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

Dynamic spreading of chromatin-mediated gene silencing and reactivation between neighboring genes in single cells

(2022) Sarah Lensch et al.   eLife

High-fidelity Cas13 variants for targeted RNA degradation with minimal collateral effects

(2022) Huawei Tong et al.   NATURE BIOTECHNOLOGY

CRISPR-RNAa: targeted activation of translation using dCas13 fusions to translation initiation factors

(2022) Peter B Otoupal et al.   NUCLEIC ACIDS RESEARCH

Negative autoregulation mitigates collateral RNase activity of repeat-targeting CRISPR-Cas13d in mammalian cells

(2022) Chase P. Kelley et al.   Cell Reports

Optimization of specific RNA knockdown in mammalian cells with CRISPR-Cas13

(2022) Brandon Joseph Davis Burris et al.   METHODS

Surface antigen-guided CRISPR screens identify regulators of myeloid leukemia differentiation

(2021) Eric Wang et al.   Cell Stem Cell

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

(2021) Efthymia Papalexi et al.   NATURE GENETICS

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Programmable RNA targeting with the single-protein CRISPR effector Cas7-11

(2021) Ahsen Özcan et al.   NATURE

Engineered pegRNAs improve prime editing efficiency

(2021) James W. Nelson et al.   NATURE BIOTECHNOLOGY

Pharmacological inhibition of LSD1 triggers myeloid differentiation by targeting GSE1 oncogenic functions in AML

(2021) Luciano Nicosia et al.   ONCOGENE

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

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

Massively parallel Cas13 screens reveal principles for guide RNA design

(2020) Hans-Hermann Wessels et al.   NATURE BIOTECHNOLOGY

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

(2020) Daniel Schraivogel et al.   NATURE METHODS

Multilayered VBC score predicts sgRNAs that efficiently generate loss-of-function alleles

(2020) Georg Michlits et al.   NATURE METHODS

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

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

Multiplexed genome engineering by Cas12a and CRISPR arrays encoded on single transcripts

(2019) Carlo C. Campa et al.   NATURE METHODS

Exploring genetic interaction manifolds constructed from rich single-cell phenotypes

(2019) Thomas M. Norman et al.   SCIENCE

The human body at cellular resolution: the NIH Human Biomolecular Atlas Program

(2019)   NATURE

CRISPR-Cas9-based mutagenesis frequently provokes on-target mRNA misregulation

(2019) Rubina Tuladhar et al.   Nature Communications

Single-cell multiomic analysis identifies regulatory programs in mixed-phenotype acute leukemia

(2019) Jeffrey M. Granja et al.   NATURE BIOTECHNOLOGY

Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors

(2018) Silvana Konermann et al.   CELL

An enhanced CRISPR repressor for targeted mammalian gene regulation

(2018) Nan Cher Yeo et al.   NATURE METHODS

Structural Basis for the RNA-Guided Ribonuclease Activity of CRISPR-Cas13d

(2018) Cheng Zhang et al.   CELL

Optimized libraries for CRISPR-Cas9 genetic screens with multiple modalities

(2018) Kendall R. Sanson et al.   Nature Communications

Simultaneous epitope and transcriptome measurement in single cells

(2017) Marlon Stoeckius et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

The Human Cell Atlas

(2017) Aviv Regev et al.   eLife

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

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench et al.   NATURE BIOTECHNOLOGY

Reprogramming eukaryotic translation with ligand-responsive synthetic RNA switches

(2016) Andrew V Anzalone et al.   NATURE METHODS

Zika virus produces noncoding RNAs using a multi-pseudoknot structure that confounds a cellular exonuclease

(2016) B. M. Akiyama 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

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

The sva package for removing batch effects and other unwanted variation in high-throughput experiments

(2012) Jeffrey T. Leek et al.   BIOINFORMATICS

Robust rank aggregation for gene list integration and meta-analysis

(2012) Raivo Kolde et al.   BIOINFORMATICS

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY