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

Integrated genomic characterization of endometrial carcinoma

(2013) Gad Getz et al.   NATURE

Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers

(2013) Alayne L Brunner et al.   GENOME BIOLOGY

miRcode: a map of putative microRNA target sites in the long non-coding transcriptome

(2012) Ashwini Jeggari et al.   BIOINFORMATICS

Global transcriptome analysis reveals distinct expression among duplicated genes during sorghum-Bipolaris sorghicola interaction

(2012) Hiroshi Mizuno et al.   BMC PLANT BIOLOGY

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

Extensive somatic L1 retrotransposition in colorectal tumors

(2012) S. Solyom 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

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

Landscape of transcription in human cells

(2012) Sarah Djebali et al.   NATURE

Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes

(2012) Jan J. Molenaar et al.   NATURE

Rfam 11.0: 10 years of RNA families

(2012) Sarah W. Burge et al.   NUCLEIC ACIDS RESEARCH

The Non-Coding Oncogene: A Case of Missing DNA Evidence?

(2012) Puja Shahrouki et al.   Frontiers in Genetics

PhyloCSF: a comparative genomics method to distinguish protein coding and non-coding regions

(2011) M. F. Lin et al.   BIOINFORMATICS

A Long Noncoding RNA Controls Muscle Differentiation by Functioning as a Competing Endogenous RNA

(2011) Marcella Cesana et al.   CELL

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

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

lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements

(2011) Chenguang Gong et al.   NATURE

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression

(2011) John R Prensner et al.   NATURE BIOTECHNOLOGY

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

Human Cancer Long Non-Coding RNA Transcriptomes

(2011) Ewan A. Gibb et al.   PLoS One

A User's Guide to the Encyclopedia of DNA Elements (ENCODE)

(2011)   PLOS BIOLOGY

Ovarian Cancer Development and Metastasis

(2010) Ernst Lengyel   AMERICAN JOURNAL OF PATHOLOGY

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Identification of differentially expressed genes using an annealing control primer system in stage III serous ovarian carcinoma

(2010) Yun-Sook Kim et al.   BMC CANCER

Recurrent Focal Copy-Number Changes and Loss of Heterozygosity Implicate Two Noncoding RNAs and One Tumor Suppressor Gene at Chromosome 3q13.31 in Osteosarcoma

(2010) I. Pasic et al.   CANCER RESEARCH

Filamin a mediates HGF/c-MET signaling in tumor cell migration

(2010) Alex-Xianghua Zhou et al.   INTERNATIONAL JOURNAL OF CANCER

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

(2010) Rajnish A. Gupta et al.   NATURE

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim 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

CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer

(2010) Jiayi Wang et al.   NUCLEIC ACIDS RESEARCH

Novel Primate-Specific Genes, RMEL 1, 2 and 3, with Highly Restricted Expression in Melanoma, Assessed by New Data Mining Tool

(2010) Josane F. Sousa et al.   PLoS One

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

An Architectural Role for a Nuclear Noncoding RNA: NEAT1 RNA Is Essential for the Structure of Paraspeckles

(2009) Christine M. Clemson et al.   MOLECULAR CELL

Conserved long noncoding RNAs transcriptionally regulated by Oct4 and Nanog modulate pluripotency in mouse embryonic stem cells

(2009) J. Sheik Mohamed et al.   RNA

Novel Molecular Subtypes of Serous and Endometrioid Ovarian Cancer Linked to Clinical Outcome

(2008) R. W. Tothill et al.   CLINICAL CANCER RESEARCH

UCA1, a non-protein-coding RNA up-regulated in bladder carcinoma and embryo, influencing cell growth and promoting invasion

(2008) Fan Wang et al.   FEBS LETTERS

The Identification of MicroRNAs in a Genomically Unstable Region of Human Chromosome 8q24

(2008) K. Huppi et al.   MOLECULAR CANCER RESEARCH

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Pvt1-encoded microRNAs in oncogenesis

(2008) Gabriele B Beck-Engeser et al.   Retrovirology