Towards quantitative and multiplexed in vivo functional cancer genomics

Comprehensive Characterization of Cancer Driver Genes and Mutations

(2018) Matthew H. Bailey et al.   CELL

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Optimized base editors enable efficient editing in cells, organoids and mice

(2018) Maria Paz Zafra et al.   NATURE BIOTECHNOLOGY

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

Mapping the in vivo fitness landscape of lung adenocarcinoma tumor suppression in mice

(2018) Zoë N. Rogers et al.   NATURE GENETICS

The emerging clinical relevance of genomics in cancer medicine

(2018) Michael F. Berger et al.   Nature Reviews Clinical Oncology

In vivo CRISPR screening unveils histone demethylase UTX as an important epigenetic regulator in lung tumorigenesis

(2018) Qibiao Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rewritable multi-event analog recording in bacterial and mammalian cells

(2018) Weixin Tang et al.   SCIENCE

An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities

(2018) Jason M Gehrke et al.   NATURE BIOTECHNOLOGY

CRISPR/Cas9 screening using unique molecular identifiers

(2017) Bernhard Schmierer et al.   Molecular Systems Biology

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

Scaling single-cell genomics from phenomenology to mechanism

(2017) Amos Tanay et al.   NATURE

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo

(2017) Weike Pei et al.   NATURE

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

Orthologous CRISPR–Cas9 enzymes for combinatorial genetic screens

(2017) Fadi J Najm et al.   NATURE BIOTECHNOLOGY

Synergistic drug combinations for cancer identified in a CRISPR screen for pairwise genetic interactions

(2017) Kyuho Han et al.   NATURE BIOTECHNOLOGY

In vivo genome editing and organoid transplantation models of colorectal cancer and metastasis

(2017) Jatin Roper et al.   NATURE BIOTECHNOLOGY

Molecular definition of a metastatic lung cancer state reveals a targetable CD109–Janus kinase–Stat axis

(2017) Chen-Hua Chuang et al.   NATURE MEDICINE

A quantitative and multiplexed approach to uncover the fitness landscape of tumor suppression in vivo

(2017) Zoë N Rogers et al.   NATURE METHODS

CRISPR-UMI: single-cell lineage tracing of pooled CRISPR–Cas9 screens

(2017) Georg Michlits et al.   NATURE METHODS

AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma

(2017) Ryan D Chow et al.   NATURE NEUROSCIENCE

Tumour heterogeneity and resistance to cancer therapies

(2017) Ibiayi Dagogo-Jack et al.   Nature Reviews Clinical Oncology

Functional variomics and network perturbation: connecting genotype to phenotype in cancer

(2017) Song Yi et al.   NATURE REVIEWS GENETICS

Building a lineage from single cells: genetic techniques for cell lineage tracking

(2017) Mollie B. Woodworth et al.   NATURE REVIEWS GENETICS

piggyBacmediates efficient in vivo CRISPR library screening for tumorigenesis in mice

(2017) Chunlong Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Krasmutant genetically engineered mouse models of human cancers are genomically heterogeneous

(2017) Wei-Jen Chung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Metabolic Interactions in the Tumor Microenvironment

(2017) Costas A. Lyssiotis et al.   TRENDS IN CELL BIOLOGY

Single-Cell Multiomics: Multiple Measurements from Single Cells

(2017) Iain C. Macaulay et al.   TRENDS IN GENETICS

Modeling the process of human tumorigenesis

(2017) Sneha Balani et al.   Nature Communications

Tissue Force Programs Cell Fate and Tumor Aggression

(2017) Jason J. Northey et al.   Cancer Discovery

Identification and analysis of mutational hotspots in oncogenes and tumour suppressors

(2017) Hanadi Baeissa et al.   Oncotarget

Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding

(2017) Stephanie Tzouanas Schmidt et al.   ACS Synthetic Biology

Analysis of 100,000 human cancer genomes reveals the landscape of tumor mutational burden

(2017) Zachary R. Chalmers et al.   Genome Medicine

Jak1–STAT3 Signals Are Essential Effectors of the USP6/TRE17 Oncogene in Tumorigenesis

(2016) Laura Quick et al.   CANCER RESEARCH

Single-Cell Sequencing for Precise Cancer Research: Progress and Prospects

(2016) Xiaoyan Zhang et al.   CANCER RESEARCH

High-Throughput, High-Resolution Mapping of Protein Localization in Mammalian Brain by In Vivo Genome Editing

(2016) Takayasu Mikuni et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

Development of a Comprehensive Genotype-to-Fitness Map of Adaptation-Driving Mutations in Yeast

(2016) Sandeep Venkataram et al.   CELL

PARP Inhibitor Activity Correlates with SLFN11 Expression and Demonstrates Synergy with Temozolomide in Small Cell Lung Cancer

(2016) Benjamin H. Lok et al.   CLINICAL CANCER RESEARCH

Genetically engineered mouse models in oncology research and cancer medicine

(2016) Kelly Kersten et al.   EMBO Molecular Medicine

Modeling invasive lobular breast carcinoma by CRISPR/Cas9-mediated somatic genome editing of the mammary gland

(2016) Stefano Annunziato et al.   GENES & DEVELOPMENT

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

An in vivo multiplexed small-molecule screening platform

(2016) Barbara M Grüner et al.   NATURE METHODS

Rapidly evolving homing CRISPR barcodes

(2016) Reza Kalhor et al.   NATURE METHODS

Engineering microdeletions and microduplications by targeting segmental duplications with CRISPR

(2016) Derek J C Tai et al.   NATURE NEUROSCIENCE

Role of non-coding sequence variants in cancer

(2016) Ekta Khurana et al.   NATURE REVIEWS GENETICS

Single-cell genome sequencing: current state of the science

(2016) Charles Gawad et al.   NATURE REVIEWS GENETICS

COSMIC: somatic cancer genetics at high-resolution

(2016) Simon A. Forbes et al.   NUCLEIC ACIDS RESEARCH

Base changes in tumour DNA have the power to reveal the causes and evolution of cancer

(2016) M Hollstein et al.   ONCOGENE

Mutational landscape ofEGFR-,MYC-, andKras-driven genetically engineered mouse models of lung adenocarcinoma

(2016) David G. McFadden et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Multiplexed barcoded CRISPR-Cas9 screening enabled by CombiGEM

(2016) Alan S. L. Wong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Multiplexed pancreatic genome engineering and cancer induction by transfection-based CRISPR/Cas9 delivery in mice

(2016) Roman Maresch et al.   Nature Communications

Apc Restoration Promotes Cellular Differentiation and Reestablishes Crypt Homeostasis in Colorectal Cancer

(2015) Lukas E. Dow et al.   CELL

Chromothripsis and Kataegis Induced by Telomere Crisis

(2015) John Maciejowski et al.   CELL

Pancreatic cancer modeling using retrograde viral vector delivery and in vivo CRISPR/Cas9-mediated somatic genome editing

(2015) Shin-Heng Chiou et al.   GENES & DEVELOPMENT

Adenovirus-Mediated Somatic Genome Editing ofPtenby CRISPR/Cas9 in Mouse Liver in Spite of Cas9-Specific Immune Responses

(2015) Dan Wang et al.   HUMAN GENE THERAPY

Barcoding reveals complex clonal dynamics of de novo transformed human mammary cells

(2015) Long V. Nguyen et al.   NATURE

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

Inducible in vivo genome editing with CRISPR-Cas9

(2015) Lukas E Dow et al.   NATURE BIOTECHNOLOGY

Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains

(2015) Junwei Shi et al.   NATURE BIOTECHNOLOGY

Toward understanding and exploiting tumor heterogeneity

(2015) Ash A Alizadeh et al.   NATURE MEDICINE

Studying clonal dynamics in response to cancer therapy using high-complexity barcoding

(2015) Hyo-eun C Bhang et al.   NATURE MEDICINE

Single-cell analysis tools for drug discovery and development

(2015) James R. Heath et al.   NATURE REVIEWS DRUG DISCOVERY

An ecosystem of cancer cell line factories to support a cancer dependency map

(2015) Jesse S. Boehm et al.   NATURE REVIEWS GENETICS

High-throughput functional genomics using CRISPR–Cas9

(2015) Ophir Shalem et al.   NATURE REVIEWS GENETICS

Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation

(2015) Antonia A. Dominguez et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

CRISPR/Cas9 somatic multiplex-mutagenesis for high-throughput functional cancer genomics in mice

(2015) Julia Weber et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Somatic CRISPR/Cas9-mediated tumour suppressor disruption enables versatile brain tumour modelling

(2015) Marc Zuckermann et al.   Nature Communications

Activation of MET via Diverse Exon 14 Splicing Alterations Occurs in Multiple Tumor Types and Confers Clinical Sensitivity to MET Inhibitors

(2015) G. M. Frampton et al.   Cancer Discovery

Modeling of the Human Alveolar Rhabdomyosarcoma Pax3-Foxo1 Chromosome Translocation in Mouse Myoblasts Using CRISPR-Cas9 Nuclease

(2015) Irina V. Lagutina et al.   PLoS Genetics

Pan-Cancer Analysis of Mutation Hotspots in Protein Domains

(2015) Martin L. Miller et al.   Cell Systems

MLL3 Is a Haploinsufficient 7q Tumor Suppressor in Acute Myeloid Leukemia

(2014) Chong Chen et al.   CANCER CELL

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

(2014) Randall J. Platt et al.   CELL

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Development and Applications of CRISPR-Cas9 for Genome Engineering

(2014) Patrick D. Hsu et al.   CELL

Rapid modelling of cooperating genetic events in cancer through somatic genome editing

(2014) Francisco J. Sánchez-Rivera et al.   NATURE

Clonal dynamics of native haematopoiesis

(2014) Jianlong Sun et al.   NATURE

In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system

(2014) Danilo Maddalo et al.   NATURE

CRISPR-mediated direct mutation of cancer genes in the mouse liver

(2014) Wen Xue et al.   NATURE

Discovery and saturation analysis of cancer genes across 21 tumour types

(2014) Michael S. Lawrence et al.   NATURE

Genome editing with Cas9 in adult mice corrects a disease mutation and phenotype

(2014) Hao Yin et al.   NATURE BIOTECHNOLOGY

The tumour-induced systemic environment as a critical regulator of cancer progression and metastasis

(2014) Sandra S. McAllister et al.   NATURE CELL BIOLOGY

In vivo RNAi screening identifies a mechanism of sorafenib resistance in liver cancer

(2014) Ramona Rudalska et al.   NATURE MEDICINE

RNAi screening comes of age: improved techniques and complementary approaches

(2014) Stephanie E. Mohr et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Direct in Vivo RNAi Screen Unveils Myosin IIa as a Tumor Suppressor of Squamous Cell Carcinomas

(2014) D. Schramek et al.   SCIENCE

Genomically encoded analog memory with precise in vivo DNA writing in living cell populations

(2014) F. Farzadfard et al.   SCIENCE

Obligate Progression Precedes Lung Adenocarcinoma Dissemination

(2014) D. R. Caswell et al.   Cancer Discovery

Simple and Rapid In Vivo Generation of Chromosomal Rearrangements using CRISPR/Cas9 Technology

(2014) Rafael B. Blasco et al.   Cell Reports

Repurposing CRISPR/Cas9 for in situ functional assays

(2013) A. Malina et al.   GENES & DEVELOPMENT

The Clinical Relevance of Cancer Cell Lines

(2013) J.-P. Gillet et al.   JNCI-Journal of the National Cancer Institute

Diverse and heritable lineage imprinting of early haematopoietic progenitors

(2013) Shalin H. Naik et al.   NATURE

Mutational heterogeneity in cancer and the search for new cancer-associated genes

(2013) Michael S. Lawrence et al.   NATURE

Tumour heterogeneity and cancer cell plasticity

(2013) Corbin E. Meacham et al.   NATURE

RNAi screens in mice identify physiological regulators of oncogenic growth

(2013) Slobodan Beronja et al.   NATURE

Pan-cancer patterns of somatic copy number alteration

(2013) Travis I Zack et al.   NATURE GENETICS

Microenvironmental regulation of tumor progression and metastasis

(2013) Daniela F Quail et al.   NATURE MEDICINE

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Emerging patterns of somatic mutations in cancer

(2013) Ian R. Watson et al.   NATURE REVIEWS GENETICS

Cancer Genome Landscapes

(2013) B. Vogelstein et al.   SCIENCE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Evolution of the cancer genome

(2012) Lucy R. Yates et al.   NATURE REVIEWS GENETICS

Causes and consequences of aneuploidy in cancer

(2012) David J. Gordon et al.   NATURE REVIEWS GENETICS

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

The cBio Cancer Genomics Portal: An Open Platform for Exploring Multidimensional Cancer Genomics Data: Figure 1.

(2012) Ethan Cerami et al.   Cancer Discovery

A Rapid and Scalable System for Studying Gene Function in Mice Using Conditional RNA Interference

(2011) Prem K. Premsrirut et al.   CELL

Hallmarks of Cancer: The Next Generation

(2011) Douglas Hanahan et al.   CELL

Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding

(2011) Rong Lu et al.   NATURE BIOTECHNOLOGY

Cellular barcoding tool for clonal analysis in the hematopoietic system

(2010) A. Gerrits et al.   BLOOD

Intestinal Crypt Homeostasis Results from Neutral Competition between Symmetrically Dividing Lgr5 Stem Cells

(2010) Hugo J. Snippert et al.   CELL

Big science: The cancer genome challenge

(2010) Heidi Ledford   NATURE

The landscape of somatic copy-number alteration across human cancers

(2010) Rameen Beroukhim et al.   NATURE

Assessing therapeutic responses in Kras mutant cancers using genetically engineered mouse models

(2010) Mallika Singh et al.   NATURE BIOTECHNOLOGY

Functional Identification of Tumor-Suppressor Genes through an In Vivo RNA Interference Screen in a Mouse Lymphoma Model

(2009) Anka Bric et al.   CANCER CELL

The cancer genome

(2009) Michael R. Stratton et al.   NATURE

In vivo RNAi screening identifies regulators of actin dynamics as key determinants of lymphoma progression

(2009) Corbin E Meacham et al.   NATURE GENETICS

Recognizing and avoiding siRNA off-target effects for target identification and therapeutic application

(2009) Aimee L. Jackson et al.   NATURE REVIEWS DRUG DISCOVERY

Recruitment of Antigen-Specific CD8+ T Cells in Response to Infection Is Markedly Efficient

(2009) J. W. J. van Heijst et al.   SCIENCE

An Oncogenomics-Based In Vivo RNAi Screen Identifies Tumor Suppressors in Liver Cancer

(2008) Lars Zender et al.   CELL

Dissecting T cell lineage relationships by cellular barcoding

(2008) Koen Schepers et al.   JOURNAL OF EXPERIMENTAL MEDICINE

The art and design of genetic screens: RNA interference

(2008) Michael Boutros et al.   NATURE REVIEWS GENETICS