Published in BMC Bioinformatics on January 18, 2010
MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev (2011) 2.66
Identification of miRNAs and their target genes in developing soybean seeds by deep sequencing. BMC Plant Biol (2011) 2.01
Analysis of microRNA transcriptome by deep sequencing of small RNA libraries of peripheral blood. BMC Genomics (2010) 1.84
Identification of novel soybean microRNAs involved in abiotic and biotic stresses. BMC Genomics (2011) 1.70
Soybean Knowledge Base (SoyKB): a web resource for soybean translational genomics. BMC Genomics (2012) 1.29
Advances in omics and bioinformatics tools for systems analyses of plant functions. Plant Cell Physiol (2011) 1.28
Function and evolution of a MicroRNA that regulates a Ca2+-ATPase and triggers the formation of phased small interfering RNAs in tomato reproductive growth. Plant Cell (2011) 1.20
Origins and evolution of microRNA genes in plant species. Genome Biol Evol (2012) 1.20
Misexpression of miR482, miR1512, and miR1515 increases soybean nodulation. Plant Physiol (2010) 1.19
Identification and characterization of microRNAs in Phaseolus vulgaris by high-throughput sequencing. BMC Genomics (2012) 1.16
Identification of soybean seed developmental stage-specific and tissue-specific miRNA targets by degradome sequencing. BMC Genomics (2012) 1.14
Genome-wide profiling of miRNAs and other small non-coding RNAs in the Verticillium dahliae-inoculated cotton roots. PLoS One (2012) 1.10
Characterization of the stress associated microRNAs in Glycine max by deep sequencing. BMC Plant Biol (2011) 1.08
Genome organization and characteristics of soybean microRNAs. BMC Genomics (2012) 1.05
Comparative analysis reveals dynamic changes in miRNAs and their targets and expression during somatic embryogenesis in longan (Dimocarpus longan Lour.). PLoS One (2013) 1.04
Genome-wide identification of soybean microRNAs and their targets reveals their organ-specificity and responses to phosphate starvation. BMC Genomics (2013) 1.01
Identification of soybean microRNAs involved in soybean cyst nematode infection by deep sequencing. PLoS One (2012) 0.97
NPK macronutrients and microRNA homeostasis. Front Plant Sci (2015) 0.94
Two microRNAs linked to nodule infection and nitrogen-fixing ability in the legume Lotus japonicus. Plant Physiol (2012) 0.94
High-throughput sequencing and characterization of the small RNA transcriptome reveal features of novel and conserved microRNAs in Panax ginseng. PLoS One (2012) 0.94
Divergent patterns of endogenous small RNA populations from seed and vegetative tissues of Glycine max. BMC Plant Biol (2012) 0.91
SFGD: a comprehensive platform for mining functional information from soybean transcriptome data and its use in identifying acyl-lipid metabolism pathways. BMC Genomics (2014) 0.88
High-throughput sequencing identification of novel and conserved miRNAs in the Brassica oleracea leaves. BMC Genomics (2013) 0.87
Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing. J Exp Bot (2014) 0.85
Identification of Cold-Responsive miRNAs and Their Target Genes in Nitrogen-Fixing Nodules of Soybean. Int J Mol Sci (2014) 0.84
Identification and Dynamic Regulation of microRNAs Involved in Salt Stress Responses in Functional Soybean Nodules by High-Throughput Sequencing. Int J Mol Sci (2013) 0.84
Systems and evolutionary characterization of microRNAs and their underlying regulatory networks in soybean cotyledons. PLoS One (2014) 0.83
Genome-wide identification of non-coding RNAs interacted with microRNAs in soybean. Front Plant Sci (2014) 0.83
Identification of miRNAs and their target genes in peach (Prunus persica L.) using high-throughput sequencing and degradome analysis. PLoS One (2013) 0.82
Elucidation of miRNAs-mediated responses to low nitrogen stress by deep sequencing of two soybean genotypes. PLoS One (2013) 0.81
The transition from primary siRNAs to amplified secondary siRNAs that regulate chalcone synthase during development of Glycine max seed coats. PLoS One (2013) 0.80
Identification of microRNAs differentially expressed involved in male flower development. Funct Integr Genomics (2015) 0.79
System approaches to study root hairs as a single cell plant model: current status and future perspectives. Front Plant Sci (2015) 0.79
Identification of MicroRNAs in Response to Different Day Lengths in Soybean Using High-Throughput Sequencing and qRT-PCR. PLoS One (2015) 0.79
A survey of the small RNA population during far-red light-induced apical hook opening. Front Plant Sci (2014) 0.78
MicroRNAs and targets in senescent litchi fruit during ambient storage and post-cold storage shelf life. BMC Plant Biol (2015) 0.77
Comparative Profiling of miRNAs and Target Gene Identification in Distant-Grafting between Tomato and Lycium (Goji Berry). Front Plant Sci (2016) 0.77
Identification of miRNAs and their targets by high-throughput sequencing and degradome analysis in cytoplasmic male-sterile line NJCMS1A and its maintainer NJCMS1B of soybean. BMC Genomics (2016) 0.76
Comparison of Small RNA Profiles of Glycine max and Glycine soja at Early Developmental Stages. Int J Mol Sci (2016) 0.75
Small RNA profiling and degradome analysis reveal regulation of microRNA in peanut embryogenesis and early pod development. BMC Genomics (2017) 0.75
Identification of novel miRNAs from drought tolerant rice variety Nagina 22. Sci Rep (2016) 0.75
Genome-wide identification of soybean microRNA responsive to soybean cyst nematodes infection by deep sequencing. BMC Genomics (2017) 0.75
CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res (1994) 392.47
tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res (1997) 142.55
RNAmmer: consistent and rapid annotation of ribosomal RNA genes. Nucleic Acids Res (2007) 85.81
A greedy algorithm for aligning DNA sequences. J Comput Biol (2000) 47.89
miRBase: tools for microRNA genomics. Nucleic Acids Res (2007) 38.61
MicroRNAs: small RNAs with a big role in gene regulation. Nat Rev Genet (2004) 37.83
RNA interference. Nature (2002) 22.28
microRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell (2005) 14.81
Microarray profiling of microRNAs reveals frequent coexpression with neighboring miRNAs and host genes. RNA (2005) 14.14
Role of microRNAs in plant and animal development. Science (2003) 12.45
Specific effects of microRNAs on the plant transcriptome. Dev Cell (2005) 8.48
Criteria for annotation of plant MicroRNAs. Plant Cell (2008) 7.49
DINAMelt web server for nucleic acid melting prediction. Nucleic Acids Res (2005) 6.90
GtRNAdb: a database of transfer RNA genes detected in genomic sequence. Nucleic Acids Res (2008) 6.07
Specialization and evolution of endogenous small RNA pathways. Nat Rev Genet (2007) 5.68
The role of RNA interference in heterochromatic silencing. Nature (2004) 4.56
The diversity of RNA silencing pathways in plants. Trends Genet (2006) 4.32
A microRNA catalog of the developing chicken embryo identified by a deep sequencing approach. Genome Res (2008) 3.74
The use of MPSS for whole-genome transcriptional analysis in Arabidopsis. Genome Res (2004) 3.30
RNA: guiding gene silencing. Science (2001) 2.50
MtHAP2-1 is a key transcriptional regulator of symbiotic nodule development regulated by microRNA169 in Medicago truncatula. Genes Dev (2006) 2.41
Identification and characterization of new plant microRNAs using EST analysis. Cell Res (2005) 2.35
MicroRNA regulation of gene expression in plants. Curr Opin Plant Biol (2004) 2.32
Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci U S A (2008) 1.92
Novel and nodulation-regulated microRNAs in soybean roots. BMC Genomics (2008) 1.92
Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data. BMC Genomics (2009) 1.66
MicroRNA166 controls root and nodule development in Medicago truncatula. Plant J (2008) 1.61
Plant gene expression in effective and ineffective root nodules of alfalfa (Medicago sativa). Plant Mol Biol (1987) 1.18
Reconstituting plant miRNA biogenesis. Proc Natl Acad Sci U S A (2008) 1.00
Genome sequence of the palaeopolyploid soybean. Nature (2010) 17.82
Designing and evaluating complex interventions to improve health care. BMJ (2007) 9.78
Elucidation of the small RNA component of the transcriptome. Science (2005) 8.66
Criteria for annotation of plant MicroRNAs. Plant Cell (2008) 7.49
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans. Nature (2009) 6.44
Global identification of microRNA-target RNA pairs by parallel analysis of RNA ends. Nat Biotechnol (2008) 6.18
Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning. Nat Genet (2006) 5.81
The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature (2011) 4.94
A critical assessment of Mus musculus gene function prediction using integrated genomic evidence. Genome Biol (2008) 4.78
Accumulation of phosphorylated repressor for gibberellin signaling in an F-box mutant. Science (2003) 4.44
The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res (2007) 4.23
MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res (2006) 4.08
Long-term monitoring shows hepatitis B virus resistance to entecavir in nucleoside-naïve patients is rare through 5 years of therapy. Hepatology (2009) 4.00
AtXRN4 degrades mRNA in Arabidopsis and its substrates include selected miRNA targets. Mol Cell (2004) 3.96
Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs. RNA (2009) 3.87
Enhanced computer vision with Microsoft Kinect sensor: a review. IEEE Trans Cybern (2013) 3.75
Slug antagonizes p53-mediated apoptosis of hematopoietic progenitors by repressing puma. Cell (2005) 3.73
A LysM receptor-like kinase plays a critical role in chitin signaling and fungal resistance in Arabidopsis. Plant Cell (2008) 3.54
An expression atlas of rice mRNAs and small RNAs. Nat Biotechnol (2007) 3.45
Legumes symbioses: absence of Nod genes in photosynthetic bradyrhizobia. Science (2007) 3.42
Routine Microsecond Molecular Dynamics Simulations with AMBER on GPUs. 1. Generalized Born. J Chem Theory Comput (2012) 3.40
Ultradeep bisulfite sequencing analysis of DNA methylation patterns in multiple gene promoters by 454 sequencing. Cancer Res (2007) 3.40
tRNA cleavage is a conserved response to oxidative stress in eukaryotes. RNA (2008) 3.39
Taking healthcare interventions from trial to practice. BMJ (2010) 3.27
Plant snoRNA database. Nucleic Acids Res (2003) 3.15
Graph embedding and extensions: a general framework for dimensionality reduction. IEEE Trans Pattern Anal Mach Intell (2007) 3.06
Role of RNA polymerase IV in plant small RNA metabolism. Proc Natl Acad Sci U S A (2007) 3.05
Plant MPSS databases: signature-based transcriptional resources for analyses of mRNA and small RNA. Nucleic Acids Res (2006) 2.95
Genome-wide analysis for discovery of rice microRNAs reveals natural antisense microRNAs (nat-miRNAs). Proc Natl Acad Sci U S A (2008) 2.92
Generation of a flanking sequence-tag database for activation-tagging lines in japonica rice. Plant J (2006) 2.69
MicroRNAs as master regulators of the plant NB-LRR defense gene family via the production of phased, trans-acting siRNAs. Genes Dev (2011) 2.66
Genome evolution following host jumps in the Irish potato famine pathogen lineage. Science (2010) 2.62
Analysis of detergent-resistant membranes in Arabidopsis. Evidence for plasma membrane lipid rafts. Plant Physiol (2004) 2.55
Transcriptome dynamics of Deinococcus radiodurans recovering from ionizing radiation. Proc Natl Acad Sci U S A (2003) 2.52
Inferring gene regulatory networks from multiple microarray datasets. Bioinformatics (2006) 2.49
B lymphocyte stimulator overexpression in patients with systemic lupus erythematosus: longitudinal observations. Arthritis Rheum (2003) 2.47
Construction of small RNA cDNA libraries for deep sequencing. Methods (2007) 2.43
An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J (2010) 2.41
Visualization of nitric oxide in living cells by a copper-based fluorescent probe. Nat Chem Biol (2006) 2.33
Patterns of positive selection in the complete NBS-LRR gene family of Arabidopsis thaliana. Genome Res (2002) 2.27
Implementing intensive control of blood glucose concentration and blood pressure in type 2 diabetes in England: cost analysis (UKPDS 63). BMJ (2002) 2.24
Local production of B lymphocyte stimulator protein and APRIL in arthritic joints of patients with inflammatory arthritis. Arthritis Rheum (2003) 2.21
Riboswitch control of gene expression in plants by splicing and alternative 3' end processing of mRNAs. Plant Cell (2007) 2.18
Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem (2008) 2.14
Identification of unstable transcripts in Arabidopsis by cDNA microarray analysis: rapid decay is associated with a group of touch- and specific clock-controlled genes. Proc Natl Acad Sci U S A (2002) 2.14
Construction of Parallel Analysis of RNA Ends (PARE) libraries for the study of cleaved miRNA targets and the RNA degradome. Nat Protoc (2009) 2.12
Genetics and functional genomics of legume nodulation. Curr Opin Plant Biol (2006) 2.09
Nitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana. Proc Natl Acad Sci U S A (2010) 2.03
Complete transcriptome of the soybean root hair cell, a single-cell model, and its alteration in response to Bradyrhizobium japonicum infection. Plant Physiol (2009) 2.00
T-DNA insertional mutagenesis for activation tagging in rice. Plant Physiol (2002) 1.99
A spatial dissection of the Arabidopsis floral transcriptome by MPSS. BMC Plant Biol (2008) 1.99
Transcriptional similarities, dissimilarities, and conservation of cis-elements in duplicated genes of Arabidopsis. Plant Physiol (2004) 1.96
Multiple genetic processes result in heterogeneous rates of evolution within the major cluster disease resistance genes in lettuce. Plant Cell (2004) 1.94
Massive analysis of rice small RNAs: mechanistic implications of regulated microRNAs and variants for differential target RNA cleavage. Plant Cell (2011) 1.93
Distinct size distribution of endogeneous siRNAs in maize: Evidence from deep sequencing in the mop1-1 mutant. Proc Natl Acad Sci U S A (2008) 1.92
Marek's disease virus encodes MicroRNAs that map to meq and the latency-associated transcript. J Virol (2006) 1.91
Understanding the unique characteristics of suicide in China: national psychological autopsy study. Biomed Environ Sci (2005) 1.90
Management of High-Throughput DNA Sequencing Projects: Alpheus. J Comput Sci Syst Biol (2008) 1.85
Divergence in expression between duplicated genes in Arabidopsis. Mol Biol Evol (2007) 1.83
Clustering gene expression data using a graph-theoretic approach: an application of minimum spanning trees. Bioinformatics (2002) 1.81
Interoperability with Moby 1.0--it's better than sharing your toothbrush! Brief Bioinform (2008) 1.80
Microarray analysis of chitin elicitation in Arabidopsis thaliana. Mol Plant Pathol (2002) 1.80
Genome-wide DNA methylation analysis reveals novel epigenetic changes in chronic lymphocytic leukemia. Epigenetics (2012) 1.80
Molecular and chromosomal evidence for allopolyploidy in soybean. Plant Physiol (2009) 1.78
Identification of 118 Arabidopsis transcription factor and 30 ubiquitin-ligase genes responding to chitin, a plant-defense elicitor. Mol Plant Microbe Interact (2007) 1.77
Epidermal growth factor-like domain 7 protects endothelial cells from hyperoxia-induced cell death. Am J Physiol Lung Cell Mol Physiol (2007) 1.75