The Genetic Architecture of the Genome-Wide Transcriptional Response to ER Stress in the Mouse

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

The Noncoding RNA Revolution—Trashing Old Rules to Forge New Ones

(2014) Thomas R. Cech et al.   CELL

RNA-Seq Alignment to Individualized Genomes Improves Transcript Abundance Estimates in Multiparent Populations

(2014) Steven C. Munger et al.   GENETICS

Using next-generation RNA sequencing to identify imprinted genes

(2014) X Wang et al.   HEREDITY

Innate Immune Activity Conditions the Effect of Regulatory Variants upon Monocyte Gene Expression

(2014) B. P. Fairfax et al.   SCIENCE

Endoplasmic reticulum stress signaling: the microRNA connection

(2013) Marion Maurel et al.   AMERICAN JOURNAL OF PHYSIOLOGY-CELL PHYSIOLOGY

CACTIN is an essential nuclear protein in Arabidopsis and may be associated with the eukaryotic spliceosome

(2013) Katherine L. Baldwin et al.   FEBS LETTERS

Analysis of Allele-Specific Expression in Mouse Liver by RNA-Seq: A Comparison With Cis -eQTL Identified Using Genetic Linkage

(2013) Sandrine Lagarrigue et al.   GENETICS

An enhanced integrated stress response ameliorates mutant SOD1-induced ALS

(2013) L. Wang et al.   HUMAN MOLECULAR GENETICS

The Collaborative Cross: A Recombinant Inbred Mouse Population for the Systems Genetic Era

(2013) D. W. Threadgill et al.   ILAR JOURNAL

Micro(RNA)managing Endoplasmic Reticulum Stress

(2013) Andrew E. Byrd et al.   IUBMB LIFE

Identification of Steroid-Sensitive Gene-1/Ccdc80 as a JAK2-Binding Protein

(2013) Erin E. O'Leary et al.   MOLECULAR ENDOCRINOLOGY

Stress-induced changes in gene interactions in human cells

(2013) Renuka R. Nayak et al.   NUCLEIC ACIDS RESEARCH

Using natural variation in Drosophila to discover previously unknown endoplasmic reticulum stress genes

(2013) C. Y. Chow et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

UPR-inducible miRNAs contribute to stressful situations

(2013) Nilesh Chitnis et al.   TRENDS IN BIOCHEMICAL SCIENCES

Regulation of the transcriptome by ER stress: non-canonical mechanisms and physiological consequences

(2013) Angela M. Arensdorf et al.   Frontiers in Genetics

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

High-Resolution Genetic Mapping Using the Mouse Diversity Outbred Population

(2012) Karen L. Svenson et al.   GENETICS

Extensive compensatory cis-trans regulation in the evolution of mouse gene expression

(2012) A. Goncalves et al.   GENOME RESEARCH

Dimer-specific regulatory mechanisms within the NF-κB family of transcription factors

(2012) Stephen T. Smale   IMMUNOLOGICAL REVIEWS

The impact of the unfolded protein response on human disease

(2012) Shiyu Wang et al.   JOURNAL OF CELL BIOLOGY

The diversity outbred mouse population

(2012) Gary A. Churchill et al.   MAMMALIAN GENOME

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

ER Stress Activates NF-κB by Integrating Functions of Basal IKK Activity, IRE1 and PERK

(2012) Arvin B. Tam et al.   PLoS One

Genetic analysis of complex traits in the emerging Collaborative Cross

(2011) David L. Aylor et al.   GENOME RESEARCH

Selective Abrogation of BiP/GRP78 Blunts Activation of NF- B through the ATF6 Branch of the UPR: Involvement of C/EBP  and mTOR-Dependent Dephosphorylation of Akt

(2011) S. Nakajima et al.   MOLECULAR AND CELLULAR BIOLOGY

Sequence-based characterization of structural variation in the mouse genome

(2011) Binnaz Yalcin et al.   NATURE

Mouse genomic variation and its effect on phenotypes and gene regulation

(2011) Thomas M. Keane et al.   NATURE

The Architecture of Gene Regulatory Variation across Multiple Human Tissues: The MuTHER Study

(2011) Alexandra C. Nica et al.   PLoS Genetics

Gene Expression and Genetic Variation in Response to Endoplasmic Reticulum Stress in Human Cells

(2010) Beth A. Dombroski et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Cytoscape 2.8: new features for data integration and network visualization

(2010) M. E. Smoot et al.   BIOINFORMATICS

The Genetic Basis for Male x Female Interactions Underlying Variation in Reproductive Phenotypes of Drosophila

(2010) C. Y. Chow et al.   GENETICS

Regulatory divergence in Drosophila revealed by mRNA-seq

(2010) C. J. McManus et al.   GENOME RESEARCH

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

The unfolded protein response in familial amyotrophic lateral sclerosis

(2010) L. Wang et al.   HUMAN MOLECULAR GENETICS

Deficiency of Suppressor Enhancer Lin12 1 Like (SEL1L) in Mice Leads to Systemic Endoplasmic Reticulum Stress and Embryonic Lethality

(2010) Adam B. Francisco et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

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

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

The Non-coding RNAgadd7Is a Regulator of Lipid-induced Oxidative and Endoplasmic Reticulum Stress

(2009) Rita T. Brookheart et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

(2009) Da Wei Huang et al.   Nature Protocols

Common Regulatory Variation Impacts Gene Expression in a Cell Type-Dependent Manner

(2009) A. S. Dimas et al.   SCIENCE

Chop deletion reduces oxidative stress, improves β cell function, and promotes cell survival in multiple mouse models of diabetes

(2008) Benbo Song et al.   JOURNAL OF CLINICAL INVESTIGATION

The Collaborative Cross at Oak Ridge National Laboratory: developing a powerful resource for systems genetics

(2008) Elissa J. Chesler et al.   MAMMALIAN GENOME

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH

Transcriptome-Wide Identification of Novel Imprinted Genes in Neonatal Mouse Brain

(2008) Xu Wang et al.   PLoS One