Long Non-Coding RNA Expression Levels Modulate Cell-Type-Specific Splicing Patterns by Altering Their Interaction Landscape with RNA-Binding Proteins

MALAT1 sponges miR-106b-5p to promote the invasion and metastasis of colorectal cancer via SLAIN2 enhanced microtubules mobility

(2019) Meng Zhuang et al.   EBioMedicine

Construction and comprehensive analysis of a ceRNA network to reveal potential prognostic biomarkers for hepatocellular carcinoma

(2019) Junyu Long et al.   Cancer Cell International

Functional Classification and Experimental Dissection of Long Noncoding RNAs

(2018) Florian Kopp et al.   CELL

High‐throughput identification of RNA nuclear enrichment sequences

(2018) Chinmay J Shukla et al.   EMBO JOURNAL

Noncoding RNA:RNA Regulatory Networks in Cancer

(2018) Jia Chan et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Structural analyses of NEAT1 lncRNAs suggest long-range RNA interactions that may contribute to paraspeckle architecture

(2018) Yizhu Lin et al.   NUCLEIC ACIDS RESEARCH

Splicing regulation by long noncoding RNAs

(2018) Natali Romero-Barrios et al.   NUCLEIC ACIDS RESEARCH

POSTAR2: deciphering the post-transcriptional regulatory logics

(2018) Yumin Zhu et al.   NUCLEIC ACIDS RESEARCH

Nuclear Speckle RNA Binding Proteins Remodel Alternative Splicing and the Non-coding Arabidopsis Transcriptome to Regulate a Cross-Talk Between Auxin and Immune Responses

(2018) Jérémie Bazin et al.   Frontiers in Plant Science

Capturing functional long non-coding RNAs through integrating large-scale causal relations from gene perturbation experiments

(2018) Jinyuan Xu et al.   EBioMedicine

CRISPR/Cas9 Knockout Strategies to Ablate CCAT1 lncRNA Gene in Cancer Cells

(2018) Khadijeh Zare et al.   BIOLOGICAL PROCEDURES ONLINE

The Gene Ontology Resource: 20 years and still GOing strong

(2018)   NUCLEIC ACIDS RESEARCH

LncRNA Structural Characteristics in Epigenetic Regulation

(2017) Chenguang Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The Reactome Pathway Knowledgebase

(2017) Antonio Fabregat et al.   NUCLEIC ACIDS RESEARCH

Mutational landscape of RNA-binding proteins in human cancers

(2017) Yaseswini Neelamraju et al.   RNA Biology

Seten: a tool for systematic identification and comparison of processes, phenotypes, and diseases associated with RNA-binding proteins from condition-specific CLIP-seq profiles

(2017) Gungor Budak et al.   RNA

RNA-binding protein HuR promotes bladder cancer progression by competitively binding to the long noncoding HOTAIR with miR-1

(2017) Dapeng Yu et al.   OncoTargets and Therapy

Identifying and Characterizing circRNA-Protein Interaction

(2017) William W Du et al.   Theranostics

Transcriptome analysis of developing lens reveals abundance of novel transcripts and extensive splicing alterations

(2017) Rajneesh Srivastava et al.   Scientific Reports

Challenges in the analysis of long noncoding RNA functionality

(2016) Sergio Leone et al.   FEBS LETTERS

A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs

(2016) Elena Rivas et al.   NATURE METHODS

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

LncRNAOIP5-AS1/cyranosponges RNA-binding protein HuR

(2016) Jiyoung Kim et al.   NUCLEIC ACIDS RESEARCH

CRISPRi-based genome-scale identification of functional long noncoding RNA loci in human cells

(2016) S. John Liu et al.   SCIENCE

Integrative analyses reveal a long noncoding RNA-mediated sponge regulatory network in prostate cancer

(2016) Zhou Du et al.   Nature Communications

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

Ensembl 2016

(2015) Andrew Yates et al.   NUCLEIC ACIDS RESEARCH

Exploiting pre-rRNA processing in Diamond Blackfan anemia gene discovery and diagnosis

(2014) Jason E. Farrar et al.   AMERICAN JOURNAL OF HEMATOLOGY

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Rise of the RNA Machines: Exploring the Structure of Long Non-Coding RNAs

(2013) Irina V. Novikova et al.   JOURNAL OF MOLECULAR BIOLOGY

iCLIP: Protein–RNA interactions at nucleotide resolution

(2013) Ina Huppertz et al.   METHODS

NEAT1 long noncoding RNA regulates transcription via protein sequestration within subnuclear bodies

(2013) Tetsuro Hirose et al.   MOLECULAR BIOLOGY OF THE CELL

SPIN90 Knockdown Attenuates the Formation and Movement of Endosomal Vesicles in the Early Stages of Epidermal Growth Factor Receptor Endocytosis

(2013) Hyejin Oh et al.   PLoS One

An integrated encyclopedia of DNA elements in the human genome

(2012)   NATURE

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Radiation Resistance in Glioma Cells Determined by DNA Damage Repair Activity of Ape1/Ref-1

(2010) Mamta D. NAIDU et al.   JOURNAL OF RADIATION RESEARCH

The Sequence Read Archive

(2010) R. Leinonen et al.   NUCLEIC ACIDS RESEARCH

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Paraspeckles: nuclear bodies built on long noncoding RNA

(2009) Charles S. Bond et al.   JOURNAL OF CELL BIOLOGY