Pan-cancer transcriptomic analysis associates long non-coding RNAs with key mutational driver events

The Dual Roles of NRF2 in Cancer

(2016) Silvia Menegon et al.   TRENDS IN MOLECULAR MEDICINE

SomInaClust: detection of cancer genes based on somatic mutation patterns of inactivation and clustering

(2015) Jimmy Van den Eynden et al.   BMC BIOINFORMATICS

TANRIC: An Interactive Open Platform to Explore the Function of lncRNAs in Cancer

(2015) Jun Li et al.   CANCER RESEARCH

NKD1 marks intestinal and liver tumors linked to aberrant Wnt signaling

(2015) Jitka Stancikova et al.   CELLULAR SIGNALLING

p53-Regulated Networks of Protein, mRNA, miRNA, and lncRNA Expression Revealed by Integrated Pulsed Stable Isotope Labeling With Amino Acids in Cell Culture (pSILAC) and Next Generation Sequencing (NGS) Analyses

(2015) Sabine Hünten et al.   MOLECULAR & CELLULAR PROTEOMICS

Gain-of-function p53 mutants co-opt chromatin pathways to drive cancer growth

(2015) Jiajun Zhu et al.   NATURE

The landscape of long noncoding RNAs in the human transcriptome

(2015) Matthew K Iyer et al.   NATURE GENETICS

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Integrative genomic analysis reveals widespread enhancer regulation by p53 in response to DNA damage

(2015) Scott T. Younger et al.   NUCLEIC ACIDS RESEARCH

Genome-wide profiling of p53-regulated enhancer RNAs uncovers a subset of enhancers controlled by a lncRNA

(2015) Nicolas Léveillé et al.   Nature Communications

MYC-repressed long noncoding RNAs antagonize MYC-induced cell proliferation and cell cycle progression

(2015) Taewan Kim et al.   Oncotarget

MYC regulates the non-coding transcriptome

(2015) Jonathan R. Hart et al.   Oncotarget

HTSeq--a Python framework to work with high-throughput sequencing data

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Genome-wide Mapping and Characterization of Notch-Regulated Long Noncoding RNAs in Acute Leukemia

(2014) Thomas Trimarchi et al.   CELL

Loss of One Copy of Zfp148 Reduces Lesional Macrophage Proliferation and Atherosclerosis in Mice by Activating p53

(2014) Volkan I. Sayin et al.   CIRCULATION RESEARCH

Long Noncoding RNA MALAT1 Regulates Endothelial Cell Function and Vessel Growth

(2014) Katharina M. Michalik et al.   CIRCULATION RESEARCH

NRF2/Long Noncoding RNA ROR Signaling Regulates Mammary Stem Cell Expansion and Protects against Estrogen Genotoxicity

(2014) Yongshu Zhang et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Brevican knockdown reduces late-stage glioma tumor aggressiveness

(2014) Chrissa A. Dwyer et al.   JOURNAL OF NEURO-ONCOLOGY

LincRNA-p21 Activates p21 In cis to Promote Polycomb Target Gene Expression and to Enforce the G1/S Checkpoint

(2014) Nadya Dimitrova et al.   MOLECULAR CELL

Sequencing depth and coverage: key considerations in genomic analyses

(2014) David Sims et al.   NATURE REVIEWS GENETICS

Parallel Profiling of the Transcriptome, Cistrome, and Epigenome in the Cellular Response to Ionizing Radiation

(2014) S. Rashi-Elkeles et al.   Science Signaling

Antioxidants Accelerate Lung Cancer Progression in Mice

(2014) V. I. Sayin et al.   Science Translational Medicine

Global analysis of p53-regulated transcription identifies its direct targets and unexpected regulatory mechanisms

(2014) Mary Ann Allen et al.   eLife

Characterization of a Novel Long Noncoding RNA, SCAL1, Induced by Cigarette Smoke and Elevated in Lung Cancer Cell Lines

(2013) Philip Thai et al.   AMERICAN JOURNAL OF RESPIRATORY CELL AND MOLECULAR BIOLOGY

X Chromosome Inactivation and Epigenetic Responses to Cellular Reprogramming

(2013) Derek Lessing et al.   Annual Review of Genomics and Human Genetics

The emerging role of the Nrf2-Keap1 signaling pathway in cancer

(2013) M. C. Jaramillo et al.   GENES & DEVELOPMENT

YY1 binds to α-synuclein 3′-flanking region SNP and stimulates antisense noncoding RNA expression

(2013) Ikuko Mizuta et al.   JOURNAL OF HUMAN GENETICS

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Integrative genomic analyses reveal clinically relevant long noncoding RNAs in human cancer

(2013) Zhou Du et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Comprehensive Analysis of Long Non-Coding RNAs in Ovarian Cancer Reveals Global Patterns and Targeted DNA Amplification

(2013) Rozita Akrami et al.   PLoS One

Pint lincRNA connects the p53 pathway with epigenetic silencing by the Polycomb repressive complex 2

(2013) Oskar Marín-Béjar et al.   GENOME BIOLOGY

Nrf2 Redirects Glucose and Glutamine into Anabolic Pathways in Metabolic Reprogramming

(2012) Yoichiro Mitsuishi et al.   CANCER CELL

Troy, a Tumor Necrosis Factor Receptor Family Member, Interacts With Lgr5 to Inhibit Wnt Signaling in Intestinal Stem Cells

(2012) Bohumil Fafilek et al.   GASTROENTEROLOGY

A triple helix stabilizes the 3' ends of long noncoding RNAs that lack poly(A) tails

(2012) J. E. Wilusz et al.   GENES & DEVELOPMENT

BRAFV600Eremodels the melanocyte transcriptome and inducesBANCRto regulate melanoma cell migration

(2012) Ross J. Flockhart et al.   GENOME RESEARCH

The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression

(2012) T. Derrien et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

LincRNA-p21 Suppresses Target mRNA Translation

(2012) Je-Hyun Yoon et al.   MOLECULAR CELL

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

(2012) Claudia Carrieri et al.   NATURE

The Cancer Cell Line Encyclopedia enables predictive modelling of anticancer drug sensitivity

(2012) Jordi Barretina et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

p53 mutations in cancer

(2012) Patricia A. J. Muller et al.   NATURE CELL BIOLOGY

Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

(2011) M. N. Cabili et al.   GENES & DEVELOPMENT

Oncogene-induced Nrf2 transcription promotes ROS detoxification and tumorigenesis

(2011) Gina M. DeNicola et al.   NATURE

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

The Emergence of lncRNAs in Cancer Biology

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

Genomewide characterization of non-polyadenylated RNAs

(2011) Li Yang et al.   GENOME BIOLOGY

Dissecting the Unique Role of the Retinoblastoma Tumor Suppressor during Cellular Senescence

(2010) Agustin Chicas et al.   CANCER CELL

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

(2010) Maite Huarte et al.   CELL

The Nuclear-Retained Noncoding RNA MALAT1 Regulates Alternative Splicing by Modulating SR Splicing Factor Phosphorylation

(2010) Vidisha Tripathi et al.   MOLECULAR CELL

Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis

(2010) Rajnish A. Gupta et al.   NATURE

Ab initio reconstruction of cell type–specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs

(2010) Mitchell Guttman et al.   NATURE BIOTECHNOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

RNAi-Mediated Silencing of Nuclear Factor Erythroid-2-Related Factor 2 Gene Expression in Non-Small Cell Lung Cancer Inhibits Tumor Growth and Increases Efficacy of Chemotherapy

(2008) A. Singh et al.   CANCER RESEARCH