meyers BC, Voytas DF, & Stupar RM (2015). microRNA maturation and microRNA target gene expression regulation are severely disrupted in soybean dicer-like1 double mutants. G3, pii, [epub]. DOI: 10.1534/g3.115.022137.

Patel P, Ramachandruni D, Kakrana A, Nakano M & Meyers BC (2015). miTRATA: a web-based tool for microRNA truncation and tailing analysis. Bioinformatics. 32(3):450-2. doi: 10.1093/bioinformatics/btv583.

Zhai J, Bischof S, Lee T-F, Teng C, Wang H, Chen X, Feng S, Gallego-Bartolome J, Park SY, Liu L, Liu W, Henderson I, Meyers BC, Ausin I & Jacobsen SE. Pol IV transcribes short RNAs that preferentially terminate at methylated cytosines by misincorporation. Cell. 163(2):445-55. doi: 10.1016/j.cell.2015.09.032.

Xia R, Xu J,Arikit S & Meyers BC (2015). Extensive families of miRNAs and PHAS loci in Norway spruce demonstrate the origins of complex phasiRNA networks in seed plants. Mol Biol Evol, 32(11):2905-18. doi: 10.1093/molbev/msv164.

Fei Q, Li P, Teng C & Meyers BC (2015). Secondary siRNAs from Medicago NB-LRRs modulated via miRNA-target interactions and their abundances. Plant J, 83(3):451-65. doi: 10.1111/tpj.12900.

Belli Kullan J, Lopes Paim Pinto D, Bertolini E, Fasoli M, Zenoni S, Tornielli GB, Pezzotti M, Meyers BC, Farina L, Pè M & Mica E (2015). miRVine: a microRNA expression atlas of grapevine based on small RNA sequencing. BMC Genomics, 16:393. doi: 10.1186/s12864-015-1610-5.

Xia R, Ye S, Liu Z, Meyers BC & Liu Z (2015). Novel and recently evolved microRNA clusters regulate expansive F-BOX gene networks through phased small interfering RNAs in wild diploid strawberry. Plant Physiol. 169(1): 594-610. doi: 10.1104/pp.15. 00253.

Yan Z, Hossain MS, Valdés-López O, Hoang NT, Zhai J, Wang J, Libault M, Brechenmacher L, Findley S, Joshi T, Qiu L, Sherrier DJ, Ji T, Meyers BC, Xu D & Stacey G (2015). Identification and functional characterization of soybean root hair microRNAs expressed in response to Bradyrhizobium japonicum infection. Plant Biotechnol J, [epub]. doi: 10.1111/ pbi.12387.

El Baidouri M, Kim KD, Abernathy B, Arikit S, Maumus F, Panaud O, Meyers BC & Jackson SA (2015). A new approach for annotation of transposable elements using small RNA mapping. Nucleic Acids Res 43(13):e84. doi:10.1093/nar/gkv257.

Yan Z, Hossain MS, Arikit S, Valdés-López O, Zhai J, Wang J, Libault M, Ji T, Qiu L, Meyers BC & Stacey G (2015). Identification of microRNAs and their mRNA targets during soybean nodule development: functional analysis of the role of miR393j-3p in soybean nodulation. New Phytol, 207(3):748-59. doi: 10.1111/nph.13365.

Tu B, Xu C, Liu L, Zhai J, Li S, Lopez MA, Zhao Y, Yu Y, Ramachandran V, Ren G, Yu B, Li S, Meyers BC, Mo B & Chen X (2015). Distinct and cooperative activities of HESO1 and URT1 nucleotidyl transferases in microRNA turnover in Arabidopsis. PLoS Genet, 11(4):e1005119. doi: 10.1371/journal.pgen.1005119.

Zhao M, Meyers BC, Cai C, Xu W, & Ma J (2015). Evolutionary patterns and coevolutionary consequences of MIRNA genes and microRNA targets triggered by multiple mechanisms of genomic duplications in soybean. Plant Cell, 27(3): 546-62. doi:10.1105/tpc.15.00048.

Zhai J, Zhang H, Arikit S, Huang K, Nan GL, Walbot V & Meyers BC (2015). Spatiotemporally dynamic, cell-type-dependent premeiotic and meiotic phasiRNAs in maize anthers. Proc. Natl. Acad. Sci. USA (PNAS), 112(10): 3146-51. doi:10.1073/pnas.1418918112.

Zhao M, Cai C, Zhai J, Lin F, Li L, Shreve J, Thimmapuram J, Hughes TJ, Meyers BC & Ma J (2015). Coordination of microRNAs, PhasiRNAs, and NB-LRR genes in response to a plant pathogen: Insights from analyses of a set of soybean Rps gene near-isogenic lines. The Plant Genome 8(1):1-13. doi:10.3835/plantgenome2014.09.0044.

Arikit S, Xia R, Kakrana A, Huang K, Zhai J, Yan Z, Valdés-López O, Prince S, Musket TA, Nguyen HT, Stacey G & Meyers BC (2014). An atlas of soybean small RNAs identifies phased siRNAs from hundreds of coding genes. Plant Cell, 26(12):4584-601. doi: 10.1105/tpc.114.131847. • Highlighted in Hofmann, NR (2014). “A world beyond Arabidopsis: Updates on small RNAs in plant development” Plant Cell, 26: 4564.

Thompson BE, Basham C, Hammond R, Ding Q, Kakrana A, Lee TF, Simon SA, Meeley R, Meyers BC & Hake S (2014). The dicerlike-1 homologue fuzzy tassel is required for the regulation of meristem determinacy in the inflorescence and vegetative growth in maize. Plant Cell, 26(12):4702-17. doi: 10.1105/tpc.114.132670. • Also highlighted in Hofmann, NR (2014). “A world beyond Arabidopsis: Updates on small RNAs in plant development” Plant Cell, 26: 4702-4717.

Kakrana A, Hammond R, Patel P, Nakano M & Meyers BC (2014). sPARTA: a parallelized pipeline for integrated analysis of plant miRNA and cleaved mRNA data sets, including new miRNA target-identification software. Nucleic Acids Res, 42(18):e139. doi:10.1093/nar/ gku693.

Wong J, Gao L, Yang Y, Zhai J, Arikit S, Yu Y, Duan S, Chan V, Xiong Q, Yan J, Li S, Liu R, Wang Y, Tang G, Meyers BC, Chen X & Ma W (2014). Roles of small RNAs in soybean defense against Phytophthora sojae infection. Plant J, 79(6):928-40. doi: 10.1111/tpj.12590.

Canto-Pastor A, Molla-Morales A, Ernst E, Dahl W, Zhai J, Yan Y, Meyers BC, Shanklin J & Martienssen RA (2014). Efficient transformation and artificial miRNA gene silencing in Lemna minor. Plant Biol, 17(Suppl1):59-65. doi: 10.1111/plb.12215.

Sasaki T, Lee T-F, Liao WW, Naumann U, Liao JL, Eun C, Huang YY, Fu JL, Chen PY, Meyers BC, Matzke AJ & Matzke M (2014). Distinct and concurrent pathways of Pol II- and Pol IV-dependent siRNA biogenesis at a repetitive trans-silencer locus in Arabidopsis thaliana. Plant J, 79(1): 127-38. doi:10.1111/tpj.12545.

Chávez Montes RA, de Fatima Rosas-Cárdenas F, De Paoli E, Accerbi M, Rymarquis LA, Mahalingam G, Marsch-Martínez N, Meyers BC*, Green PJ* & de Folter S* (2014). Sample sequencing of vascular plants demonstrates widespread conservation and divergence of microRNAs. Nature Comm, 5:3722. doi: 10.1038/ncomms4722.

Venu RC, Ma J, Jia Y, Liu G, Jia MH, Nobuta K, Sreerekha MV, Moldenhauer K, McClung AM, Meyers BC, & Wang GL (2014). Identification of candidate genes associated with positive and negative heterosis in rice. PLoS ONE, 9(4):e95178. doi:10.1371/journal.pone.0095178.

Wei L, Gu L, Song X, Cui X, Lu Z, Zhou M, Wang L, Hu F, Zhai J, Meyers BC & Cao X (2014). Dicer-like 3 produces transposable element-associated 24-nt siRNAs that control agricultural traits in rice. Proc Natl Acad Sci USA, 111(10):3877-82. doi: 10.1073/pnas. 1318131111.

Creasey KM, Zhai J, Borges F, Van Ex F, Regulski M, Meyers BC & Martienssen RA (2014). miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature, 508(7496): 411-5. doi: 10.1038/nature13069.

Zhai J, Arikit S, Simon SA, Kingham BF & Meyers BC (2014). Rapid construction of parallel analysis of RNA end (PARE) libraries for Illumina sequencing. Methods, 67(1):84-90. doi: 10.1016/j.ymeth.2013.06.025.

Jeong DH, Schmidt SA, Rymarquis LA, Park S, Ganssmann M, German MA, Accerbi M, Zhai J, Fahlgren N, Fox SE, Garvin DF, Mockler TC, Carrington JC, Meyers BC & Green PJ (2013). Parallel Analysis of RNA Ends enhances global investigation of microRNAs and target RNAs of Brachypodium distachyon. Genome Biol, 14(12):R145. doi: 10.1186/gb-2013-14-12-r145.

Gong L, Kakrana A, Arikit S, Meyers BC & Wendel JF (2013). Composition and expression of conserved microRNA genes in diploid cotton (Gossypium) species. Genome Biol Evol, 5(12):2449-59. doi: 10.1093/gbe/evt196.

Venkataramanan KP, Jones SW, McCormick KP, Kunjeti SG, Ralston MT, Meyers BC & Papoutsakis ET (2013). The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolic stress in C. acetobutylicum. BMC Genomics, 14:849. doi: 10.1186/1471-2164-14-849.

Schapire AL, Bologna NG, Moro B, Zhai J, Meyers BC & Palatnik JF (2013). Construction of Specific Parallel Amplification of RNA Ends (SPARE) libraries for the systematic identification of plant microRNA processing intermediates. Methods, 64(3):283-91. doi: 10.1016/j.ymeth. 2013.08.032.

The Amborella Genome Project [Meyers is a member and senior co-author] (2013). The Amborella genome and the evolution of flowering plants. Science, 342(6165):1241089. doi: 10.1126/science.1241089.

Bologna NG, Schapire AL, Zhai J, Chorostecki U, Boisbouvier J, Meyers BC & Palatnik J (2013). Multiple RNA recognition patterns during miRNA biogenesis in plants. Genome Res, 23(10):1675-89. doi: 10.1101/gr.153387.112.

Zhai J, Zhao Y, Simon SA, Huang S, Petsch K, Arikit S, Pillay M, Ji L, Xie M, Cao X, Yu B, Timmermans M, Yang B, Chen X & Meyers BC (2013). Plant MicroRNAs display differential 3' truncation and tailing, modifications which are ARGONAUTE1 dependent and conserved across species. Plant Cell, 25(7):2417-28. doi: 10.1105/tpc.113.114603.

Nandety RS, Caplan JL, Cavanaugh K, Perroud B, Wroblewski T, Michelmore RW & Meyers BC (2013). The role of TIR-NBS and TIR-X proteins in plant basal defense responses. Plant Physiol, 162(3):1459-72. doi: 10.1104/pp.113.219162.

Jeong DH, Thatcher SR, Brown RS, Zhai J, Park S, Rymarquis LA, Meyers BC & Green PJ (2013). Comprehensive investigation of microRNAs enhanced by analysis of sequence variants, expression patterns, ARGONAUTE loading, and target cleavage. Plant Physiol, 162(3):1225-45. doi: 10.1104/pp.113.219873.

Raman V, Simon SA, Romag A, Demirci F, Mathioni SM, Zhai J, Meyers BC & Donofrio NM (2013). Physiological stressors and invasive plant infections alter the small RNA transcriptome of the rice blast fungus, Magnaporthe oryzae. BMC Genomics, 14:326. doi: 10.1186/1471-2164-14-326.

Chen S, Songkumarn P, Venu RC, Gowda M, Bellizzi M, Hu J, Liu W, Ebbole D, Meyers B, Mitchell T, & Wang GL. (2013) Identification and characterization of in planta-expressed secreted effector proteins from Magnaporthe oryzae that induce cell death in rice. Mol Plant Microbe Interact, 26(2):191-202. http://dx.doi.org/10.1094/MPMI-05-12-0117-R.

Xia R, Meyers BC, Liu Z, Beers EP, Ye S & Liu Z (2013). MicroRNA superfamilies descend from miR390 and their roles in secondary small interfering RNA biogenesis in Eudicots. Plant Cell, 25(5):1555-72. doi: 10.1105/tpc.113.110957.

Venu RC, Sreerekha MV, Sheshu Madhav M, Nobuta K, Mohan M, Chen S, Jia Y, Meyers B & Wang GL (2013). Deep transcriptome sequencing reveals the expression of key functional and regulatory genes involved in the abiotic stress signaling pathways in rice. J. Plant Biol, 56: 216-231. doi: 10.1007/s12374-013-0075-9.

Stroud H, Ding B, Simon SA, Feng S, Bellizzi M, Pellegrini M, Wang GL, Meyers BC & Jacobsen SE (2013). Plants regenerated from tissue culture contain stable epigenome changes in rice. eLife, 2:e00354. doi: 10.7554/eLife.00354.

Ding B, Bellizi Mdel R, Ning Y, Meyers BC & Wang GL (2012). HDT701, a histone H4 deacetylase, negatively regulates plant innate immunity by modulating histone H4 acetylation of defense-related genes in rice. Plant Cell, 24(9):3783-94. doi: 10.1105/tpc.112.101972.

The International Arabidopsis Informatics Consortium. [Meyers is the interim director and a primary contributor] (2012). Taking the next step: Building an Arabidopsis Information Portal. Plant Cell, 24(6):2248-2256. doi: 10.1105/tpc.112.100669.

The EPIC Planning Committee [Meyers is a member and primary contributor] (2012). Reading the second code: Mapping epigenomes to understand plant growth, development, and adaptation to the environment. Plant Cell, 24: 2257-2261. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3406913/pdf/2257.pdf

Chodavarapu RK, Feng S, Ding B, Simon SA, Lopez D, Jia Y, Wang GL, Meyers BC, Jacobsen S & Pellegrini M (2012). Transcriptome and methylome interactions in rice hybrids. Proc. Natl. Acad. Sci. USA (PNAS), 109(30):12040-5. doi: 10.1073/pnas.1209297109.

Ausin I, Greenberg MV, Simanshu DK, Hale CJ, Vashist AA, Simon SA, Lee T-F, Feng S, Espanola S, Meyers BC, Wohlshlegel JA, Patel DJ & Jacobsen SE (2012). INVOLVED IN DE NOVO 2-containing complex involved in RNA-directed DNA methylation in Arabidopsis. Proc. Natl. Acad. Sci. USA (PNAS), 109(22):8374-81. doi: 10.1073/pnas/1206638109.

Lee TF, Gurazada SG, Zhai J, Li S, Simon SA, Matzke M, Chen X & Meyers BC (2012). RNA Polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeats. Epigenetics,7(7):781-95. doi: 10.4161/epi.20290.

Barbour JE, Liao IT, Stonaker JL, Lim JP, Lee CC, Parkinson SE, Kermicle J, Simon SA, Meyers BC, Williams-Carrier R, Barkan A & Hollick JB (2012). required to maintain repression2 is a novel protein that facilitates locus-specific paramutation in maize. Plant Cell, 24(5):1761-75. doi: 10.1105/tpc.112.097618.

Sánchez-León N, Arteaga-Vázquez M, Alvarez-Mejía C, Mendiola-Soto J, Durán-Figueroa N, Rodríguez-Leal D, Rodríguez-Arévalo I, García-Campayo V, Garcia-Aguilar M, Olmedo-Monfil V, Arteaga-Sánchez M, de la Vega OM, Nobuta K, Vemaraju K, Meyers BC & Vielle-Calzada JP (2012). Transcriptional analysis of the Arabidopsis ovule by massively parallel signature sequencing. J. Exp. Bot, 63(10):3829-42. doi: 10.1093/jxb/ers075.

The Tomato Genome Sequencing Consortium [Meyers is a member and senior co-author] (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485(7400):635-41. doi: 10.1038/nature11119.

You W, Tyczewska A, Spencer M, Daxinger L, Schmid MW, Grossniklaus U, Simon SA, Meyers BC, Matzke AJ & Matzke M (2012). Atypical DNA methylation of genes encoding cysteine-rich peptides in Arabidopsis thaliana. BMC Plant Biol, 12:51. doi: 10.1186/1471-2229-12-51.

Zhao Y, Yu Y, Zhai J, Ramachandran V, Dinh TT, Meyers BC, Mo B & Chen X (2012). The Arabidopsis nucleotidyl transferase HESO1 uridylates unmethylated small RNAs to trigger their degradation. Current Biol, 22(8):689-94. doi: 10.1016/j.cub.2012.02.051.

Gao D, Chen J, Chen M, Meyers BC & Jackson S (2012). A highly conserved, small LTR retrotransposon that preferentially targets genes in grass genomes. PLoS One, 7(2):e32010. doi: 10.1371/journal.pone.0032010.

Committee on Gene Symbolization, Nomenclature and Linkage, Rice Genetics Cooperative [Meyers is a member and co-author] (2012). Nomenclature report on rice WRKY's - Conflict regarding gene names and its solution. RICE, 5:3. doi:10.1186/1939-8433-5-3.

Yue JX, Meyers BC, Chen JQ, Tian D & Yang S (2012). Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes. New Phytol, 193(4):1049-63. doi: 10.1111/j.1469-8137.2011.04006.x.

Song X, Li P, Zhai J, Zhou M, Ma L, Liu B, Jeong DH, Nakano M, Cao S, Liu C, Chu C, Wang XJ, Green PJ, Meyers BC & Cao X (2012). Roles of DCL4 and DCL3b in rice phased small RNA biogenesis. Plant J, 69(3):462-74. doi: 10.1111/j.1365-313X.2011.04805.x.

Zhai J, Jeong DH, De Paoli E, Park S, Rosen BD, Li Y, González AJ, Yan Z, Kitto SL, Grusak MA, Jackson SA, Stacey G, Cook DR, Green PJ, Sherrier DJ & Meyers BC (2011). MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes & Dev, 25(23):2540 -53. doi: 10.1101/gad.177527.111.

Kunjeti SG, Evans TA, Marsh AG, Gregory NF, Kunjeti S, Meyers BC, Kalavacharla VS & Donofrio NM (2011). RNA-Seq reveals infection-related global gene changes in Phytophthora phawseoli, the causal agent of lima bean downy mildew. Mol. Plant Pathol, 13(5):454-66. doi: 10.1111/j.1364-3703.2011.00761.x.

Young ND, Debellé F, Oldroyd G, Geurts R, Cannon SB, Mayer KFX, Gouzy J, Van de Peer Y, Schoof H, Udvardi MK, Cook DR, Meyers BC…(106 co- authors)… & Roe BA (2011). The Medicago genome provides insight into evolution of rhizobial symbiosis. Nature, 480(7378):520-4. doi: 10.1038/nature10625.

Jeong DH, Park S, Zhai J, Gurazada SG, De Paoli E, Meyers BC & Green PJ (2011). Massive analysis of rice small RNAs: mechanistic implications of regulated miRNAs and variants for differential target RNA cleavage. Plant Cell 23, (12):4185-207. doi: 10.1105/tpc.111.089045.

La H, Ding B, Mishra GP, Zhou B, Yang H, Bellizzi Mdel R, Chen S, Meyers BC, Peng Z, Zhu JK & Wang GL (2011). A 5-methylcytosine DNA glycosylase/lyase demethylates the retrotransposon Tos17 and promotes its transposition in rice. Proc Natl Acad Sci USA, 108(37):15498-503. doi: 10.1073/pnas.1112704108.

Eun C, Lorkovic ZJ, Naumann U, Long Q, Havecker ER, Simon SA, Meyers BC, Matzke AJ & Matzke M (2011). AGO6 functions in RNA-mediated transcriptional gene silencing in shoot and root meristems in Arabidopsis thaliana. PLoS ONE, 6(10):e25730. doi:10.1371/journal. pone.0025730.

Kalavacharla V, Liu Z, Meyers BC, Thimmapuram J & Melmaiee K (2011). Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencing. BMC Plant Biol, 11:135. doi: 10.1186/1471-2229-11-135.

Shen Y, Venu RC, Nobuta K, Wu X, Notibula V, Demirci C, Meyers BC, Wang GL & Li QQ (2011). Transcriptome dynamics through alternative polyadenylation in developmental and environmental responses in plants revealed by deep sequencing. Genome Res, 21(9):1478-86.

Venu RC, Sreerekha M, Nobuta K, Beló A, Ning Y, An G, Meyers BC & Wang GL (2011). Deep sequencing reveals the complex and coordinated transcriptional regulation of genes related to grain quality in rice cultivars. BMC Genomics, 12:190. doi: 10.1186/1471-2164-12-190.

Waidner LA, Burnside J, Anderson AS, Bernberg EL, German MA, Meyers BC, Green PJ & Morgan RW (2011). A microRNA of infectious laryngotracheitis virus can downregulate and direct cleavage of ICP4 mRNA. Virology, 411(1):25 -31. doi: 10.1016/j.virol.2010.12.023.

Raffaele S, Farrer RA, Cano LM, Studholme DJ, MacLean D, Thines M, Jiang RH, Zody MC, Kunjeti SG, Donofrio NM, Meyers BC, Nusbaum C & Kamoun S (2010). Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science, 330(6010):1540-3. doi: 10.1126/science.1193070.

Arteaga-Vazquez M, Sidorenko L, Rabanal FA, Shrivistava R, Nobuta K, Green PJ, Meyers BC & Chandler VL (2010). RNA-mediated trans-communication can establish paramutation at the b1 locus in maize. Proc Natl Acad Sci USA, 107(29):12986-91. doi: 10.1073/pnas. 1007972107.

Yu B, Bi L, Zhai J, Agarwal M, Li S, Wu Q, Ding SW, Meyers BC, Vaucheret H & Chen X (2010). siRNAs compete with miRNAs for methylation by HEN1 in Arabidopsis. Nucleic Acid Res, 38(17):5844-50. doi: 10.193/nar/gkq348.

Venu RC, Sheshu Madhav M, Sreerekha MV, Nobuta K, Zhang Y, Carswell P, Boehm MJ, Meyers BC, Korth KL & Wang GL (2010). Deep and comparative transcriptome analysis of rice plants infested by the beet armyworm (Spodoptera exigua) and water weevil (Lissorhoptrus oryzophilus). RICE, 3:22-35. http://rd.springer.com/article/10.1007/s12284-010-9037-8.

Joshi T, Yan Z, Libault M, Jeong DH, Park S, Green PJ, Sherrier DJ, Farmer A, May G, Meyers BC, Xu D & Stacey G (2010). Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics, 11 Suppl1:S14. doi: 10.1186/1471-2105-11-S1-S14.

Swaminathan K, Alabady MS, Varala K, De Paoli E, Ho I, Rokhsar DS, Arumuganathan AK, Ming R, Green PJ, Meyers BC, Moose SP & Hudson ME (2010). Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. Genome Biol, 11(2):R12. doi: 10.1186/gb-2010-11-2-r12.

The International Brachypodium Initiative [Meyers is a member and co-author] (2010). Genome sequencing and analysis of the model grass Brachypodium distachyon. Nature, 463(7282):763-8. doi: 10.1038/nature08747.

Kanno T, Bucher E, Daxinger L, Huettel B, Kreil DP, Breinig F, Lind M, Schmitt MJ, Simon SA, Gurazada SG, Meyers BC, Lorkovic ZJ, Matzke AJ & Matzke M (2010). RNA-directed DNA methylation and plant development require an IWR1-type transcription factor. EMBO Rep, 11(1):65-71. doi: 10.1038/embor.2009.246.

Wei F…(45 co-authors)…Meyers BC, Bennetzen J, Martienssen RA, McCombie WR, Aluru S, Clifton SW, Schnable PS, Ware D, Wilson RK & Wing RA (2009). Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genetics, 5(11):e1000728. doi: 10.1371/journal.pgen.1000728.

Haas BJ…(117 co-authors) …Meyers BC, van West P, Ristaino J, Govers F, Birch PR, Whisson SC, Judelson HS & Nusbaum C (2009). Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature, 461(7262):393-8. doi: 10.1038/nature08358.

De Paoli E, Dorantes-Acosta A, Zhai J, Accerbi M, Jeong DH, Park S, Meyers BC, Jorgensen RA & Green PJ (2009). Distinct extremely abundant siRNAs associated with cosuppression in Petunia. RNA, 15(11):1965-70. doi: 10.1261/rna.1706109.

Waidner LA, Morgan RW, Anderson AS, Bernberg EL, Kamboj S, Garcia M, Riblet SM, Ouyang M, Isaacs GK, Markis M, Meyers BC, Green PJ & Burnside J (2009). MicroRNAs of Gallid and Meleagrid Herpesviruses show generally conserved genomic locations and are virus-specific. Virology, 388(1):128-36. doi: 10.1016/j.virol.2009.02.043.

German MA, Luo S, Schroth G, Meyers BC & Green PJ (2009). Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nature Protoco, 4(3):356-62. doi: 10.1038/nprot.2009.8. 79. Hanada K, Vallejo V, Nobuta K, Slotkin RK, Lisch D, Meyers BC, Shiu SH & Jiang N (2009). The functional role of pack-MULEs in rice inferred from purifying selection and expression profile. Plant Cell, 21(1):25-38. doi: 10.1105/tpc.108.063206.

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 (2008). Criteria for annotation of plant microRNAs. Plant Cell, 20(12):3186-90. doi: 10.1105/tpc.108.064311.

Morgan RW, Anderson A, Bernberg E, Kamboj S, Huang E, Lagasse G, Isaacs G, Parcells M, Meyers BC, Green PJ & Burnside J (2008). Sequence conservation and differential expression of Marek's disease virus microRNAs. J. Virol, 82(24):12213-20. doi: 10.1128/JVI.01722-08.

Nobuta K, Lu C, Shrivastava R, Pillay M, De Paoli E, Accerbi M, Arteaga-Vasquez M, Sidorenko L, Jeong DH, Yen Y, Green PJ, Chandler V* & Meyers BC* (2008). Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci USA, 105(39):14958-63. doi: 10.1073/pnas.0808066105.

German MA, Pillay M, Jeong DH, Hetawal A, Luo S, Janardhanan P, Kannan V, Rymarquis LA, Nobuta K, German R, De Paoli E, Lu C, Schroth G, Meyers BC* & Green PJ* (2008). Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nature Biotech, 26(8):941-6. doi: 10.1038/nbt1417.

Iandolino A, Nobuta K, da Silva FG, Cook DR & Meyers BC (2008). Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures. BMC Plant Biol, 8:53. doi: 10.1186/1471-2229-8-53.

Burnside J, Ouyang M, Anderson A, Bernberg E, Lu C, Meyers BC, Green PJ, Markis M, Isaacs G, Huang E & Morgan RW (2008). Deep sequencing of chicken microRNAs. BMC Genomics, 9:185. doi: 10.1186/1471-2164-9-185.

Peiffer JA, Kaushik S, Sakai H, Arteaga-Vazquez M, Sanchez-Leon N, Ghazal H, Vielle-Calzada JP & Meyers BC (2008). A Spatial Dissection of the Arabidopsis Floral Transcriptome by MPSS. BMC Plant Biol, 8:43. doi: 10.1186/1471-2229-8-43.

Beló A, Nobuta K, Venu RC, Janardhanan PE, Wang GL & Meyers BC (2008). Transposable element regulation in rice and Arabidopsis: diverse patterns of active expression and siRNA-mediated silencing. Tropical Plant Biol, 1:72-84. doi: 10.1007/s12042-007-9008-4.

Zhai J, Liu J, Li PC, Meyers BC, Chen X & Cao X (2008). Small RNA-directed epigenetic natural variation in Arabidopsis thaliana. PLoS Genetics, 4(4):e1000056. doi: 10.1371/journal.pgen.1000056.

Lin H, Ouyang S, Egan A, Nobuta K, Haas BJ, Gu X, Silva JC, Meyers BC & Buell CR (2008). Characterization of paralogous protein families in rice. BMC Plant Biol, 8:18. doi: 10.1186/1471-2229-8-18.

Adams-Phillips L, Wan J, Tan X, Dunning FM, Meyers BC, Michelmore RW & Bent AF (2008). Discovery of ADP-ribosylation and other plant defense pathway elements through expression profiling of four different Arabidopsis-Pseudomonas R/avr interactions. Mol Plant Microbe Interact, 21(5):646-57. doi: 10.1094/MPMI-21-5-0646.

Lu C, Jeong DH, Kulkarni K, Pillay M, Nobuta K, German R, Thatcher SR, Maher C, Zhang L, Ware D, Liu B, Cao X, Meyers BC & Green PJ (2008). Genome-wide analysis for discovery of new rice miRNAs reveals natural antisense miRNAs (nat- miRNAs). Proc. Natl. Acad. Sci. USA (PNAS), 105(12):4951-6. doi: 10.1073/pnas.0708743105.

Kohler A, Rinaldi C, Duplessis S, Baucher M, Geelen D, Duchaussoy F, Meyers BC, Boerjan W & Martin F (2008). Genome-wide identification of NBS resistance genes in Populus trichocarpa. Plant Mol Biol, 66(6):619-36. doi: 10.1007/s11103-008-9293-9.

Kuang H, Caldwell KS, Meyers BC & Michelmore RW (2008). Frequent sequence exchanges between homologs of RPP8 in Arabidopsis are not necessarily associated with genomic proximity. Plant J, 54(1):69-80. doi: 10.1111/j.1365-313X.2008.03408.x.

Rice Annotation Project: Tanaka T…92 authors…Meyers BC, Chaparro C, Piegu B, Panaud O & Echeverria M (2008). The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res, 36(Database issue):D1028-33.

Chen J, Agrawal V, Rattray M, West MA, St.Clair DA, Michelmore RW, Coughlan SJ & Meyers BC (2007). A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis. BMC Genomics, 8:414.

Tan X, Meyers BC, Kozik A, West MA, Morgante M, St. Clair DA, Bent AF & Michelmore RW (2007). Global expression analysis of nucleotide binding site-leucine rich repeat-encoding genes in Arabidopsis. BMC Plant Biol, 7:56.

Ganko EW, Meyers BC & Vision TJ (2007). Divergence in expression between duplicated genes in Arabidopsis. Mol Biol Evol, 24(10):2298 -309.

Nobuta K, Venu RC, Lu C, Belo A, Vemaraju K, Kulkarni K, Wang W, Pillay M, Green PJ, Wang GL & Meyers BC (2007). An expression atlas of rice mRNAs and small RNAs. Nature Biotech, 25(4):473-7.

Gowda M, Venu RC, Raghupathy MB, Nobuta K, Li H, Wing R, Stahlberg E, Coughlan S, Haudenschild CD, Dean R, Meyers BC* & Wang GL* (2006). Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methods. BMC Genomics, 7:310.

Lu C, Kulkarni K, Souret FF, MuthuValliappan R, Tej SS, Poethig RS, Henderson IR, Jacobsen SE, Wang W, Green PJ* & Meyers BC* (2006). MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res, 16(10):1276-88.

Yan H, Ito H, Nobuta K, Ouyang S, Jin W, Tian S, Lu C, Venu RC, Wang GL, Green PJ, Wing RA, Buell CR, Meyers BC & Jiang J (2006). Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromere. Plant Cell, 18(9):2123-33.

Burnside J, Bernberg E, Anderson A, Lu C, Meyers BC, Green PJ, Jain N, Isaacs G & Morgan RW (2006). Marek's disease virus encodes MicroRNAs that map to meq and the latency-associated transcript. J Virol, 80(17):8778-86.

Henderson IR, Zhang X, Lu C, Johnson L, Meyers BC, Green PJ & Jacobsen SE (2006). Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing, and DNA methylation patterning. Nature Genet, 38(6):721-5.

Tetko IV, Haberer G, Rudd S, Meyers BC, Mewes HW & Mayer KFX (2006). Spatiotemporal Expression Control correlates with Intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana. PLoS Comput Biol, 2(3):e67. doi: 10.1371/journal.pcbi.0020021.

Nakano M, Nobuta K, Vemeraju K, Tej SS, Skogen JW & Meyers BC (2006). Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res, 34(Database issue):D731-5.

Moreno-Vázquez S, Ning J & Meyers BC (2005). hATpin, a family of MITE-like hAT mobile elements conserved in diverse plant species that forms highly stable secondary structures. Plant Mol Biol, 58(6):869-86.

Lu C, Tej SS, Luo S, Haudenschild CD, Meyers BC* & Green PJ*(2005). Elucidation of the small RNA component of the transcriptome. Science, 309(5740):1567-9.

Meyers BC, Tej SS, Vu TH, Haudenschild CD, Agrawal V, Edberg SB, Ghazal H & Decola S (2004). The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res, 14(8):1641-53.

Meyers BC, Vu TH, Tej SS, Ghazal H, Matvienko M, Agrawal V & Haudenschild CD (2004). Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencing. Nat Biotech, 22(8):1006-11.

Kuang H, Woo SS, Meyers BC, Nevo E & Michelmore RW (2004). Multiple genetic processes result in heterogeneous rates of evolution within the major cluster disease resistance genes in lettuce. Plant Cell, 16(11):2870-94.

Wright SI, Yau CB, Looseley M & Meyers BC (2004). Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Mol Biol Evol, 21(9):1719-26.

Meyers BC, Lee DK, Vu TH, Tej SS, Edberg SB, Matvienko M & Tindell LD (2004). Arabidopsis MPSS: an online resource for quantitative expression analysis. Plant Physiol, 135(2):801-13.

Rudd S, Frisch M, Grote K, Meyers BC, Mayer K & Werner T (2004). Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expression. Plant Physiol, 135(2):715-22.

Haberer G, Hindemitt T, Meyers BC & Mayer K (2004). Transcriptional similarities, dissimilarities and conservation of cis-elements in duplicated genes of Arabidopsis. Plant Physiol, 136(2):3009-22.

Meyers BC, Kozik A, Griego A, Kuang H & Michelmore RW (2003). Genome-wide analysis of NBS-LRR-encoding genes in Arabidopsis. Plant Cell, 15(4):809-34. · Highlighted in Eckardt & Innes (2003) “Resistance Rodeo: Rounding up the Full Complement of Arabidopsis NBS-LRR Genes” Plant Cell, 15(4):806 -807. doi:10.1105/tpc.150470

Meyers BC, Morgante M & Michelmore RW (2002). TIR-X and TIR-NBS proteins: two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomes. Plant J, 32(1):77-92.

Mondragon-Palomino M, Meyers BC, Michelmore RW & Gaut BS (2002). Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res, 12(9):1305-15.

Shen KA, Chin DB, Arroyo-Garcia R, Ochoa OE, Lavelle DO, Wroblewski T, Meyers BC & Michelmore RW (2002). Dm3 is one member of a large constitutively expressed family of nucleotide binding site-leucine-rich repeat encoding genes. Mol Plant Microbe Interact, 15(3):251-61.