Elimination of PCR duplicates in RNA-seq and small RNA-seq using unique molecular identifiers

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Comparative Analysis of Single-Cell RNA Sequencing Methods

(2017) Christoph Ziegenhain et al.   MOLECULAR CELL

An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites

(2017) Peter J Skene et al.   eLife

dupRadar: a Bioconductor package for the assessment of PCR artifacts in RNA-Seq data

(2016) Sergi Sayols et al.   BMC BIOINFORMATICS

Je, a versatile suite to handle multiplexed NGS libraries with unique molecular identifiers

(2016) Charles Girardot et al.   BMC BIOINFORMATICS

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data

(2016) Melanie Schirmer et al.   BMC BIOINFORMATICS

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Modeling Enzyme Processivity Reveals that RNA-Seq Libraries Are Biased in Characteristic and Correctable Ways

(2016) Nathan Archer et al.   Cell Systems

The impact of amplification on differential expression analyses by RNA-seq

(2016) Swati Parekh et al.   Scientific Reports

High-throughput and quantitative genome-wide messenger RNA sequencing for molecular phenotyping

(2015) John E. Collins et al.   BMC GENOMICS

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Computational and analytical challenges in single-cell transcriptomics

(2015) Oliver Stegle et al.   NATURE REVIEWS GENETICS

Practical guidelines for B-cell receptor repertoire sequencing analysis

(2015) Gur Yaari et al.   Genome Medicine

Scalable microfluidics for single-cell RNA printing and sequencing

(2015) Sayantan Bose et al.   GENOME BIOLOGY

Strategies for Achieving High Sequencing Accuracy for Low Diversity Samples and Avoiding Sample Bleeding Using Illumina Platform

(2015) Abhishek Mitra et al.   PLoS One

Digital Encoding of Cellular mRNAs Enabling Precise and Absolute Gene Expression Measurement by Single-Molecule Counting

(2014) Glenn K. Fu et al.   ANALYTICAL CHEMISTRY

piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing

(2014) Bo W. Han et al.   BIOINFORMATICS

The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila

(2014) Fabio Mohn et al.   CELL

The HP1 Homolog Rhino Anchors a Nuclear Complex that Suppresses piRNA Precursor Splicing

(2014) Zhao Zhang et al.   CELL

The exon junction complex is required for definition and excision of neighboring introns inDrosophila

(2014) Rippei Hayashi et al.   GENES & DEVELOPMENT

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

Targeted sequencing for gene discovery and quantification using RNA CaptureSeq

(2014) Tim R Mercer et al.   Nature Protocols

Full-length RNA-seq from single cells using Smart-seq2

(2014) Simone Picelli et al.   Nature Protocols

Molecular indexing enables quantitative targeted RNA sequencing and reveals poor efficiencies in standard library preparations

(2014) Glenn K. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

An Ancient Transcription Factor Initiates the Burst of piRNA Production during Early Meiosis in Mouse Testes

(2013) Xin Zhiguo Li et al.   MOLECULAR CELL

Comparative analysis of RNA sequencing methods for degraded or low-input samples

(2013) Xian Adiconis et al.   NATURE METHODS

Quantitative single-cell RNA-seq with unique molecular identifiers

(2013) Saiful Islam et al.   NATURE METHODS

Cellular Source and Mechanisms of High Transcriptome Complexity in the Mammalian Testis

(2013) Magali Soumillon et al.   Cell Reports

Selective Depletion of rRNA Enables Whole Transcriptome Profiling of Archival Fixed Tissue

(2012) John D. Morlan et al.   PLoS One

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

(2012) K. Shiroguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Heterotypic piRNA Ping-Pong Requires Qin, a Protein with Both E3 Ligase and Tudor Domains

(2011) Zhao Zhang et al.   MOLECULAR CELL

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

Counting individual DNA molecules by the stochastic attachment of diverse labels

(2011) G. K. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

(2011) Daniel Aird et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Collapse of Germline piRNAs in the Absence of Argonaute3 Reveals Somatic piRNAs in Flies

(2009) Chengjian Li et al.   CELL

ChIP–seq: advantages and challenges of a maturing technology

(2009) Peter J. Park   NATURE REVIEWS GENETICS

Endogenous siRNA and miRNA Targets Identified by Sequencing of the Arabidopsis Degradome

(2008) Charles Addo-Quaye et al.   CURRENT BIOLOGY

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

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