MACHETE identifies interferon-encompassing chromosome 9p21.3 deletions as mediators of immune evasion and metastasis

All is not lost: learning from 9p21 loss in cancer

(2022) Pavlina Spiliopoulou et al.   TRENDS IN IMMUNOLOGY

9p21 loss confers a cold tumor immune microenvironment and primary resistance to immune checkpoint therapy

(2021) Guangchun Han et al.   Nature Communications

Type I interferon activates MHC class I-dressed CD11b+ conventional dendritic cells to promote protective anti-tumor CD8+ T cell immunity

(2021) Ellen Duong et al.   IMMUNITY

Differential abundance testing on single-cell data using k-nearest neighbor graphs

(2021) Emma Dann et al.   NATURE BIOTECHNOLOGY

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

(2020) Sushant Kumar et al.   CELL

Patterns of somatic structural variation in human cancer genomes

(2020) Yilong Li et al.   NATURE

Transcription phenotypes of pancreatic cancer are driven by genomic events during tumor evolution

(2020) Michelle Chan-Seng-Yue et al.   NATURE GENETICS

Senescence-Induced Vascular Remodeling Creates Therapeutic Vulnerabilities in Pancreas Cancer

(2020) Marcus Ruscetti et al.   CELL

Interplay of somatic alterations and immune infiltration modulates response to PD-1 blockade in advanced clear cell renal cell carcinoma

(2020) David A. Braun et al.   NATURE MEDICINE

Approaches to treat immune hot, altered and cold tumours with combination immunotherapies

(2019) Jérôme Galon et al.   NATURE REVIEWS DRUG DISCOVERY

Generation of focal mutations and large genomic deletions in the pancreas using inducible in vivo genome editing

(2019) Amrendra Mishra et al.   CARCINOGENESIS

Genomic and Functional Approaches to Understanding Cancer Aneuploidy

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

Cytosolic DNA Sensing in Organismal Tumor Control

(2018) Claire Vanpouille-Box et al.   CANCER CELL

Single-Cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment

(2018) Elham Azizi et al.   CELL

Cell-of-Origin Patterns Dominate the Molecular Classification of 10,000 Tumors from 33 Types of Cancer

(2018) Katherine A. Hoadley et al.   CELL

Prevalent Homozygous Deletions of Type I Interferon and Defensin Genes in Human Cancers Associate with Immunotherapy Resistance

(2018) Zhenqing Ye et al.   CLINICAL CANCER RESEARCH

Tumor Cell-Intrinsic Factors Underlie Heterogeneity of Immune Cell Infiltration and Response to Immunotherapy

(2018) Jinyang Li et al.   IMMUNITY

Nivolumab plus Ipilimumab in Lung Cancer with a High Tumor Mutational Burden

(2018) Matthew D. Hellmann et al.   NEW ENGLAND JOURNAL OF MEDICINE

Evolutionary routes and KRAS dosage define pancreatic cancer phenotypes

(2018) Sebastian Mueller et al.   NATURE

Precancerous neoplastic cells can move through the pancreatic ductal system

(2018) Alvin P. Makohon-Moore et al.   NATURE

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

(2018) Joan C Smith et al.   eLife

GuideScan software for improved single and paired CRISPR guide RNA design

(2017) Alexendar R Perez et al.   NATURE BIOTECHNOLOGY

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

(2016) Yanyan Cai et al.   CANCER CELL

Loss of IFN-γ Pathway Genes in Tumor Cells as a Mechanism of Resistance to Anti-CTLA-4 Therapy

(2016) Jianjun Gao et al.   CELL

Immune Cytolytic Activity Stratifies Molecular Subsets of Human Pancreatic Cancer

(2016) David Balli et al.   CLINICAL CANCER RESEARCH

Chromosome engineering in zygotes with CRISPR/Cas9

(2016) Katharina Boroviak et al.   GENESIS

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

(2016) Yu Liu et al.   NATURE

Highly Efficient Genome Editing of Murine and Human Hematopoietic Progenitor Cells by CRISPR/Cas9

(2016) Michael C. Gundry et al.   Cell Reports

Data-Driven Phenotypic Dissection of AML Reveals Progenitor-like Cells that Correlate with Prognosis

(2015) Jacob H. Levine et al.   CELL

Optimizing sparse sequencing of single cells for highly multiplex copy number profiling

(2015) Timour Baslan et al.   GENOME RESEARCH

Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets (MSK-IMPACT)

(2015) Donavan T. Cheng et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Interferon α/β Enhances the Cytotoxic Response of MEK Inhibition in Melanoma

(2015) Oren Litvin et al.   MOLECULAR CELL

Virtual microdissection identifies distinct tumor- and stroma-specific subtypes of pancreatic ductal adenocarcinoma

(2015) Richard A Moffitt et al.   NATURE GENETICS

Robust enumeration of cell subsets from tissue expression profiles

(2015) Aaron M Newman et al.   NATURE METHODS

IL35-Producing B Cells Promote the Development of Pancreatic Neoplasia

(2015) Y. Pylayeva-Gupta et al.   Cancer Discovery

Highly efficient targeted chromosome deletions using CRISPR/Cas9

(2014) Zuyong He et al.   BIOTECHNOLOGY AND BIOENGINEERING

A modular and flexible ESC-based mouse model of pancreatic cancer

(2014) M. Saborowski et al.   GENES & DEVELOPMENT

Engagement of the ICOS pathway markedly enhances efficacy of CTLA-4 blockade in cancer immunotherapy

(2014) Xiaozhou Fan et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Conditional Reverse Tet-Transactivator Mouse Strains for the Efficient Induction of TRE-Regulated Transgenes in Mice

(2014) Lukas E. Dow et al.   PLoS One

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

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

Interferon-  Protects the Female Reproductive Tract from Viral and Bacterial Infection

(2013) K. Y. Fung et al.   SCIENCE

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

(2013) J. Gao et al.   Science Signaling

Review: a meta-analysis of GWAS and age-associated diseases

(2012) William R. Jeck et al.   AGING CELL

Oncogenic Kras-Induced GM-CSF Production Promotes the Development of Pancreatic Neoplasia

(2012) Yuliya Pylayeva-Gupta et al.   CANCER CELL

Overview. Type I interferons as primers, activators and inhibitors of innate and adaptive immune responses

(2012) Paul J Hertzog   IMMUNOLOGY AND CELL BIOLOGY

Expression of tumour-specific antigens underlies cancer immunoediting

(2012) Michel DuPage et al.   NATURE

Silencing of Irf7 pathways in breast cancer cells promotes bone metastasis through immune escape

(2012) Bradley N Bidwell et al.   NATURE MEDICINE

A cluster of cooperating tumor-suppressor gene candidates in chromosomal deletions

(2012) W. Xue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Type I interferon response and innate immune sensing of cancer

(2012) Mercedes B. Fuertes et al.   TRENDS IN IMMUNOLOGY

Tumour evolution inferred by single-cell sequencing

(2011) Nicholas Navin et al.   NATURE

Oncogenic KRas Suppresses Inflammation-Associated Senescence of Pancreatic Ductal Cells

(2010) Kyoung Eun Lee et al.   CANCER CELL

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Mice Heterozygous for Germ-line Mutations in Methylthioadenosine Phosphorylase (MTAP) Die Prematurely of T-Cell Lymphoma

(2009) Y. Kadariya et al.   CANCER RESEARCH

The cancer genome

(2009) Michael R. Stratton et al.   NATURE