RNA-seq data science: From raw data to effective interpretation

Nanopore sequencing technology, bioinformatics and applications

(2021) Yunhao Wang et al.   NATURE BIOTECHNOLOGY

Allele-Specific QTL Fine Mapping with PLASMA

(2020) Austin T. Wang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Visualization of circular RNAs and their internal splicing events from transcriptomic data

(2020) Yi Zheng et al.   BIOINFORMATICS

Accurate quantification of circular RNAs identifies extensive circular isoform switching events

(2020) Jinyang Zhang et al.   Nature Communications

GenomeScope 2.0 and Smudgeplot for reference-free profiling of polyploid genomes

(2020) T. Rhyker Ranallo-Benavidez et al.   Nature Communications

Combining short and long read sequencing to characterize antimicrobial resistance genes on plasmids applied to an unauthorized genetically modified Bacillus

(2020) Bas Berbers et al.   Scientific Reports

Profiling immunoglobulin repertoires across multiple human tissues using RNA sequencing

(2020) Igor Mandric et al.   Nature Communications

Transcriptomic signatures across human tissues identify functional rare genetic variation

(2020) Nicole M. Ferraro et al.   SCIENCE

Reconstruction of full-length circular RNAs enables isoform-level quantification

(2019) Yi Zheng et al.   Genome Medicine

Machine learning analysis of gene expression data reveals novel diagnostic and prognostic biomarkers and identifies therapeutic targets for soft tissue sarcomas

(2019) David G. P. van IJzendoorn et al.   PLoS Computational Biology

Expanded Expression Landscape and Prioritization of Circular RNAs in Mammals

(2019) Peifeng Ji et al.   Cell Reports

MLSeq: Machine learning interface for RNA-sequencing data

(2019) Dincer Goksuluk et al.   COMPUTER METHODS AND PROGRAMS IN BIOMEDICINE

RNA sequencing: the teenage years

(2019) Rory Stark et al.   NATURE REVIEWS GENETICS

Challenges and recommendations to improve the installability and archival stability of omics computational tools

(2019) Serghei Mangul et al.   PLOS BIOLOGY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

The biogenesis, biology and characterization of circular RNAs

(2019) Lasse S. Kristensen et al.   NATURE REVIEWS GENETICS

Ularcirc: visualization and enhanced analysis of circular RNAs via back and canonical forward splicing

(2019) David T Humphreys et al.   NUCLEIC ACIDS RESEARCH

Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes

(2019) Nicola De Maio et al.   Microbial Genomics

Modeling allele-specific expression at the gene and SNP levels simultaneously by a Bayesian logistic mixed regression model

(2019) Jing Xie et al.   BMC BIOINFORMATICS

Genetic regulatory variation in populations informs transcriptome analysis in rare disease

(2019) Pejman Mohammadi et al.   SCIENCE

CDSeq: A novel complete deconvolution method for dissecting heterogeneous samples using gene expression data

(2019) Kai Kang et al.   PLoS Computational Biology

Leveraging allelic imbalance to refine fine-mapping for eQTL studies

(2019) Jennifer Zou et al.   PLoS Genetics

Hierarchical analysis of RNA-seq reads improves the accuracy of allele-specific expression

(2018) Narayanan Raghupathy et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

Long reads: their purpose and place

(2018) Martin O Pollard et al.   HUMAN MOLECULAR GENETICS

Piercing the dark matter: bioinformatics of long-range sequencing and mapping

(2018) Fritz J. Sedlazeck et al.   NATURE REVIEWS GENETICS

Computational Strategies for Exploring Circular RNAs

(2018) Yuan Gao et al.   TRENDS IN GENETICS

CIRCpedia v2: An Updated Database for Comprehensive Circular RNA Annotation and Expression Comparison

(2018) Rui Dong et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

An Enumerative Combinatorics Model for Fragmentation Patterns in RNA Sequencing Provides Insights into Nonuniformity of the Expected Fragment Starting-Point and Coverage Profile

(2017) Celine Prakash et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Annotation-free quantification of RNA splicing using LeafCutter

(2017) Yang I. Li et al.   NATURE GENETICS

Allele-specific expression reveals interactions between genetic variation and environment

(2017) David A Knowles et al.   NATURE METHODS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

CSCD: a database for cancer-specific circular RNAs

(2017) Siyu Xia et al.   NUCLEIC ACIDS RESEARCH

Mixture models reveal multiple positional bias types in RNA-Seq data and lead to accurate transcript concentration estimates

(2017) Andreas Tuerk et al.   PLoS Computational Biology

Rail-RNA: scalable analysis of RNA-seq splicing and coverage

(2016) Abhinav Nellore et al.   BIOINFORMATICS

Assembly-based inference of B-cell receptor repertoires from short read RNA sequencing data with V’DJer

(2016) Lisle E. Mose et al.   BIOINFORMATICS

RapMap: a rapid, sensitive and accurate tool for mapping RNA-seq reads to transcriptomes

(2016) Avi Srivastava et al.   BIOINFORMATICS

Diverse alternative back-splicing and alternative splicing landscape of circular RNAs

(2016) Xiao-Ou Zhang et al.   GENOME RESEARCH

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Landscape of tumor-infiltrating T cell repertoire of human cancers

(2016) Bo Li et al.   NATURE GENETICS

Detecting circular RNAs: bioinformatic and experimental challenges

(2016) Linda Szabo et al.   NATURE REVIEWS GENETICS

Comprehensive identification of internal structure and alternative splicing events in circular RNAs

(2016) Yuan Gao et al.   Nature Communications

Specific identification and quantification of circular RNAs from sequencing data

(2015) Jun Cheng et al.   BIOINFORMATICS

Fast and efficient QTL mapper for thousands of molecular phenotypes

(2015) Halit Ongen et al.   BIOINFORMATICS

ASEQ: fast allele-specific studies from next-generation sequencing data

(2015) Alessandro Romanel et al.   BMC Medical Genomics

Proper Use of Allele-Specific Expression Improves Statistical Power forcis-eQTL Mapping with RNA-Seq Data

(2015) Yi-Juan Hu et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Fine-mapping cellular QTLs with RASQUAL and ATAC-seq

(2015) Natsuhiko Kumasaka et al.   NATURE GENETICS

WASP: allele-specific software for robust molecular quantitative trait locus discovery

(2015) Bryce van de Geijn et al.   NATURE METHODS

MiXCR: software for comprehensive adaptive immunity profiling

(2015) Dmitriy A Bolotin et al.   NATURE METHODS

Identification of novel fusion genes in lung cancer using breakpoint assembly of transcriptome sequencing data

(2015) Lynnette Fernandez-Cuesta et al.   GENOME BIOLOGY

Alignment of Short Reads: A Crucial Step for Application of Next-Generation Sequencing Data in Precision Medicine

(2015) Hao Ye et al.   Pharmaceutics

Rcount: simple and flexible RNA-Seq read counting

(2014) M. W. Schmid et al.   BIOINFORMATICS

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

(2014) S. Anders et al.   BIOINFORMATICS

QuASAR: quantitative allele-specific analysis of reads

(2014) Chris T. Harvey et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer

(2014) Francesco Abate et al.   BMC Systems Biology

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

(2014) Sheng Li et al.   NATURE BIOTECHNOLOGY

Sailfish enables alignment-free isoform quantification from RNA-seq reads using lightweight algorithms

(2014) Rob Patro et al.   NATURE BIOTECHNOLOGY

Normalization of RNA-seq data using factor analysis of control genes or samples

(2014) Davide Risso et al.   NATURE BIOTECHNOLOGY

RNA CoMPASS: A Dual Approach for Pathogen and Host Transcriptome Analysis of RNA-Seq Datasets

(2014) Guorong Xu et al.   PLoS One

Identification of genetic variants associated with alternative splicing using sQTLseekeR

(2014) Jean Monlong et al.   Nature Communications

A multi-split mapping algorithm for circular RNA, splicing, trans-splicing and fusion detection

(2014) Steve Hoffmann et al.   GENOME BIOLOGY

TIGAR: transcript isoform abundance estimation method with gapped alignment of RNA-Seq data by variational Bayesian inference

(2013) Naoki Nariai et al.   BIOINFORMATICS

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

HTQC: a fast quality control toolkit for Illumina sequencing data

(2013) Xi Yang et al.   BMC BIOINFORMATICS

Genomics: the state of the art in RNA-seq analysis

(2013) Ian Korf   NATURE METHODS

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Systematic evaluation of spliced alignment programs for RNA-seq data

(2013) Pär G Engström et al.   NATURE METHODS

Probabilistic error correction for RNA sequencing

(2013) Hai-Son Le et al.   NUCLEIC ACIDS RESEARCH

Identifying differentially expressed transcripts from RNA-seq data with biological variation

(2012) Peter Glaus et al.   BIOINFORMATICS

Matrix eQTL: ultra fast eQTL analysis via large matrix operations

(2012) A. A. Shabalin   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

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

(2012) Cole Trapnell et al.   Nature Protocols

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

Estimation of alternative splicing isoform frequencies from RNA-Seq data

(2011) Marius Nicolae et al.   Algorithms for Molecular Biology

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

A powerful and flexible statistical framework for testing hypotheses of allele-specific gene expression from RNA-seq data

(2011) D. A. Skelly et al.   GENOME RESEARCH

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Uncovering the Complexity of Transcriptomes with RNA-Seq

(2010) Valerio Costa et al.   JOURNAL OF BIOMEDICINE AND BIOTECHNOLOGY

Advancing RNA-Seq analysis

(2010) Brian J Haas et al.   NATURE BIOTECHNOLOGY

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Transcript length bias in RNA-seq data confounds systems biology

(2009) Alicia Oshlack et al.   Biology Direct

Next-generation DNA sequencing

(2008) Jay Shendure et al.   NATURE BIOTECHNOLOGY

Simple and Globally Convergent Methods for Accelerating the Convergence of Any EM Algorithm

(2008) RAVI VARADHAN et al.   SCANDINAVIAN JOURNAL OF STATISTICS

Real-Time DNA Sequencing from Single Polymerase Molecules

(2008) J. Eid et al.   SCIENCE