bioconductor: DriverNet | Projects

10.1186/s12864-017-4423-x

Integration of multiple networks and pathways identifies cancer driver genes in pan-cancer analysis
Cited by: 31
Author(s): Claudia Cava, Gloria Bertoli, Antonio Colaprico, Catharina Olsen, Gianluca Bontempi, Isabella Castiglioni
Software Mentions: 12
Published: almost 7 years ago

10.3389/fgene.2016.00002

Strategies for Integrated Analysis of Genetic, Epigenetic, and Gene Expression Variation in Cancer: Addressing the Challenges
Cited by: 16
Author(s): Louise B. Thingholm, Lars van Brakel Andersen, Enes Makalic, Melissa C. Southey, Mads Thomassen, Lise Lotte Hansen
Software Mentions: 6
Published: over 8 years ago

10.1371/journal.pcbi.1007520

A novel network control model for identifying personalized driver genes in cancer
Cited by: 39
Author(s): Weifeng Guo, Shao-Wu Zhang, Tao Zeng, Yan Li, Jianxi Gao, Luonan Chen
Software Mentions: 5
Published: almost 5 years ago

10.7150/thno.63416

Mapping the landscape of synthetic lethal interactions in liver cancer
Cited by: 7
Author(s): Chen Yang, Yuchen Guo, Ruolan Qian, Yi‐Wen Huang, Linmeng Zhang, Jun Wang, Xiaowen Huang, Zhicheng Liu, Wenxin Qin, Cun Wang, Huimin Chen, Xuhui Ma, Dayong Zhang
Software Mentions: 5
Published: almost 4 years ago

10.3389/fgene.2020.564839

FI-Net: Identification of Cancer Driver Genes by Using Functional Impact Prediction Neural Network
Cited by: 6
Author(s): Hong Gu, Xin Xu, Pan Qin, Jia Wang
Software Mentions: 4
Published: almost 4 years ago

10.3389/fmolb.2021.671309

Cancer-Associated circRNA–miRNA–mRNA Regulatory Networks: A Meta-Analysis
Cited by: 21
Author(s): Shaheerah Khan, Atimukta Jha, Amaresh C. Panda, Anshuman Dixit
Software Mentions: 4
Published: over 3 years ago

10.1186/s13073-015-0228-1

A genome-wide approach to link genotype to clinical outcome by utilizing next generation sequencing and gene chip data of 6,697 breast cancer patients
Cited by: 65
Author(s): Lőrinc Sándor Pongor, M Kormos, Christos Hatzis, Lajos Pusztai, András Szabó, Balázs Győrffy
Software Mentions: 3
Published: almost 9 years ago

10.7717/peerj.2568

The use of gene interaction networks to improve the identification of cancer driver genes
Cited by: 11
Author(s): Emilie Ramsahai, Kheston Walkins, Vrijesh Tripathi, McCormick John
Software Mentions: 3
Published: over 7 years ago

10.1371/journal.pcbi.1007381

LOTUS: A single- and multitask machine learning algorithm for the prediction of cancer driver genes
Cited by: 25
Author(s): Olivier Collier, Véronique Stoven, Jean-Philippe Vert
Software Mentions: 3
Published: about 5 years ago

10.1186/s12859-021-04203-7

driveR: a novel method for prioritizing cancer driver genes using somatic genomics data
Cited by: 6
Author(s): Ege Ülgen, Osman Uğur Sezerman
Software Mentions: 3
Published: over 3 years ago

10.1002/path.4230

Distinct evolutionary trajectories of primary high‐grade serous ovarian cancers revealed through spatial mutational profiling
Cited by: 351
Author(s): Ali Bashashati, Gavin Ha, Alicia A. Tone, Jiarui Ding, Leah M Prentice, Andrew Roth, Jamie Rosner, Karey Shumansky, Steve E. Kalloger, Janine Senz, Winnie Yang, Melissa K. McConechy, Nataliya Melnyk, Michael S. Anglesio, Margaret Luk, Kane Tse, Thomas Zeng, Richard A. Moore, Yongjun Zhao, Marco A. Marra, Blake Gilks, Stephen Yip, David G. Huntsman, Jessica N. McAlpine, Sohrab P. Shah
Software Mentions: 3
Published: about 11 years ago

10.1186/s13059-016-0989-x

MUFFINN: cancer gene discovery via network analysis of somatic mutation data
Cited by: 118
Author(s): Ara Cho, Jung Eun Shim, Eiru Kim, Fran Supek, Ben Lehner, Insuk Lee
Software Mentions: 3
Published: over 8 years ago

10.7150/thno.52670

Computational methods for cancer driver discovery: A survey
Cited by: 16
Author(s): Vu Viet Hoang Pham, Lin Liu, Cameron P. Bracken, Gregory J. Goodall, Jiuyong Li, Thuc Duy Le
Software Mentions: 2
Published: almost 4 years ago

10.1186/s12859-019-2847-9

A random walk-based method to identify driver genes by integrating the subcellular localization and variation frequency into bipartite graph
Cited by: 20
Author(s): Junrong Song, Wei Peng, Rui Wang
Software Mentions: 2
Published: over 5 years ago

10.1186/s12859-021-03989-w

Ranking cancer drivers via betweenness-based outlier detection and random walks
Cited by: 5
Author(s): Cesim Erten, Aissa Houdjedj, Hilal Kazan
Software Mentions: 2
Published: over 3 years ago

10.1186/s12864-016-2727-x

Hotspot mutations delineating diverse mutational signatures and biological utilities across cancer types
Cited by: 24
Author(s): Tenghui Chen, Zixing Wang, Wanding Zhou, Zechen Chong, Funda Meric‐Bernstam, Gordon B. Mills, Ken Chen
Software Mentions: 2
Published: over 8 years ago

10.1186/s12920-019-0582-8

MECoRank: cancer driver genes discovery simultaneously evaluating the impact of SNVs and differential expression on transcriptional networks
Cited by: 3
Author(s): Ying Hui, Pi-Jing Wei, Junfeng Xia, Yutian Wang, Chun-Hou Zheng
Software Mentions: 2
Published: almost 5 years ago

10.1186/s12920-019-0619-z

Identifying driver genes involving gene dysregulated expression, tissue-specific expression and gene-gene network
Cited by: 9
Author(s): Junrong Song, Wei Peng, Rui Wang, Jianxin Wang
Software Mentions: 2
Published: almost 5 years ago

10.1371/journal.pcbi.1007538

CBNA: A control theory based method for identifying coding and non-coding cancer drivers
Cited by: 20
Author(s): Vu Viet Hoang Pham, Lin Liu, Cameron P. Bracken, Gregory J. Goodall, Qi Long, Jiuyong Li, Thuc Duy Le
Software Mentions: 2
Published: almost 5 years ago

10.3389/fgene.2015.00341

A Network-Based Model of Oncogenic Collaboration for Prediction of Drug Sensitivity
Cited by: 5
Author(s): Ted Laderas, Laura M. Heiser, Kemal Sönmez
Software Mentions: 2
Published: almost 9 years ago

10.3389/fgene.2020.607798

DriverSubNet: A Novel Algorithm for Identifying Cancer Driver Genes by Subnetwork Enrichment Analysis
Cited by: 3
Author(s): Di Zhang, Yannan Bin
Software Mentions: 2
Published: over 3 years ago

10.1186/s13059-014-0489-9

MSEA: detection and quantification of mutation hotspots through mutation set enrichment analysis
Cited by: 48
Author(s): Peilin Jia, Quan Wang, Qingxia Chen, Katherine E. Hutchinson, William Pao, Zhongming Zhao
Software Mentions: 2
Published: about 10 years ago

10.1186/s13073-014-0056-8

DawnRank: discovering personalized driver genes in cancer
Cited by: 194
Author(s): Jack P. Hou, Jian Ma
Software Mentions: 2
Published: over 10 years ago

10.1186/s13073-021-00830-0

Pan-cancer detection of driver genes at the single-patient resolution
Cited by: 12
Author(s): Joel Nulsen, Hrvoje Mišetić, Christopher Yau, Francesca D. Ciccarelli
Software Mentions: 2
Published: over 3 years ago

10.18632/oncotarget.19481

Integrating omics data and protein interaction networks to prioritize driver genes in cancer
Cited by: 11
Author(s): Tiejun Zhang, Di Zhang
Software Mentions: 2
Published: about 7 years ago

10.18632/oncotarget.21643

ndmaSNF: cancer subtype discovery based on integrative framework assisted by network diffusion model
Cited by: 13
Author(s): Chao Yang, Shuguang Ge, Chun-Hou Zheng
Software Mentions: 2
Published: about 7 years ago

10.1186/1471-2164-15-605

Identification of collaborative driver pathways in breast cancer
Cited by: 10
Author(s): Yang Liu, Zhenjun Hu
Software Mentions: 1
Published: almost 11 years ago

10.1186/gb-2012-13-12-r124

DriverNet: uncovering the impact of somatic driver mutations on transcriptional networks in cancer
Cited by: 241
Author(s): Ali Bashashati, Gholamreza Haffari, Jiarui Ding, Gavin Ha, Kenneth Lui, Jamie Rosner, David G. Huntsman, Carlos Caldas, Samuel Aparicio, Sohrab P. Shah
Software Mentions: 1
Published: almost 13 years ago

10.1186/s12859-016-1332-y

LNDriver: identifying driver genes by integrating mutation and expression data based on gene-gene interaction network
Cited by: 27
Author(s): Pi-Jing Wei, Di Zhang, Junfeng Xia, Chun-Hou Zheng
Software Mentions: 1
Published: almost 8 years ago

10.1186/s12859-018-2218-y

Discovering mutated driver genes through a robust and sparse co-regularized matrix factorization framework with prior information from mRNA expression patterns and interaction network
Cited by: 19
Author(s): Jianing Xi, Minghui Wang, Ao Li
Software Mentions: 1
Published: over 6 years ago

10.18632/oncotarget.10536

Ranking novel cancer driving synthetic lethal gene pairs using TCGA data
Cited by: 28
Author(s): Hao Ye, Xun Zhang, Yunqin Chen, Qi Liu, Jia Wei
Software Mentions: 1
Published: about 8 years ago

10.1186/s12859-021-04377-0

Identification of driver genes based on gene mutational effects and network centrality
Cited by: 2
Author(s): Yaning Tang, Pi-Jing Wei, Jianping Zhao, Junfeng Xia, Ruifen Cao, Chun-Hou Zheng
Software Mentions: 1
Published: over 3 years ago

10.1186/s12859-017-1869-4

QuaDMutEx: quadratic driver mutation explorer
Cited by: 7
Author(s): Yahya Bokhari, Tomasz Arodź
Software Mentions: 1
Published: almost 7 years ago

10.1038/s41598-021-91656-8

Evaluating machine learning methodologies for identification of cancer driver genes
Cited by: 36
Author(s): Sharaf J. Malebary, Yaser Daanial Khan
Software Mentions: 1
Published: over 3 years ago

10.1371/journal.pone.0196939

Cancer driver mutation prediction through Bayesian integration of multi-omic data
Cited by: 16
Author(s): Zixing Wang, Kwok Shing Ng, Tenghui Chen, Tae Beom Kim, Fang Wang, Kenna Mills Shaw, Kenneth L. Scott, Funda Meric‐Bernstam, Gordon B. Mills, Ken Chen
Software Mentions: 1
Published: over 6 years ago

10.3389/fgene.2021.608042

NEM-Tar: A Probabilistic Graphical Model for Cancer Regulatory Network Inference and Prioritization of Potential Therapeutic Targets From Multi-Omics Data
Cited by: 1
Author(s): Yuchen Zhang, Lina Zhu, Xin Wang
Software Mentions: 1
Published: over 3 years ago

10.1038/s41598-021-93917-y

Predicting pathogenic non-coding SVs disrupting the 3D genome in 1646 whole cancer genomes using multiple instance learning
Cited by: 1
Author(s): Marleen M. Nieboer, Luan Thanh Nguyen, Jeroen de Ridder
Software Mentions: 1
Published: about 3 years ago

10.1371/journal.pcbi.1004350

An Evolutionary Approach for Identifying Driver Mutations in Colorectal Cancer
Cited by: 23
Author(s): Jasmine Foo, Lin L. Liu, Kevin Leder, Markus Riester, Yoh Iwasa, Christoph Lengauer, Franziska Michor
Software Mentions: 1
Published: about 9 years ago

Projects: bioconductor: DriverNet

Papers Mentioning DriverNet 41