RNA-seq data analysis at the gene and CDS levels provides a comprehensive view of transcriptome responses induced by 4-hydroxynonenal

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

(2013) Mar Gonzàlez-Porta et al.   GENOME BIOLOGY

Inhibition of NF-κB Activation by 4-Hydroxynonenal Contributes to Liver Injury in a Mouse Model of Alcoholic Liver Disease

(2012) Xiaobing Dou et al.   AMERICAN JOURNAL OF PATHOLOGY

Lipid peroxidation dysregulation in ischemic stroke: Plasma 4-HNE as a potential biomarker?

(2012) Wan-Chi Lee et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Downregulation of miR-144 is associated with colorectal cancer progression via activation of mTOR signaling pathway

(2012) Takeshi Iwaya et al.   CARCINOGENESIS

Synthesis and antioxidant activity of 1,3,4-oxadiazole tagged thieno[2,3-d]pyrimidine derivatives

(2012) Y. Kotaiah et al.   EUROPEAN JOURNAL OF MEDICINAL CHEMISTRY

Identifying differentially spliced genes from two groups of RNA-seq samples

(2012) Weichen Wang et al.   GENE

Detecting differential usage of exons from RNA-seq data

(2012) S. Anders et al.   GENOME RESEARCH

Structure-based prediction of protein–protein interactions on a genome-wide scale

(2012) Qiangfeng Cliff Zhang et al.   NATURE

Differential analysis of gene regulation at transcript resolution with RNA-seq

(2012) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

A comprehensive comparison of RNA-Seq-based transcriptome analysis from reads to differential gene expression and cross-comparison with microarrays: a case study in Saccharomyces cerevisiae

(2012) Intawat Nookaew et al.   NUCLEIC ACIDS RESEARCH

PrePPI: a structure-informed database of protein–protein interactions

(2012) Qiangfeng Cliff Zhang et al.   NUCLEIC ACIDS RESEARCH

RNA-Seq Provides New Insights in the Transcriptome Responses Induced by the Carcinogen Benzo[a]pyrene

(2012) J. van Delft et al.   TOXICOLOGICAL SCIENCES

4-Hydroxynonenal Induces Mitochondrial-Mediated Apoptosis and Oxidative Stress in SH-SY5Y Human Neuronal Cells

(2011) Sunny O. Abarikwu et al.   BASIC & CLINICAL PHARMACOLOGY & TOXICOLOGY

Molecular signatures database (MSigDB) 3.0

(2011) A. Liberzon et al.   BIOINFORMATICS

Structure−Activity Analysis of Diffusible Lipid Electrophiles Associated with Phospholipid Peroxidation: 4-Hydroxynonenal and 4-Oxononenal Analogues

(2011) Colleen E. McGrath et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Comparing Next-Generation Sequencing and Microarray Technologies in a Toxicological Study of the Effects of Aristolochic Acid on Rat Kidneys

(2011) Zhenqiang Su et al.   CHEMICAL RESEARCH IN TOXICOLOGY

Relating protein adduction to gene expression changes: a systems approach

(2011) Bing Zhang et al.   Molecular BioSystems

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Regulation of the DNA Damage Response and Gene Expression by the Dot1L Histone Methyltransferase and the 53Bp1 Tumour Suppressor

(2011) Jennifer FitzGerald et al.   PLoS One

From RNA-seq reads to differential expression results

(2011) Alicia Oshlack et al.   GENOME BIOLOGY

Systems Analysis of Protein Modification and Cellular Responses Induced by Electrophile Stress

(2010) Aaron T. Jacobs et al.   ACCOUNTS OF CHEMICAL RESEARCH

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

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

RNA sequencing shows no dosage compensation of the active X-chromosome

(2010) Yuanyan Xiong et al.   NATURE GENETICS

Alternative expression analysis by RNA sequencing

(2010) Malachi Griffith et al.   NATURE METHODS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Reduced cellular redox status induces 4-hydroxynonenal-mediated caspase 3 activation leading to erythrocyte death during chronic arsenic exposure in rats

(2010) Debabrata Biswas et al.   TOXICOLOGY AND APPLIED PHARMACOLOGY

Noisy Splicing Drives mRNA Isoform Diversity in Human Cells

(2010) Joseph K. Pickrell et al.   PLoS Genetics

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Synthesis of novel indolyl-pyrimidine antiinflammatory, antioxidant and antibacterial agents

(2009) SS Panda et al.   INDIAN JOURNAL OF PHARMACEUTICAL SCIENCES

4-Hydroxynonenal induces p53-mediated apoptosis in retinal pigment epithelial cells

(2008) Abha Sharma et al.   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS

The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

(2008) Leming Shi et al.   BMC BIOINFORMATICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS