Published in Nucleic Acids Res on May 01, 2003
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics (2005) 3.69
Searching for IRES. RNA (2006) 2.78
Unique folding of precursor microRNAs: quantitative evidence and implications for de novo identification. RNA (2006) 1.85
Repertoire and evolution of miRNA genes in four divergent nematode species. Genome Res (2009) 1.64
X-inactivation: quantitative predictions of protein interactions in the Xist network. Nucleic Acids Res (2012) 1.01
Global mRNA stability is not associated with levels of gene expression in Drosophila melanogaster but shows a negative correlation with codon bias. J Mol Evol (2005) 0.88
Boltzmann ensemble features of RNA secondary structures: a comparative analysis of biological RNA sequences and random shuffles. J Math Biol (2007) 0.80
On the normalization of the minimum free energy of RNAs by sequence length. PLoS One (2014) 0.80
Novel Approach to Analyzing MFE of Noncoding RNA Sequences. Genomics Insights (2016) 0.75
An abundant class of tiny RNAs with probable regulatory roles in Caenorhabditis elegans. Science (2001) 44.16
Expanded sequence dependence of thermodynamic parameters improves prediction of RNA secondary structure. J Mol Biol (1999) 41.48
Estimation of secondary structure in ribonucleic acids. Nature (1971) 20.52
WormBase: network access to the genome and biology of Caenorhabditis elegans. Nucleic Acids Res (2001) 18.52
Coaxial stacking of helixes enhances binding of oligoribonucleotides and improves predictions of RNA folding. Proc Natl Acad Sci U S A (1994) 8.06
Transposons but not retrotransposons are located preferentially in regions of high recombination rate in Caenorhabditis elegans. Genetics (2000) 1.85
Repetitive-DNA elements are similarly distributed on Caenorhabditis elegans autosomes. Proc Natl Acad Sci U S A (2000) 1.64
Genomewide analysis of PRC1 and PRC2 occupancy identifies two classes of bivalent domains. PLoS Genet (2008) 11.17
Large-scale mapping and validation of Escherichia coli transcriptional regulation from a compendium of expression profiles. PLoS Biol (2007) 10.46
Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev Cell (2004) 3.85
A customized and versatile high-density genotyping array for the mouse. Nat Methods (2009) 3.53
topoSNP: a topographic database of non-synonymous single nucleotide polymorphisms with and without known disease association. Nucleic Acids Res (2004) 3.50
Predicting protein function from protein/protein interaction data: a probabilistic approach. Bioinformatics (2003) 3.24
Structural location of disease-associated single-nucleotide polymorphisms. J Mol Biol (2003) 3.20
Whole-genome annotation by using evidence integration in functional-linkage networks. Proc Natl Acad Sci U S A (2004) 2.93
Evidence of a large-scale functional organization of mammalian chromosomes. PLoS Genet (2005) 2.73
The recombinational anatomy of a mouse chromosome. PLoS Genet (2008) 2.66
Network-based analysis of affected biological processes in type 2 diabetes models. PLoS Genet (2007) 2.54
Computational identification of operons in microbial genomes. Genome Res (2002) 2.35
Identification of functional links between genes using phylogenetic profiles. Bioinformatics (2003) 2.33
Gene-specific RNA polymerase II phosphorylation and the CTD code. Nat Struct Mol Biol (2010) 2.22
RankGene: identification of diagnostic genes based on expression data. Bioinformatics (2003) 1.96
Deep sequencing of the oral microbiome reveals signatures of periodontal disease. PLoS One (2012) 1.96
Extracting conserved gene expression motifs from gene expression data. Pac Symp Biocomput (2003) 1.95
Genomic functional annotation using co-evolution profiles of gene clusters. Genome Biol (2002) 1.76
COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. Nucleic Acids Res (2010) 1.72
Global changes in processing of mRNA 3' untranslated regions characterize clinically distinct cancer subtypes. Cancer Res (2009) 1.70
Cracking the egg: molecular dynamics and evolutionary aspects of the transition from the fully grown oocyte to embryo. Genes Dev (2006) 1.67
PACdb: PolyA Cleavage Site and 3'-UTR Database. Bioinformatics (2005) 1.63
A ubiquitous and conserved signal for RNA localization in chordates. Curr Biol (2002) 1.60
The art of gene function prediction. Nat Biotechnol (2006) 1.56
Systematic variation in mRNA 3'-processing signals during mouse spermatogenesis. Nucleic Acids Res (2006) 1.56
Identification of transcription factor binding sites upstream of human genes regulated by the phosphatidylinositol 3-kinase and MEK/ERK signaling pathways. J Biol Chem (2004) 1.49
A systems biology approach identifies inflammatory abnormalities between mouse strains prior to development of metabolic disease. Diabetes (2010) 1.41
Probabilistic protein function prediction from heterogeneous genome-wide data. PLoS One (2007) 1.41
Towards the identification of essential genes using targeted genome sequencing and comparative analysis. BMC Genomics (2006) 1.39
A Bayesian framework for combining gene predictions. Bioinformatics (2002) 1.37
Immediate-early and delayed primary response genes are distinct in function and genomic architecture. J Biol Chem (2007) 1.37
An aberrant transcription factor network essential for Wnt signaling and stem cell maintenance in glioblastoma. Cell Rep (2013) 1.35
Signals for pre-mRNA cleavage and polyadenylation. Wiley Interdiscip Rev RNA (2011) 1.31
GC/AT-content spikes as genomic punctuation marks. Proc Natl Acad Sci U S A (2004) 1.30
MuPlex: multi-objective multiplex PCR assay design. Nucleic Acids Res (2005) 1.28
RimO, a MiaB-like enzyme, methylthiolates the universally conserved Asp88 residue of ribosomal protein S12 in Escherichia coli. Proc Natl Acad Sci U S A (2008) 1.27
Accelerated postnatal growth increases lipogenic gene expression and adipocyte size in low-birth weight mice. Diabetes (2009) 1.25
A multispecies comparison of the metazoan 3'-processing downstream elements and the CstF-64 RNA recognition motif. BMC Genomics (2006) 1.25
Biological context networks: a mosaic view of the interactome. Mol Syst Biol (2006) 1.24
The COMBREX project: design, methodology, and initial results. PLoS Biol (2013) 1.24
Human-mouse gene identification by comparative evidence integration and evolutionary analysis. Genome Res (2003) 1.14
Glycogen synthase kinase-3 represses cyclic AMP response element-binding protein (CREB)-targeted immediate early genes in quiescent cells. J Biol Chem (2007) 1.12
Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers. Genome Biol (2008) 1.11
GEMS: a web server for biclustering analysis of expression data. Nucleic Acids Res (2005) 1.10
Position-dependent motif characterization using non-negative matrix factorization. Bioinformatics (2008) 1.09
Hypermutable DNA chronicles the evolution of human colon cancer. Proc Natl Acad Sci U S A (2014) 1.02
Probe-level analysis of expression microarrays characterizes isoform-specific degradation during mouse oocyte maturation. PLoS One (2009) 1.01
Hierarchical tree snipping: clustering guided by prior knowledge. Bioinformatics (2007) 1.01
Biological process linkage networks. PLoS One (2009) 1.00
Integration of relational and hierarchical network information for protein function prediction. BMC Bioinformatics (2008) 0.99
Phylogenetic detection of conserved gene clusters in microbial genomes. BMC Bioinformatics (2005) 0.97
Patterns of recombination activity on mouse chromosome 11 revealed by high resolution mapping. PLoS One (2010) 0.96
Triplet repeat length bias and variation in the human transcriptome. Proc Natl Acad Sci U S A (2009) 0.95
Evidence of a large-scale functional organization of Mammalian chromosomes. PLoS Biol (2007) 0.94
Gene expression module discovery using gibbs sampling. Genome Inform (2004) 0.93
Less is more: towards an optimal universal description of protein folds. Bioinformatics (2005) 0.93
Genes involved in complex adaptive processes tend to have highly conserved upstream regions in mammalian genomes. BMC Genomics (2005) 0.92
Identification of genes with fast-evolving regions in microbial genomes. Nucleic Acids Res (2004) 0.91
Segmentally variable genes: a new perspective on adaptation. PLoS Biol (2004) 0.91
Quantitative comparison of EST libraries requires compensation for systematic biases in cDNA generation. BMC Bioinformatics (2006) 0.91
Thousands of missed genes found in bacterial genomes and their analysis with COMBREX. Biol Direct (2012) 0.90
Integration of heterogeneous expression data sets extends the role of the retinol pathway in diabetes and insulin resistance. Bioinformatics (2009) 0.90
A predictive phosphorylation signature of lung cancer. PLoS One (2009) 0.90
Quantitative analysis of single nucleotide polymorphisms within copy number variation. PLoS One (2008) 0.89
Functional characterization of the YmcB and YqeV tRNA methylthiotransferases of Bacillus subtilis. Nucleic Acids Res (2010) 0.86
CGDSNPdb: a database resource for error-checked and imputed mouse SNPs. Database (Oxford) (2010) 0.85
A comparative genomic method for computational identification of prokaryotic translation initiation sites. Nucleic Acids Res (2002) 0.85
Quantifying DNA-protein binding specificities by using oligonucleotide mass tags and mass spectroscopy. Proc Natl Acad Sci U S A (2007) 0.83
Computational tradeoffs in multiplex PCR assay design for SNP genotyping. BMC Genomics (2005) 0.83
Biochemical networks: the evolution of gene annotation. Nat Chem Biol (2010) 0.82
Seeing the forest for the trees: using the Gene Ontology to restructure hierarchical clustering. Bioinformatics (2009) 0.80
Interrogating the transcriptome of oocytes and preimplantation embryos. Methods Enzymol (2010) 0.80
Biochemical Characterization of Hypothetical Proteins from Helicobacter pylori. PLoS One (2013) 0.79
Characterization of two new aminopeptidases in Escherichia coli. J Bacteriol (2005) 0.78
To supplement or not to supplement: a metabolic network framework for human nutritional supplements. PLoS One (2013) 0.77
Multi-node graphs: a framework for multiplexed biological assays. J Comput Biol (2006) 0.77
Predicting malaria interactome classifications from time-course transcriptomic data along the intraerythrocytic developmental cycle. Artif Intell Med (2010) 0.76
Systems biology characterization of engineered tissues. Annu Rev Biomed Eng (2013) 0.75
Context specific protein function prediction. Genome Inform (2007) 0.75
The complete genome sequence of a dog: a perspective. Bioessays (2006) 0.75