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

Synonymous Mutations Frequently Act as Driver Mutations in Human Cancers

(2014) Fran Supek et al.   CELL

Realizing the promise of cancer predisposition genes

(2014) Nazneen Rahman   NATURE

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

(2014) Peilin Jia et al.   PLoS Computational Biology

INstruct: a database of high-quality 3D structurally resolved protein interactome networks

(2013) Michael J. Meyer et al.   BIOINFORMATICS

No Gene-Specific Optimization of Mutation Rate in Escherichia coli

(2013) X. Chen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Construction of human activity-based phosphorylation networks

(2013) R. H. Newman et al.   Molecular Systems Biology

Mutational landscape and significance across 12 major cancer types

(2013) Cyriac Kandoth et al.   NATURE

The Implications of Clonal Genome Evolution for Cancer Medicine

(2013) Samuel Aparicio et al.   NEW ENGLAND JOURNAL OF MEDICINE

Yin and Yang of disease genes and death genes between reciprocally scale-free biological networks

(2013) Hyun Wook Han et al.   NUCLEIC ACIDS RESEARCH

Exonic Transcription Factor Binding Directs Codon Choice and Affects Protein Evolution

(2013) A. B. Stergachis et al.   SCIENCE

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

An Inhibitor of Mutant IDH1 Delays Growth and Promotes Differentiation of Glioma Cells

(2013) D. Rohle et al.   SCIENCE

Targeted Inhibition of Mutant IDH2 in Leukemia Cells Induces Cellular Differentiation

(2013) F. Wang et al.   SCIENCE

Genomic evidence for elevated mutation rates in highly expressed genes

(2012) Chungoo Park et al.   EMBO REPORTS

Evolutionary Meta-Analysis of Association Studies Reveals Ancient Constraints Affecting Disease Marker Discovery

(2012) J. T. Dudley et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coevolution Reveals a Network of Human Proteins Originating with Multicellularity

(2012) A. Bezginov et al.   MOLECULAR BIOLOGY AND EVOLUTION

Clonal evolution in cancer

(2012) Mel Greaves et al.   NATURE

Navigating cancer network attractors for tumor-specific therapy

(2012) Pau Creixell et al.   NATURE BIOTECHNOLOGY

Evolutionary diagnosis method for variants in personal exomes

(2012) Sudhir Kumar et al.   NATURE METHODS

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

Database resources of the National Center for Biotechnology Information

(2012)   NUCLEIC ACIDS RESEARCH

Evolution of the cancer genome

(2012) Ondrej Podlaha et al.   TRENDS IN GENETICS

Network physiology reveals relations between network topology and physiological function

(2012) Amir Bashan et al.   Nature Communications

Differential network entropy reveals cancer system hallmarks

(2012) James West et al.   Scientific Reports

ProteinHistorian: Tools for the Comparative Analysis of Eukaryote Protein Origin

(2012) John A. Capra et al.   PLoS Computational Biology

The Orphan Disease Networks

(2011) Minlu Zhang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Global cancer statistics

(2011) Ahmedin Jemal et al.   CA-A CANCER JOURNAL FOR CLINICIANS

Principles and Strategies for Developing Network Models in Cancer

(2011) Dana Pe'er et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

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

(2011) I. Lee et al.   GENOME RESEARCH

On the Origins of Mendelian Disease Genes in Man: The Impact of Gene Duplication

(2011) J. E. Dickerson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Network of Cancer Genes (NCG 3.0): integration and analysis of genetic and network properties of cancer genes

(2011) M. D'Antonio et al.   NUCLEIC ACIDS RESEARCH

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

PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse

(2011) P. V. Hornbeck et al.   NUCLEIC ACIDS RESEARCH

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

(2011) Sudhir Kumar et al.   TRENDS IN GENETICS

Gene enrichment profiles reveal T-cell development, differentiation, and lineage-specific transcription factors including ZBTB25 as a novel NF-AT repressor

(2010) Y. Benita et al.   BLOOD

The Amphimedon queenslandica genome and the evolution of animal complexity

(2010) Mansi Srivastava et al.   NATURE

Phospho.ELM: a database of phosphorylation sites--update 2011

(2010) H. Dinkel et al.   NUCLEIC ACIDS RESEARCH

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

OMA 2011: orthology inference among 1000 complete genomes

(2010) A. M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

(2009) Gabriela Bindea et al.   BIOINFORMATICS

The human protein coevolution network

(2009) E. R.M. Tillier et al.   GENOME RESEARCH

Oncogenes and Cancer

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

Human Protein Reference Database--2009 update

(2008) T. S. Keshava Prasad et al.   NUCLEIC ACIDS RESEARCH

Network properties of genes harboring inherited disease mutations

(2008) I. Feldman et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA