HRT Atlas v1.0 database: redefining human and mouse housekeeping genes and candidate reference transcripts by mining massive RNA-seq datasets

Short paired-end reads trump long single-end reads for expression analysis

(2020) Adam H. Freedman et al.   BMC BIOINFORMATICS

EpiRegio: analysis and retrieval of regulatory elements linked to genes

(2020) Nina Baumgarten et al.   NUCLEIC ACIDS RESEARCH

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

(2019) Gianni Monaco et al.   Cell Reports

Predictability of human differential gene expression

(2019) Megan Crow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Retinal transcriptome and eQTL analyses identify genes associated with age-related macular degeneration

(2019) Rinki Ratnapriya et al.   NATURE GENETICS

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

(2018) Jianhong Ou et al.   BMC GENOMICS

Massive mining of publicly available RNA-seq data from human and mouse

(2018) Alexander Lachmann et al.   Nature Communications

A Comprehensive Mouse Transcriptomic BodyMap across 17 Tissues by RNA-seq

(2017) Bin Li et al.   Scientific Reports

Identification and analysis of house-keeping and tissue-specific genes based on RNA-seq data sets across 15 mouse tissues

(2016) Jingyao Zeng et al.   GENE

Unstable Expression of Commonly Used Reference Genes in Rat Pancreatic Islets Early after Isolation Affects Results of Gene Expression Studies

(2016) Lucie Kosinová et al.   PLoS One

The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins

(2016) Andrew D. Rouillard et al.   Database-The Journal of Biological Databases and Curation

Tissue-based map of the human proteome

(2015) M. Uhlen et al.   SCIENCE

The Impact of Normalization Methods on RNA-Seq Data Analysis

(2015) J. Zyprych-Walczak et al.   Biomed Research International

Do Housekeeping Genes Exist?

(2015) Yijuan Zhang et al.   PLoS One

Union Exon Based Approach for RNA-Seq Gene Quantification: To Be or Not to Be?

(2015) Shanrong Zhao et al.   PLoS One

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

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

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

Pseudogenes as Weaknesses of ACTB (Actb) and GAPDH (Gapdh) Used as Reference Genes in Reverse Transcription and Polymerase Chain Reactions

(2012) Yuan Sun et al.   PLoS One

Estimation of alternative splicing isoform frequencies from RNA-Seq data

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

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Gene Expression in Chicken Reveals Correlation with Structural Genomic Features and Conserved Patterns of Transcription in the Terrestrial Vertebrates

(2010) Haisheng Nie et al.   PLoS One

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

The MIQE Guidelines: Minimum Information for Publication of Quantitative Real-Time PCR Experiments

(2009) S. A. Bustin et al.   CLINICAL CHEMISTRY

The UCSC Genome Browser database: update 2010

(2009) B. Rhead et al.   NUCLEIC ACIDS RESEARCH

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

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

Does this band make sense? Limits to expression based cancer studies

(2008) Timothy K. Williams et al.   CANCER LETTERS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

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

(2008) M. Sultan et al.   SCIENCE

On the nature of human housekeeping genes

(2008) Jiang Zhu et al.   TRENDS IN GENETICS