Published in PLoS Comput Biol on November 01, 2007
Retracted An endogenous, systemic RNAi pathway in plants. EMBO J (2010) 2.82
Identification of nutrient-responsive Arabidopsis and rapeseed microRNAs by comprehensive real-time polymerase chain reaction profiling and small RNA sequencing. Plant Physiol (2009) 2.33
Concern Misregulation of AUXIN RESPONSE FACTOR 8 underlies the developmental abnormalities caused by three distinct viral silencing suppressors in Arabidopsis. PLoS Pathog (2011) 2.12
PMRD: plant microRNA database. Nucleic Acids Res (2009) 1.94
Differential effects of viral silencing suppressors on siRNA and miRNA loading support the existence of two distinct cellular pools of ARGONAUTE1. EMBO J (2012) 1.62
Plants Encode a General siRNA Suppressor That Is Induced and Suppressed by Viruses. PLoS Biol (2015) 1.41
Discovery of barley miRNAs through deep sequencing of short reads. BMC Genomics (2011) 1.40
Transcriptome-wide analysis of uncapped mRNAs in Arabidopsis reveals regulation of mRNA degradation. Plant Cell (2008) 1.29
Genome-wide profiling of populus small RNAs. BMC Genomics (2009) 1.28
Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing. BMC Med Genomics (2009) 1.10
Integrated microRNA and mRNA expression profiling in a rat colon carcinogenesis model: effect of a chemo-protective diet. Physiol Genomics (2011) 1.10
Lessons on RNA silencing mechanisms in plants from eukaryotic argonaute structures. Plant Cell (2013) 1.02
In silico miRNA prediction in metazoan genomes: balancing between sensitivity and specificity. BMC Genomics (2009) 1.01
Cloning and validation of novel miRNA from basmati rice indicates cross talk between abiotic and biotic stresses. Mol Genet Genomics (2009) 0.96
Identification of novel maize miRNAs by measuring the precision of precursor processing. BMC Plant Biol (2011) 0.96
miRNA regulation in the early development of barley seed. BMC Plant Biol (2012) 0.94
Plant siRNAs from introns mediate DNA methylation of host genes. RNA (2011) 0.94
Computational prediction of the localization of microRNAs within their pre-miRNA. Nucleic Acids Res (2013) 0.94
A cross-species transcriptomics approach to identify genes involved in leaf development. BMC Genomics (2008) 0.93
Computational prediction and experimental validation of microRNAs in the brown alga Ectocarpus siliculosus. Nucleic Acids Res (2013) 0.81
Fast selection of miRNA candidates based on large-scale pre-computed MFE sets of randomized sequences. BMC Res Notes (2014) 0.81
Analysis of antisense expression by whole genome tiling microarrays and siRNAs suggests mis-annotation of Arabidopsis orphan protein-coding genes. PLoS One (2010) 0.80
Bioinformatic analysis of epigenetic and microRNA mediated regulation of drought responsive genes in rice. PLoS One (2012) 0.79
Arabidopsis RNASE THREE LIKE2 Modulates the Expression of Protein-Coding Genes via 24-Nucleotide Small Interfering RNA-Directed DNA Methylation. Plant Cell (2016) 0.78
Construction of microRNA functional families by a mixture model of position weight matrices. PeerJ (2013) 0.77
Fine tuning of auxin signaling by miRNAs. Physiol Mol Biol Plants (2008) 0.77
A specific dsRNA-binding protein complex selectively sequesters endogenous inverted-repeat siRNA precursors and inhibits their processing. Nucleic Acids Res (2017) 0.76
A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science (2002) 42.78
miRBase: microRNA sequences, targets and gene nomenclature. Nucleic Acids Res (2006) 39.25
A uniform system for microRNA annotation. RNA (2003) 20.28
Vienna RNA secondary structure server. Nucleic Acids Res (2003) 19.69
Prediction of plant microRNA targets. Cell (2002) 19.20
The microRNAs of Caenorhabditis elegans. Genes Dev (2003) 17.70
Vertebrate microRNA genes. Science (2003) 17.42
Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution. Science (2005) 16.82
Automatic clustering of orthologs and in-paralogs from pairwise species comparisons. J Mol Biol (2001) 16.47
Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet (2005) 15.96
A pattern-based method for the identification of MicroRNA binding sites and their corresponding heteroduplexes. Cell (2006) 14.70
MicroRNAS and their regulatory roles in plants. Annu Rev Plant Biol (2006) 14.44
Computational identification of plant microRNAs and their targets, including a stress-induced miRNA. Mol Cell (2004) 12.97
A diverse and evolutionarily fluid set of microRNAs in Arabidopsis thaliana. Genes Dev (2006) 11.71
Endogenous and silencing-associated small RNAs in plants. Plant Cell (2002) 10.07
Elucidation of the small RNA component of the transcriptome. Science (2005) 8.66
Specific effects of microRNAs on the plant transcriptome. Dev Cell (2005) 8.48
High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MIRNA genes. PLoS One (2007) 7.34
RNA polymerase III transcribes human microRNAs. Nat Struct Mol Biol (2006) 6.81
Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nat Genet (2004) 6.34
Functions of microRNAs and related small RNAs in plants. Nat Genet (2006) 5.66
Many novel mammalian microRNA candidates identified by extensive cloning and RAKE analysis. Genome Res (2006) 5.23
Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function. Trends Genet (2005) 5.07
Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics (2004) 4.95
MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res (2006) 4.08
Detection of 91 potential conserved plant microRNAs in Arabidopsis thaliana and Oryza sativa identifies important target genes. Proc Natl Acad Sci U S A (2004) 3.97
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics (2005) 3.69
Prediction and identification of Arabidopsis thaliana microRNAs and their mRNA targets. Genome Biol (2004) 3.66
Conservation and divergence of plant microRNA genes. Plant J (2006) 3.64
AGRIS: Arabidopsis gene regulatory information server, an information resource of Arabidopsis cis-regulatory elements and transcription factors. BMC Bioinformatics (2003) 3.61
Mammalian microRNAs derived from genomic repeats. Trends Genet (2005) 3.60
Identification of transcribed sequences in Arabidopsis thaliana by using high-resolution genome tiling arrays. Proc Natl Acad Sci U S A (2005) 3.21
Computational prediction of miRNAs in Arabidopsis thaliana. Genome Res (2005) 2.86
A family of human microRNA genes from miniature inverted-repeat transposable elements. PLoS One (2007) 2.63
Transcript annotation in FANTOM3: mouse gene catalog based on physical cDNAs. PLoS Genet (2006) 2.48
Origin and evolution of human microRNAs from transposable elements. Genetics (2007) 2.39
Identification and characterization of new plant microRNAs using EST analysis. Cell Res (2005) 2.35
Tagging mammalian transcription complexity. Trends Genet (2006) 2.27
Alu elements within human mRNAs are probable microRNA targets. Trends Genet (2006) 2.20
Evolution of Arabidopsis microRNA families through duplication events. Genome Res (2006) 1.96
Computational evidence for hundreds of non-conserved plant microRNAs. BMC Genomics (2005) 1.43
The four Rs of RNA-directed evolution. Nat Genet (2004) 1.04
The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov (2012) 26.98
Integrative analysis of complex cancer genomics and clinical profiles using the cBioPortal. Sci Signal (2013) 19.54
A combined transmembrane topology and signal peptide prediction method. J Mol Biol (2004) 15.77
JASPAR, the open access database of transcription factor-binding profiles: new content and tools in the 2008 update. Nucleic Acids Res (2007) 8.79
Ancient human genome sequence of an extinct Palaeo-Eskimo. Nature (2010) 7.51
Programmed cell death 4 (PDCD4) is an important functional target of the microRNA miR-21 in breast cancer cells. J Biol Chem (2007) 7.46
Prediction of lipoprotein signal peptides in Gram-negative bacteria. Protein Sci (2003) 6.85
EasyGene--a prokaryotic gene finder that ranks ORFs by statistical significance. BMC Bioinformatics (2003) 6.63
The transcriptional network that controls growth arrest and differentiation in a human myeloid leukemia cell line. Nat Genet (2009) 6.02
Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas. N Engl J Med (2015) 5.71
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res (2007) 5.29
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics (2005) 4.25
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
Reliability measures for membrane protein topology prediction algorithms. J Mol Biol (2003) 3.13
An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics (2005) 3.05
The genome of the fire ant Solenopsis invicta. Proc Natl Acad Sci U S A (2011) 2.74
A code for transcription initiation in mammalian genomes. Genome Res (2007) 2.71
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res (2008) 2.60
Population genetic analysis of shotgun assemblies of genomic sequences from multiple individuals. Genome Res (2008) 2.46
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics (2002) 2.23
The phenotypic spectrum of SCN8A encephalopathy. Neurology (2015) 2.12
microRNA-101 is a potent inhibitor of autophagy. EMBO J (2011) 2.00
Whole-genome sequencing of cultivated and wild peppers provides insights into Capsicum domestication and specialization. Proc Natl Acad Sci U S A (2014) 1.91
Molecular composition of IMP1 ribonucleoprotein granules. Mol Cell Proteomics (2007) 1.80
Integrated analyses of microRNAs demonstrate their widespread influence on gene expression in high-grade serous ovarian carcinoma. PLoS One (2012) 1.76
Signatures of RNA binding proteins globally coupled to effective microRNA target sites. Genome Res (2010) 1.75
The genome of the leaf-cutting ant Acromyrmex echinatior suggests key adaptations to advanced social life and fungus farming. Genome Res (2011) 1.70
MicroRNA-145 targets YES and STAT1 in colon cancer cells. PLoS One (2010) 1.64
Improving ancient DNA read mapping against modern reference genomes. BMC Genomics (2012) 1.59
Sampling realistic protein conformations using local structural bias. PLoS Comput Biol (2006) 1.56
A generative, probabilistic model of local protein structure. Proc Natl Acad Sci U S A (2008) 1.50
miR-449 inhibits cell proliferation and is down-regulated in gastric cancer. Mol Cancer (2011) 1.46
Asap: a framework for over-representation statistics for transcription factor binding sites. PLoS One (2008) 1.46
Social insect genomes exhibit dramatic evolution in gene composition and regulation while preserving regulatory features linked to sociality. Genome Res (2013) 1.45
miR-34a repression in proneural malignant gliomas upregulates expression of its target PDGFRA and promotes tumorigenesis. PLoS One (2012) 1.44
Computational evidence for hundreds of non-conserved plant microRNAs. BMC Genomics (2005) 1.43
An epidemiologic and genomic investigation into the obesity paradox in renal cell carcinoma. J Natl Cancer Inst (2013) 1.42
Small RNA sequencing and functional characterization reveals MicroRNA-143 tumor suppressor activity in liposarcoma. Cancer Res (2011) 1.40
A hidden Markov model approach for determining expression from genomic tiling micro arrays. BMC Bioinformatics (2006) 1.40
Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns. Genome Biol (2012) 1.34
Hypomorphic mutations in PGAP2, encoding a GPI-anchor-remodeling protein, cause autosomal-recessive intellectual disability. Am J Hum Genet (2013) 1.34
Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii. Nat Commun (2013) 1.31
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Res (2006) 1.29
MicroRNA transfection and AGO-bound CLIP-seq data sets reveal distinct determinants of miRNA action. RNA (2011) 1.26
RpoD promoters in Campylobacter jejuni exhibit a strong periodic signal instead of a -35 box. J Mol Biol (2003) 1.25
The genomic impact of 100 million years of social evolution in seven ant species. Trends Genet (2011) 1.25
miRMaid: a unified programming interface for microRNA data resources. BMC Bioinformatics (2010) 1.20
MicroRNA-143 down-regulates Hexokinase 2 in colon cancer cells. BMC Cancer (2012) 1.16
Genome-wide nucleosome map and cytosine methylation levels of an ancient human genome. Genome Res (2013) 1.12
Identification and analysis of miRNAs in human breast cancer and teratoma samples using deep sequencing. BMC Med Genomics (2009) 1.10
MASTR: multiple alignment and structure prediction of non-coding RNAs using simulated annealing. Bioinformatics (2007) 1.10
Comparing cancer vs normal gene expression profiles identifies new disease entities and common transcriptional programs in AML patients. Blood (2013) 1.09
Laccase detoxification mediates the nutritional alliance between leaf-cutting ants and fungus-garden symbionts. Proc Natl Acad Sci U S A (2012) 1.05
Bias of purine stretches in sequenced chromosomes. Comput Chem (2002) 1.05
Discovery of regulatory elements is improved by a discriminatory approach. PLoS Comput Biol (2009) 1.04
The fungal symbiont of Acromyrmex leaf-cutting ants expresses the full spectrum of genes to degrade cellulose and other plant cell wall polysaccharides. BMC Genomics (2013) 1.00
Comprehensive analysis of long non-coding RNAs in ovarian cancer reveals global patterns and targeted DNA amplification. PLoS One (2013) 0.99
Reconstructing genome evolution in historic samples of the Irish potato famine pathogen. Nat Commun (2013) 0.95
An evolutionary method for learning HMM structure: prediction of protein secondary structure. BMC Bioinformatics (2007) 0.95
microRNA-146a inhibits G protein-coupled receptor-mediated activation of NF-κB by targeting CARD10 and COPS8 in gastric cancer. Mol Cancer (2012) 0.95
Comparative Metagenomics of Eight Geographically Remote Terrestrial Hot Springs. Microb Ecol (2015) 0.93
Oligonucleotide ligation assay-based DNA chip for multiplex detection of single nucleotide polymorphism. Biosens Bioelectron (2004) 0.92
Bayesian transcriptome assembly. Genome Biol (2014) 0.92
CCHMM_PROF: a HMM-based coiled-coil predictor with evolutionary information. Bioinformatics (2009) 0.91
Loss of miR-10a activates lpo and collaborates with activated Wnt signaling in inducing intestinal neoplasia in female mice. PLoS Genet (2013) 0.91
Modeling promoter grammars with evolving hidden Markov models. Bioinformatics (2008) 0.90
Automatic generation of gene finders for eukaryotic species. BMC Bioinformatics (2006) 0.90
Teaching computers to fold proteins. Phys Rev E Stat Nonlin Soft Matter Phys (2004) 0.88
Long- and short-term selective forces on malaria parasite genomes. PLoS Genet (2010) 0.86
Training HMM structure with genetic algorithm for biological sequence analysis. Bioinformatics (2004) 0.86
A short-read multiplex sequencing method for reliable, cost-effective and high-throughput genotyping in large-scale studies. Hum Mutat (2013) 0.84
DivA: detection of non-homologous and very divergent regions in protein sequence alignments. BMC Res Notes (2014) 0.83
BayesMD: flexible biological modeling for motif discovery. J Comput Biol (2008) 0.83
Novel overlapping coding sequences in Chlamydia trachomatis. FEMS Microbiol Lett (2006) 0.82
Alterations in polyadenylation and its implications for endocrine disease. Front Endocrinol (Lausanne) (2013) 0.81
Hidden Markov Models for prediction of protein features. Methods Mol Biol (2008) 0.79
Sequence and expression analysis of gaps in human chromosome 20. Nucleic Acids Res (2012) 0.79
On the accuracy of short read mapping. Methods Mol Biol (2013) 0.77
Long-term results of a phase II trial of high-dose radiotherapy (60 Gy) and UFT/l-leucovorin in patients with non-resectable locally advanced rectal cancer (LARC). Acta Oncol (2008) 0.77
SNPest: a probabilistic graphical model for estimating genotypes. BMC Res Notes (2014) 0.76
Biparental inheritance of chromosomal abnormalities in male twins with non-syndromic mental retardation. Eur J Med Genet (2011) 0.76
Old soldiers never die .... Genome Biol (2012) 0.75
Erratum. Eur Heart J Qual Care Clin Outcomes (2017) 0.75
Corrigendum: Genome-wide adaptive complexes to underground stresses in blind mole rats Spalax. Nat Commun (2015) 0.75