Published in BMC Bioinformatics on January 30, 2009
MicroRNAs: New Biomarkers for Diagnosis, Prognosis, Therapy Prediction and Therapeutic Tools for Breast Cancer. Theranostics (2015) 1.62
Genome-wide microRNA expression analysis of clear cell renal cell carcinoma by next generation deep sequencing. PLoS One (2012) 1.41
Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans. Genome Res (2010) 1.31
First survey of the wheat chromosome 5A composition through a next generation sequencing approach. PLoS One (2011) 1.09
Bioinformatic tools for microRNA dissection. Nucleic Acids Res (2015) 1.02
Root precursors of microRNAs in wild emmer and modern wheats show major differences in response to drought stress. Funct Integr Genomics (2015) 0.98
A Review of Computational Tools in microRNA Discovery. Front Genet (2013) 0.98
HuntMi: an efficient and taxon-specific approach in pre-miRNA identification. BMC Bioinformatics (2013) 0.96
A computational-based update on microRNAs and their targets in barley (Hordeum vulgare L.). BMC Genomics (2010) 0.94
Computational prediction of the localization of microRNAs within their pre-miRNA. Nucleic Acids Res (2013) 0.94
Review of current methodological approaches for characterizing microRNAs in plants. Int J Plant Genomics (2009) 0.93
Wheat miRNA ancestors: evident by transcriptome analysis of A, B, and D genome donors. Funct Integr Genomics (2016) 0.90
Next-generation survey sequencing and the molecular organization of wheat chromosome 6B. DNA Res (2013) 0.89
Combination of measures distinguishes pre-miRNAs from other stem-loops in the genome of the newly sequenced Anopheles darlingi. BMC Genomics (2010) 0.85
NOVOMIR: De Novo Prediction of MicroRNA-Coding Regions in a Single Plant-Genome. J Nucleic Acids (2010) 0.83
New wheat microRNA using whole-genome sequence. Funct Integr Genomics (2014) 0.82
ZIKV - CDB: A Collaborative Database to Guide Research Linking SncRNAs and ZIKA Virus Disease Symptoms. PLoS Negl Trop Dis (2016) 0.77
Small RNAs in metastatic and non-metastatic oral squamous cell carcinoma. BMC Med Genomics (2015) 0.77
An integrative approach to identify hexaploid wheat miRNAome associated with development and tolerance to abiotic stress. BMC Genomics (2015) 0.77
A framework for improving microRNA prediction in non-human genomes. Nucleic Acids Res (2015) 0.77
Role of bioinformatics in establishing microRNAs as modulators of abiotic stress responses: the new revolution. Front Physiol (2015) 0.76
MicroRNA prediction using a fixed-order Markov model based on the secondary structure pattern. PLoS One (2012) 0.76
Non-coding RNA gene families in the genomes of anopheline mosquitoes. BMC Genomics (2014) 0.76
The prediction of the porcine pre-microRNAs in genome-wide based on support vector machine (SVM) and homology searching. BMC Genomics (2012) 0.75
Identification and Characterization of Microsatellite Loci in Maqui (Aristotelia chilensis [Molina] Stunz) Using Next-Generation Sequencing (NGS). PLoS One (2016) 0.75
Integrating genetics and epigenetics in breast cancer: biological insights, experimental, computational methods and therapeutic potential. BMC Syst Biol (2015) 0.75
Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction. Comput Struct Biotechnol J (2016) 0.75
Computational Detection of piRNA in Human Using Support Vector Machine. Avicenna J Med Biotechnol (2016) 0.75
The human genome browser at UCSC. Genome Res (2002) 168.23
Conserved seed pairing, often flanked by adenosines, indicates that thousands of human genes are microRNA targets. Cell (2005) 96.87
The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell (1993) 64.62
The 21-nucleotide let-7 RNA regulates developmental timing in Caenorhabditis elegans. Nature (2000) 39.31
The nuclear RNase III Drosha initiates microRNA processing. Nature (2003) 35.49
Identification of tissue-specific microRNAs from mouse. Curr Biol (2002) 34.55
Posttranscriptional regulation of the heterochronic gene lin-14 by lin-4 mediates temporal pattern formation in C. elegans. Cell (1993) 33.79
Asymmetry in the assembly of the RNAi enzyme complex. Cell (2003) 22.18
MicroRNA genes are transcribed by RNA polymerase II. EMBO J (2004) 20.65
Vienna RNA secondary structure server. Nucleic Acids Res (2003) 19.69
The microRNAs of Caenorhabditis elegans. Genes Dev (2003) 17.70
Exportin-5 mediates the nuclear export of pre-microRNAs and short hairpin RNAs. Genes Dev (2003) 17.64
Identification of hundreds of conserved and nonconserved human microRNAs. Nat Genet (2005) 15.96
TRBP recruits the Dicer complex to Ago2 for microRNA processing and gene silencing. Nature (2005) 13.44
Identification of microRNAs of the herpesvirus family. Nat Methods (2005) 12.98
Human microRNAs are processed from capped, polyadenylated transcripts that can also function as mRNAs. RNA (2004) 11.52
Computational identification of Drosophila microRNA genes. Genome Biol (2003) 9.86
Modulation of microRNA processing and expression through RNA editing by ADAR deaminases. Nat Struct Mol Biol (2005) 7.49
miRBase: the microRNA sequence database. Methods Mol Biol (2006) 6.17
Computational and experimental identification of C. elegans microRNAs. Mol Cell (2003) 5.22
Approaches to microRNA discovery. Nat Genet (2006) 4.32
Classification of real and pseudo microRNA precursors using local structure-sequence features and support vector machine. BMC Bioinformatics (2005) 3.69
HEN1 recognizes 21-24 nt small RNA duplexes and deposits a methyl group onto the 2' OH of the 3' terminal nucleotide. Nucleic Acids Res (2006) 3.14
Identification of clustered microRNAs using an ab initio prediction method. BMC Bioinformatics (2005) 2.76
Human microRNA prediction through a probabilistic co-learning model of sequence and structure. Nucleic Acids Res (2005) 2.48
Patterns of flanking sequence conservation and a characteristic upstream motif for microRNA gene identification. RNA (2004) 2.17
Profile-based detection of microRNA precursors in animal genomes. Bioinformatics (2004) 1.79
MicroRNAs: expression, avoidance and subversion by vertebrate viruses. Nat Rev Microbiol (2006) 1.54
Plant and animal microRNAs: similarities and differences. Funct Integr Genomics (2005) 1.51
miRRim: a novel system to find conserved miRNAs with high sensitivity and specificity. RNA (2007) 1.21
Conserved microRNA characteristics in mammals. Oligonucleotides (2006) 1.08
The opossum genome: insights and opportunities from an alternative mammal. Genome Res (2008) 0.94
A genomic regulatory network for development. Science (2002) 9.67
Genome of the marsupial Monodelphis domestica reveals innovation in non-coding sequences. Nature (2007) 7.91
STAMP: a web tool for exploring DNA-binding motif similarities. Nucleic Acids Res (2007) 4.92
enoLOGOS: a versatile web tool for energy normalized sequence logos. Nucleic Acids Res (2005) 4.03
Inhibition and role of let-7d in idiopathic pulmonary fibrosis. Am J Respir Crit Care Med (2010) 3.02
Human transcriptome subtraction by using short sequence tags to search for tumor viruses in conjunctival carcinoma. J Virol (2007) 2.68
DNA familial binding profiles made easy: comparison of various motif alignment and clustering strategies. PLoS Comput Biol (2007) 2.37
Features of mammalian microRNA promoters emerge from polymerase II chromatin immunoprecipitation data. PLoS One (2009) 2.29
A provisional regulatory gene network for specification of endomesoderm in the sea urchin embryo. Dev Biol (2002) 2.26
Mesenchymal glioma stem cells are maintained by activated glycolytic metabolism involving aldehyde dehydrogenase 1A3. Proc Natl Acad Sci U S A (2013) 2.25
Reconstructing an ancestral mammalian immune supercomplex from a marsupial major histocompatibility complex. PLoS Biol (2006) 2.17
Mapping and identification of essential gene functions on the X chromosome of Drosophila. EMBO Rep (2001) 1.83
mirConnX: condition-specific mRNA-microRNA network integrator. Nucleic Acids Res (2011) 1.62
ComiR: Combinatorial microRNA target prediction tool. Nucleic Acids Res (2013) 1.39
Profibrotic role of miR-154 in pulmonary fibrosis. Am J Respir Cell Mol Biol (2012) 1.30
Improved detection of DNA motifs using a self-organized clustering of familial binding profiles. Bioinformatics (2005) 1.29
Combined analysis reveals a core set of cycling genes. Genome Biol (2007) 1.10
Footer: a quantitative comparative genomics method for efficient recognition of cis-regulatory elements. Genome Res (2005) 1.09
High throughput determination of TGFβ1/SMAD3 targets in A549 lung epithelial cells. PLoS One (2011) 1.02
Inferring protein-DNA dependencies using motif alignments and mutual information. Bioinformatics (2007) 1.01
FOOTER: a web tool for finding mammalian DNA regulatory regions using phylogenetic footprinting. Nucleic Acids Res (2005) 0.99
Novel modeling of combinatorial miRNA targeting identifies SNP with potential role in bone density. PLoS Comput Biol (2012) 0.97
The role of RNA folding free energy in the evolution of the polymerase genes of the influenza A virus. Genome Biol (2009) 0.93
Overexpression of microRNA-1 promotes cardiomyocyte commitment from human cardiovascular progenitors via suppressing WNT and FGF signaling pathways. J Mol Cell Cardiol (2013) 0.90
Regulatory conservation of protein coding and microRNA genes in vertebrates: lessons from the opossum genome. Genome Biol (2007) 0.90
A sequence alignment-independent method for protein classification. Appl Bioinformatics (2004) 0.90
Deregulation of common genes by c-Myc and its direct target, MT-MC1. Proc Natl Acad Sci U S A (2005) 0.89
Large scale comparison of innate responses to viral and bacterial pathogens in mouse and macaque. PLoS One (2011) 0.87
RNA deep sequencing reveals differential microRNA expression during development of sea urchin and sea star. PLoS One (2011) 0.86
Finding subtypes of transcription factor motif pairs with distinct regulatory roles. Nucleic Acids Res (2011) 0.85
Extracting biologically significant patterns from short time series gene expression data. BMC Bioinformatics (2009) 0.85
Estrogen represses gene expression through reconfiguring chromatin structures. Nucleic Acids Res (2013) 0.85
Expression of regulatory platelet microRNAs in patients with sickle cell disease. PLoS One (2013) 0.84
SOP3: a web-based tool for selection of oligonucleotide primers for single nucleotide polymorphism analysis by Pyrosequencing. Biotechniques (2005) 0.84
T-ReCS: stable selection of dynamically formed groups of features with application to prediction of clinical outcomes. Pac Symp Biocomput (2015) 0.81
To bind or not to bind--FoxA1 determines estrogen receptor action in breast cancer progression. Breast Cancer Res (2012) 0.81
Self-organizing neural networks to support the discovery of DNA-binding motifs. Neural Netw (2006) 0.81
Electrostatic hot spot on DNA-binding domains mediates phosphate desolvation and the pre-organization of specificity determinant side chains. Nucleic Acids Res (2010) 0.80
Spectral clustering strategies for heterogeneous disease expression data. Pac Symp Biocomput (2013) 0.78
Regulatory heterochronies and loose temporal scaling between sea star and sea urchin regulatory circuits. Int J Dev Biol (2017) 0.75
Eric Davidson (1937-2015) and the past, present and future of EvoDevo. Evol Dev (2016) 0.75
Web-based primer design software for genome-scale genotyping by pyrosequencing. Methods Mol Biol (2007) 0.75