Network-Based Approaches to Explore Complex Biological Systems towards Network Medicine

Long non-coding RNA PVT1 as a novel candidate for targeted therapy in hematologic malignancies

(2018) Mohammad Houshmand et al.   INTERNATIONAL JOURNAL OF BIOCHEMISTRY & CELL BIOLOGY

lncRNA PVT1 promotes the angiogenesis of vascular endothelial cell by targeting miR‑26b to activate CTGF/ANGPT2

(2018) Jifu Zheng et al.   INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE

Long non-coding RNA PVT1 predicts poor prognosis and induces radioresistance by regulating DNA repair and cell apoptosis in nasopharyngeal carcinoma

(2018) Yi He et al.   Cell Death & Disease

Molecular mechanisms of long noncoding RNAs and their role in disease pathogenesis

(2018) Guoku Hu et al.   Oncotarget

Computational identification of specific genes for glioblastoma stem-like cells identity

(2018) Giulia Fiscon et al.   Scientific Reports

Effect of long non-coding RNA PVT1 on cell proliferation and migration in melanoma

(2017) Lamei Chen et al.   INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE

lncRNA PVT1 and its splicing variant function as competing endogenous RNA to regulate clear cell renal cell carcinoma progression

(2017) Tao Yang et al.   Oncotarget

SWIM: a computational tool to unveiling crucial nodes in complex biological networks

(2017) Paola Paci et al.   Scientific Reports

Understanding Tissue-Specific Gene Regulation

(2017) Abhijeet Rajendra Sonawane et al.   Cell Reports

Role of the long non-coding RNA PVT1 in the dysregulation of the ceRNA-ceRNA network in human breast cancer

(2017) Federica Conte et al.   PLoS One

GenePANDA—a novel network-based gene prioritizing tool for complex diseases

(2017) Tianshu Yin et al.   Scientific Reports

Computational methods for identifying miRNA sponge interactions

(2016) Thuc Duy Le et al.   BRIEFINGS IN BIOINFORMATICS

Competing endogenous RNA networks in human cancer: hypothesis, validation, and perspectives

(2016) Chao Yang et al.   Oncotarget

The lncRNA PVT1 Contributes to the Cervical Cancer Phenotype and Associates with Poor Patient Prognosis

(2016) Marissa Iden et al.   PLoS One

ceRNA in cancer: possible functions and clinical implications

(2015) Xiaolong Qi et al.   JOURNAL OF MEDICAL GENETICS

PTEN ceRNA networks in human cancer

(2015) Laura Poliseno et al.   METHODS

Long non-coding RNA PVT1 as a novel biomarker for diagnosis and prognosis of non-small cell lung cancer

(2015) Di Cui et al.   TUMOR BIOLOGY

Long noncoding RNA PVT1 modulates thyroid cancer cell proliferation by recruiting EZH2 and regulating thyroid-stimulating hormone receptor (TSHR)

(2015) Qinyi Zhou et al.   TUMOR BIOLOGY

Oncocers: ceRNA-mediated cross-talk by sponging miRNAs in oncogenic pathways

(2015) Sercan Ergun et al.   TUMOR BIOLOGY

Review The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge

(2015) Katarzyna Tomczak et al.   Wspolczesna Onkologia-Contemporary Oncology

Tetracycline-inducible shRNA targeting long non-coding RNA PVT1 inhibits cell growth and induces apoptosis in bladder cancer cells

(2015) Chengle Zhuang et al.   Oncotarget

A DIseAse MOdule Detection (DIAMOnD) Algorithm Derived from a Systematic Analysis of Connectivity Patterns of Disease Proteins in the Human Interactome

(2015) Susan Dina Ghiassian et al.   PLoS Computational Biology

PVT1: A Rising Star among Oncogenic Long Noncoding RNAs

(2015) Teresa Colombo et al.   Biomed Research International

Computational analysis identifies a sponge interaction network between long non-coding RNAs and messenger RNAs in human breast cancer

(2014) Paola Paci et al.   BMC Systems Biology

Reconstructing and Reprogramming the Tumor-Propagating Potential of Glioblastoma Stem-like Cells

(2014) Mario L. Suvà et al.   CELL

Oncofetal long noncoding RNA PVT1 promotes proliferation and stem cell-like property of hepatocellular carcinoma cells by stabilizing NOP2

(2014) Fang Wang et al.   HEPATOLOGY

PVT1 dependence in cancer with MYC copy-number increase

(2014) Yuen-Yi Tseng et al.   NATURE

Integrated Network Analysis Identifies Fight-Club Nodes as a Class of Hubs Encompassing Key Putative Switch Genes That Induce Major Transcriptome Reprogramming during Grapevine Development

(2014) Maria Concetta Palumbo et al.   PLANT CELL

Finding reproducible cluster partitions for the k-means algorithm

(2013) Paulo JG Lisboa et al.   BMC BIOINFORMATICS

Natural RNA circles function as efficient microRNA sponges

(2013) Thomas B. Hansen et al.   NATURE

Circular RNAs are a large class of animal RNAs with regulatory potency

(2013) Sebastian Memczak et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Passing Messages between Biological Networks to Refine Predicted Interactions

(2013) Kimberly Glass et al.   PLoS One

Role of the AP-1 transcription factor FOSL1 in endothelial cells adhesion and migration

(2013) Federico Galvagni et al.   Cell Adhesion & Migration

Non-coding RNA and antisense RNA. Nature’s trash or treasure?

(2011) Stuart Knowling et al.   BIOCHIMIE

PRINCIPLE: a tool for associating genes with diseases via network propagation

(2011) A. Gottlieb et al.   BIOINFORMATICS

ProDiGe: Prioritization Of Disease Genes with multitask machine learning from positive and unlabeled examples

(2011) Fantine Mordelet et al.   BMC BIOINFORMATICS

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

A ceRNA Hypothesis: The Rosetta Stone of a Hidden RNA Language?

(2011) Leonardo Salmena et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Glioblastoma stem cells

(2011) Ghazaleh Tabatabai et al.   CELL AND TISSUE RESEARCH

The central role of RNA in human development and cognition

(2011) John S. Mattick   FEBS LETTERS

A distinct subset of glioma cell lines with stem cell-like properties reflects the transcriptional phenotype of glioblastomas and overexpresses CXCR4 as therapeutic target

(2011) Alexander Schulte et al.   GLIA

Whole genome RNA expression profiling of endoscopic biliary brushings provides data suitable for biomarker discovery in cholangiocarcinoma

(2011) Michael H. Chapman et al.   JOURNAL OF HEPATOLOGY

Non-coding RNAs in human disease

(2011) Manel Esteller   NATURE REVIEWS GENETICS

A Functional Variant at a Prostate Cancer Predisposition Locus at 8q24 Is Associated with PVT1 Expression

(2011) Kerstin B. Meyer et al.   PLoS Genetics

DA DA: Degree-Aware Algorithms for Network-Based Disease Gene Prioritization

(2011) Sinan Erten et al.   BioData Mining

A coding-independent function of gene and pseudogene mRNAs regulates tumour biology

(2010) Laura Poliseno et al.   NATURE

Network medicine: a network-based approach to human disease

(2010) Albert-László Barabási et al.   NATURE REVIEWS GENETICS

MapSplice: Accurate mapping of RNA-seq reads for splice junction discovery

(2010) Kai Wang et al.   NUCLEIC ACIDS RESEARCH

Associating Genes and Protein Complexes with Disease via Network Propagation

(2010) Oron Vanunu et al.   PLoS Computational Biology

Evolution and Functions of Long Noncoding RNAs

(2009) Chris P. Ponting et al.   CELL

Long non-coding RNAs: insights into functions

(2009) Tim R. Mercer et al.   NATURE REVIEWS GENETICS

Walking the Interactome for Prioritization of Candidate Disease Genes

(2008) Sebastian Köhler et al.   AMERICAN JOURNAL OF HUMAN GENETICS

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS