CRISPR screening in hematology research: from bulk to single-cell level

A transcription factor atlas of directed differentiation

(2023) Julia Joung et al.   CELL

Predicting cellular responses to complex perturbations in high‐throughput screens

(2023) Mohammad Lotfollahi et al.   Molecular Systems Biology

Microfluidics-free single-cell genomics with templated emulsification

(2023) Iain C. Clark et al.   NATURE BIOTECHNOLOGY

Discovery of target genes and pathways at GWAS loci by pooled single-cell CRISPR screens

(2023) John A. Morris et al.   SCIENCE

Massively parallel phenotyping of coding variants in cancer with Perturb-seq

(2022) Oana Ursu et al.   NATURE BIOTECHNOLOGY

Pooled genetic perturbation screens with image-based phenotypes

(2022) David Feldman et al.   Nature Protocols

Disruption of dNTPs Homeostasis by Ribonucleotide Reductase Hyperactivation Overcomes AML Differentiation Blockade

(2022) Hanying Wang et al.   BLOOD

Spatial CRISPR genomics identifies regulators of the tumor microenvironment

(2022) Maxime Dhainaut et al.   CELL

Genome-wide CRISPR screens of T cell exhaustion identify chromatin remodeling factors that limit T cell persistence

(2022) Julia A. Belk et al.   CANCER CELL

Mapping information-rich genotype-phenotype landscapes with genome-scale Perturb-seq

(2022) Joseph M. Replogle et al.   CELL

Live-seq enables temporal transcriptomic recording of single cells

(2022) Wanze Chen et al.   NATURE

Efficient combinatorial targeting of RNA transcripts in single cells with Cas13 RNA Perturb-seq

(2022) Hans-Hermann Wessels et al.   NATURE METHODS

A balanced measure shows superior performance of pseudobulk methods in single-cell RNA-sequencing analysis

(2022) Alan E. Murphy et al.   Nature Communications

Advanced single-cell pooled CRISPR screening identifies C19orf53 required for cell proliferation based on mTORC1 regulators

(2021) Yulong Tang et al.   CELL BIOLOGY AND TOXICOLOGY

Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens

(2021) Efthymia Papalexi et al.   NATURE GENETICS

Multimodal pooled Perturb-CITE-seq screens in patient models define mechanisms of cancer immune evasion

(2021) Chris J. Frangieh et al.   NATURE GENETICS

Combinatorial CRISPR screen identifies fitness effects of gene paralogues

(2021) Nicola A. Thompson et al.   Nature Communications

Evaluating Capture Sequence Performance for Single-Cell CRISPR Activation Experiments

(2021) Xin Yi Choo et al.   ACS Synthetic Biology

Decoding Neuronal Diversification by Multiplexed Single-cell RNA-Seq

(2021) Joachim Luginbühl et al.   Stem Cell Reports

Profiling the genetic determinants of chromatin accessibility with scalable single-cell CRISPR screens

(2021) Noa Liscovitch-Brauer et al.   NATURE BIOTECHNOLOGY

BTK inhibition sensitizes Acute Lymphoblastic Leukemia to asparaginase by suppressing the Amino Acid Response pathway

(2021) Miriam Butler et al.   BLOOD

Genome wide CRISPR screening reveals a role for sialylation in the tumorigenesis and chemoresistance of acute myeloid leukemia cells

(2021) Dong-hee Lee et al.   CANCER LETTERS

Metabolic control of TFH cells and humoral immunity by phosphatidylethanolamine

(2021) Guotong Fu et al.   NATURE

Ultra-high-throughput single-cell RNA sequencing and perturbation screening with combinatorial fluidic indexing

(2021) Paul Datlinger et al.   NATURE METHODS

Genome-wide CRISPRi/a screens in human neurons link lysosomal failure to ferroptosis

(2021) Ruilin Tian et al.   NATURE NEUROSCIENCE

In vivo genome-wide CRISPR screen reveals breast cancer vulnerabilities and synergistic mTOR/Hippo targeted combination therapy

(2021) Meiou Dai et al.   Nature Communications

High-resolution characterization of gene function using single-cell CRISPR tiling screen

(2021) Lu Yang et al.   Nature Communications

High-throughput single-cell chromatin accessibility CRISPR screens enable unbiased identification of regulatory networks in cancer

(2021) Sarah E. Pierce et al.   Nature Communications

Genome-wide CRISPR screen identifies CDK6 as a therapeutic target in Adult T-cell leukemia/lymphoma

(2021) Takashi Ishio et al.   BLOOD

Functional single-cell genomics of human cytomegalovirus infection

(2021) Marco Y. Hein et al.   NATURE BIOTECHNOLOGY

Joint single-cell measurements of nuclear proteins and RNA in vivo

(2021) Hattie Chung et al.   NATURE METHODS

KAT6A and ENL Form an Epigenetic Transcriptional Control Module to Drive Critical Leukemogenic Gene-Expression Programs

(2021) Fangxue Yan et al.   Cancer Discovery

High-throughput analysis of the activities of xCas9, SpCas9-NG and SpCas9 at matched and mismatched target sequences in human cells

(2020) Hui Kwon Kim et al.   Nature Biomedical Engineering

Pooled Knockin Targeting for Genome Engineering of Cellular Immunotherapies

(2020) Theodore L. Roth et al.   CELL

Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing

(2020) Joseph M. Replogle et al.   NATURE BIOTECHNOLOGY

Targeted Perturb-seq enables genome-scale genetic screens in single cells

(2020) Daniel Schraivogel et al.   NATURE METHODS

Coupled scRNA-Seq and Intracellular Protein Activity Reveal an Immunosuppressive Role of TREM2 in Cancer

(2020) Yonatan Katzenelenbogen et al.   CELL

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

A Three-Way Combinatorial CRISPR Screen for Analyzing Interactions among Druggable Targets

(2020) Peng Zhou et al.   Cell Reports

A Single-Cell Transcriptomics CRISPR-Activation Screen Identifies Epigenetic Regulators of the Zygotic Genome Activation Program

(2020) Celia Alda-Catalinas et al.   Cell Systems

CRISPR screen identifies genes that sensitize AML cells to double negative T cell therapy

(2020) Fraser Soares et al.   BLOOD

Genome-wide CRISPR screen identifies regulators of MAPK and MTOR pathways mediating sorafenib resistance in acute myeloid leukemia

(2020) Alisa Damnernsawad et al.   HAEMATOLOGICA

HyPR-seq: Single-cell quantification of chosen RNAs via hybridization and sequencing of DNA probes

(2020) Jamie L. Marshall et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

In vivo Perturb-Seq reveals neuronal and glial abnormalities associated with autism risk genes

(2020) Xin Jin et al.   SCIENCE

A Genome-wide Framework for Mapping Gene Regulation via Cellular Genetic Screens

(2019) Molly Gasperini et al.   CELL

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

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Multiplexed detection of proteins, transcriptomes, clonotypes and CRISPR perturbations in single cells

(2019) Eleni P. Mimitou et al.   NATURE METHODS

The next generation of CRISPR–Cas technologies and applications

(2019) Adrian Pickar-Oliver et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Single-Cell RNA-Sequencing-Based CRISPRi Screening Resolves Molecular Drivers of Early Human Endoderm Development

(2019) Ryan M.J. Genga et al.   Cell Reports

Modular one-pot assembly of CRISPR arrays enables library generation and reveals factors influencing crRNA biogenesis

(2019) Chunyu Liao et al.   Nature Communications

Model-based understanding of single-cell CRISPR screening

(2019) Bin Duan et al.   Nature Communications

Mitochondrial Reprogramming Underlies Resistance to BCL-2 Inhibition in Lymphoid Malignancies

(2019) Romain Guièze et al.   CANCER CELL

CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons

(2019) Ruilin Tian et al.   NEURON

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

(2019) Thomas M. Norman et al.   SCIENCE

Optical Pooled Screens in Human Cells

(2019) David Feldman et al.   CELL

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

Genome-wide CRISPR/Cas9 library screening identified PHGDH as a critical driver for Sorafenib resistance in HCC

(2019) Lai Wei et al.   Nature Communications

Integrated drug profiling and CRISPR screening identify essential pathways for CAR T-cell cytotoxicity

(2019) Olli Dufva et al.   BLOOD

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Single-cell characterization of haematopoietic progenitors and their trajectories in homeostasis and perturbed haematopoiesis

(2018) Amir Giladi et al.   NATURE CELL BIOLOGY

On the design of CRISPR-based single-cell molecular screens

(2018) Andrew J Hill et al.   NATURE METHODS

SAVER: gene expression recovery for single-cell RNA sequencing

(2018) Mo Huang et al.   NATURE METHODS

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function

(2018) Eric Shifrut et al.   CELL

Protein Barcodes Enable High-Dimensional Single-Cell CRISPR Screens

(2018) Aleksandra Wroblewska et al.   CELL

Coupled Single-Cell CRISPR Screening and Epigenomic Profiling Reveals Causal Gene Regulatory Networks

(2018) Adam J. Rubin et al.   CELL

Comparative Analysis of Droplet-Based Ultra-High-Throughput Single-Cell RNA-Seq Systems

(2018) Xiannian Zhang et al.   MOLECULAR CELL

Simultaneous multiplexed amplicon sequencing and transcriptome profiling in single cells

(2018) Mridusmita Saikia et al.   NATURE METHODS

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells

(2017) Shiqi Xie et al.   MOLECULAR CELL

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

(2017) Kyuho Han et al.   NATURE BIOTECHNOLOGY

Multiplexed quantification of proteins and transcripts in single cells

(2017) Vanessa M Peterson et al.   NATURE BIOTECHNOLOGY

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

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

(2017) John Paul Shen et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

(2017) Julia Joung et al.   Nature Protocols

Am I ready for CRISPR? A user's guide to genetic screens

(2017) John G. Doench   NATURE REVIEWS GENETICS

RNA editing with CRISPR-Cas13

(2017) David B. T. Cox et al.   SCIENCE

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

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

(2016) Britt Adamson et al.   CELL

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

(2016) Alexis C. Komor et al.   NATURE

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 High-Throughput Strategy for Dissecting Mammalian Genetic Interactions

(2016) Victoria B. Stockman et al.   PLoS One

Droplet Barcoding for Single-Cell Transcriptomics Applied to Embryonic Stem Cells

(2015) Allon M. Klein et al.   CELL

Highly Parallel Genome-wide Expression Profiling of Individual Cells Using Nanoliter Droplets

(2015) Evan Z. Macosko et al.   CELL

Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System

(2015) Bernd Zetsche et al.   CELL

Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems

(2015) Sergey Shmakov et al.   MOLECULAR CELL

Massively parallel high-order combinatorial genetics in human cells

(2015) Alan S L Wong et al.   NATURE BIOTECHNOLOGY

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

(2015) Je Hyuk Lee et al.   Nature Protocols

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

Combinatorial labeling of single cells for gene expression cytometry

(2015) H. C. Fan et al.   SCIENCE

Highly effective combination of LSD1 (KDM1A) antagonist and pan-histone deacetylase inhibitor against human AML cells

(2014) W Fiskus et al.   LEUKEMIA

Low-coverage single-cell mRNA sequencing reveals cellular heterogeneity and activated signaling pathways in developing cerebral cortex

(2014) Alex A Pollen et al.   NATURE BIOTECHNOLOGY

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Massively Parallel Single-Cell RNA-Seq for Marker-Free Decomposition of Tissues into Cell Types

(2014) D. A. Jaitin et al.   SCIENCE

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells

(2013) Ophir Shalem 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

Full-length mRNA-Seq from single-cell levels of RNA and individual circulating tumor cells

(2012) Daniel Ramsköld et al.   NATURE BIOTECHNOLOGY

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

(2012) M. Jinek et al.   SCIENCE

Characterization of the single-cell transcriptional landscape by highly multiplex RNA-seq

(2011) S. Islam et al.   GENOME RESEARCH

Genomic Screening with RNAi: Results and Challenges

(2010) Stephanie Mohr et al.   Annual Review of Biochemistry