Prediction of small, noncoding RNAs in bacteria using heterogeneous data.

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Small non-coding RNAs in Streptomyces coelicolor. Nucleic Acids Res (2008) 1.31

Deep sequencing-based identification of small non-coding RNAs in Streptomyces coelicolor. RNA Biol (2011) 1.15

TargetRNA2: identifying targets of small regulatory RNAs in bacteria. Nucleic Acids Res (2014) 1.04

Directional RNA-seq reveals highly complex condition-dependent transcriptomes in E. coli K12 through accurate full-length transcripts assembling. BMC Genomics (2013) 0.94

Computational small RNA prediction in bacteria. Bioinform Biol Insights (2013) 0.88

Non-coding RNA detection methods combined to improve usability, reproducibility and precision. BMC Bioinformatics (2010) 0.86

Using RNA inverse folding to identify IRES-like structural subdomains. RNA Biol (2013) 0.83

nocoRNAc: characterization of non-coding RNAs in prokaryotes. BMC Bioinformatics (2011) 0.82

Inferring the relation between transcriptional and posttranscriptional regulation from expression compendia. BMC Microbiol (2014) 0.81

Small regulatory RNAs in Archaea. RNA Biol (2014) 0.80

Identification and validation of sRNAs in Edwardsiella tarda S08. PLoS One (2017) 0.75

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Vertebrate microRNA genes. Science (2003) 17.42

Computational identification of Drosophila microRNA genes. Genome Biol (2003) 9.86

The small RNA chaperone Hfq and multiple small RNAs control quorum sensing in Vibrio harveyi and Vibrio cholerae. Cell (2004) 8.89

Fast and reliable prediction of noncoding RNAs. Proc Natl Acad Sci U S A (2005) 8.15

Integrating genomic homology into gene structure prediction. Bioinformatics (2001) 7.92

Identification of novel small RNAs using comparative genomics and microarrays. Genes Dev (2001) 7.65

Novel small RNA-encoding genes in the intergenic regions of Escherichia coli. Curr Biol (2001) 7.56

Noncoding RNA gene detection using comparative sequence analysis. BMC Bioinformatics (2001) 7.07

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RNA expression analysis using a 30 base pair resolution Escherichia coli genome array. Nat Biotechnol (2000) 6.36

The small RNA regulators of Escherichia coli: roles and mechanisms*. Annu Rev Microbiol (2004) 5.72

Prediction of transcription terminators in bacterial genomes. J Mol Biol (2000) 5.28

Global analysis of small RNA and mRNA targets of Hfq. Mol Microbiol (2003) 4.98

Prediction of rho-independent Escherichia coli transcription terminators. A statistical analysis of their RNA stem-loop structures. J Mol Biol (1990) 4.78

Computational identification of noncoding RNAs in E. coli by comparative genomics. Curr Biol (2001) 4.58

SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res (2003) 4.17

Comparative gene prediction in human and mouse. Genome Res (2003) 4.13

A survey of small RNA-encoding genes in Escherichia coli. Nucleic Acids Res (2003) 4.10

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Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res (2003) 3.18

Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res (2006) 2.90

Computational gene prediction using multiple sources of evidence. Genome Res (2004) 2.58

Transcriptome analysis of Escherichia coli using high-density oligonucleotide probe arrays. Nucleic Acids Res (2002) 2.40

A bioinformatics based approach to discover small RNA genes in the Escherichia coli genome. Biosystems (2002) 2.31

A computational approach to identify genes for functional RNAs in genomic sequences. Nucleic Acids Res (2001) 2.28

GAZE: a generic framework for the integration of gene-prediction data by dynamic programming. Genome Res (2002) 2.20

Regulatory roles for small RNAs in bacteria. Curr Opin Microbiol (2003) 2.03

MSARI: multiple sequence alignments for statistical detection of RNA secondary structure. Proc Natl Acad Sci U S A (2004) 1.85

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sRNAPredict: an integrative computational approach to identify sRNAs in bacterial genomes. Nucleic Acids Res (2005) 1.52

PromEC: An updated database of Escherichia coli mRNA promoters with experimentally identified transcriptional start sites. Nucleic Acids Res (2001) 1.36

Identifying operons and untranslated regions of transcripts using Escherichia coli RNA expression analysis. Bioinformatics (2002) 1.19

Human-mouse gene identification by comparative evidence integration and evolutionary analysis. Genome Res (2003) 1.14

Target prediction for small, noncoding RNAs in bacteria. Nucleic Acids Res (2006) 2.90

TargetRNA: a tool for predicting targets of small RNA action in bacteria. Nucleic Acids Res (2008) 1.64

An approach for clustering gene expression data with error information. BMC Bioinformatics (2006) 1.05