Discovery of putative tumor suppressors from CRISPR screens reveals rewired lipid metabolism in acute myeloid leukemia cells

CRISPR screens in physiologic medium reveal conditionally essential genes in human cells

(2021) Nicholas J. Rossiter et al.   Cell Metabolism

SciPy 1.0: fundamental algorithms for scientific computing in Python

(2020) Pauli Virtanen et al.   NATURE METHODS

Visualizing and interpreting cancer genomics data via the Xena platform

(2020) Mary J. Goldman et al.   NATURE BIOTECHNOLOGY

Optimization of AsCas12a for combinatorial genetic screens in human cells

(2020) Peter C. DeWeirdt et al.   NATURE BIOTECHNOLOGY

Array programming with NumPy

(2020) Charles R. Harris et al.   NATURE

Engineered CRISPR–Cas12a variants with increased activities and improved targeting ranges for gene, epigenetic and base editing

(2019) Benjamin P. Kleinstiver et al.   NATURE BIOTECHNOLOGY

CHP1 Regulates Compartmentalized Glycerolipid Synthesis by Activating GPAT4

(2019) Xiphias Ge Zhu et al.   MOLECULAR CELL

Probing the Global Cellular Responses to Lipotoxicity Caused by Saturated Fatty Acids

(2019) Manuele Piccolis et al.   MOLECULAR CELL

JACKS: joint analysis of CRISPR/Cas9 knockout screens

(2019) Felicity Allen et al.   GENOME RESEARCH

Prioritization of cancer therapeutic targets using CRISPR–Cas9 screens

(2019) Fiona M. Behan et al.   NATURE

Next-generation characterization of the Cancer Cell Line Encyclopedia

(2019) Mahmoud Ghandi et al.   NATURE

The landscape of cancer cell line metabolism

(2019) Haoxin Li et al.   NATURE MEDICINE

Integrated Analysis of TP53 Gene and Pathway Alterations in The Cancer Genome Atlas

(2019) Lawrence A. Donehower et al.   Cell Reports

Identifying chemogenetic interactions from CRISPR screens with drugZ

(2019) Medina Colic et al.   Genome Medicine

Paralog buffering contributes to the variable essentiality of genes in cancer cell lines

(2019) Barbara De Kegel et al.   PLoS Genetics

Cell culture models of fatty acid overload: Problems and solutions

(2018) Nour Alsabeeh et al.   BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR AND CELL BIOLOGY OF LIPIDS

Mapping the Genetic Landscape of Human Cells

(2018) Max A. Horlbeck et al.   CELL

Combinatorial CRISPR-Cas9 Metabolic Screens Reveal Critical Redox Control Points Dependent on the KEAP1-NRF2 Regulatory Axis

(2018) Dongxin Zhao et al.   MOLECULAR CELL

Toward an integrated map of genetic interactions in cancer cells

(2018) Benedikt Rauscher et al.   Molecular Systems Biology

Interrogation of Mammalian Protein Complex Structure, Function, and Membership Using Genome-Scale Fitness Screens

(2018) Joshua Pan et al.   Cell Systems

Unsupervised correction of gene-independent cell responses to CRISPR-Cas9 targeting

(2018) Francesco Iorio et al.   BMC GENOMICS

Cell Model Passports—a hub for clinical, genetic and functional datasets of preclinical cancer models

(2018) Dieudonne van der Meer et al.   NUCLEIC ACIDS RESEARCH

High‐resolution mapping of cancer cell networks using co‐functional interactions

(2018) Evan A Boyle et al.   Molecular Systems Biology

Functional genomic landscape of acute myeloid leukaemia

(2018) Jeffrey W. Tyner et al.   NATURE

GENCODE reference annotation for the human and mouse genomes

(2018) Adam Frankish et al.   NUCLEIC ACIDS RESEARCH

HumanNet v2: human gene networks for disease research

(2018) Sohyun Hwang et al.   NUCLEIC ACIDS RESEARCH

Fatty acid synthase (FASN) as a therapeutic target in breast cancer

(2017) Javier A. Menendez et al.   EXPERT OPINION ON THERAPEUTIC TARGETS

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

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

Combinatorial CRISPR–Cas9 screens for de novo mapping of genetic interactions

(2017) John Paul Shen et al.   NATURE METHODS

Genetic interaction mapping in mammalian cells using CRISPR interference

(2017) Dan Du et al.   NATURE METHODS

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation

(2017) Shashikant Pujar et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2018

(2017) Daniel R Zerbino et al.   NUCLEIC ACIDS RESEARCH

PICKLES: the database of pooled in-vitro CRISPR knockout library essentiality screens

(2017) Walter F Lenoir et al.   NUCLEIC ACIDS RESEARCH

Evaluation and Design of Genome-Wide CRISPR/SpCas9 Knockout Screens

(2017) Traver Hart et al.   G3-Genes Genomes Genetics

Complex heatmaps reveal patterns and correlations in multidimensional genomic data

(2016) Zuguang Gu et al.   BIOINFORMATICS

BAGEL: a computational framework for identifying essential genes from pooled library screens

(2016) Traver Hart et al.   BMC BIOINFORMATICS

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

A global genetic interaction network maps a wiring diagram of cellular function

(2016) M. Costanzo et al.   SCIENCE

Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting

(2016) A. J. Aguirre et al.   Cancer Discovery

A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia

(2016) Konstantinos Tzelepis et al.   Cell Reports

PRROC: computing and visualizing precision-recall and receiver operating characteristic curves in R

(2015) Jan Grau et al.   BIOINFORMATICS

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

(2015) Traver Hart et al.   CELL

Defective autophagy is a key feature of cerebral cavernous malformations

(2015) Saverio Marchi et al.   EMBO Molecular Medicine

Differential genetic interactions of yeast stress response MAPK pathways

(2015) H. Martin et al.   Molecular Systems Biology

High-throughput functional genomics using CRISPR–Cas9

(2015) Ophir Shalem et al.   NATURE REVIEWS GENETICS

Loss of endothelial programmed cell death 10 activates glioblastoma cells and promotes tumor growth

(2015) Yuan Zhu et al.   NEURO-ONCOLOGY

Identification and characterization of essential genes in the human genome

(2015) T. Wang et al.   SCIENCE

mixtools: AnRPackage for Analyzing Finite Mixture Models

(2015) Tatiana Benaglia et al.   Journal of Statistical Software

circlize implements and enhances circular visualization in R

(2014) Zuguang Gu et al.   BIOINFORMATICS

Measuring error rates in genomic perturbation screens: gold standards for human functional genomics

(2014) T. Hart et al.   Molecular Systems Biology

Area under Precision-Recall Curves for Weighted and Unweighted Data

(2014) Jens Keilwagen et al.   PLoS One

Cas9 as a versatile tool for engineering biology

(2013) Prashant Mali et al.   NATURE METHODS

Genomic and Epigenomic Landscapes of Adult De Novo Acute Myeloid Leukemia

(2013)   NEW ENGLAND JOURNAL OF MEDICINE

RNA-Guided Human Genome Engineering via Cas9

(2013) P. Mali et al.   SCIENCE

Genetic Screens in Human Cells Using the CRISPR-Cas9 System

(2013) Tim Wang et al.   SCIENCE

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

The mTOR Signalling Pathway in Human Cancer

(2012) Helena Pópulo et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Differential network biology

(2012) Trey Ideker et al.   Molecular Systems Biology

A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity

(2012) M. Jinek et al.   SCIENCE

Palmitate Increases the Susceptibility of Cells to Drug-Induced Toxicity: An In Vitro Method to Identify Drugs With Potential Contraindications in Patients With Metabolic Disease

(2012) Yi et al.   TOXICOLOGICAL SCIENCES

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

(2012) Ethan Cerami et al.   Cancer Discovery

Quantitative Genetic Interactions Reveal Biological Modularity

(2010) Pedro Beltrao et al.   CELL

Fatty acid synthase as a potential therapeutic target in cancer

(2010) Richard Flavin et al.   Future Oncology

Rewiring of Genetic Networks in Response to DNA Damage

(2010) S. Bandyopadhyay et al.   SCIENCE

The Genetic Landscape of a Cell

(2010) M. Costanzo et al.   SCIENCE

NF2/Merlin Is a Novel Negative Regulator of mTOR Complex 1, and Activation of mTORC1 Is Associated with Meningioma and Schwannoma Growth

(2009) M. F. James et al.   MOLECULAR AND CELLULAR BIOLOGY

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

The TSC1-TSC2 Complex Is Required for Proper Activation of mTOR Complex 2

(2008) J. Huang et al.   MOLECULAR AND CELLULAR BIOLOGY

Conservation and Rewiring of Functional Modules Revealed by an Epistasis Map in Fission Yeast

(2008) A. Roguev et al.   SCIENCE