SWAN pathway-network identification of common aneuploidy-based oncogenic drivers

Aneuploid senescent cells activate NF‐κB to promote their immune clearance by NK cells

(2021) Ruoxi W Wang et al.   EMBO REPORTS

Comparison of pathway and gene-level models for cancer prognosis prediction

(2020) Xingyu Zheng et al.   BMC BIOINFORMATICS

Passenger Mutations in More Than 2,500 Cancer Genomes: Overall Molecular Functional Impact and Consequences

(2020) Sushant Kumar et al.   CELL

Loss of BAP1 expression is associated with an immunosuppressive microenvironment in uveal melanoma, with implications for immunotherapy development

(2020) Carlos R. Figueiredo et al.   JOURNAL OF PATHOLOGY

THE MOLECULAR ANALYSIS FOR THERAPY CHOICE (NCI-MATCH) TRIAL: LESSONS for GENOMIC TRIAL DESIGN

(2020) Keith T Flaherty et al.   JNCI-Journal of the National Cancer Institute

Our best weapons against cancer are not magic bullets

(2020) Vinay Prasad   NATURE

Genomic basis for RNA alterations in cancer

(2020) Claudia Calabrese et al.   NATURE

Tobacco smoking and somatic mutations in human bronchial epithelium

(2020) Kenichi Yoshida et al.   NATURE

Homologous recombination deficiency status-based classification of high-grade serous ovarian carcinoma

(2020) Hisamitsu Takaya et al.   Scientific Reports

Autophagy gene haploinsufficiency drives chromosome instability, increases migration, and promotes early ovarian tumors

(2020) Joe R. Delaney et al.   PLoS Genetics

The mutational landscape of normal human endometrial epithelium

(2020) Luiza Moore et al.   NATURE

The mutational constraint spectrum quantified from variation in 141,456 humans

(2020) Konrad J. Karczewski et al.   NATURE

Transcriptomic changes involved in the dedifferentiation of myofibroblasts derived from the lung of a patient with idiopathic pulmonary fibrosis

(2020) Kenichi Suzuki et al.   Molecular Medicine Reports

Cancer prognosis prediction using somatic point mutation and copy number variation data: a comparison of gene-level and pathway-based models

(2020) Xingyu Zheng et al.   BMC BIOINFORMATICS

Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens

(2019) Fiona M. Behan et al.   NATURE

SRSF3-Regulated RNA Alternative Splicing Promotes Glioblastoma Tumorigenicity by Affecting Multiple Cellular Processes

(2019) Xiao Song et al.   CANCER RESEARCH

Context is everything: aneuploidy in cancer

(2019) Uri Ben-David et al.   NATURE REVIEWS GENETICS

The landscape of somatic mutation in normal colorectal epithelial cells

(2019) Henry Lee-Six et al.   NATURE

PathTracer: High-sensitivity detection of differential pathway activity in tumours

(2019) Ståle Nygård et al.   Scientific Reports

Personalized Medicine for Primary Treatment of Serous Ovarian Cancer

(2019) Dan L. Longo   NEW ENGLAND JOURNAL OF MEDICINE

PCNA Unloading Is Negatively Regulated by BET Proteins

(2019) Mi-Sun Kang et al.   Cell Reports

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

(2018) Alison M. Taylor et al.   CANCER CELL

Profound Tissue Specificity in Proliferation Control Underlies Cancer Drivers and Aneuploidy Patterns

(2018) Laura Magill Sack et al.   CELL

Timing the Landmark Events in the Evolution of Clear Cell Renal Cell Cancer: TRACERx Renal

(2018) Thomas J. Mitchell et al.   CELL

Chromosomal instability drives metastasis through a cytosolic DNA response

(2018) Samuel F. Bakhoum et al.   NATURE

Sequencing of prostate cancers identifies new cancer genes, routes of progression and drug targets

(2018) David C. Wedge et al.   NATURE GENETICS

BRD4 facilitates replication stress-induced DNA damage response

(2018) Jingwen Zhang et al.   ONCOGENE

Spatially constrained tandem bromodomain inhibition bolsters sustained repression of BRD4 transcriptional activity for TNBC cell growth

(2018) Chunyan Ren et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TORC1 inhibition enhances immune function and reduces infections in the elderly

(2018) Joan B. Mannick et al.   Science Translational Medicine

CREBBP/EP300 bromodomains are critical to sustain the GATA1/MYC regulatory axis in proliferation

(2018) Veronica Garcia-Carpizo et al.   Epigenetics & Chromatin

Targeting adenosine for cancer immunotherapy

(2018) Robert D. Leone et al.   Journal for ImmunoTherapy of Cancer

Distinct mechanisms govern the phosphorylation of different SR protein splicing factors

(2018) Yunxin Long et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

An evolving story of the metastatic voyage of ovarian cancer cells: cellular and molecular orchestration of the adipose-rich metastatic microenvironment

(2018) Takeshi Motohara et al.   ONCOGENE

Somatic mutant clones colonize the human esophagus with age

(2018) Iñigo Martincorena et al.   SCIENCE

BET Inhibition Induces HEXIM1- and RAD51-Dependent Conflicts between Transcription and Replication

(2018) Akhil Bowry et al.   Cell Reports

Systematic identification of mutations and copy number alterations associated with cancer patient prognosis

(2018) Joan C Smith et al.   eLife

Racial disparities in treatment and survival from ovarian cancer

(2018) Janet S. Hildebrand et al.   Cancer Epidemiology

Cadmium exposure and endometrial cancer risk: A large midwestern U.S. population-based case-control study

(2017) Jane A. McElroy et al.   PLoS One

Crosstalk between Cytoplasmic RIG-I and STING Sensing Pathways

(2017) Alessandra Zevini et al.   TRENDS IN IMMUNOLOGY

Tumour-associated macrophages secrete pleiotrophin to promote PTPRZ1 signalling in glioblastoma stem cells for tumour growth

(2017) Yu Shi et al.   Nature Communications

Haploinsufficiency networks identify targetable patterns of allelic deficiency in low mutation ovarian cancer

(2017) Joe Ryan Delaney et al.   Nature Communications

DNA copy number changes define spatial patterns of heterogeneity in colorectal cancer

(2017) Soulafa Mamlouk et al.   Nature Communications

Loss of Chromosome 8p Governs Tumor Progression and Drug Response by Altering Lipid Metabolism

(2016) Yanyan Cai et al.   CANCER CELL

Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer

(2016) Hui Zhang et al.   CELL

Deletions linked to TP53 loss drive cancer through p53-independent mechanisms

(2016) Yu Liu et al.   NATURE

The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2016 update

(2016) Enis Afgan et al.   NUCLEIC ACIDS RESEARCH

No current evidence for widespread dosage compensation in S. cerevisiae

(2016) Eduardo M Torres et al.   eLife

Selective advantage of trisomic human cells cultured in non-standard conditions

(2016) Samuel D. Rutledge et al.   Scientific Reports

Aneuploidy-induced cellular stresses limit autophagic degradation

(2015) Stefano Santaguida et al.   GENES & DEVELOPMENT

Positive Feedback Regulation of Type I IFN Production by the IFN-Inducible DNA Sensor cGAS

(2015) Feng Ma et al.   JOURNAL OF IMMUNOLOGY

Multiple Pathways for Protein Transport to Peroxisomes

(2015) P.K. Kim et al.   JOURNAL OF MOLECULAR BIOLOGY

Whole–genome characterization of chemoresistant ovarian cancer

(2015) Ann-Marie Patch et al.   NATURE

Comprehensive, Integrative Genomic Analysis of Diffuse Lower-Grade Gliomas

(2015)   NEW ENGLAND JOURNAL OF MEDICINE

High burden and pervasive positive selection of somatic mutations in normal human skin

(2015) I. Martincorena et al.   SCIENCE

Uveal Melanoma Cells Utilize a Novel Route for Transendothelial Migration

(2014) Michael D. Onken et al.   PLoS One

mTOR inhibition improves immune function in the elderly

(2014) J. B. Mannick et al.   Science Translational Medicine

BRCA1 haploinsufficiency for replication stress suppression in primary cells

(2014) Shailja Pathania et al.   Nature Communications

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

(2013) Teresa Davoli et al.   CELL

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

SurvExpress: An Online Biomarker Validation Tool and Database for Cancer Gene Expression Data Using Survival Analysis

(2013) Raul Aguirre-Gamboa et al.   PLoS One

Pathway-based personalized analysis of cancer

(2013) Y. Drier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrative Analysis of Complex Cancer Genomics and Clinical Profiles Using the cBioPortal

(2013) J. Gao et al.   Science Signaling

Evolutionary dynamics of cancer in response to targeted combination therapy

(2013) Ivana Bozic et al.   eLife

The UCSC genome browser and associated tools

(2012) R. M. Kuhn et al.   BRIEFINGS IN BIOINFORMATICS

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets

(2012) Andreas Wilm et al.   NUCLEIC ACIDS RESEARCH

Recurrent Hemizygous Deletions in Cancers May Optimize Proliferative Potential

(2012) N. L. Solimini et al.   SCIENCE

Telomeric Allelic Imbalance Indicates Defective DNA Repair and Sensitivity to DNA-Damaging Agents

(2012) Nicolai J. Birkbak et al.   Cancer Discovery

Control-FREEC: a tool for assessing copy number and allelic content using next-generation sequencing data

(2011) Valentina Boeva et al.   BIOINFORMATICS

Aquaporins at a glance

(2011) A. S. Verkman   JOURNAL OF CELL SCIENCE

Integrated genomic analyses of ovarian carcinoma

(2011) D. Bell et al.   NATURE

Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM

(2010) Charles J. Vaske et al.   BIOINFORMATICS

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

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

VarScan: variant detection in massively parallel sequencing of individual and pooled samples

(2009) Daniel C. Koboldt et al.   BIOINFORMATICS

An online survival analysis tool to rapidly assess the effect of 22,277 genes on breast cancer prognosis using microarray data of 1,809 patients

(2009) Balazs Györffy et al.   BREAST CANCER RESEARCH AND TREATMENT

The tale of transforming growth factor-beta (TGFβ) signaling: A soigné enigma

(2009) Arindam Chaudhury et al.   IUBMB LIFE

Prognostic relevance of DNA copy number changes in colorectal cancer

(2009) George Poulogiannis et al.   JOURNAL OF PATHOLOGY

Part I: Milestones in personalised medicine—imatinib

(2008) Carlo Gambacorti-Passerini   LANCET ONCOLOGY