A novel network control model for identifying personalized driver genes in cancer

deepDriver: Predicting Cancer Driver Genes Based on Somatic Mutations Using Deep Convolutional Neural Networks

(2019) Ping Luo et al.   Frontiers in Genetics

DriverML: a machine learning algorithm for identifying driver genes in cancer sequencing studies

(2019) Yi Han et al.   NUCLEIC ACIDS RESEARCH

Transposable elements drive widespread expression of oncogenes in human cancers

(2019) Hyo Sik Jang et al.   NATURE GENETICS

Optimal control nodes in disease-perturbed networks as targets for combination therapy

(2019) Yuxuan Hu et al.   Nature Communications

Discovering personalized driver mutation profiles of single samples in cancer by network control strategy

(2018) Wei-Feng Guo et al.   BIOINFORMATICS

Facilitating Anti-Cancer Combinatorial Drug Discovery by Targeting Epistatic Disease Genes

(2018) Yuan Quan et al.   MOLECULES

Constrained target controllability of complex networks

(2017) Wei-Feng Guo et al.   JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT

Network control principles predict neuron function in the Caenorhabditis elegans connectome

(2017) Gang Yan et al.   NATURE

Comparison of algorithms for the detection of cancer drivers at subgene resolution

(2017) Eduard Porta-Pardo et al.   NATURE METHODS

Structure-based control of complex networks with nonlinear dynamics

(2017) Jorge Gomez Tejeda Zañudo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Personalized characterization of diseases using sample-specific networks

(2016) Xiaoping Liu et al.   NUCLEIC ACIDS RESEARCH

A geometrical approach to control and controllability of nonlinear dynamical networks

(2016) Le-Zhi Wang et al.   Nature Communications

Advances in computational approaches for prioritizing driver mutations and significantly mutated genes in cancer genomes

(2015) Feixiong Cheng et al.   BRIEFINGS IN BIOINFORMATICS

DriverDBv2: a database for human cancer driver gene research

(2015) I-Fang Chung et al.   NUCLEIC ACIDS RESEARCH

Convergence behaviour and Control in Non-Linear Biological Networks

(2015) Stefan Karl et al.   Scientific Reports

Pan-cancer network analysis identifies combinations of rare somatic mutations across pathways and protein complexes

(2014) Mark D M Leiserson et al.   NATURE GENETICS

Target control of complex networks

(2014) Jianxi Gao et al.   Nature Communications

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

Dynamics and Control at Feedback Vertex Sets. I: Informative and Determining Nodes in Regulatory Networks

(2013) Bernold Fiedler et al.   Journal of Dynamics and Differential Equations

Dynamics and control at feedback vertex sets. II: A faithful monitor to determine the diversity of molecular activities in regulatory networks

(2013) Atsushi Mochizuki et al.   JOURNAL OF THEORETICAL BIOLOGY

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

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

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Realistic control of network dynamics

(2013) Sean P. Cornelius et al.   Nature Communications

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

(2013) Ali Bashashati et al.   GENOME BIOLOGY

Controlling edge dynamics in complex networks

(2012) Tamás Nepusz et al.   Nature Physics

Dominating scale-free networks with variable scaling exponent: heterogeneous networks are not difficult to control

(2012) Jose C Nacher et al.   NEW JOURNAL OF PHYSICS

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

Exome sequencing identifies GRIN2A as frequently mutated in melanoma

(2011) Xiaomu Wei et al.   NATURE GENETICS

KEGG for integration and interpretation of large-scale molecular data sets

(2011) M. Kanehisa et al.   NUCLEIC ACIDS RESEARCH

Network medicine: a network-based approach to human disease

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

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

(2010) Guanming Wu et al.   GENOME BIOLOGY

Scale-Free Networks: A Decade and Beyond

(2009) Albert-László Barabási   SCIENCE

Power-Law Distributions in Empirical Data

(2009) Aaron Clauset et al.   SIAM REVIEW

PID: the Pathway Interaction Database

(2008) Carl F. Schaefer et al.   NUCLEIC ACIDS RESEARCH

Human Gene Coexpression Landscape: Confident Network Derived from Tissue Transcriptomic Profiles

(2008) Carlos Prieto et al.   PLoS One