Computational identification of epigenetically regulated lncRNAs and their associated genes based on integrating genomic data

The evolution of lncRNA repertoires and expression patterns in tetrapods

(2014) Anamaria Necsulea et al.   NATURE

Microarray Profiling and Co-Expression Network Analysis of Circulating lncRNAs and mRNAs Associated with Major Depressive Disorder

(2014) Zhifen Liu et al.   PLoS One

The Long Non-Coding HOTAIR Is Modulated by Cyclic Stretch and WNT/β-CATENIN in Human Aortic Valve Cells and Is a Novel Repressor of Calcification Genes

(2014) Katrina Carrion et al.   PLoS One

A mesenchymal glioma stem cell profile is related to clinical outcome

(2014) A Balbous et al.   Oncogenesis

Hyaluronan synthases (HAS1–3) in stromal and malignant cells correlate with breast cancer grade and predict patient survival

(2013) Päivi Auvinen et al.   BREAST CANCER RESEARCH AND TREATMENT

 1 Integrin Targeting Potentiates Antiangiogenic Therapy and Inhibits the Growth of Bevacizumab-Resistant Glioblastoma

(2013) W. S. Carbonell et al.   CANCER RESEARCH

Poised Chromatin at the ZEB1 Promoter Enables Breast Cancer Cell Plasticity and Enhances Tumorigenicity

(2013) Christine L. Chaffer et al.   CELL

Integrated Systems Approach Identifies Genetic Nodes and Networks in Late-Onset Alzheimer’s Disease

(2013) Bin Zhang et al.   CELL

Integration of Genome-wide Approaches Identifies lncRNAs of Adult Neural Stem Cells and Their Progeny In Vivo

(2013) Alexander D. Ramos et al.   Cell Stem Cell

Long Noncoding RNA in Prostate, Bladder, and Kidney Cancer

(2013) Elena S. Martens-Uzunova et al.   EUROPEAN UROLOGY

Reproducibility of high-throughput mRNA and small RNA sequencing across laboratories

(2013) Peter A C 't Hoen et al.   NATURE BIOTECHNOLOGY

Long non-coding RNAs: new players in cell differentiation and development

(2013) Alessandro Fatica et al.   NATURE REVIEWS GENETICS

Regulation of nucleosome dynamics by histone modifications

(2013) Gabriel E Zentner et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Structure and function of long noncoding RNAs in epigenetic regulation

(2013) Tim R Mercer et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Long Non-coding RNAs: Novel Targets for Nervous System Disease Diagnosis and Therapy

(2013) Irfan A. Qureshi et al.   Neurotherapeutics

HOXA1 drives melanoma tumor growth and metastasis and elicits an invasion gene expression signature that prognosticates clinical outcome

(2013) J Wardwell-Ozgo et al.   ONCOGENE

Pervasive Transcription of the Human Genome Produces Thousands of Previously Unidentified Long Intergenic Noncoding RNAs

(2013) Matthew J. Hangauer et al.   PLoS Genetics

Cancer Epigenetics: From Mechanism to Therapy

(2012) Mark A. Dawson et al.   CELL

Regulatory long non-coding RNA and its functions

(2012) Yong Huang et al.   JOURNAL OF PHYSIOLOGY AND BIOCHEMISTRY

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Long non-coding RNA expression profiles predict clinical phenotypes in glioma

(2012) Xiaoqin Zhang et al.   NEUROBIOLOGY OF DISEASE

Genome-wide analysis reveals distinct patterns of epigenetic features in long non-coding RNA loci

(2012) Satish Sati et al.   NUCLEIC ACIDS RESEARCH

Noncoder: a web interface for exon array-based detection of long non-coding RNAs

(2012) Pascal Gellert et al.   NUCLEIC ACIDS RESEARCH

HOTAIR is a negative prognostic factor and exhibits pro-oncogenic activity in pancreatic cancer

(2012) K Kim et al.   ONCOGENE

Long non-coding RNAs and cancer: a new frontier of translational research?

(2012) R Spizzo et al.   ONCOGENE

Negative Correlation between Expression Level and Evolutionary Rate of Long Intergenic Noncoding RNAs

(2011) David Managadze et al.   Genome Biology and Evolution

Global DNA hypomethylation coupled to repressive chromatin domain formation and gene silencing in breast cancer

(2011) G. C. Hon et al.   GENOME RESEARCH

The Human Hyaluronan Synthase 2 (HAS2) Gene and Its Natural Antisense RNA Exhibit Coordinated Expression in the Renal Proximal Tubular Epithelial Cell

(2011) Daryn R. Michael et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Identification of Novel GDNF Isoforms andcis-Antisense GDNFOS Gene and Their Regulation in Human Middle Temporal Gyrus of Alzheimer Disease

(2011) Mikko Airavaara et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Regulation by Small RNAs in Bacteria: Expanding Frontiers

(2011) Gisela Storz et al.   MOLECULAR CELL

Genomic Maps of Long Noncoding RNA Occupancy Reveal Principles of RNA-Chromatin Interactions

(2011) Ci Chu et al.   MOLECULAR CELL

Molecular Mechanisms of Long Noncoding RNAs

(2011) Kevin C. Wang et al.   MOLECULAR CELL

RNA-Seq unleashed

(2011) Matthew K Iyer et al.   NATURE BIOTECHNOLOGY

Genome-wide views of long non-coding RNAs

(2011) Mary Muers   NATURE REVIEWS GENETICS

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

Large-scale prediction of long non-coding RNA functions in a coding–non-coding gene co-expression network

(2011) Qi Liao et al.   NUCLEIC ACIDS RESEARCH

The Emergence of lncRNAs in Cancer Biology

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

Role of H3K27 methylation in the regulation of lncRNA expression

(2010) Susan C Wu et al.   CELL RESEARCH

Large non-coding RNAs: missing links in cancer?

(2010) M. Huarte et al.   HUMAN MOLECULAR GENETICS

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

(2010) Rajnish A. Gupta et al.   NATURE

Epigenetic modifications and human disease

(2010) Anna Portela et al.   NATURE BIOTECHNOLOGY

Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells

(2010) Sabine Loewer et al.   NATURE GENETICS

Charting histone modifications and the functional organization of mammalian genomes

(2010) Vicky W. Zhou et al.   NATURE REVIEWS GENETICS

Long Noncoding RNA as Modular Scaffold of Histone Modification Complexes

(2010) M.-C. Tsai et al.   SCIENCE

Noncoding RNA Gas5 Is a Growth Arrest- and Starvation-Associated Repressor of the Glucocorticoid Receptor

(2010) T. Kino et al.   Science Signaling

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster

(2009) X. Zhang et al.   BLOOD

Non-coding RNAs: regulators of disease

(2009) Ryan J Taft et al.   JOURNAL OF PATHOLOGY

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

(2009) Mitchell Guttman et al.   NATURE

Combinatorial network of primary and secondary microRNA-driven regulatory mechanisms

(2009) Kang Tu et al.   NUCLEIC ACIDS RESEARCH

Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression

(2009) Ahmad M. Khalil et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Linkage and Association Study of Late-Onset Alzheimer Disease Families Linked to 9p21.3

(2008) S. Züchner et al.   ANNALS OF HUMAN GENETICS

Serum  2-HS Glycoprotein Predicts Survival in Patients with Glioblastoma

(2008) V. Petrik et al.   CLINICAL CHEMISTRY

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE