Trupti Joshi, Zhe Yan, Marc Libault, Dong-Hoon Jeong,, Sunhee Park, Pamela J Green, D Janine Sherrier, Andrew Farmer, Greg May, Blake C Meyers, Dong Xu and Gary Stacey (2010) Prediction of novel miRNAs and associated target genes in Glycine max. Bioinformatics 2010, 11(Suppl 1):S.

Stacey A. Simon, Blake C. Meyers, and D. Janine Sherrier (2009) MicroRNAs in the Rhizobia Legume Symbiosis. Plant Physiol. 151: 1002-1008.

Lee TF, Zhai J, Meyers BC. (2010) Conservation and divergence in eukaryotic DNA methylation. Proc Natl Acad Sci U S A. 2010 May 18;107(20):9027-8.

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 Acids Res. 2010 May 6.

Venu, R. C., Madhav, M.S., Sreerekha, M. V., Nobuta, K., Zhang, Y., Carswell, P., Boehm, M.J., Meyers, B.C., Korth, K.L., and G.L. Wang. (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.

Joshi, T., Yan, Z., Libault, M., Jeong, D.H., Park, S., Green, P.J., Sherrier, D.J., Farmer, A., May, G., Meyers, B.C., Xu, D., and G. Stacey. (2010) Prediction of novel miRNAs and associated target genes in Glycine max. BMC Bioinformatics. 11: Suppl 1, S14.

Meyers BC, Simon SA, Zhai J. (2010) MicroRNA processing: battle of the bulge. Curr Biol. 2010 Jan 26;20(2):R68-70.

Swaminathan, K., Alabady, M., Varala, K., De Paoli, E., Ho, I., Rokhsar, D., Ming, R., Green, P.J., Meyers, B.C., Moose, S.P., and M.E. Hudson. (2010) Surveying the structure and expression of genomic repetitive elements from Miscanthus x giganteus. Genome Biology. 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. 463:763-768.

Kanno, T., Bucher, E., Daxinger, L., Huettel, B., Kreil, D.P., Breinig, F., Lind, M., Schmitt, M.J., Simon, S.A., Gurazada, S.G.R, Meyers, B.C., Lorkovic, Z.J., Matzke, A.J.M., and M. Matzke. (2010) RNA-directed DNA methylation and plant development require an IWR1-type transcription factor. EMBO Reports. 11:65-71.

2009

Wei, F., …(45 co-authors)…, Meyers, B.C., Bennetzen, J., Martienssen, R., McCombie, W.R., Aluru, S., Clifton, S.W., Schnable, P.S., Ware, D., Wilson, R.K, and R.A. Wing. (2009) Detailed analysis of a contiguous 22-Mb region of the maize genome. PLoS Genetics 5:e1000728.

Haas, B., …(117 co-authors)...Meyers, B.C., van West, P., Ristaino, J., Govers, F., Birch, P.R., Whisson, S.C., Judelson, H.S., and C. Nusbaum. (2009) The genome sequence of the Irish potato famine pathogen Phytophthora infestans. Nature. 461:393-398.

De Paoli, E., Dorantes-Acosta, A., Zhai, J., Accerbi, M., Jeong, D.H., Meyers, B.C., Jorgensen, R.A., and P. J. Green (2009) Distinct extremely abundant siRNAs associated with cosuppression in Petunia. RNA. 15:1965-70.

Waidner, L. Morgan, R., Anderson, A., Bernberg, E., Kamboj, S., Garcia, M., Riblet, S., Ouyang, M., Isaacs, G., Markis, M., Meyers, B.C., Green, P.J., and J. Burnside. (2009) MicroRNAs of Gallid and Meleagrid Herpesviruses show generally conserved genomic locations and are virus-specific. Virology. 388:128-36.

German, M.A., Luo, S., Schroth, G., Meyers, B.C., and P. J. Green (2009) Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nature Protocols. 4:356-362.

Hanada, K., Vallejo, V., Nobuta, K., Slotkin, R.K., Lisch, D., Meyers, B.C., Shiu, S.H., and N. Jiang. (2009). Expression and functional indication of Pack-MULEs in rice. Plant Cell. 21: 25-38.

2008

Meyers, B.C.*, Axtell, M.J.*, Bartel, B., Bartel, D.P., Baulcombe, D., Bowman, J.L., Cao, X., Carrington, J.C., Chen, X., Green, P.J., Griffiths-Jones, S., Jacobsen, S.E., Mallory, A.C., Martienssen, R.A., Poethig, R.S., Qi, Y., Vaucheret, H., Voinnet, O., Watanabe, Y., Weigel, D., and J.K. Zhu. (2008) Criteria for annotation of plant microRNAs. Plant Cell. 20: 3186-3190.
* indicates co-corresponding authors.

Morgan, R.W., Anderson, A., Bernberg, E., Kamboj, S., Huang, E., Lagasse, G., Isaacs, G., Parcells, M., Meyers, B.C., Green, P.J., and J. Burnside (2008) Sequence conservation and differential expression of Marek’s disease virus microRNAs. J. Virology. 82:12213-20.

Nobuta, K., Lu, C., Shrivastava, R., Pillay, M., De Paoli, E., Accerbi, M., Arteaga-Vasquez, M., Sidorenko, L., Jeong, D.-H., Yen, Y., Green, P.J., Chandler, V. *, and B.C. Meyers *. (2008) A novel size distribution of endogeneous siRNAs in maize: evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci USA. 105:14958-63.
* indicates co-corresponding authors.

German, M.A., Pillay, M., Jeong, D.-H., Hetawal, A., Luo, S., Janardhanan, P., Kannan, V., Rymarquis, L., Nobuta, K., German, R., De Paoli, E., Lu, C., Schroth, G., Meyers, B.C. *, and P.J. Green *. (2008) Novel microRNA-target RNA pairs revealed by Parallel Analysis of RNA Ends (PARE). Nature Biotechnology. 26:941-946.
* indicates co-corresponding author.

Iandolino, A., Nobuta, K., Goes da Silva, F., Wu, H., D. Cook, and B.C. Meyers. (2008). Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signatures. BMC Plant Biology. 8:53.

Burnside, J., Ouyang, M., Anderson, A., Bernberg, E., Lu, C., Meyers, B.C., Green, P.J., Isaacs, G., and R.W. Morgan. (2008) Deep sequencing of chicken microRNAs. BMC Genomics. 9:185.

Peiffer, J.A., Kaushik, S., Sakai, H., Arteaga-Vazquez, M., Sanchez-Leon, N., Ghazal, H., Vielle-Calzada, J.P., and B.C. Meyers. (2008) A Spatial Dissection of the Arabidopsis Floral Transcriptome by MPSS. BMC Plant Biology. 8:43.

Beló, A., Nobuta, K., Venu, R.C., Janardhanan, P.E., Wang, G.-L., and B.C. Meyers. (2008) Transposable element regulation in rice and Arabidopsis: diverse patterns of active expression and siRNA-mediated silencing. Tropical Plant Biology. 1:72-84.

Zhai, J., Liu, J., Li, P.C., Meyers, B.C., Chen, X., and X. Cao. (2008) Small RNA-directed epigenetic natural variation between Arabidopsis ecotypes. PLoS Genetics. 4:e1000056.

Lin, H., Ouyang, S., Egan, A., Nobuta, K., Haas, B., Gu, X., Silva, J.C., Meyers, B.C., and C.R. Buell. (2008) Characterization of paralogous protein families in rice. BMC Plant Biology. 8:18.

Adams-Phillips, L., Wan, J., Tan, X., Dunning, M., Meyers, B.C., Michelmore, R.W., and A. Bent. (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. 21:646-657.

 Lu, C., Jeong, D.-H., Kulkarni, K., Pillay, M., Nobuta, K., German, R., Thatcher, S., Maher, C. Zhang, L., Ware, D., Liu, B., Cao, X., Meyers, B.C.,  and P.J. Green. (2008) Genome-wide analysis for discovery of new rice miRNAs reveals natural antisense miRNAs (nat-miRNAs). Proc Natl Acad Sci USA. 105:4951-4956.  

Kohler, A., Rinaldi, C., Duplessis, S., Baucher, M., Geelen, D., Hellsten, U., Frédéric Duchaussoy,  Meyers, B.C., DiFazio, S., Boerjan, W. and F. Martin. (2008) Genome-wide identification of NBS resistance genes in Populus trichocarpa. Plant Molecular Biology. 66:619-636.

Kuang, H., Caldwell, K., Meyers, B.C.,  and R.W. Michelmore. (2008) Frequent sequence exchanges between homologs of RPP8 in Arabidopsis are not necessarily associated with genomic proximity. The Plant Journal. 54:69-80.

Tanaka, T., B.A. Antonio, S. Kikuchi, T. Matsumoto, Y. Nagamura, H. Numa, H. Sakai, J. Wu, T. Itoh, T. Sasaki, R. Aono, Y. Fujii, T. Habara, E. Harada, M. Kanno, Y. Kawahara, H. Kawashima, H. Kubooka, A. Matsuya, H. Nakaoka, N. Saichi, R. Sanbonmatsu, Y. Sato, Y. Shinso, M. Suzuki, J. Takeda, M. Tanino, F. Todokoro, K. Yamaguchi, N. Yamamoto, C. Yamasaki, T. Imanishi, T. Okido, M. Tada, K. Ikeo, Y. Tateno, T. Gojobori, Y.C. Lin, F.J. Wei, Y.I. Hsing, Q. Zhao, B. Han, M.R. Kramer, R.W. McCombie, D. Lonsdale, C.C. O'Donovan, E.J. Whitfield, R. Apweiler, K.O. Koyanagi, J.P. Khurana, S. Raghuvanshi, N.K. Singh, A.K. Tyagi, G. Haberer, M. Fujisawa, S. Hosokawa, Y. Ito, H. Ikawa, M. Shibata, M. Yamamoto, R.M. Bruskiewich, D.R. Hoen, T.E. Bureau, N. Namiki, H. Ohyanagi, Y. Sakai, S. Nobushima, K. Sakata, R.A. Barrero, Y. Sato, A. Souvorov, B. Smith-White, T. Tatusova, S. An, G. An, O.O. S, G. Fuks, G. Fuks, J. Messing, K.R. Christie, D. Lieberherr, H. Kim, A. Zuccolo, R.A. Wing, K. Nobuta, P.J. Green, C. Lu, B.C. Meyers, C. Chaparro, B. Piegu, O. Panaud, and M. Echeverria.  (2008). The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Research. 36(Database issue):D1028-33.

Chen, J., Agrawal, V., Rattray, M., West, M.A.L., St.Clair, D.A., Michelmore, R.W., Coughlan, S.J., and B.C. Meyers. (2007) A comparison of microarray and MPSS technology platforms for expression analysis of Arabidopsis. BMC Genomics. 8:414.

Tan, X., Meyers, B.C., Kozik, A., West, M.A.L., Morgante, M., St. Clair, D.A., Bent, A.F., and R.W. Michelmore. (2007) Global expression analysis of nucleotide binding site-leucine rich repeat-encoding genes in Arabidopsis. BMC Plant Biology. 7:56.

Ganko, E.W., Meyers, B.C., and T.J. Vision. (2007) Divergence in expression between duplicated genes in Arabidopsis. Mol. Biol. Evolution. 24(10):2298–2309

Nobuta, N., Venu, R.C., Lu, C., Belo, A., Vemaraju, K., Kulkarni, K., Wang, W., Pillay, M., Green, P.J., Wang, G.-L., and B.C. Meyers. (2007) An expression atlas of rice mRNA and small RNA. Nature Biotechnology. 25:473-477.

Gowda, M., Venu, R.C., Li, H., Nobuta, K., Raghupathy, M., Kim, H., Stahlberg, E., Coughlan, S., Haudenschild, C.D., Dean, R., Meyers, B.C.*, and G. Wang*. (2007). Deep and comprehensive transcriptome analysis of Magnaporthe grisea using MPSS, RL-SAGE, and microarrays. BMC Genomics. 8:310-326.* indicates co-corresponding authors.

Nobuta, K., Vemaraju, K., and Meyers, B.C. (2006).  Method for analysis of gene expression in plants using MPSS. Methods in Molecular Biology. 406:387-408.

Lu, C., Kulkarni, K., Souret, F.F., Valliappan, R.M., Tej, S.S., Poethig, R.S., Henderson, I. R., Jacobsen,  S.E., Wang, W., P.J. Green* and B.C. Meyers*. (2006) microRNAs and other small RNAs enriched in the Arabidopsis RNA-DEPENDENT RNA POLYMERASE-2 mutant. Genome Research. 16:1276-1288.      * indicates co-corresponding authors.

Yan, H., Ito,H., Nobuta, K., Ouyang, S., Jin, W., Tian, S., Lu, C., Venu, R.C., Wang, G.L., Green, P.J., Wing, R.A., Buell, C.R., Meyers, B.C., and J. Jiang. (2006) Genomic and genetic characterization of rice Cen3 reveals evolutionary remnants of a complex centromere. Plant Cell. 18:2123-2133.

Burnside, J. Bernberg, E., Anderson, A., Lu, C., Meyers, B. C., Green, P.J., Jain, N., Isaac, G., and R. Morgan. (2006) Cloning and expression of microRNAs flanking the meq oncogene of Marek's disease virus. J. Virology. 80:8778-8786.

Henderson, I.R., Zhang, X., Lu, C., Johnson, L., Meyers, B.C., Green, P.J., and Jacobsen, S.E. (2006). Dissecting Arabidopsis DICER function in small RNA processing, gene silencing, and DNA methylation patterning. Nature Genetics. 38:721-725.

Tetko IV, Haberer G, Rudd S, Meyers B, Mewes HW, Mayer KF (2006). Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana. PLoS Comput Biol. 2006 Mar;2(3):e21.

Meyers, B.C., Souret, FF, Lu, C. and Green, P.J.  (2006). Sweating the small stuff: microRNA discovery in plants. Current Opinion in Biotechnology. April 17 (2) :139-146

I.V. Tetko, G. Haberer, S. Rudd, Meyers, B.C., H.W. Mewes, K.F.X. Mayer. (2006). Spatio-Temporal Expression Control mediated through intragenic Scaffold Matrix Attachment Regions (S/MARs) in Arabidopsis thaliana. PLoS Computational Biology. 2:e21.

Nakano, M., Nobuta, K., Vemeraju, K., Tej, S.S., Skogen, J. W. and Meyers, B.C. (2006).  Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Research. 34(Database issue):D731-5.

Moreno-Vázquez, S., Ning, J. and Meyers, B.C. (2005).  hATpin, a family of hAT mobile elements with MITE-like features that is conserved in diverse plant species. Plant Molecular Biology. 58: 869-886.

Lu, C., Tej, S.S., Luo, S., Haudenschild, C.D., Meyers, B.C.*, and P.J. Green*. (2005). Elucidation of the small RNA component of the transcriptome. Science. 309:1567-1569.
* co-corresponding authors.

Meyers, B.C., Kaushik, K. and Nandety, R.S. (2005).  Evolving disease resistance genes. Current Opinion in Plant Biology. April 8 (2) :129-134

Nobuta, K. and Meyers, B.C. (2005).  Pseudomonas versus Arabidopsis: models for genomic research into plant disease resistance. BioScience. 55(8): 679-686

Haberer, G., Hindemitt, T. Meyers, B.C., and K. Mayer. (2004). Transcriptional similarities, dissimilarities and conservation of cis elements in duplicated genes of Arabidopsis thaliana. Plant Physiology. 136: 3009-3022.

Kuang, H., Woo, S.-S., Meyers, B.C., Nevo, E. and R.W. Michelmore. (2004). Multiple genetic processes result in heterogeneous rates of evolution within the major cluster disease resistance genes in lettuce.  Plant Cell. 16: 2870-2894.

Meyers, B.C., Scalabrin, S. and Morgante, M. (2004). Mapping and sequencing complex genomes: Let's get physical. Nature Reviews Genetics.5(8):578-88.

Meyers, B.C., Tej, S.S., Vu, T.H., Haudenschild, C.D., Agrawal, V., Edberg, S.B., Ghazal, H. and S. Decola. (2004). The use of MPSS for whole- genome transcriptional analysis in Arabidopsis. Genome Research. 14:1641-1653.

Meyers, B.C., Vu, T.H., Tej, S.S., Matvienko, M., Ghazal, H., Agrawal, V., and C.D. Haudenschild. (2004). Analysis of the transcriptional complexity of Arabidopsis by massively parallel signature sequencing. Nature Biotechnology. 22:1006-1011.

Meyers, B.C., Lee, D.K., Vu, T.H., Tej, S.S., Edberg, S.B., Matvienko, M., and L.D. Tindell. (2004). Arabidopsis MPSS: an online resource for quantitative expression analysis. Plant Physiology. 135: 801-813.

Meyers, B.C., Galbraith, D.W., Nelson, T., and V. Agrawal. (2004). Methods for transcriptional profiling in plants: be fruitful and replicate. Plant Physiology. 135: 637-652.

Coughlan, S., Agrawal, V. and B.C. Meyers. (2004). A comparison of global gene expression measurement technologies in Arabidopsis thaliana. Comparative and Functional Genomics 5: 245-252.

Rudd, S., Frisch, M., Grote, K., Meyers, B.C., Mayer, K. and T. Werner. (2004). Genome-wide in silico mapping of S/MARs in Arabidopsis thaliana suggests correlation of intragenic S/MARs with gene expression. Plant Physiology. 135: 715-722.

Wright, S.I., Yau, C.B.K, Looseley, M. and B.C. Meyers. (2004). Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrata. Molecular Biology and Evolution.

2003

Meyers, B.C., Kozik.A., Griego,A., Kuang H., and Michelmore, R.W. (2003).  Genome-wide analysis of NBS-LRR encoding genes in Arabidopsis. Plant Cell. 15:809-834.

2002

Meyers, B.C., Morgante, M., and R.W. Michelmore (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. The Plant Journal. 32.77-92

Mondragon-Palomino, M., Meyers, B.C., Michelmore, R.W. and B.S. Gaut. (2002). Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Research. 12:1305-1315.

Shen, K.A., Chin, D.B., Arroyo-Garcia, R., Ochoa, O.E., Lavelle, D.O., Wroblewski, T., Meyers, B.C., and R.W. Michelmore. (2002). Dm3 is one member of a large constitutively-expressed family of NBS-LRR-encoding genes. Mol. Plant Microbe Interact. 15:251-261.

2001

Meyers, B.C., Tingey, S.V., and M. Morgante (2001). Abundance, distribution and transcriptional activity of repetitive elements in the maize genome. Genome Research. 11:1660-1676.

1999

Meyers, B.C.*, Dickerman, A.W.*, Michelmore, R.W., Sivaramakrishnan, S., Sobral, B.W., and N.D. Young. (1999). Plant disease resistance genes encode members of an ancient and diverse protein family within the nucleotide-binding superfamily. The Plant Journal. 20:317-332. *co-first authors

Sivaramakrishnan, S., Meyers, B. C., Shen, K. A., Lavelle, D. O., and R. W. Michelmore. (1999). Isolation of putative disease resistance genes from chickpean and pigeonpea. International Chickpea and Pigeonpea Newsletter. 6:33-36.

1998

Meyers, B. C., Chin, D. B., Shen, K. A., Sivaramakrishnan, S., Lavelle, D. O., Zhang, Z., and R. W. Michelmore. (1998). The major resistance gene cluster in lettuce is highly duplicated and spans several megabases. Plant Cell. 10: 1817-1832.

Meyers, B. C., Shen, K. A., Rohani, P., Gaut, B., and R. W. Michelmore. (1998). Receptor-like genes in the major resistance locus of lettuce are subject to divergent selection. Plant Cell. 10: 1833-1846.

Michelmore, R.W. and B.C. Meyers. (1998). Clusters of resistance genes in plants evolve by divergent selection and a birth-and-death process. Genome Research. 8: 1113-1130.

Shen*, K.A., Meyers*, B.C., Islam-Faridi, N., Chin, D.B., Stelly, D.M., and R.W. Michelmore. (1998). Resistance gene candidates identified by PCR with degenerate oligonucleotide primers map to clusters of resistance genes in lettuce. Mol Plant-Microbe Interact. 11: 815-823. *co-first authors

1997

Okubara, P.A., Arroyo-Garcia, R., Shen, K.A., Mazier, M., Meyers, B.C., Ochoa, O.E., Kim, S., Yang, C.-H., and R.W. Michelmore. (1997).  A transgenic mutant of Lactuca sativa (Lettuce) with a T-DNA tightly linked to the loss of downy mildew resistance. Mol. Plant-Microbe Inter. 10: 970-977.

Mayer, S., Charlesworth, D. and B. Meyers. (1996). Inbreeding depression in four populations of Collinsia heterophylla Nutt (Scrophulariaceae). Evolution. 50: 879-891.

Anderson, P.A., Okubara, P.A., Arroyo-Garcia, R., Meyers, B.C., and R.W. Michelmore. (1996). Molecular analysis of irradiation-induced and spontaneous deletion mutants at a disease resistance locus in Lactuca sativa. Mol. Gen. Genet. 251: 316-325.