SePIA: RNA and small RNA sequence processing, integration, and analysis
Published 2016 View Full Article
- Home
- Publications
- Publication Search
- Publication Details
Title
SePIA: RNA and small RNA sequence processing, integration, and analysis
Authors
Keywords
Sequencing, Integration, miRNA, totalRNA, RNA, Breast cancer
Journal
BioData Mining
Volume 9, Issue 1, Pages -
Publisher
Springer Nature
Online
2016-05-22
DOI
10.1186/s13040-016-0099-z
References
Ask authors/readers for more resources
Related references
Note: Only part of the references are listed.- Fast and accurate approximate inference of transcript expression from RNA-seq data
- (2015) James Hensman et al. BIOINFORMATICS
- Estrogen receptor α inhibitor activates the unfolded protein response, blocks protein synthesis, and induces tumor regression
- (2015) Neal D. Andruska et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Global miRNA expression and correlation with mRNA levels in primary human bone cells
- (2015) N. Laxman et al. RNA
- Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine
- (2015) Hao Ye et al. Pharmaceutics
- Trimmomatic: a flexible trimmer for Illumina sequence data
- (2014) Anthony M. Bolger et al. BIOINFORMATICS
- Elevated expression of myosin X in tumours contributes to breast cancer aggressiveness and metastasis
- (2014) R Cao et al. BRITISH JOURNAL OF CANCER
- Mapping the miRNA interactome by cross-linking ligation and sequencing of hybrids (CLASH)
- (2014) Aleksandra Helwak et al. Nature Protocols
- Ahnak functions as a tumor suppressor via modulation of TGFβ/Smad signaling pathway
- (2014) I H Lee et al. ONCOGENE
- Reliable Identification of Genomic Variants from RNA-Seq Data
- (2013) Robert Piskol et al. AMERICAN JOURNAL OF HUMAN GENETICS
- iMir: An integrated pipeline for high-throughput analysis of small non-coding RNA data obtained by smallRNA-Seq
- (2013) Giorgio Giurato et al. BMC BIOINFORMATICS
- Elevated cyclin B2 expression in invasive breast carcinoma is associated with unfavorable clinical outcome
- (2013) Emman Shubbar et al. BMC CANCER
- Prooncogenic Factors miR-23b and miR-27b Are Regulated by Her2/Neu, EGF, and TNF- in Breast Cancer
- (2013) L. Jin et al. CANCER RESEARCH
- The miR-17/92 cluster: a comprehensive update on its genomics, genetics, functions and increasingly important and numerous roles in health and disease
- (2013) E Mogilyansky et al. CELL DEATH AND DIFFERENTIATION
- Systematic evaluation of spliced alignment programs for RNA-seq data
- (2013) Pär G Engström et al. NATURE METHODS
- miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions
- (2013) Sheng-Da Hsu et al. NUCLEIC ACIDS RESEARCH
- Integrated MicroRNA and mRNA Signatures Associated with Survival in Triple Negative Breast Cancer
- (2013) Luciano Cascione et al. PLoS One
- Tumor Suppressive Function of mir-205 in Breast Cancer Is Linked to HMGB3 Regulation
- (2013) Ola A. Elgamal et al. PLoS One
- MicroRNA-143 is downregulated in breast cancer and regulates DNA methyltransferases 3A in breast cancer cells
- (2013) Enders K. O. Ng et al. TUMOR BIOLOGY
- RSeQC: quality control of RNA-seq experiments
- (2012) Liguo Wang et al. BIOINFORMATICS
- RNA-SeQC: RNA-seq metrics for quality control and process optimization
- (2012) David S. DeLuca et al. BIOINFORMATICS
- STAR: ultrafast universal RNA-seq aligner
- (2012) Alexander Dobin et al. BIOINFORMATICS
- Detecting miRNAs in deep-sequencing data: a software performance comparison and evaluation
- (2012) V. Williamson et al. BRIEFINGS IN BIOINFORMATICS
- Joint analysis of miRNA and mRNA expression data
- (2012) A. Muniategui et al. BRIEFINGS IN BIOINFORMATICS
- miR-187 Is an Independent Prognostic Factor in Breast Cancer and Confers Increased Invasive Potential In Vitro
- (2012) L. Mulrane et al. CLINICAL CANCER RESEARCH
- Detecting differential usage of exons from RNA-seq data
- (2012) S. Anders et al. GENOME RESEARCH
- Comprehensive molecular portraits of human breast tumours
- (2012) Daniel C. Koboldt et al. NATURE
- Differential analysis of gene regulation at transcript resolution with RNA-seq
- (2012) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- Streaming fragment assignment for real-time analysis of sequencing experiments
- (2012) Adam Roberts et al. NATURE METHODS
- Fast gapped-read alignment with Bowtie 2
- (2012) Ben Langmead et al. NATURE METHODS
- Transcriptomic landscape of breast cancers through mRNA sequencing
- (2012) Jeyanthy Eswaran et al. Scientific Reports
- From snoRNA to miRNA: Dual function regulatory non-coding RNAs
- (2011) Michelle S. Scott et al. BIOCHIMIE
- wapRNA: a web-based application for the processing of RNA sequences
- (2011) Wenming Zhao et al. BIOINFORMATICS
- A pipeline for RNA-seq data processing and quality assessment
- (2011) Angela Goncalves et al. BIOINFORMATICS
- Bambino: a variant detector and alignment viewer for next-generation sequencing data in the SAM/BAM format
- (2011) M. N. Edmonson et al. BIOINFORMATICS
- ChimeraScan: a tool for identifying chimeric transcription in sequencing data
- (2011) Matthew K. Iyer et al. BIOINFORMATICS
- RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome
- (2011) Bo Li et al. BMC BIOINFORMATICS
- Down-regulation of the cavin family proteins in breast cancer
- (2011) Lin Bai et al. JOURNAL OF CELLULAR BIOCHEMISTRY
- Caveolin Involvement and Modulation in Breast Cancer
- (2011) M. N. Aoki et al. MINI-REVIEWS IN MEDICINAL CHEMISTRY
- miRanalyzer: an update on the detection and analysis of microRNAs in high-throughput sequencing experiments
- (2011) M. Hackenberg et al. NUCLEIC ACIDS RESEARCH
- miRDeep2 accurately identifies known and hundreds of novel microRNA genes in seven animal clades
- (2011) Marc R. Friedländer et al. NUCLEIC ACIDS RESEARCH
- Integrated Analysis of miRNA and mRNA Expression in Childhood Medulloblastoma Compared with Neural Stem Cells
- (2011) Laura A. Genovesi et al. PLoS One
- deFuse: An Algorithm for Gene Fusion Discovery in Tumor RNA-Seq Data
- (2011) Andrew McPherson et al. PLoS Computational Biology
- Evaluation of statistical methods for normalization and differential expression in mRNA-Seq experiments
- (2010) James H Bullard et al. BMC BIOINFORMATICS
- The Myc-miR-17 92 Axis Blunts TGF Signaling and Production of Multiple TGF -Dependent Antiangiogenic Factors
- (2010) M. Dews et al. CANCER RESEARCH
- mir-17-92, a cluster of miRNAs in the midst of the cancer network
- (2010) Virginie Olive et al. INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY
- Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
- (2010) Cole Trapnell et al. NATURE BIOTECHNOLOGY
- Biases in Illumina transcriptome sequencing caused by random hexamer priming
- (2010) Kasper D. Hansen et al. NUCLEIC ACIDS RESEARCH
- ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
- (2010) K. Wang et al. NUCLEIC ACIDS RESEARCH
- An oncogenic role of eIF3e/INT6 in human breast cancer
- (2010) M Grzmil et al. ONCOGENE
- Large-scale data integration framework provides a comprehensive view on glioblastoma multiforme
- (2010) Kristian Ovaska et al. Genome Medicine
- Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
- (2010) Jeremy Goecks et al. GENOME BIOLOGY
- Differential expression analysis for sequence count data
- (2010) Simon Anders et al. GENOME BIOLOGY
- TopHat: discovering splice junctions with RNA-Seq
- (2009) Cole Trapnell et al. BIOINFORMATICS
- The Sequence Alignment/Map format and SAMtools
- (2009) H. Li et al. BIOINFORMATICS
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- edgeR: a Bioconductor package for differential expression analysis of digital gene expression data
- (2009) M. D. Robinson et al. BIOINFORMATICS
- Correlation of expression profiles between microRNAs and mRNA targets using NCI-60 data
- (2009) Yu-Ping Wang et al. BMC GENOMICS
- Next-generation gap
- (2009) John D McPherson NATURE METHODS
- DIANA-microT web server: elucidating microRNA functions through target prediction
- (2009) M. Maragkakis et al. NUCLEIC ACIDS RESEARCH
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- A novel signaling pathway impact analysis
- (2008) Adi Laurentiu Tarca et al. BIOINFORMATICS
- A Human snoRNA with MicroRNA-Like Functions
- (2008) Christine Ender et al. MOLECULAR CELL
Find Funding. Review Successful Grants.
Explore over 25,000 new funding opportunities and over 6,000,000 successful grants.
ExploreDiscover Peeref hubs
Discuss science. Find collaborators. Network.
Join a conversation