Consistent RNA sequencing contamination in GTEx and other data sets

DoubletFinder: Doublet Detection in Single-Cell RNA Sequencing Data Using Artificial Nearest Neighbors

(2019) Christopher S. McGinnis et al.   Cell Systems

Atlas of RNA sequencing profiles for normal human tissues

(2019) Maria Suntsova et al.   Scientific Data

Adipose Tissue Gene Expression Associations Reveal Hundreds of Candidate Genes for Cardiometabolic Traits

(2019) Chelsea K. Raulerson et al.   AMERICAN JOURNAL OF HUMAN GENETICS

DoubletDecon: Deconvoluting Doublets from Single-Cell RNA-Sequencing Data

(2019) Erica A.K. DePasquale et al.   Cell Reports

Detection and removal of barcode swapping in single-cell RNA-seq data

(2018) Jonathan A. Griffiths et al.   Nature Communications

xMD-miRNA-seq to generate near in vivo miRNA expression estimates in colon epithelial cells

(2018) Avi Z. Rosenberg et al.   Scientific Reports

Single-cell transcriptomics of 20 mouse organs creates a Tabula Muris

(2018) et al.   NATURE

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

Reference component analysis of single-cell transcriptomes elucidates cellular heterogeneity in human colorectal tumors

(2017) Huipeng Li et al.   NATURE GENETICS

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

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

Complex Sources of Variation in Tissue Expression Data: Analysis of the GTEx Lung Transcriptome

(2016) Matthew N. McCall et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Optimizing Workflows and Processing of Cytologic Samples for Comprehensive Analysis by Next-Generation Sequencing: Memorial Sloan Kettering Cancer Center Experience

(2016) Shaozhou Ken Tian et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

Transcript-level expression analysis of RNA-seq experiments with HISAT, StringTie and Ballgown

(2016) Mihaela Pertea et al.   Nature Protocols

Transcriptomic variation of pharmacogenes in multiple human tissues and lymphoblastoid cell lines

(2016) A Chhibber et al.   PHARMACOGENOMICS JOURNAL

Human Contamination in Public Genome Assemblies

(2016) Kirill Kryukov et al.   PLoS One

Toward the promise of microRNAs – Enhancing reproducibility and rigor in microRNA research

(2016) Kenneth W. Witwer et al.   RNA Biology

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

A Single-Cell Transcriptome Atlas of the Human Pancreas

(2016) Mauro J. Muraro et al.   Cell Systems

A Single-Cell Transcriptomic Map of the Human and Mouse Pancreas Reveals Inter- and Intra-cell Population Structure

(2016) Maayan Baron et al.   Cell Systems

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

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

Combining tumor genome simulation with crowdsourcing to benchmark somatic single-nucleotide-variant detection

(2015) Adam D Ewing et al.   NATURE METHODS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Cell types in the mouse cortex and hippocampus revealed by single-cell RNA-seq

(2015) A. Zeisel et al.   SCIENCE

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

(2015) et al.   SCIENCE

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

Library preparation methods for next-generation sequencing: Tone down the bias

(2014) Erwin L. van Dijk et al.   EXPERIMENTAL CELL RESEARCH

Whole-exome sequencing and clinical interpretation of formalin-fixed, paraffin-embedded tumor samples to guide precision cancer medicine

(2014) Eliezer M Van Allen et al.   NATURE MEDICINE

Diverse and Widespread Contamination Evident in the Unmapped Depths of High Throughput Sequencing Data

(2014) Richard W. Lusk   PLoS One

Mining of public sequencing databases supports a non-dietary origin for putative foreign miRNAs: underestimated effects of contamination in NGS

(2014) J. P. Tosar et al.   RNA

Unexpected cross-species contamination in genome sequencing projects

(2014) Samier Merchant et al.   PeerJ

Analysis of the Human Tissue-specific Expression by Genome-wide Integration of Transcriptomics and Antibody-based Proteomics

(2013) Linn Fagerberg et al.   MOLECULAR & CELLULAR PROTEOMICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Smart-seq2 for sensitive full-length transcriptome profiling in single cells

(2013) Simone Picelli et al.   NATURE METHODS

MR Imaging Predictors of Molecular Profile and Survival: Multi-institutional Study of the TCGA Glioblastoma Data Set

(2013) David A. Gutman et al.   RADIOLOGY

Analysis of plant-derived miRNAs in animal small RNA datasets

(2012) Yuanji Zhang et al.   BMC GENOMICS

Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration

(2012) H. Thorvaldsdottir et al.   BRIEFINGS IN BIOINFORMATICS

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

(2012) Oliver Stegle et al.   Nature Protocols

ContEst: estimating cross-contamination of human samples in next-generation sequencing data

(2011) Kristian Cibulskis et al.   BIOINFORMATICS

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

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

(2011) Bo Li 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

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform

(2011) Martin Kircher et al.   NUCLEIC ACIDS RESEARCH

Abundant Human DNA Contamination Identified in Non-Primate Genome Databases

(2011) Mark S. Longo et al.   PLoS One

Towards a knowledge-based Human Protein Atlas

(2010) Mathias Uhlen et al.   NATURE BIOTECHNOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS