Identifying driver genes for individual patients through inductive matrix completion

DRIMC: an improved drug repositioning approach using Bayesian inductive matrix completion

(2020) Wenjuan Zhang et al.   BIOINFORMATICS

Visualizing and interpreting cancer genomics data via the Xena platform

(2020) Mary J. Goldman et al.   NATURE BIOTECHNOLOGY

Towards a data-integrated cell

(2019) Noël Malod-Dognin et al.   Nature Communications

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

(2019) Yi Han et al.   NUCLEIC ACIDS RESEARCH

Identification of survival-related predictors in hepatocellular carcinoma through integrated genomic, transcriptomic, and proteomic analyses

(2019) Fangyuan Dong et al.   BIOMEDICINE & PHARMACOTHERAPY

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

(2019) Wei-Feng Guo et al.   PLoS Computational Biology

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

(2019) Vu V. H. Pham et al.   PLoS Computational Biology

Whole-exome mutational and transcriptional landscapes of combined hepatocellular cholangiocarcinoma and intrahepatic cholangiocarcinoma reveal molecular diversity

(2018) Zhen-Hao Liu et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR BASIS OF DISEASE

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

(2018) Wei-Feng Guo et al.   BIOINFORMATICS

Robust Inductive Matrix Completion Strategy to Explore Associations between LincRNAs and Human Disease Phenotypes

(2018) Ashis Biswas et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

New approach for understanding genome variations in KEGG

(2018) Minoru Kanehisa et al.   NUCLEIC ACIDS RESEARCH

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

Discovering potential driver genes through an integrated model of somatic mutation profiles and gene functional information

(2017) Jianing Xi et al.   Molecular BioSystems

Dynein axonemal heavy chain 8 promotes androgen receptor activity and associates with prostate cancer progression

(2016) Yu Wang et al.   Oncotarget

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

(2015) Feixiong Cheng et al.   BRIEFINGS IN BIOINFORMATICS

Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles

(2015) Denis Bertrand et al.   NUCLEIC ACIDS RESEARCH

DriverDBv2: a database for human cancer driver gene research

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

Inductive matrix completion for predicting gene-disease associations

(2014) N. Natarajan et al.   BIOINFORMATICS

DawnRank: discovering personalized driver genes in cancer

(2014) Jack P Hou et al.   Genome Medicine

Identifying driver mutations in sequenced cancer genomes: computational approaches to enable precision medicine

(2014) Benjamin J Raphael et al.   Genome Medicine

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

(2013) David Tamborero et al.   BIOINFORMATICS

Journeys into the genome of cancer cells

(2013) Michael R. Stratton   EMBO Molecular Medicine

Facing the cold start problem in recommender systems

(2013) Blerina Lika et al.   EXPERT SYSTEMS WITH APPLICATIONS

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

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Identification and Characterization of Cancer Mutations in Japanese Lung Adenocarcinoma without Sequencing of Normal Tissue Counterparts

(2013) Ayako Suzuki et al.   PLoS One

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

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

(2013) Ali Bashashati et al.   GENOME BIOLOGY

Principles and Strategies for Developing Network Models in Cancer

(2011) Dana Pe'er et al.   CELL

Controllability of complex networks

(2011) Yang-Yu Liu et al.   NATURE

Functional SNP in the microRNA-367 binding site in the 3'UTR of the calcium channel ryanodine receptor gene 3 (RYR3) affects breast cancer risk and calcification

(2011) L. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

GOSemSim: an R package for measuring semantic similarity among GO terms and gene products

(2010) G. Yu et al.   BIOINFORMATICS

Advances in understanding cancer genomes through second-generation sequencing

(2010) Matthew Meyerson et al.   NATURE REVIEWS GENETICS

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

Protein networks in disease

(2008) T. Ideker et al.   GENOME RESEARCH

Finding common genes in multiple cancer types through meta–analysis of microarray experiments: A rank aggregation approach

(2008) V. Pihur et al.   GENOMICS

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

(2008) Da Wei Huang et al.   NUCLEIC ACIDS RESEARCH