A Gene Gravity Model for the Evolution of Cancer Genomes: A Study of 3,000 Cancer Genomes across 9 Cancer Types

TP53 loss creates therapeutic vulnerability in colorectal cancer

(2015) Yunhua Liu et al.   NATURE

Studying Tumorigenesis through Network Evolution and Somatic Mutational Perturbations in the Cancer Interactome

(2014) Feixiong Cheng et al.   MOLECULAR BIOLOGY AND EVOLUTION

Realizing the promise of cancer predisposition genes

(2014) Nazneen Rahman   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

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

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

TCGA-Assembler: open-source software for retrieving and processing TCGA data

(2014) Yitan Zhu et al.   NATURE METHODS

VarWalker: Personalized Mutation Network Analysis of Putative Cancer Genes from Next-Generation Sequencing Data

(2014) Peilin Jia et al.   PLoS Computational Biology

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

(2013) David Tamborero et al.   BIOINFORMATICS

Depletion of a Putatively Druggable Class of Phosphatidylinositol Kinases Inhibits Growth of p53-Null Tumors

(2013) Brooke M. Emerling et al.   CELL

Hypermutation of the Inactive X Chromosome Is a Frequent Event in Cancer

(2013) Natalie Jäger et al.   CELL

Cumulative Haploinsufficiency and Triplosensitivity Drive Aneuploidy Patterns and Shape the Cancer Genome

(2013) Teresa Davoli et al.   CELL

Clinical Significance of Serum COL6A3 in Pancreatic Ductal Adenocarcinoma

(2013) Christopher Y. Kang et al.   JOURNAL OF GASTROINTESTINAL SURGERY

Genome-wide Consequences of Deleting Any Single Gene

(2013) Xinchen Teng et al.   MOLECULAR CELL

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

Signatures of mutational processes in human cancer

(2013) Ludmil B. Alexandrov et al.   NATURE

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Single-cell sequencing-based technologies will revolutionize whole-organism science

(2013) Ehud Shapiro et al.   NATURE REVIEWS GENETICS

Integrative approaches for finding modular structure in biological networks

(2013) Koyel Mitra et al.   NATURE REVIEWS GENETICS

COL11A1 promotes tumor progression and predicts poor clinical outcome in ovarian cancer

(2013) Y-H Wu et al.   ONCOGENE

AHNAK and Inflammatory Markers Predict Poor Survival in Laryngeal Carcinoma

(2013) Claudia A. Dumitru et al.   PLoS One

Functional Roles of Pulsing in Genetic Circuits

(2013) J. H. Levine et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

The mutational landscape of chromatin regulatory factors across 4,623 tumor samples

(2013) Abel Gonzalez-Perez et al.   GENOME BIOLOGY

A Whole-Cell Computational Model Predicts Phenotype from Genotype

(2012) Jonathan R. Karr et al.   CELL

Genomic Landscape of Non-Small Cell Lung Cancer in Smokers and Never-Smokers

(2012) Ramaswamy Govindan et al.   CELL

Profiles of Genomic Instability in High-Grade Serous Ovarian Cancer Predict Treatment Outcome

(2012) Z. C. Wang et al.   CLINICAL CANCER RESEARCH

Dissecting the genomic complexity underlying medulloblastoma

(2012) David T. W. Jones et al.   NATURE

A universal model for mobility and migration patterns

(2012) Filippo Simini et al.   NATURE

Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes

(2012) Zhi Jiang Zang et al.   NATURE GENETICS

Evolutionary diagnosis method for variants in personal exomes

(2012) Sudhir Kumar et al.   NATURE METHODS

Chromatin and the genome integrity network

(2012) Manolis Papamichos-Chronakis et al.   NATURE REVIEWS GENETICS

TSGene: a web resource for tumor suppressor genes

(2012) Min Zhao et al.   NUCLEIC ACIDS RESEARCH

InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

(2012) Karin Breuer et al.   NUCLEIC ACIDS RESEARCH

Evolution of the cancer genome

(2012) Ondrej Podlaha et al.   TRENDS IN GENETICS

Large-Scale Functional Organization of Long-Range Chromatin Interaction Networks

(2012) Kuljeet Singh Sandhu et al.   Cell Reports

Identification of Fat4 and Tsc22d1 as Novel Candidate Genes for Spontaneous Pulmonary Adenomas

(2011) A. Berndt et al.   CANCER RESEARCH

Principles and Strategies for Developing Network Models in Cancer

(2011) Dana Pe'er et al.   CELL

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

PINA v2.0: mining interactome modules

(2011) Mark J. Cowley et al.   NUCLEIC ACIDS RESEARCH

OGEE: an online gene essentiality database

(2011) Wei-Hua Chen et al.   NUCLEIC ACIDS RESEARCH

Mutational Inactivation of STAG2 Causes Aneuploidy in Human Cancer

(2011) D. A. Solomon et al.   SCIENCE

Tumor-specific expression and alternative splicing of the COL6A3 gene in pancreatic cancer

(2011) Hwyda Arafat et al.   SURGERY

Phylomedicine: an evolutionary telescope to explore and diagnose the universe of disease mutations

(2011) Sudhir Kumar et al.   TRENDS IN GENETICS

Multi-cancer computational analysis reveals invasion-associated variant of desmoplastic reaction involving INHBA, THBS2 and COL11A1

(2010) Hoon Kim et al.   BMC Medical Genomics

ESR1/SYNE1 Polymorphism and Invasive Epithelial Ovarian Cancer Risk: An Ovarian Cancer Association Consortium Study

(2010) J. A. Doherty et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Pseudopodial Actin Dynamics Control Epithelial-Mesenchymal Transition in Metastatic Cancer Cells

(2010) Jay Shankar et al.   CANCER RESEARCH

Genomic instability — an evolving hallmark of cancer

(2010) Simona Negrini et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

REPAIRtoire--a database of DNA repair pathways

(2010) K. Milanowska et al.   NUCLEIC ACIDS RESEARCH

COSMIC: mining complete cancer genomes in the Catalogue of Somatic Mutations in Cancer

(2010) S. A. Forbes et al.   NUCLEIC ACIDS RESEARCH

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

Associating Genes and Protein Complexes with Disease via Network Propagation

(2010) Oron Vanunu et al.   PLoS Computational Biology

Edgetic perturbation models of human inherited disorders

(2009) Quan Zhong et al.   Molecular Systems Biology

Cancer attractors: A systems view of tumors from a gene network dynamics and developmental perspective

(2009) Sui Huang et al.   SEMINARS IN CELL & DEVELOPMENTAL BIOLOGY

Involvement of Members of the Cadherin Superfamily in Cancer

(2009) G. Berx et al.   Cold Spring Harbor Perspectives in Biology

Identification of Fat4 as a candidate tumor suppressor gene in breast cancers

(2008) Chao Qi et al.   INTERNATIONAL JOURNAL OF CANCER

Oncogenes and Cancer

(2008) Carlo M. Croce   NEW ENGLAND JOURNAL OF MEDICINE