CBNA: A control theory based method for identifying coding and non-coding cancer drivers

microRNA-130a suppresses breast cancer cell migration and invasion by targeting FOSL1 and upregulating ZO-1

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FYN promotes mesenchymal phenotypes of basal type breast cancer cells through STAT5/NOTCH2 signaling node

(2018) Ga-Hang Lee et al.   ONCOGENE

Loss of PTEN in high grade advanced stage triple negative breast ductal cancers in African American women

(2018) Farhan Khan et al.   PATHOLOGY RESEARCH AND PRACTICE

Combinatorial Targeting by MicroRNAs Co-ordinates Post-transcriptional Control of EMT

(2018) Joseph Cursons et al.   Cell Systems

NetSig: network-based discovery from cancer genomes

(2017) Heiko Horn et al.   NATURE METHODS

Individual-specific edge-network analysis for disease prediction

(2017) Xiangtian Yu et al.   NUCLEIC ACIDS RESEARCH

Computational Methods for Characterizing Cancer Mutational Heterogeneity

(2017) Fabio Vandin   Frontiers in Genetics

Predicting the recurrence of noncoding regulatory mutations in cancer

(2016) Woojin Yang et al.   BMC BIOINFORMATICS

Update of the FANTOM web resource: high resolution transcriptome of diverse cell types in mammals

(2016) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

Personalized characterization of diseases using sample-specific networks

(2016) Xiaoping Liu et al.   NUCLEIC ACIDS RESEARCH

Evaluating the evaluation of cancer driver genes

(2016) Collin J. Tokheim et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Controllability analysis of the directed human protein interaction network identifies disease genes and drug targets

(2016) Arunachalam Vinayagam et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Computational approaches for the identification of cancer genes and pathways

(2016) Christos M. Dimitrakopoulos et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes

(2016) Bernard Pereira et al.   Nature Communications

Identifying Cancer Subtypes from miRNA-TF-mRNA Regulatory Networks and Expression Data

(2016) Taosheng Xu et al.   PLoS One

Non-coding recurrent mutations in chronic lymphocytic leukaemia

(2015) Xose S. Puente et al.   NATURE

miRWalk2.0: a comprehensive atlas of microRNA-target interactions

(2015) Harsh Dweep et al.   NATURE METHODS

miRTarBase 2016: updates to the experimentally validated miRNA-target interactions database

(2015) Chih-Hung Chou et al.   NUCLEIC ACIDS RESEARCH

Identification of Constrained Cancer Driver Genes Based on Mutation Timing

(2015) Thomas Sakoparnig et al.   PLoS Computational Biology

Predicting effective microRNA target sites in mammalian mRNAs

(2015) Vikram Agarwal et al.   eLife

Epithelial-mesenchymal transition spectrum quantification and its efficacy in deciphering survival and drug responses of cancer patients

(2014) T. Z. Tan et al.   EMBO Molecular Medicine

E2F1 induces miR-224/452 expression to drive EMT through TXNIP downregulation

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Analysis of Changes in SUMO-2/3 Modification during Breast Cancer Progression and Metastasis

(2014) Divya Subramonian et al.   JOURNAL OF PROTEOME RESEARCH

Genome-wide analysis of noncoding regulatory mutations in cancer

(2014) Nils Weinhold et al.   NATURE GENETICS

COSMIC: exploring the world's knowledge of somatic mutations in human cancer

(2014) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

DIANA-TarBase v7.0: indexing more than half a million experimentally supported miRNA:mRNA interactions

(2014) Ioannis S. Vlachos et al.   NUCLEIC ACIDS RESEARCH

miR-223 Is a Coordinator of Breast Cancer Progression as Revealed by Bioinformatics Predictions

(2014) Eva Maria Pinatel et al.   PLoS One

DawnRank: discovering personalized driver genes in cancer

(2014) Jack P Hou et al.   Genome Medicine

OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes

(2013) David Tamborero et al.   BIOINFORMATICS

Discovering causal pathways linking genomic events to transcriptional states using Tied Diffusion Through Interacting Events (TieDIE)

(2013) Evan O. Paull et al.   BIOINFORMATICS

Identification of mutated core cancer modules by integrating somatic mutation, copy number variation, and gene expression data

(2013) Junhua Zhang et al.   BMC Systems Biology

Systematic analysis of somatic mutations in phosphorylation signaling predicts novel cancer drivers

(2013) J. Reimand et al.   Molecular Systems Biology

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer

(2013) Ali Bashashati et al.   GENOME BIOLOGY

The landscape of cancer genes and mutational processes in breast cancer

(2012) Philip J. Stephens et al.   NATURE

Comprehensive molecular portraits of human breast tumours

(2012) Daniel C. Koboldt et al.   NATURE

Functional impact bias reveals cancer drivers

(2012) Abel Gonzalez-Perez et al.   NUCLEIC ACIDS RESEARCH

Mutual exclusivity analysis identifies oncogenic network modules

(2011) G. Ciriello et al.   GENOME RESEARCH

Controllability of complex networks

(2011) Yang-Yu Liu et al.   NATURE

A Directed Protein Interaction Network for Investigating Intracellular Signal Transduction

(2011) A. Vinayagam et al.   Science Signaling

Cdc42-Interacting Protein 4 Promotes Breast Cancer Cell Invasion and Formation of Invadopodia through Activation of N-WASp

(2010) C. S. Pichot et al.   CANCER RESEARCH

The genetic basis of kidney cancer: a metabolic disease

(2010) W. Marston Linehan et al.   Nature Reviews Urology

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

A human functional protein interaction network and its application to cancer data analysis

(2010) Guanming Wu et al.   GENOME BIOLOGY

Cancer-Specific High-Throughput Annotation of Somatic Mutations: Computational Prediction of Driver Missense Mutations

(2009) H. Carter et al.   CANCER RESEARCH

Supervised Risk Predictor of Breast Cancer Based on Intrinsic Subtypes

(2009) Joel S. Parker et al.   JOURNAL OF CLINICAL ONCOLOGY

TransmiR: a transcription factor–microRNA regulation database

(2009) Juan Wang et al.   NUCLEIC ACIDS RESEARCH

The miR-200 family determines the epithelial phenotype of cancer cells by targeting the E-cadherin repressors ZEB1 and ZEB2

(2008) S.-M. Park et al.   GENES & DEVELOPMENT

Somatic mutations affect key pathways in lung adenocarcinoma

(2008) Li Ding et al.   NATURE

The miR-200 family and miR-205 regulate epithelial to mesenchymal transition by targeting ZEB1 and SIP1

(2008) Philip A. Gregory et al.   NATURE CELL BIOLOGY

Core Signaling Pathways in Human Pancreatic Cancers Revealed by Global Genomic Analyses

(2008) S. Jones et al.   SCIENCE