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

Complementing tissue characterization by integrating transcriptome profiling from the Human Protein Atlas and from the FANTOM5 consortium

(2015) Nancy Yiu-Lin Yu et al.   NUCLEIC ACIDS RESEARCH

The human transcriptome across tissues and individuals

(2015) M. Mele et al.   SCIENCE

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

(2015) et al.   SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Comparison of CAGE and RNA-seq transcriptome profiling using clonally amplified and single-molecule next-generation sequencing

(2014) H. Kawaji et al.   GENOME RESEARCH

A comparative encyclopedia of DNA elements in the mouse genome

(2014) Feng Yue et al.   NATURE

A promoter-level mammalian expression atlas

(2014)   NATURE

The Mouse Genome Database (MGD): facilitating mouse as a model for human biology and disease

(2014) Janan T. Eppig et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2015

(2014) Fiona Cunningham et al.   NUCLEIC ACIDS RESEARCH

Genomic responses in mouse models greatly mimic human inflammatory diseases

(2014) Keizo Takao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Noninvasive in vivo monitoring of tissue-specific global gene expression in humans

(2014) W. Koh et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next-Generation Sequencing: Methodology and Application

(2013) Ayman Grada et al.   JOURNAL OF INVESTIGATIVE DERMATOLOGY

Genomic responses in mouse models poorly mimic human inflammatory diseases

(2013) Junhee Seok et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

mRNA enrichment protocols determine the quantification characteristics of external RNA spike-in controls in RNA-Seq studies

(2013) Tao Qing et al.   Science China-Life Sciences

Human housekeeping genes, revisited

(2013) Eli Eisenberg et al.   TRENDS IN GENETICS

eMouseAtlas, EMAGE, and the spatial dimension of the transcriptome

(2012) Chris Armit et al.   MAMMALIAN GENOME

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Unamplified cap analysis of gene expression on a single-molecule sequencer

(2011) M. Kanamori-Katayama et al.   GENOME RESEARCH

Identification of Human Housekeeping Genes and Tissue-Selective Genes by Microarray Meta-Analysis

(2011) Cheng-Wei Chang et al.   PLoS One

Large scale comparison of global gene expression patterns in human and mouse

(2011) Xiangqun Zheng-Bradley et al.   GENOME BIOLOGY

TiSGeD: a database for tissue-specific genes

(2010) S. J. Xiao et al.   BIOINFORMATICS

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Housekeeping genes; expression levels may change with density of cultured cells

(2010) Samantha Greer et al.   JOURNAL OF IMMUNOLOGICAL METHODS

A global map of human gene expression

(2010) Margus Lukk et al.   NATURE BIOTECHNOLOGY

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

A scaling normalization method for differential expression analysis of RNA-seq data

(2010) Mark D Robinson et al.   GENOME BIOLOGY

Applications of New Sequencing Technologies for Transcriptome Analysis

(2009) Olena Morozova et al.   Annual Review of Genomics and Human Genetics

Definition, conservation and epigenetics of housekeeping and tissue-enriched genes

(2009) Xinwei She et al.   BMC GENOMICS

Genetics of gene expression and its effect on disease

(2008) Valur Emilsson et al.   NATURE

From gene expression to disease risk

(2008) Emmanouil T Dermitzakis   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

A large-scale analysis of tissue-specific pathology and gene expression of human disease genes and complexes

(2008) K. Lage et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

On the nature of human housekeeping genes

(2008) Jiang Zhu et al.   TRENDS IN GENETICS