Gene Expression Nebulas (GEN): a comprehensive data portal integrating transcriptomic profiles across multiple species at both bulk and single-cell levels

COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas

(2021) Xianwen Ren et al.   CELL

The Genome Sequence Archive Family: Toward Explosive Data Growth and Diverse Data Types

(2021) Tingting Chen et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

High-Throughput Transcriptome Profiling in Drug and Biomarker Discovery

(2020) Xiaonan Yang et al.   Frontiers in Genetics

IC4R-2.0: Rice Genome Reannotation Using Massive RNA-seq Data

(2020) Jian Sang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

Database resources of the National Center for Biotechnology Information

(2020) Eric W Sayers et al.   NUCLEIC ACIDS RESEARCH

pblat: a multithread blat algorithm speeding up aligning sequences to genomes

(2019) Meng Wang et al.   BMC BIOINFORMATICS

Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage

(2019) Dvir Aran et al.   NATURE IMMUNOLOGY

RNA-Seq Signatures Normalized by mRNA Abundance Allow Absolute Deconvolution of Human Immune Cell Types

(2019) Gianni Monaco et al.   Cell Reports

Deep-learning augmented RNA-seq analysis of transcript splicing

(2019) Zijun Zhang et al.   NATURE METHODS

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Remodeling of epigenome and transcriptome landscapes with aging in mice reveals widespread induction of inflammatory responses

(2019) Bérénice A. Benayoun et al.   GENOME RESEARCH

Genomic and transcriptomic profiling expands precision cancer medicine: the WINTHER trial

(2019) Jordi Rodon et al.   NATURE MEDICINE

Single-Cell RNA-Seq Technologies and Related Computational Data Analysis

(2019) Geng Chen et al.   Frontiers in Genetics

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Current best practices in single‐cell RNA‐seq analysis: a tutorial

(2019) Malte D Luecken et al.   Molecular Systems Biology

RNA sequencing: the teenage years

(2019) Rory Stark et al.   NATURE REVIEWS GENETICS

The EMBL-EBI search and sequence analysis tools APIs in 2019

(2019) Fábio Madeira et al.   NUCLEIC ACIDS RESEARCH

Cerebro: interactive visualization of scRNA-seq data

(2019) Roman Hillje et al.   BIOINFORMATICS

OUP accepted manuscript

(2018)   BIOINFORMATICS

A single-cell RNA-seq survey of the developmental landscape of the human prefrontal cortex

(2018) Suijuan Zhong et al.   NATURE

Impact of Genetic Polymorphisms on Human Immune Cell Gene Expression

(2018) Benjamin J. Schmiedel et al.   CELL

Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems

(2018) Xiannian Zhang et al.   MOLECULAR CELL

Database Resources of the BIG Data Center in 2019

(2018) et al.   NUCLEIC ACIDS RESEARCH

Editome Disease Knowledgebase (EDK): a curated knowledgebase of editome-disease associations in human

(2018) Guangyi Niu et al.   NUCLEIC ACIDS RESEARCH

NucMap: a database of genome-wide nucleosome positioning map across species

(2018) Yongbing Zhao et al.   NUCLEIC ACIDS RESEARCH

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

ICG: a wiki-driven knowledgebase of internal control genes for RT-qPCR normalization

(2017) Jian Sang et al.   NUCLEIC ACIDS RESEARCH

Araport11: a complete reannotation of theArabidopsis thalianareference genome

(2017) Chia-Yi Cheng et al.   PLANT JOURNAL

Single-cell transcriptomics to explore the immune system in health and disease

(2017) Michael J. T. Stubbington et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

GSA: Genome Sequence Archive *

(2017) Yanqing Wang et al.   GENOMICS PROTEOMICS & BIOINFORMATICS

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

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

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

(2016) Mihaela Pertea et al.   Nature Protocols

REDIportal: a comprehensive database of A-to-I RNA editing events in humans

(2016) Ernesto Picardi et al.   NUCLEIC ACIDS RESEARCH

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

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

(2015) Allon M. Klein et al.   CELL

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

(2015) Evan Z. Macosko et al.   CELL

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells

(2014) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next generation sequencing technologies for next generation plant breeding

(2014) Soham Ray et al.   Frontiers in Plant Science

REDItools: high-throughput RNA editing detection made easy

(2013) Ernesto Picardi et al.   BIOINFORMATICS

An expression atlas of human primary cells: inference of gene function from coexpression networks

(2013) Neil A Mabbott et al.   BMC GENOMICS

BLUEPRINT: mapping human blood cell epigenomes

(2013) J. H. A. Martens et al.   HAEMATOLOGICA

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

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

NCBI GEO: archive for functional genomics data sets—update

(2012) Tanya Barrett et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Densely Interconnected Transcriptional Circuits Control Cell States in Human Hematopoiesis

(2011) Noa Novershtern et al.   CELL

The DNA Data Bank of Japan launches a new resource, the DDBJ Omics Archive of functional genomics experiments

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

The sequence read archive: explosive growth of sequencing data

(2011) Y. Kodama et al.   NUCLEIC ACIDS RESEARCH

Disease Ontology: a backbone for disease semantic integration

(2011) L. M. Schriml et al.   NUCLEIC ACIDS RESEARCH

Inferring Regulatory Networks from Expression Data Using Tree-Based Methods

(2010) Vân Anh Huynh-Thu et al.   PLoS One

GeneCards Version 3: the human gene integrator

(2010) M. Safran et al.   Database-The Journal of Biological Databases and Curation

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

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

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

The Immunological Genome Project: networks of gene expression in immune cells

(2008) Tracy S P Heng et al.   NATURE IMMUNOLOGY

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS