Published in BioData Min on May 20, 2016
Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol (2009) 235.12
The Sequence Alignment/Map format and SAMtools. Bioinformatics (2009) 232.39
MicroRNAs: genomics, biogenesis, mechanism, and function. Cell (2004) 198.59
Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics (2009) 190.94
Fast gapped-read alignment with Bowtie 2. Nat Methods (2012) 83.79
TopHat: discovering splice junctions with RNA-Seq. Bioinformatics (2009) 81.13
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol (2010) 75.21
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics (2009) 67.17
Differential expression analysis for sequence count data. Genome Biol (2010) 64.56
Comprehensive molecular portraits of human breast tumours. Nature (2012) 47.39
Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics (2014) 44.23
ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res (2010) 43.51
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biol (2010) 39.63
miRBase: tools for microRNA genomics. Nucleic Acids Res (2007) 38.61
MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell (2007) 38.42
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol (2014) 27.48
RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics (2011) 25.76
STAR: ultrafast universal RNA-seq aligner. Bioinformatics (2012) 25.21
HTSeq--a Python framework to work with high-throughput sequencing data. Bioinformatics (2014) 23.22
Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments. BMC Bioinformatics (2010) 19.86
The role of site accessibility in microRNA target recognition. Nat Genet (2007) 18.52
Differential analysis of gene regulation at transcript resolution with RNA-seq. Nat Biotechnol (2012) 14.01
Biases in Illumina transcriptome sequencing caused by random hexamer priming. Nucleic Acids Res (2010) 9.08
AdapterRemoval: easy cleaning of next-generation sequencing reads. BMC Res Notes (2012) 7.94
Detecting differential usage of exons from RNA-seq data. Genome Res (2012) 6.34
A human snoRNA with microRNA-like functions. Mol Cell (2008) 5.84
miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades. Nucleic Acids Res (2011) 5.83
DIANA-microT web server: elucidating microRNA functions through target prediction. Nucleic Acids Res (2009) 5.23
A novel signaling pathway impact analysis. Bioinformatics (2008) 5.06
deFuse: an algorithm for gene fusion discovery in tumor RNA-Seq data. PLoS Comput Biol (2011) 4.66
Streaming fragment assignment for real-time analysis of sequencing experiments. Nat Methods (2012) 4.43
RSeQC: quality control of RNA-seq experiments. Bioinformatics (2012) 4.31
miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res (2013) 4.19
Using expression profiling data to identify human microRNA targets. Nat Methods (2007) 3.37
mir-17-92, a cluster of miRNAs in the midst of the cancer network. Int J Biochem Cell Biol (2010) 3.15
RNA-SeQC: RNA-seq metrics for quality control and process optimization. Bioinformatics (2012) 2.94
Systematic evaluation of spliced alignment programs for RNA-seq data. Nat Methods (2013) 2.92
ChimeraScan: a tool for identifying chimeric transcription in sequencing data. Bioinformatics (2011) 2.74
The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease. Cell Death Differ (2013) 2.41
miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments. Nucleic Acids Res (2011) 2.25
The myc-miR-17~92 axis blunts TGF{beta} signaling and production of multiple TGF{beta}-dependent antiangiogenic factors. Cancer Res (2010) 2.13
Next-generation gap. Nat Methods (2009) 2.01
Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme. Genome Med (2010) 1.94
A pipeline for RNA-seq data processing and quality assessment. Bioinformatics (2011) 1.85
Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data. BMC Genomics (2009) 1.66
Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format. Bioinformatics (2011) 1.61
Elevated cyclin B2 expression in invasive breast carcinoma is associated with unfavorable clinical outcome. BMC Cancer (2013) 1.61
Decorin suppresses tumor cell-mediated angiogenesis. Oncogene (2002) 1.57
Reliable identification of genomic variants from RNA-seq data. Am J Hum Genet (2013) 1.55
Integrated microRNA and mRNA signatures associated with survival in triple negative breast cancer. PLoS One (2013) 1.43
From snoRNA to miRNA: Dual function regulatory non-coding RNAs. Biochimie (2011) 1.35
Prooncogenic factors miR-23b and miR-27b are regulated by Her2/Neu, EGF, and TNF-α in breast cancer. Cancer Res (2013) 1.31
Joint analysis of miRNA and mRNA expression data. Brief Bioinform (2012) 1.21
wapRNA: a web-based application for the processing of RNA sequences. Bioinformatics (2011) 1.17
Transcriptomic landscape of breast cancers through mRNA sequencing. Sci Rep (2012) 1.08
miR-187 is an independent prognostic factor in breast cancer and confers increased invasive potential in vitro. Clin Cancer Res (2012) 1.04
GCIP/CCNDBP1, a helix-loop-helix protein, suppresses tumorigenesis. J Cell Biochem (2007) 1.03
Tumor suppressive function of mir-205 in breast cancer is linked to HMGB3 regulation. PLoS One (2013) 1.02
An oncogenic role of eIF3e/INT6 in human breast cancer. Oncogene (2010) 1.01
Down-regulation of the cavin family proteins in breast cancer. J Cell Biochem (2012) 0.99
iMir: an integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq. BMC Bioinformatics (2013) 0.99
Ahnak functions as a tumor suppressor via modulation of TGFβ/Smad signaling pathway. Oncogene (2014) 0.98
Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH). Nat Protoc (2014) 0.96
MicroRNA-143 is downregulated in breast cancer and regulates DNA methyltransferases 3A in breast cancer cells. Tumour Biol (2013) 0.95
Elevated expression of myosin X in tumours contributes to breast cancer aggressiveness and metastasis. Br J Cancer (2014) 0.94
Integrated analysis of miRNA and mRNA expression in childhood medulloblastoma compared with neural stem cells. PLoS One (2011) 0.93
Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation. Brief Bioinform (2012) 0.92
Estrogen receptor α inhibitor activates the unfolded protein response, blocks protein synthesis, and induces tumor regression. Proc Natl Acad Sci U S A (2015) 0.92
Global Approaches to the Role of miRNAs in Drug-Induced Changes in Gene Expression. Front Genet (2012) 0.87
Fast and accurate approximate inference of transcript expression from RNA-seq data. Bioinformatics (2015) 0.81
Global miRNA expression and correlation with mRNA levels in primary human bone cells. RNA (2015) 0.80
Anima: modular workflow system for comprehensive image data analysis. Front Bioeng Biotechnol (2014) 0.77
Caveolin involvement and modulation in breast cancer. Mini Rev Med Chem (2011) 0.77
Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine. Pharmaceutics (2015) 0.76