Research Topics
Genomes and GenesSpecies | Blake C MeyersSummaryAffiliation: University of Delaware Country: USA Publications
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Publications
Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutantKan Nobuta
Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
Proc Natl Acad Sci U S A 105:14958-63. 2008..The enrichment of miRNAs and loss of 24-nt heterochromatic siRNAs in mop1-1 should be advantageous for miRNA discovery as the maize genome becomes more fully sequenced...- Identification and analysis of common bean (Phaseolus vulgaris L.) transcriptomes by massively parallel pyrosequencingVenu Kalavacharla
College of Agriculture and Related Sciences, Delaware State University, Dover, DE 19901, USA
BMC Plant Biol 11:135. 2011..However, the number and description of common bean sequences are very limited, which greatly inhibits genome and transcriptome research. Here we used 454 pyrosequencing to obtain a substantial transcriptome dataset for common bean... - Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grassesKankshita Swaminathan
Department of Crop Sciences, University of Illinois at Urbana Champaign, Urbana, IL 61801, USA
Genome Biol 11:R12. 2010..The essentially uncharacterized triploid genome (3n = 57, x = 19) of Mxg is likely critical for the rapid growth of this vegetatively propagated interspecific hybrid... - Characterization of paralogous protein families in riceHaining Lin
The Institute for Genomic Research, 9712 Medical Center Dr, Rockville, MD 20850, USA
BMC Plant Biol 8:18. 2008..This, coupled with other genetic events such as tandem duplications, has resulted in a substantial number of its genes, and resulting proteins, occurring in paralogous families... - Comparative expression profiling in grape (Vitis vinifera) berries derived from frequency analysis of ESTs and MPSS signaturesAlberto Iandolino
Department of Plant Pathology and College of Agricultural and Environmental Sciences Genomics Facility, University of California, One Shields Avenue, Davis, CA 95616, USA
BMC Plant Biol 8:53. 2008..The sequence depth of MPSS allowed us to capture and quantify almost all the transcripts at a specific stage in the development of the grape berry... 
Global expression analysis of nucleotide binding site-leucine rich repeat-encoding and related genes in ArabidopsisXiaoping Tan
The Genome Center, University of California, Davis, California 95616, USA
BMC Plant Biol 7:56. 2007..8% of all ORFs so far annotated in Arabidopsis ecotype Col-0. Despite their prevalence in the genome and functional importance, there was little information regarding expression of these genes...- Deep and comparative analysis of the mycelium and appressorium transcriptomes of Magnaporthe grisea using MPSS, RL-SAGE, and oligoarray methodsMalali Gowda
Department of Plant Pathology, Ohio State University, Columbus, OH 43210, USA
BMC Genomics 7:310. 2006.... - A comparison of microarray and MPSS technology platforms for expression analysis of ArabidopsisJunfeng Chen
School of Computer Science, University of Manchester, Oxford Road, Manchester, M13 9PL, UK
BMC Genomics 8:414. 2007.... - Prediction of novel miRNAs and associated target genes in Glycine maxTrupti Joshi
Digital Biology Laboratory, Computer Science Department and Christopher S, Bond Life Sciences Center, University of Missouri, Columbia, MO 65211, USA
BMC Bioinformatics 11:S14. 2010..Many plant miRNAs play critical roles in nutrient homeostasis, developmental processes, abiotic stress and pathogen responses. Currently, only 70 miRNA have been identified in soybean... 
Evolving disease resistance genesBlake C Meyers
Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19714, USA
Curr Opin Plant Biol 8:129-34. 2005..Diversity within populations is maintained by balancing selection. Analyses of whole-genome sequences have and will continue to provide new insight into the dynamics of resistance gene evolution...- Experimental design, preprocessing, normalization and differential expression analysis of small RNA sequencing experimentsKevin P McCormick
Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
Silence 2:2. 2011..While our focus is on sRNA sequencing experiments, many of the principles discussed are applicable to the sequencing of other RNA populations... - Sweating the small stuff: microRNA discovery in plantsBlake C Meyers
Delaware Biotechnology Institute and Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19714, USA
Curr Opin Biotechnol 17:139-46. 2006.... - Criteria for annotation of plant MicroRNAsBlake C Meyers
Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
Plant Cell 20:3186-90. 2008..Herein, we update the specific criteria required for the annotation of plant miRNAs, including experimental and computational data, as well as refinements to standard nomenclature... - Arabidopsis MPSS. An online resource for quantitative expression analysisBlake C Meyers
Department of Plant and Soil Sciences, University of Delaware, Newark, USA
Plant Physiol 135:801-13. 2004 - The use of MPSS for whole-genome transcriptional analysis in ArabidopsisBlake C Meyers
Department of Plant and Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19714, USA
Genome Res 14:1641-53. 2004..More than 89% of the sum of the expressed signature abundances matched the Arabidopsis genome, and many of the unmatched signatures found in high abundances were predicted to match to previously uncharacterized transcripts... - Methods for transcriptional profiling in plants. Be fruitful and replicateBlake C Meyers
Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
Plant Physiol 135:637-52. 2004 - Analysis of the transcriptional complexity of Arabidopsis thaliana by massively parallel signature sequencingBlake C Meyers
Delaware Biotechnology Institute, 15 Innovation Way, University of Delaware, Newark, Delaware 19714, USA
Nat Biotechnol 22:1006-11. 2004..thaliana genes transcribed in these libraries. The MPSS expression data suggest that the A. thaliana transcriptome is complex and contains many as-yet uncharacterized variants of normal coding transcripts... - Deep sequencing of chicken microRNAsJoan Burnside
Department of Animal and Food Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
BMC Genomics 9:185. 2008..We have applied this approach to the identification of chicken microRNAs and to the comparison of microRNAs in chicken embryo fibroblasts (CEF) infected with Marek's disease virus (MDV) to those present in uninfected CEF... - A spatial dissection of the Arabidopsis floral transcriptome by MPSSJason A Peiffer
Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19711, USA
BMC Plant Biol 8:43. 2008.... - An expression atlas of rice mRNAs and small RNAsKan Nobuta
Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
Nat Biotechnol 25:473-7. 2007..Among these, numerous clusters of highly regulated small RNAs were readily observed. We developed a genome browser (http://mpss.udel.edu/rice) for public access to the transcriptional profiling data for this important crop... - Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavageDong Hoon Jeong
Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19711, USA
Plant Cell 23:4185-207. 2011..This high-resolution analysis of rice miRNAs should be relevant to plant miRNAs in general, particularly in the Poaceae... - Elucidation of the small RNA component of the transcriptomeCheng Lu
Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
Science 309:1567-9. 2005..Targets of antisense RNA or miRNA did not appear to be preferentially associated with siRNAs. Many genomic regions previously considered featureless were found to be sites of numerous small RNAs... 
A microRNA of infectious laryngotracheitis virus can downregulate and direct cleavage of ICP4 mRNALisa A Waidner
Elcriton, Inc 15 Innovation Way, Suite 288, Newark, DE 19711, USA
Virology 411:25-31. 2011..Thus, in this system, iltv-miR-I5 decreased ILTV ICP4 mRNA levels via transcript cleavage and degradation. Downregulation of ICP4 could impact the balance between the lytic and latent states of the virus in vivo...- Global identification of microRNA-target RNA pairs by parallel analysis of RNA endsMarcelo A German
Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
Nat Biotechnol 26:941-6. 2008..This versatile approach will affect the study of other aspects of RNA processing beyond miRNA-target RNA pairs... - Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNAMayumi Nakano
Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19714, USA
Nucleic Acids Res 34:D731-5. 2006..Interpretation of the small RNA MPSS data is facilitated by the inclusion of extensive repeat data in our genome viewer. All the data and the tools introduced in this article are available at http://mpss.udel.edu... - Sequence conservation and differential expression of Marek's disease virus microRNAsRobin Morgan
Department of Animal and Food Sciences, Delaware Biotechnology Institute, University of Delaware, 15 Innovation Way, Newark, DE 19711, USA
J Virol 82:12213-20. 2008..These data suggest that the meq cluster microRNAs play an important role in the pathogenicity of MDV... - RNA polymerase V-dependent small RNAs in Arabidopsis originate from small, intergenic loci including most SINE repeatsTzuu Fen Lee
Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
Epigenetics 7:781-95. 2012..RNAP V, along with RNAP IV and DRM1/2, may target and silence a set of small, intergenic transposable elements located in dispersed genomic regions for silencing. Silencing at these loci may be actively reinforced by RdDM... - Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs)Cheng Lu
Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
Proc Natl Acad Sci U S A 105:4951-6. 2008..These findings suggest that other natural cis-antisense loci with similar exon-intron arrangements could be another source of miRNA genes... - Methods for analysis of gene expression in plants using MPSSKan Nobuta
Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
Methods Mol Biol 406:387-408. 2007..Here, we focus on a subset of these tools (e.g., Gene Analysis [GA], Chromosome Viewer [CV], and Library Analysis [LIBAN]) and describe how the users can analyze and interpret our MPSS expression data... - Use of massively parallel signature sequencing to study genes expressed during the plant defense responseBlake C Meyers
Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, USA
Methods Mol Biol 354:105-19. 2007.... - Construction of small RNA cDNA libraries for deep sequencingCheng Lu
Department of Plant and Soil Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
Methods 43:110-7. 2007..Here, we describe the methods used in our laboratory to construct small RNA cDNA libraries for high-throughput sequencing using technologies such as MPSS, 454 or SBS... - MicroRNAs of Gallid and Meleagrid herpesviruses show generally conserved genomic locations and are virus-specificLisa A Waidner
Department of Animal and Food Sciences, Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
Virology 388:128-36. 2009..The prevalence of microRNAs in the genomic repeat regions as well as in local repeats suggests the importance of genetic plasticity in herpesviruses for microRNA evolution and preservation of function... - MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutantCheng Lu
Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
Genome Res 16:1276-88. 2006..Deep sequencing of mutants provides a genetic approach for the dissection and characterization of diverse small RNA populations and the identification of low abundance miRNAs... - Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradomeMarcelo A German
Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
Nat Protoc 4:356-62. 2009..The data are then matched to cDNAs and analyzed through bioinformatics filters. We describe the high-throughput protocol in detail and indicate alternative uses for PARE. The procedure presented here can be accomplished in 6-7 d... - Bioinformatics analysis of small RNAs in plants using next generation sequencing technologiesKan Nobuta
Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
Methods Mol Biol 592:89-106. 2010..Here, we describe the challenges and our strategies to handle the very large quantity of small RNA data generated by these next-generation sequencing technologies... - MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAsJixian Zhai
Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware 19717, USA
Genes Dev 25:2540-53. 2011.... - Short-read sequencing technologies for transcriptional analysesStacey A Simon
Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
Annu Rev Plant Biol 60:305-33. 2009.... - Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genesJia Xing Yue
State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing 210093, China
New Phytol 193:1049-63. 2012.... - MicroRNA processing: battle of the bulgeBlake C Meyers
Department of Plant and Soil Sciences, and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
Curr Biol 20:R68-70. 2010..Several recent analyses of plant microRNA precursors define the contributions of secondary structure to the precise positions at which processing of these precursors occurs... - Computational methods for comparative analysis of plant small RNAsGayathri Mahalingam
Delaware Biotechnology Institute, University of Delaware, Newark, DE, USA
Methods Mol Biol 592:163-81. 2010..Here, we focus on these tools, and we describe how the users can implement these tools to analyze and interpret the small RNA data and how the users could use similar approaches for other sets of plant small RNAs from diverse species... - Marek's disease virus encodes MicroRNAs that map to meq and the latency-associated transcriptJoan Burnside
Department of Animal and Food Sciences, University of Delaware, Newark, 19711, USA
J Virol 80:8778-86. 2006..We propose that the MDV miRNAs function to enable MDV pathogenesis and contribute to MDV-induced transformation of chicken T cells... - Small RNA-mediated epigenetic modifications in plantsStacey A Simon
Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711, USA
Curr Opin Plant Biol 14:148-55. 2011..As the multiple layers of epigenetic regulation in plants are dissected, a more comprehensive understanding of the biological importance of epigenetic marks and states has been developed... - RNA-Seq reveals infection-related global gene changes in Phytophthora phaseoli, the causal agent of lima bean downy mildewSridhara G Kunjeti
Department of Plant and Soil Sciences, University of Delaware, Newark, DE 19716, USA
Mol Plant Pathol 13:454-66. 2012..These results are discussed with respect to the differences and similarities in the pathogenicity mechanisms of P. phaseoli and P. infestans... - Mapping and sequencing complex genomes: let's get physical!Blake C Meyers
Department of Plant and Soil Sciences and Delaware Biotechnology Institute, University of Delaware, Newark, Delaware 19711, USA
Nat Rev Genet 5:578-88. 2004 - Genome-wide in silico mapping of scaffold/matrix attachment regions in Arabidopsis suggests correlation of intragenic scaffold/matrix attachment regions with gene expressionStephen Rudd
Munich Information Center for Protein Sequences/Institute for Bioinformatics, GSF-National Research Center for Environment and Health, 85764 Neuherberg, Germany
Plant Physiol 135:715-22. 2004..On the basis of a genome-wide in silico S/MAR analysis, we found a significant correlation between the presence of intragenic S/MARs and transcriptional down-regulation... - Small RNA-directed epigenetic natural variation in Arabidopsis thalianaJixian Zhai
State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China
PLoS Genet 4:e1000056. 2008..Methylation analysis revealed that 88% of the examined loci (37 out of 42) were specifically methylated in Ler but not Col, suggesting that small RNA can direct epigenetic differences between two closely related Arabidopsis ecotypes... - TIR-X and TIR-NBS proteins: two new families related to disease resistance TIR-NBS-LRR proteins encoded in Arabidopsis and other plant genomesBlake C Meyers
Department of Vegetable Crops, University of California, Davis, CA 95616, USA
Plant J 32:77-92. 2002..These TX and TN proteins could be plant analogues of small TIR-adapter proteins that function in mammalian innate immune responses such as MyD88 and Mal... - Genome-wide analysis of NBS-LRR-encoding genes in ArabidopsisBlake C Meyers
Department of Vegetable Crops, University of California, Davis, California 95616, USA
Plant Cell 15:809-34. 2003..The observed diversity of these NBS-LRR proteins indicates the variety of recognition molecules available in an individual genotype to detect diverse biotic challenges... - Effects of gene expression on molecular evolution in Arabidopsis thaliana and Arabidopsis lyrataStephen I Wright
ICAPB, University of Edinburgh Ashworth Labs, Edinburgh, UK
Mol Biol Evol 21:1719-26. 2004.... - Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of ArabidopsisGeorg Haberer
Munich Information Center for Protein Sequences, Institute for Bioinformatics, GSF Research Center for Environment and Health, 85758 Neuherberg, Germany
Plant Physiol 136:3009-22. 2004..Our work lays a foundation for future comparative studies to elucidate the molecular manifestation of regulatory similarities and dissimilarities of duplicated genes... - Multiple genetic processes result in heterogeneous rates of evolution within the major cluster disease resistance genes in lettuceHanhui Kuang
Department of Vegetable Crops, University of California, Davis, California 95616, USA
Plant Cell 16:2870-94. 2004..Unequal crossover, insertion/deletion, and point mutation events were distributed unequally through the gene. Different evolutionary forces have impacted different parts of the LRR... - Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thalianaMariana Mondragon-Palomino
Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92612, USA
Genome Res 12:1305-15. 2002..LRRs also contain substantial indel variation, suggesting elasticity in LRR length could also influence resistance specificity... - Genomic and genetic characterization of rice Cen3 reveals extensive transcription and evolutionary implications of a complex centromereHuihuang Yan
Department of Horticulture, University of Wisconsin, Madison, 53706, USA
Plant Cell 18:2123-33. 2006..These results support the hypothesis that centromeres can evolve from gene-containing genomic regions... - Divergence in expression between duplicated genes in ArabidopsisEric W Ganko
Department of Biology, University of North Carolina at Chapel Hill, USA
Mol Biol Evol 24:2298-309. 2007.... - The Rice Annotation Project Database (RAP-DB): 2008 updateTsuyoshi Tanaka
National Institute of Agrobiological Sciences, Ibaraki 305 8602, Japan
Nucleic Acids Res 36:D1028-33. 2008..We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/... - Frequent sequence exchanges between homologs of RPP8 in Arabidopsis are not necessarily associated with genomic proximityHanhui Kuang
The Genome Center and Department of Plant Sciences, University of California, Davis, CA 95616, USA
Plant J 54:69-80. 2008..Therefore, the differentiation of type I and type II RPP8 homologs seems to have occurred before speciation of A. thaliana, A. arenosa and A. lyrata... - Genome-wide identification of NBS resistance genes in Populus trichocarpaAnnegret Kohler
Unité Mixte de Recherche INRA UHP 1136 Interactions Arbres Microorganismes, Institut National de la Recherche Agronomique, Centre de Recherches de Nancy, 54280 Champenoux, France
Plant Mol Biol 66:619-36. 2008..The transcripts of only 34 NBS-LRR genes were detected in rust-infected and non-infected leaves using a whole-genome oligoarray. None showed an altered expression two days post inoculation... - Discovery of ADP-ribosylation and other plant defense pathway elements through expression profiling of four different Arabidopsis-Pseudomonas R-avr interactionsLori Adams-Phillips
Department of Plant Pathology, University of Wisconsin Madison, Madison, WI 53706, USA
Mol Plant Microbe Interact 21:646-57. 2008.... - Dm3 is one member of a large constitutively expressed family of nucleotide binding site-leucine-rich repeat encoding genesKatherine A Shen
Department of Vegetable Crops, University of California, Davis 95616, USA
Mol Plant Microbe Interact 15:251-61. 2002..In a wildtype Dm3-expressing genotype, many of the RGC2 family members are expressed at low levels throughout the plant... - hATpin, a family of MITE-like hAT mobile elements conserved in diverse plant species that forms highly stable secondary structuresSantiago Moreno-Vázquez
Departamento de Biologia Vegetal, E T S Ingenieros Agronomos, Universidad Politecnica de Madrid, Ciudad Universitaria, 28040, Madrid, Spain
Plant Mol Biol 58:869-86. 2005..This family of class II mobile elements is found primarily in monocot species, but is also present in dicot species...