Contrasting expression patterns of coding and noncoding parts of the human genome upon oxidative stress

An interplay between the p38 MAPK pathway and AUBPs regulatesc-fosmRNA stability during mitogenic stimulation

(2015) Maria Sol Degese et al.   BIOCHEMICAL JOURNAL

ngs.plot: Quick mining and visualization of next-generation sequencing data by integrating genomic databases

(2014) Li Shen et al.   BMC GENOMICS

Control of Cdc28 CDK1 by a Stress-Induced lncRNA

(2014) Mariona Nadal-Ribelles et al.   MOLECULAR CELL

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

Global MEF2 target gene analysis in cardiac and skeletal muscle reveals novel regulation of DUSP6 by p38MAPK-MEF2 signaling

(2014) Stephanie Wales et al.   NUCLEIC ACIDS RESEARCH

Divergent Transcription: A Driving Force for New Gene Origination?

(2013) Xuebing Wu et al.   CELL

HINCUTs in cancer: hypoxia-induced noncoding ultraconserved transcripts

(2013) J Ferdin et al.   CELL DEATH AND DIFFERENTIATION

ELABELA: A Hormone Essential for Heart Development Signals via the Apelin Receptor

(2013) Serene C. Chng et al.   DEVELOPMENTAL CELL

Extensive regulation of the non-coding transcriptome by hypoxia: role of HIF in releasing paused RNApol2

(2013) Hani Choudhry et al.   EMBO REPORTS

Promoter directionality is controlled by U1 snRNP and polyadenylation signals

(2013) Albert E. Almada et al.   NATURE

Polyadenylation site–induced decay of upstream transcripts enforces promoter directionality

(2013) Evgenia Ntini et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Divergent transcription of long noncoding RNA/mRNA gene pairs in embryonic stem cells

(2013) A. A. Sigova et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Set3 HDAC Mediates Effects of Overlapping Noncoding Transcription on Gene Induction Kinetics

(2012) TaeSoo Kim et al.   CELL

Coordinated regulation of neuronal mRNA steady-state levels through developmentally controlled intron retention

(2012) K. Yap et al.   GENES & DEVELOPMENT

Long non-coding antisense RNA controls Uchl1 translation through an embedded SINEB2 repeat

(2012) Claudia Carrieri et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

Peptidomic discovery of short open reading frame–encoded peptides in human cells

(2012) Sarah A Slavoff et al.   Nature Chemical Biology

Symmetric dimethylation of H3R2 is a newly identified histone mark that supports euchromatin maintenance

(2012) Valentina Migliori et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Identification and Characterization of Novel Genotoxic Stress-Inducible Nuclear Long Noncoding RNAs in Mammalian Cells

(2012) Rena Mizutani et al.   PLoS One

Gene Loops Enhance Transcriptional Directionality

(2012) S. M. Tan-Wong et al.   SCIENCE

Systematic Localization of Common Disease-Associated Variation in Regulatory DNA

(2012) M. T. Maurano et al.   SCIENCE

Ending the message: poly(A) signals then and now

(2011) N. J. Proudfoot   GENES & DEVELOPMENT

A dynamic model of proteome changes reveals new roles for transcript alteration in yeast

(2011) M. V. Lee et al.   Molecular Systems Biology

Antisense expression increases gene expression variability and locus interdependency

(2011) Z. Xu et al.   Molecular Systems Biology

Nascent transcript sequencing visualizes transcription at nucleotide resolution

(2011) L. Stirling Churchman et al.   NATURE

Exploring long non-coding RNAs through sequencing

(2011) Sophie R. Atkinson et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

The Emergence of lncRNAs in Cancer Biology

(2011) J. R. Prensner et al.   Cancer Discovery

Analysis of DNA strand-specific differential expression with high density tiling microarrays

(2010) Luis Quintales et al.   BMC BIOINFORMATICS

Complex sense-antisense architecture of TNFAIP1/POLDIP2 on 17q11.2 represents a novel transcriptional structural-functional gene module involved in breast cancer progression

(2010) Oleg V Grinchuk et al.   BMC GENOMICS

Whole genome analysis of p38 SAPK-mediated gene expression upon stress

(2010) Isabel Ferreiro et al.   BMC GENOMICS

c-Myc Regulates Transcriptional Pause Release

(2010) Peter B. Rahl et al.   CELL

A Large Intergenic Noncoding RNA Induced by p53 Mediates Global Gene Repression in the p53 Response

(2010) Maite Huarte et al.   CELL

Dark Matter Transcripts: Sound and Fury, Signifying Nothing?

(2010) Richard Robinson   PLOS BIOLOGY

The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing

(2009) L. Redrup et al.   DEVELOPMENT

Transcriptional repression of Kruppel like factor-2 by the adaptor protein p66shc

(2009) Ajay Kumar et al.   FASEB JOURNAL

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

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

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals

(2009) Mitchell Guttman et al.   NATURE

Widespread bidirectional promoters are the major source of cryptic transcripts in yeast

(2009) Helen Neil et al.   NATURE

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

(2009) Da Wei Huang et al.   Nature Protocols

Transcriptional responses to oxidative stress: Pathological and toxicological implications

(2009) Qiang Ma   PHARMACOLOGY & THERAPEUTICS

NRF2 and KEAP1 mutations: permanent activation of an adaptive response in cancer

(2009) John D. Hayes et al.   TRENDS IN BIOCHEMICAL SCIENCES

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

(2009) Daniel Ramsköld et al.   PLoS Computational Biology

Posttranscriptional gene regulation by RNA-binding proteins during oxidative stress: implications for cellular senescence

(2008) Kotb Abdelmohsen et al.   BIOLOGICAL CHEMISTRY

A Hierarchical Network Controls Protein Translation during Murine Embryonic Stem Cell Self-Renewal and Differentiation

(2008) Prabha Sampath et al.   Cell Stem Cell

Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation

(2008) M. E. Dinger et al.   GENOME RESEARCH

Specific expression of long noncoding RNAs in the mouse brain

(2008) T. R. Mercer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Divergent Transcription from Active Promoters

(2008) Amy C. Seila et al.   SCIENCE

Nascent RNA Sequencing Reveals Widespread Pausing and Divergent Initiation at Human Promoters

(2008) Leighton J. Core et al.   SCIENCE