Multi-perspective quality control of Illumina RNA sequencing data analysis

A micro-RNA expression signature for human NAFLD progression

(2016) Yan Guo et al.   JOURNAL OF GASTROENTEROLOGY

Transfer RNA detection by small RNA deep sequencing and disease association with myelodysplastic syndromes

(2015) Yan Guo et al.   BMC GENOMICS

Mining diverse small RNA species in the deep transcriptome

(2015) Kasey C. Vickers et al.   TRENDS IN BIOCHEMICAL SCIENCES

RNAseq by Total RNA Library Identifies Additional RNAs Compared to Poly(A) RNA Library

(2015) Yan Guo et al.   Biomed Research International

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Detection of internal exon deletion with exon Del

(2014) Yan Guo et al.   BMC BIOINFORMATICS

Alternative applications for distinct RNA sequencing strategies

(2014) Leng Han et al.   BRIEFINGS IN BIOINFORMATICS

Multi-perspective quality control of Illumina exome sequencing data using QC3

(2014) Yan Guo et al.   GENOMICS

Detecting and correcting systematic variation in large-scale RNA sequencing data

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

Advanced Heat Map and Clustering Analysis Using Heatmap3

(2014) Shilin Zhao et al.   Biomed Research International

MultiRankSeq: Multiperspective Approach for RNAseq Differential Expression Analysis and Quality Control

(2014) Yan Guo et al.   Biomed Research International

IVT-seq reveals extreme bias in RNA sequencing

(2014) Nicholas F Lahens et al.   GENOME BIOLOGY

MitoSeek: extracting mitochondria information and performing high-throughput mitochondria sequencing analysis

(2013) Yan Guo et al.   BIOINFORMATICS

Landscape of DNA Virus Associations across Human Malignant Cancers: Analysis of 3,775 Cases Using RNA-Seq

(2013) J. D. Khoury et al.   JOURNAL OF VIROLOGY

Sensitive detection of somatic point mutations in impure and heterogeneous cancer samples

(2013) Kristian Cibulskis et al.   NATURE BIOTECHNOLOGY

TeloTool: a new tool for telomere length measurement from terminal restriction fragment analysis with improved probe intensity correction

(2013) Janett Göhring et al.   NUCLEIC ACIDS RESEARCH

miRBase: annotating high confidence microRNAs using deep sequencing data

(2013) Ana Kozomara et al.   NUCLEIC ACIDS RESEARCH

QC-Chain: Fast and Holistic Quality Control Method for Next-Generation Sequencing Data

(2013) Qian Zhou et al.   PLoS One

Large Scale Comparison of Gene Expression Levels by Microarrays and RNAseq Using TCGA Data

(2013) Yan Guo et al.   PLoS One

Evaluation of Allele Frequency Estimation Using Pooled Sequencing Data Simulation

(2013) Yan Guo et al.   TheScientificWorldJOURNAL

Finding the lost treasures in exome sequencing data

(2013) David C. Samuels et al.   TRENDS IN GENETICS

A new approach to bias correction in RNA-Seq

(2012) Daniel C. Jones et al.   BIOINFORMATICS

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

Exome sequencing generates high quality data in non-target regions

(2012) Yan Guo et al.   BMC GENOMICS

RNA-Seq quantification of the human small airway epithelium transcriptome

(2012) Neil R Hackett et al.   BMC GENOMICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Using probabilistic estimation of expression residuals (PEER) to obtain increased power and interpretability of gene expression analyses

(2012) Oliver Stegle et al.   Nature Protocols

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

Summarizing and correcting the GC content bias in high-throughput sequencing

(2012) Yuval Benjamini et al.   NUCLEIC ACIDS RESEARCH

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel et al.   PLoS One

The Complex Exogenous RNA Spectra in Human Plasma: An Interface with Human Gut Biota?

(2012) Kai Wang et al.   PLoS One

Hints of tRNA-Derived Small RNAs Role in RNA Silencing Mechanisms

(2012) Maria Rosa Garcia-Silva et al.   Genes

Pathogen detection using short-RNA deep sequencing subtraction and assembly

(2011) O. Isakov et al.   BIOINFORMATICS

Quality control and preprocessing of metagenomic datasets

(2011) R. Schmieder et al.   BIOINFORMATICS

Bias detection and correction in RNA-Sequencing data

(2011) Wei Zheng et al.   BMC BIOINFORMATICS

GC-Content Normalization for RNA-Seq Data

(2011) Davide Risso et al.   BMC BIOINFORMATICS

Exogenous plant MIR168a specifically targets mammalian LDLRAP1: evidence of cross-kingdom regulation by microRNA

(2011) Lin Zhang et al.   CELL RESEARCH

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Evaluating Gene Expression in C57BL/6J and DBA/2J Mouse Striatum Using RNA-Seq and Microarrays

(2011) Daniel Bottomly et al.   PLoS One

Improving RNA-Seq expression estimates by correcting for fragment bias

(2011) Adam Roberts et al.   GENOME BIOLOGY

SNP discovery in the bovine milk transcriptome using RNA-Seq technology

(2010) Angela Cánovas et al.   MAMMALIAN GENOME

Defining the transcriptome and proteome in three functionally different human cell lines

(2010) Emma Lundberg et al.   Molecular Systems Biology

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

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

3' tag digital gene expression profiling of human brain and universal reference RNA using Illumina Genome Analyzer

(2009) Yan W Asmann et al.   BMC GENOMICS

The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants

(2009) Peter J. A. Cock et al.   NUCLEIC ACIDS RESEARCH

Direct Metagenomic Detection of Viral Pathogens in Nasal and Fecal Specimens Using an Unbiased High-Throughput Sequencing Approach

(2009) Shota Nakamura et al.   PLoS One

Filtering of deep sequencing data reveals the existence of abundant Dicer-dependent small RNAs derived from tRNAs

(2009) C. Cole et al.   RNA

An Abundance of Ubiquitously Expressed Genes Revealed by Tissue Transcriptome Sequence Data

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

Genetic Detection and Characterization of Lujo Virus, a New Hemorrhagic Fever–Associated Arenavirus from Southern Africa

(2009) Thomas Briese et al.   PLoS Pathogens

Stress induces tRNA cleavage by angiogenin in mammalian cells

(2008) Hanjiang Fu et al.   FEBS LETTERS

RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays

(2008) J. C. Marioni et al.   GENOME RESEARCH

Accurate whole human genome sequencing using reversible terminator chemistry

(2008) David R. Bentley et al.   NATURE

Stem cell transcriptome profiling via massive-scale mRNA sequencing

(2008) Nicole Cloonan et al.   NATURE METHODS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

A New Arenavirus in a Cluster of Fatal Transplant-Associated Diseases

(2008) Gustavo Palacios et al.   NEW ENGLAND JOURNAL OF MEDICINE

Substantial biases in ultra-short read data sets from high-throughput DNA sequencing

(2008) J. C. Dohm et al.   NUCLEIC ACIDS RESEARCH

A Global View of Gene Activity and Alternative Splicing by Deep Sequencing of the Human Transcriptome

(2008) M. Sultan et al.   SCIENCE