Understanding Genotype-Phenotype Effects in Cancer via Network Approaches

MEMCover: integrated analysis of mutual exclusivity and functional network reveals dysregulated pathways across multiple cancer types

(2015) Yoo-Ah Kim et al.   BIOINFORMATICS

Probabilistic topic modeling for the analysis and classification of genomic sequences

(2015) Massimo La Rosa et al.   BMC BIOINFORMATICS

Cancer type-dependent genetic interactions between cancer driver alterations indicate plasticity of epistasis across cell types

(2015) S. Park et al.   Molecular Systems Biology

Understanding multicellular function and disease with human tissue-specific networks

(2015) Casey S Greene et al.   NATURE GENETICS

A statistical framework for revealing signaling pathways perturbed by DNA variants

(2015) R. Wilentzik et al.   NUCLEIC ACIDS RESEARCH

Network-based Phenome-Genome Association Prediction by Bi-Random Walk

(2015) MaoQiang Xie et al.   PLoS One

Uncovering disease-disease relationships through the incomplete interactome

(2015) J. Menche et al.   SCIENCE

Identifying Driver Genomic Alterations in Cancers by Searching Minimum-Weight, Mutually Exclusive Sets

(2015) Songjian Lu et al.   PLoS Computational Biology

Systematic identification of cancer driving signaling pathways based on mutual exclusivity of genomic alterations

(2015) Özgün Babur et al.   GENOME BIOLOGY

Dynamic networks reveal key players in aging

(2014) Fazle E. Faisal et al.   BIOINFORMATICS

Discovery of co-occurring driver pathways in cancer

(2014) Junhua Zhang et al.   BMC BIOINFORMATICS

Predicting Cancer-Specific Vulnerability via Data-Driven Detection of Synthetic Lethality

(2014) Livnat Jerby-Arnon et al.   CELL

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

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

Similarity network fusion for aggregating data types on a genomic scale

(2014) Bo Wang et al.   NATURE METHODS

Relating Diseases by Integrating Gene Associations and Information Flow through Protein Interaction Network

(2014) Mehdi Bagheri Hamaneh et al.   PLoS One

Angiogenesis Interactome and Time Course Microarray Data Reveal the Distinct Activation Patterns in Endothelial Cells

(2014) Liang-Hui Chu et al.   PLoS One

Modeling Mutual Exclusivity of Cancer Mutations

(2014) Ewa Szczurek et al.   PLoS Computational Biology

Synthetic sickness or lethality points at candidate combination therapy targets in glioblastoma

(2013) Ewa Szczurek et al.   INTERNATIONAL JOURNAL OF CANCER

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

Dissecting cancer heterogeneity with a probabilistic genotype-phenotype model

(2013) Dong-Yeon Cho et al.   NUCLEIC ACIDS RESEARCH

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Network Signatures of Survival in Glioblastoma Multiforme

(2013) Vishal N. Patel et al.   PLoS Computational Biology

Simultaneous Identification of Multiple Driver Pathways in Cancer

(2013) Mark D. M. Leiserson et al.   PLoS Computational Biology

Efficient methods for identifying mutated driver pathways in cancer

(2012) Junfei Zhao et al.   BIOINFORMATICS

HINT: High-quality protein interactomes and their applications in understanding human disease

(2012) Jishnu Das et al.   BMC Systems Biology

Probabilistic topic models

(2012) David M. Blei   COMMUNICATIONS OF THE ACM

SteinerNet: a web server for integrating 'omic' data to discover hidden components of response pathways

(2012) N. Tuncbag et al.   NUCLEIC ACIDS RESEARCH

Integrative Subtype Discovery in Glioblastoma Using iCluster

(2012) Ronglai Shen et al.   PLoS One

Inferring functional modules of protein families with probabilistic topic models

(2011) Sebastian GA Konietzny et al.   BMC BIOINFORMATICS

Discovering functional modules by identifying recurrent and mutually exclusive mutational patterns in tumors

(2011) Christopher A Miller et al.   BMC Medical Genomics

De novo discovery of mutated driver pathways in cancer

(2011) F. Vandin et al.   GENOME RESEARCH

Prioritizing candidate disease genes by network-based boosting of genome-wide association data

(2011) I. Lee et al.   GENOME RESEARCH

Mutual exclusivity analysis identifies oncogenic network modules

(2011) G. Ciriello et al.   GENOME RESEARCH

Algorithms for Detecting Significantly Mutated Pathways in Cancer

(2011) Fabio Vandin et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Rare De Novo and Transmitted Copy-Number Variation in Autistic Spectrum Disorders

(2011) Dan Levy et al.   NEURON

Rare De Novo Variants Associated with Autism Implicate a Large Functional Network of Genes Involved in Formation and Function of Synapses

(2011) Sarah R. Gilman et al.   NEURON

Using Electronic Patient Records to Discover Disease Correlations and Stratify Patient Cohorts

(2011) Francisco S. Roque et al.   PLoS Computational Biology

Identifying Causal Genes and Dysregulated Pathways in Complex Diseases

(2011) Yoo-Ah Kim et al.   PLoS Computational Biology

Proteins Encoded in Genomic Regions Associated with Immune-Mediated Disease Physically Interact and Suggest Underlying Biology

(2011) Elizabeth J. Rossin et al.   PLoS Genetics

Identifying functional miRNA–mRNA regulatory modules with correspondence latent dirichlet allocation

(2010) Bing Liu et al.   BIOINFORMATICS

Toward the dynamic interactome: it's about time

(2010) T. M. Przytycka et al.   BRIEFINGS IN BIOINFORMATICS

Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1

(2010) Roel G.W. Verhaak et al.   CANCER CELL

Network medicine: a network-based approach to human disease

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

Automated Network Analysis Identifies Core Pathways in Glioblastoma

(2010) Ethan Cerami et al.   PLoS One

DEGAS: De Novo Discovery of Dysregulated Pathways in Human Diseases

(2010) Igor Ulitsky et al.   PLoS One

Finding undetected protein associations in cell signaling by belief propagation

(2010) M. Bailly-Bechet et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network-Based Elucidation of Human Disease Similarities Reveals Common Functional Modules Enriched for Pluripotent Drug Targets

(2010) Silpa Suthram et al.   PLoS Computational Biology

Associating Genes and Protein Complexes with Disease via Network Propagation

(2010) Oron Vanunu et al.   PLoS Computational Biology

Bridging high-throughput genetic and transcriptional data reveals cellular responses to alpha-synuclein toxicity

(2009) Esti Yeger-Lotem et al.   NATURE GENETICS

Integrating Proteomic, Transcriptional, and Interactome Data Reveals Hidden Components of Signaling and Regulatory Networks

(2009) S.-s. C. Huang et al.   Science Signaling

Walking the Interactome for Prioritization of Candidate Disease Genes

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

eQED: an efficient method for interpreting eQTL associations using protein networks

(2008) Silpa Suthram et al.   Molecular Systems Biology

Regulatory networks define phenotypic classes of human stem cell lines

(2008) Franz-Josef Müller et al.   NATURE

Comprehensive genomic characterization defines human glioblastoma genes and core pathways

(2008) Roger McLendon et al.   NATURE

Why Do Hubs in the Yeast Protein Interaction Network Tend To Be Essential: Reexamining the Connection between the Network Topology and Essentiality

(2008) Elena Zotenko et al.   PLoS Computational Biology