Inferring and analyzing module-specific lncRNA–mRNA causal regulatory networks in human cancer

lncRInter: A database of experimentally validated long non-coding RNA interaction

(2017) Chun-Jie Liu et al.   Journal of Genetics and Genomics

Comprehensive analysis of long noncoding RNA–mRNA co-expression patterns in thyroid cancer

(2017) Yaying Du et al.   Molecular BioSystems

The specificity of long noncoding RNA expression

(2016) Brian S. Gloss et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

lnCaNet: pan-cancer co-expression network for human lncRNA and cancer genes

(2016) Yining Liu et al.   BIOINFORMATICS

BmncRNAdb: a comprehensive database of non-coding RNAs in the silkworm, Bombyx mori

(2016) Qiu-Zhong Zhou et al.   BMC BIOINFORMATICS

Comprehensive prediction of lncRNA–RNA interactions in human transcriptome

(2016) Goro Terai et al.   BMC GENOMICS

Long Noncoding RNAs in Cancer Pathways

(2016) Adam M. Schmitt et al.   CANCER CELL

Expression Profile of Long Noncoding RNAs in Peripheral Blood Mononuclear Cells from Multiple Sclerosis Patients

(2016) Fang Zhang et al.   CNS Neuroscience & Therapeutics

A fast PC algorithm for high dimensional causal discovery with multi-core PCs

(2016) Thuc Le et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Dynamic co-expression network analysis of lncRNAs and mRNAs associated with venous congestion

(2016) Jinshun Li et al.   Molecular Medicine Reports

DisGeNET: a comprehensive platform integrating information on human disease-associated genes and variants

(2016) Janet Piñero et al.   NUCLEIC ACIDS RESEARCH

Part mutual information for quantifying direct associations in networks

(2016) Juan Zhao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

IRNdb: the database of immunologically relevant non-coding RNAs

(2016) Elena Denisenko et al.   Database-The Journal of Biological Databases and Curation

NPInter v3.0: an upgraded database of noncoding RNA-associated interactions

(2016) Yajing Hao et al.   Database-The Journal of Biological Databases and Curation

lncRNATargets: A platform for lncRNA target prediction based on nucleic acid thermodynamics

(2016) Ruifeng Hu et al.   Journal of Bioinformatics and Computational Biology

Identification of Potential Key Long Non-Coding RNAs and Target Genes Associated with Pneumonia Using Long Non-Coding RNA Sequencing (lncRNA-Seq): A Preliminary Study

(2016) Sai Huang et al.   MEDICAL SCIENCE MONITOR

Tissue-specific Co-expression of Long Non-coding and Coding RNAs Associated with Breast Cancer

(2016) Wenting Wu et al.   Scientific Reports

LncRNA2Function: a comprehensive resource for functional investigation of human lncRNAs based on RNA-seq data

(2015) Qinghua Jiang et al.   BMC GENOMICS

Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers

(2015) Shangwei Ning et al.   NUCLEIC ACIDS RESEARCH

Expression profile of long noncoding RNAs in cartilage from knee osteoarthritis patients

(2015) M. Fu et al.   OSTEOARTHRITIS AND CARTILAGE

LncReg: a reference resource for lncRNA-associated regulatory networks

(2015) Zhong Zhou et al.   Database-The Journal of Biological Databases and Curation

Comprehensive analysis of lncRNA-mRNA co-expression patterns identifies immune-associated lncRNA biomarkers in ovarian cancer malignant progression

(2015) Qiuyan Guo et al.   Scientific Reports

FastRFunctions for Robust Correlations and Hierarchical Clustering

(2015) Peter Langfelder et al.   Journal of Statistical Software

lncRNAtor: a comprehensive resource for functional investigation of long non-coding RNAs

(2014) Charny Park et al.   BIOINFORMATICS

LncTar: a tool for predicting the RNA targets of long noncoding RNAs

(2014) Jianwei Li et al.   BRIEFINGS IN BIOINFORMATICS

lncRNAMap: A map of putative regulatory functions in the long non-coding transcriptome

(2014) Wen-Ling Chan et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

LncRNA2Target: a database for differentially expressed genes after lncRNA knockdown or overexpression

(2014) Qinghua Jiang et al.   NUCLEIC ACIDS RESEARCH

Conditional mutual inclusive information enables accurate quantification of associations in gene regulatory networks

(2014) Xiujun Zhang et al.   NUCLEIC ACIDS RESEARCH

The Role of Cyclic Nucleotide Signaling Pathways in Cancer: Targets for Prevention and Treatment

(2014) Alexandra Fajardo et al.   Cancers

Long Noncoding RNAs: Past, Present, and Future

(2013) J. T. Y. Kung et al.   GENETICS

Targeting long non-coding RNA to therapeutically upregulate gene expression

(2013) Claes Wahlestedt   NATURE REVIEWS DRUG DISCOVERY

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

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

starBase v2.0: decoding miRNA-ceRNA, miRNA-ncRNA and protein–RNA interaction networks from large-scale CLIP-Seq data

(2013) Jun-Hao Li et al.   NUCLEIC ACIDS RESEARCH

Mammalian ncRNA-disease repository: a global view of ncRNA-mediated disease network

(2013) Y Wang et al.   Cell Death & Disease

lncRNome: a comprehensive knowledgebase of human long noncoding RNAs

(2013) Deeksha Bhartiya et al.   Database-The Journal of Biological Databases and Curation

From Hub Proteins to Hub Modules: The Relationship Between Essentiality and Centrality in the Yeast Interactome at Different Scales of Organization

(2013) Jimin Song et al.   PLoS Computational Biology

RIsearch: fast RNA–RNA interaction search using a simplified nearest-neighbor energy model

(2012) Anne Wenzel et al.   BIOINFORMATICS

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

(2012) T. Derrien et al.   GENOME RESEARCH

Posttranscriptional Gene Regulation by Long Noncoding RNA

(2012) Je-Hyun Yoon et al.   JOURNAL OF MOLECULAR BIOLOGY

LncRNADisease: a database for long-non-coding RNA-associated diseases

(2012) Geng Chen et al.   NUCLEIC ACIDS RESEARCH

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Inferring gene regulatory networks from gene expression data by path consistency algorithm based on conditional mutual information

(2011) Xiujun Zhang et al.   BIOINFORMATICS

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

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

PETcofold: predicting conserved interactions and structures of two multiple alignments of RNA sequences

(2010) Stefan E. Seemann et al.   BIOINFORMATICS

RactIP: fast and accurate prediction of RNA-RNA interaction using integer programming

(2010) Yuki Kato et al.   BIOINFORMATICS

Predicting causal effects in large-scale systems from observational data

(2010) Marloes H Maathuis et al.   NATURE METHODS

Tumor necrosis factor and cancer, buddies or foes?

(2009) Xia Wang et al.   ACTA PHARMACOLOGICA SINICA

Estimating high-dimensional intervention effects from observational data

(2009) Marloes H. Maathuis et al.   ANNALS OF STATISTICS

IntaRNA: efficient prediction of bacterial sRNA targets incorporating target site accessibility and seed regions

(2008) Anke Busch et al.   BIOINFORMATICS

RNAplex: a fast tool for RNA–RNA interaction search

(2008) Hakim Tafer et al.   BIOINFORMATICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS