Publications | AbuGoot Lab

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The

Abudayyeh–Gootenberg Lab

Published Works

Rapid protein evolution by few-shot learning with a protein language model

Rapid protein evolution by few-shot learning with a protein language model

Science

2024-11-21

Programmable RNA writing with trans-splicing

Programmable RNA writing with trans-splicing

bioRxiv

2024-02-01

Advances in genome, epigenome, and transcriptome editing using CRISPR effectors,

Advances in genome, epigenome, and transcriptome editing using CRISPR effectors,

Nature Reviews Molecular Cell Biology

2023-11-01

Generative Distribution Embeddings

Generative Distribution Embeddings

arXiv

2025-05-23

Reprogramming site-specific retrotransposon activity to new DNA sites

Reprogramming site-specific retrotransposon activity to new DNA sites

Nature

2025-04-09

Precise kilobase-scale genomic insertions in mammalian cells using PASTE

Precise kilobase-scale genomic insertions in mammalian cells using PASTE

Nature Protocols

2024-12-15

Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox

Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox

Biochemistry

2023-12-19

Programmable RNA-guided DNA endonucleases are widespread in eukaryotes and their viruses

Programmable RNA-guided DNA endonucleases are widespread in eukaryotes and their viruses

Science Advances

2023-09-27

A Transcription Factor Atlas of Directed Differentiation

A Transcription Factor Atlas of Directed Differentiation

Cell

2023-01-05

Drag-and-drop genome insertion without DNA cleavage with CRISPR-directed integrases.

Drag-and-drop genome insertion without DNA cleavage with CRISPR-directed integrases.

Nature Biotechnology

2022-11-24

A multiplexed Cas13-based assay with point-of-care attributes for simultaneous COVID-19 diagnosis and variant surveillance

A multiplexed Cas13-based assay with point-of-care attributes for simultaneous COVID-19 diagnosis and variant surveillance

The CRISPR Journal

2022-11-11

RNA-triggered protein cleavage and cell death by the RNA-guided type III-E CRISPR-Cas nuclease-protease complex

RNA-triggered protein cleavage and cell death by the RNA-guided type III-E CRISPR-Cas nuclease-protease complex

Science

2022-11-03

RNA-activated protein cleavage with a CRISPR-associated endopeptidase

RNA-activated protein cleavage with a CRISPR-associated endopeptidase

Science

2022-11-03

Programmable eukaryotic protein expression with RNA sensors

Programmable eukaryotic protein expression with RNA sensors

Nature Biotechnology

2022-10-27

Structure and engineering of the type III-E CRISPR-Cas7-11 effector
complex

Structure and engineering of the type III-E CRISPR-Cas7-11 effector
complex

Cell

2022-06-23

Drag-and-drop genome insertion without DNA cleavage with CRISPR-directed integrases

Drag-and-drop genome insertion without DNA cleavage with CRISPR-directed integrases

bioRxiv

2021-11-01

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

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

Nature

2021-09-06

CRISPR-based diagnostics

CRISPR-based diagnostics

Nat Biomed Eng

2021-06-30

A global metagenomic map of urban microbiomes and antimicrobial resistance

A global metagenomic map of urban microbiomes and antimicrobial resistance

Cell

2021-06-24

CRISPR diagnostics

CRISPR diagnostics

Science

2021-05-28

Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay

Rapid SARS-CoV-2 testing in primary material based on a novel multiplex RT-LAMP assay

PLoS One

2020-11-02

Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing

Detection of SARS-CoV-2 with SHERLOCK One-Pot Testing

N. Engl. J. Med.

2020-10-08

A Survey of Genome Editing Activity for 16 Cas12a Orthologs

A Survey of Genome Editing Activity for 16 Cas12a Orthologs

Keio J. Med.

2020-09-25

Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA

Clinical validation of a Cas13-based assay for the detection of SARS-CoV-2 RNA

Nat Biomed Eng

2020-08-26

Rapid and accurate species identification for ecological studies and monitoring using CRISPR-based SHERLOCK

Rapid and accurate species identification for ecological studies and monitoring using CRISPR-based SHERLOCK

Mol. Ecol. Resour.

2020-06-30

A 5-min RNA preparation method for COVID-19 detection with RT-qPCR

A 5-min RNA preparation method for COVID-19 detection with RT-qPCR

medRxiv

2020-05-08

A Protocol for Detection of COVID-19 Using CRISPR Diagnostics

A Protocol for Detection of COVID-19 Using CRISPR Diagnostics

White paper

2020-01-31

Programmable Inhibition and Detection of RNA Viruses Using Cas13

Programmable Inhibition and Detection of RNA Viruses Using Cas13

Mol. Cell

2019-12-05

SHERLOCK: nucleic acid detection with CRISPR nucleases

SHERLOCK: nucleic acid detection with CRISPR nucleases

Nat. Protoc.

2019-09-23

A cytosine deaminase for programmable single-base RNA editing

A cytosine deaminase for programmable single-base RNA editing

Science

2019-07-11

Nucleic Acid Detection of Plant Genes Using CRISPR-Cas13

Nucleic Acid Detection of Plant Genes Using CRISPR-Cas13

CRISPR J

2019-05-31

Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9

Structural basis for the promiscuous PAM recognition by Corynebacterium diphtheriae Cas9

Nat. Commun.

2019-04-29

Chipping in on Diagnostics

Chipping in on Diagnostics

CRISPR J

2019-03-31

High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage

High-Resolution Structure of Cas13b and Biochemical Characterization of RNA Targeting and Cleavage

Cell Rep.

2019-03-26

Engineered CRISPR-Cas9 nuclease with expanded targeting space

Engineered CRISPR-Cas9 nuclease with expanded targeting space

Science

2018-09-21

Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells

Pairwise library screen systematically interrogates Staphylococcus aureus Cas9 specificity in human cells

Nat. Commun.

2018-07-27

Field-deployable viral diagnostics using CRISPR-Cas13

Field-deployable viral diagnostics using CRISPR-Cas13

Science

2018-04-27

Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6

Multiplexed and portable nucleic acid detection platform with Cas13, Cas12a, and Csm6

Science

2018-04-27

RNA editing with CRISPR-Cas13

RNA editing with CRISPR-Cas13

Science

2017-11-24

RNA targeting with CRISPR‚ÄìCas13

RNA targeting with CRISPR‚ÄìCas13

Nature

2017-10-04

Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States

Decomposing Oncogenic Transcriptional Signatures to Generate Maps of Divergent Cellular States

Cell Systems

2017-08-23

Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood

Genome-scale activation screen identifies a lncRNA locus regulating a gene neighbourhood

Nature

2017-08-17

Nucleic acid detection with CRISPR-Cas13a/C2c2

Nucleic acid detection with CRISPR-Cas13a/C2c2

Science

2017-04-13

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

Genome-scale CRISPR-Cas9 knockout and transcriptional activation screening

Nat. Protoc.

2017-03-31

Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems

Crystal Structure of the Minimal Cas9 from Campylobacter jejuni Reveals the Molecular Diversity in the CRISPR-Cas9 Systems

Mol. Cell

2017-03-16

Diversity and evolution of class 2 CRISPR-Cas systems

Diversity and evolution of class 2 CRISPR-Cas systems

Nat. Rev. Microbiol.

2017-02-28

Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

Cas13b Is a Type VI-B CRISPR-Associated RNA-Guided RNase Differentially Regulated by Accessory Proteins Csx27 and Csx28

Mol. Cell

2017-02-16

Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array

Multiplex gene editing by CRISPR-Cpf1 using a single crRNA array

Nature

2016-12-05

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector

Science

2016-08-05

Characterizing genomic alterations in cancer by complementary functional associations

Characterizing genomic alterations in cancer by complementary functional associations

Nat. Biotechnol.

2016-04-30

Structure and Engineering of Francisella novicida Cas9

Structure and Engineering of Francisella novicida Cas9

Cell

2016-02-25

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

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

Mol. Cell

2015-11-05

Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease

Orthogonal gene knockout and activation with a catalytically active Cas9 nuclease

Nat. Biotechnol.

2015-10-31

Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system

Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system

Cell

2015-10-22

In vivo genome editing using Staphylococcus aureus Cas9

In vivo genome editing using Staphylococcus aureus Cas9

Nature

2015-04-09

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

Nature

2015-01-29

A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors

A melanoma cell state distinction influences sensitivity to MAPK pathway inhibitors

Cancer Discov.

2014-06-30

Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity

Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity

Cell

2013-09-12

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