Published in BMC Bioinformatics on January 14, 2010
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Analysis of microRNA-target interactions across diverse cancer types. Nat Struct Mol Biol (2013) 1.41
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miRNAMap 2.0: genomic maps of microRNAs in metazoan genomes. Nucleic Acids Res (2007) 3.05
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microRNAs and cancer: an overview. Cell Cycle (2008) 2.80
MicroRNA and mRNA integrated analysis (MMIA): a web tool for examining biological functions of microRNA expression. Nucleic Acids Res (2009) 2.03
miROrtho: computational survey of microRNA genes. Nucleic Acids Res (2008) 1.60
TranspoGene and microTranspoGene: transposed elements influence on the transcriptome of seven vertebrates and invertebrates. Nucleic Acids Res (2007) 1.30
MicroRNA silencing in primates: towards development of novel therapeutics. Cancer Res (2009) 1.29
UCbase & miRfunc: a database of ultraconserved sequences and microRNA function. Nucleic Acids Res (2008) 1.19
A combined transmembrane topology and signal peptide prediction method. J Mol Biol (2004) 15.77
MicroRNA expression in zebrafish embryonic development. Science (2005) 15.52
LNA-mediated microRNA silencing in non-human primates. Nature (2008) 11.45
Therapeutic silencing of microRNA-122 in primates with chronic hepatitis C virus infection. Science (2009) 10.30
Treatment of HCV infection by targeting microRNA. N Engl J Med (2013) 9.91
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
In situ detection of miRNAs in animal embryos using LNA-modified oligonucleotide probes. Nat Methods (2006) 6.67
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
Antagonism of microRNA-122 in mice by systemically administered LNA-antimiR leads to up-regulation of a large set of predicted target mRNAs in the liver. Nucleic Acids Res (2007) 5.67
Advantages of combined transmembrane topology and signal peptide prediction--the Phobius web server. Nucleic Acids Res (2007) 5.29
Altered MicroRNA expression confined to specific epithelial cell subpopulations in breast cancer. Cancer Res (2007) 5.25
Loss of microRNA cluster miR-29a/b-1 in sporadic Alzheimer's disease correlates with increased BACE1/beta-secretase expression. Proc Natl Acad Sci U S A (2008) 5.24
RAKE and LNA-ISH reveal microRNA expression and localization in archival human brain. RNA (2005) 4.91
An Aboriginal Australian genome reveals separate human dispersals into Asia. Science (2011) 4.84
Silencing of microRNA families by seed-targeting tiny LNAs. Nat Genet (2011) 4.81
Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics (2005) 4.25
Diagnostic and prognostic microRNAs in stage II colon cancer. Cancer Res (2008) 4.20
Sensitive and specific detection of microRNAs by northern blot analysis using LNA-modified oligonucleotide probes. Nucleic Acids Res (2004) 3.97
LNA-modified oligonucleotides mediate specific inhibition of microRNA function. Gene (2006) 3.49
Recalibrating Equus evolution using the genome sequence of an early Middle Pleistocene horse. Nature (2013) 3.45
A functional screen implicates microRNA-138-dependent regulation of the depalmitoylation enzyme APT1 in dendritic spine morphogenesis. Nat Cell Biol (2009) 3.44
Reliability measures for membrane protein topology prediction algorithms. J Mol Biol (2003) 3.13
MicroRNA expression in the adult mouse central nervous system. RNA (2008) 3.12
An HMM posterior decoder for sequence feature prediction that includes homology information. Bioinformatics (2005) 3.05
Stress-dependent cardiac remodeling occurs in the absence of microRNA-21 in mice. J Clin Invest (2010) 3.04
MicroRNA-31 functions as an oncogenic microRNA in mouse and human lung cancer cells by repressing specific tumor suppressors. J Clin Invest (2010) 2.87
Detection of microRNAs in frozen tissue sections by fluorescence in situ hybridization using locked nucleic acid probes and tyramide signal amplification. Nat Protoc (2007) 2.80
Genomic profiling of microRNAs in bladder cancer: miR-129 is associated with poor outcome and promotes cell death in vitro. Cancer Res (2009) 2.80
A code for transcription initiation in mammalian genomes. Genome Res (2007) 2.71
miR-200b mediates post-transcriptional repression of ZFHX1B. RNA (2007) 2.67
Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE. Genome Res (2008) 2.60
The liver-specific microRNA miR-122 controls systemic iron homeostasis in mice. J Clin Invest (2011) 2.30
A sequence-profile-based HMM for predicting and discriminating beta barrel membrane proteins. Bioinformatics (2002) 2.23
Uncovering growth-suppressive MicroRNAs in lung cancer. Clin Cancer Res (2009) 2.19
MicroRNA-138 regulates osteogenic differentiation of human stromal (mesenchymal) stem cells in vivo. Proc Natl Acad Sci U S A (2011) 2.05
Inhibition of microRNA function by antimiR oligonucleotides. Silence (2012) 2.02
MicroRNA-219 modulates NMDA receptor-mediated neurobehavioral dysfunction. Proc Natl Acad Sci U S A (2009) 2.00
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
Brain expressed microRNAs implicated in schizophrenia etiology. PLoS One (2007) 1.85
The utility of LNA in microRNA-based cancer diagnostics and therapeutics. Semin Cancer Biol (2008) 1.84
Molecular composition of IMP1 ribonucleoprotein granules. Mol Cell Proteomics (2007) 1.80
Signatures of RNA binding proteins globally coupled to effective microRNA target sites. Genome Res (2010) 1.75
Silencing of microRNA-155 in mice during acute inflammatory response leads to derepression of c/ebp Beta and down-regulation of G-CSF. Nucleic Acids Res (2009) 1.72
Therapeutic inhibition of the miR-34 family attenuates pathological cardiac remodeling and improves heart function. Proc Natl Acad Sci U S A (2012) 1.72
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
OligoDesign: Optimal design of LNA (locked nucleic acid) oligonucleotide capture probes for gene expression profiling. Nucleic Acids Res (2003) 1.59
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
Fluorescence-based codetection with protein markers reveals distinct cellular compartments for altered MicroRNA expression in solid tumors. Clin Cancer Res (2010) 1.44
Spatio-temporal accumulation of microRNAs is highly coordinated in developing plant tissues. Plant J (2006) 1.44
Pep-13, a plant defense-inducing pathogen-associated pattern from Phytophthora transglutaminases. EMBO J (2002) 1.44
Computational evidence for hundreds of non-conserved plant microRNAs. BMC Genomics (2005) 1.43
LNA-mediated anti-miR-155 silencing in low-grade B-cell lymphomas. Blood (2012) 1.42
A hidden Markov model approach for determining expression from genomic tiling micro arrays. BMC Bioinformatics (2006) 1.40
Silencing of microRNA-21 in vivo ameliorates autoimmune splenomegaly in lupus mice. EMBO Mol Med (2011) 1.38
Regulation of acute graft-versus-host disease by microRNA-155. Blood (2012) 1.35
Mammalian tissues defective in nonsense-mediated mRNA decay display highly aberrant splicing patterns. Genome Biol (2012) 1.34
MiR-155 is overexpressed in patients with atopic dermatitis and modulates T-cell proliferative responses by targeting cytotoxic T lymphocyte-associated antigen 4. J Allergy Clin Immunol (2010) 1.32
Genome analysis reveals insights into physiology and longevity of the Brandt's bat Myotis brandtii. Nat Commun (2013) 1.31
Experimental identification of microRNA-140 targets by silencing and overexpressing miR-140. RNA (2008) 1.29
MicroRNA silencing in primates: towards development of novel therapeutics. Cancer Res (2009) 1.29
PONGO: a web server for multiple predictions of all-alpha transmembrane proteins. Nucleic Acids Res (2006) 1.29
Silencing of the miR-17~92 cluster family inhibits medulloblastoma progression. Cancer Res (2013) 1.28
Discovering the first microRNA-targeted drug. J Cell Biol (2012) 1.26
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
MicroRNA profiling identifies microRNA-155 as an adverse mediator of cardiac injury and dysfunction during acute viral myocarditis. Circ Res (2012) 1.19
microRNA-9 targets the long non-coding RNA MALAT1 for degradation in the nucleus. Sci Rep (2013) 1.18
The therapeutic potential of microRNAs in cancer. Cancer J (2012) 1.18
microRNAs in CNS disorders. Neuromolecular Med (2009) 1.17
Mechanisms in endocrinology: micro-RNAs: targets for enhancing osteoblast differentiation and bone formation. Eur J Endocrinol (2011) 1.16
Intragenomic matching reveals a huge potential for miRNA-mediated regulation in plants. PLoS Comput Biol (2007) 1.16
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
Recombinant Adeno-Associated Virus-Mediated microRNA Delivery into the Postnatal Mouse Brain Reveals a Role for miR-134 in Dendritogenesis in Vivo. Front Neural Circuits (2010) 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