BeWith: A Between-Within method to discover relationships between cancer modules via integrated analysis of mutual exclusivity, co-occurrence and functional interactions

A new correlation clustering method for cancer mutation analysis

(2016) Jack P. Hou et al.   BIOINFORMATICS

A weighted exact test for mutually exclusive mutations in cancer

(2016) Mark D.M. Leiserson et al.   BIOINFORMATICS

Landscape of somatic mutations in 560 breast cancer whole-genome sequences

(2016) Serena Nik-Zainal et al.   NATURE

Co-occurrence of MYC amplification and TP53 mutations in human cancer

(2016) Peter Ulz et al.   NATURE GENETICS

The topography of mutational processes in breast cancer genomes

(2016) Sandro Morganella et al.   Nature Communications

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

(2015) Yoo-Ah Kim et al.   BIOINFORMATICS

Combined MYC and P53 Defects Emerge at Medulloblastoma Relapse and Define Rapidly Progressive, Therapeutically Targetable Disease

(2015) Rebecca M. Hill et al.   CANCER CELL

Comprehensive Molecular Portraits of Invasive Lobular Breast Cancer

(2015) Giovanni Ciriello et al.   CELL

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

(2015) Özgün Babur et al.   GENOME BIOLOGY

Discovery of co-occurring driver pathways in cancer

(2014) Junhua Zhang et al.   BMC BIOINFORMATICS

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

PIK3CA Mutations Frequently Coexist with EGFR/KRAS Mutations in Non-Small Cell Lung Cancer and Suggest Poor Prognosis in EGFR/KRAS Wildtype Subgroup

(2014) Lei Wang et al.   PLoS One

An APOBEC cytidine deaminase mutagenesis pattern is widespread in human cancers

(2013) Steven A Roberts et al.   NATURE GENETICS

Network-based stratification of tumor mutations

(2013) Matan Hofree et al.   NATURE METHODS

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

Deciphering Signatures of Mutational Processes Operative in Human Cancer

(2013) Ludmil B. Alexandrov et al.   Cell Reports

Simultaneous Identification of Multiple Driver Pathways in Cancer

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

Mutational Processes Molding the Genomes of 21 Breast Cancers

(2012) Serena Nik-Zainal et al.   CELL

GATA3 acts upstream of FOXA1 in mediating ESR1 binding by shaping enhancer accessibility

(2012) V. Theodorou et al.   GENOME RESEARCH

Comprehensive molecular characterization of human colon and rectal cancer

(2012)   NATURE

FOXA1 represses the molecular phenotype of basal breast cancer cells

(2012) G M Bernardo et al.   ONCOGENE

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

Mutual exclusivity analysis identifies oncogenic network modules

(2011) G. Ciriello et al.   GENOME RESEARCH

Cellular reprogramming by the conjoint action of ER , FOXA1, and GATA3 to a ligand-inducible growth state

(2011) S. L. Kong et al.   Molecular Systems Biology

FOXA1 is an essential determinant of ER  expression and mammary ductal morphogenesis

(2010) G. M. Bernardo et al.   DEVELOPMENT

Membrane-bound mucins: the mechanistic basis for alterations in the growth and survival of cancer cells

(2010) S Bafna et al.   ONCOGENE

Activation of the PI3K Pathway in Cancer Through Inhibition of PTEN by Exchange Factor P-REX2a

(2009) B. Fine et al.   SCIENCE