A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation (Q28552981)

April 2022 Public Data File from Crossref

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cites work

Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease

1 reference

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Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

19 March 2017

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Structures of Cas9 Endonucleases Reveal RNA-Mediated Conformational Activation

19 March 2017

1 reference

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Genome engineering using the CRISPR-Cas9 system

19 March 2017

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Cas9 as a versatile tool for engineering biology

19 March 2017

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Tunable and multifunctional eukaryotic transcription factors based on CRISPR/Cas

19 March 2017

1 reference

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RNA-guided gene activation by CRISPR-Cas9-based transcription factors

19 March 2017

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Heritable genome editing in C. elegans via a CRISPR-Cas9 system

19 March 2017

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Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems

19 March 2017

1 reference

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RNA-guided editing of bacterial genomes using CRISPR-Cas systems

19 March 2017

1 reference

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RNA-guided human genome engineering via Cas9

19 March 2017

1 reference

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Multiplex genome engineering using CRISPR/Cas systems

19 March 2017

1 reference

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

19 March 2017

1 reference

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CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Enzymatic assembly of DNA molecules up to several hundred kilobases

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Organization of supercoil domains and their reorganization by transcription

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

The thermodynamics of DNA structural motifs

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Fluctuations in superhelical DNA

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

One-step generation of mice carrying mutations in multiple genes by CRISPR/Cas-mediated genome engineering

6 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Improving CRISPR-Cas nuclease specificity using truncated guide RNAs

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Genome-scale CRISPR-Cas9 knockout screening in human cells

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

DNA targeting specificity of RNA-guided Cas9 nucleases

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Conformational control of DNA target cleavage by CRISPR-Cas9.

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Inducible in vivo genome editing with CRISPR-Cas9

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

A split-Cas9 architecture for inducible genome editing and transcription modulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Multiplex CRISPR/Cas9-based genome engineering from a single lentiviral vector

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

RNA-directed gene editing specifically eradicates latent and prevents new HIV-1 infection.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Comparison of non-canonical PAMs for CRISPR/Cas9-mediated DNA cleavage in human cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Direct observation of R-loop formation by single RNA-guided Cas9 and Cascade effector complexes.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Unravelling the structural and mechanistic basis of CRISPR-Cas systems

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

CRISPR transcriptional repression devices and layered circuits in mammalian cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Degenerate target sites mediate rapid primed CRISPR adaptation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Generation of gene-modified cynomolgus monkey via Cas9/RNA-mediated gene targeting in one-cell embryos.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

DNA interrogation by the CRISPR RNA-guided endonuclease Cas9.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Translation rate is controlled by coupled trade-offs between site accessibility, selective RNA unfolding and sliding at upstream standby sites.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Simple and efficient CRISPR/Cas9-mediated targeted mutagenesis in Xenopus tropicalis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Orthogonal Cas9 proteins for RNA-guided gene regulation and editing

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Heritable gene knockout in Caenorhabditis elegans by direct injection of Cas9-sgRNA ribonucleoproteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Harnessing the CRISPR/Cas9 system to disrupt latent HIV-1 provirus

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Heritable and precise zebrafish genome editing using a CRISPR-Cas system

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Highly efficient targeted mutagenesis of Drosophila with the CRISPR/Cas9 system.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Programmable repression and activation of bacterial gene expression using an engineered CRISPR-Cas system

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Characterization of 582 natural and synthetic terminators and quantification of their design constraints

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

CRISPR-mediated adaptive immune systems in bacteria and archaea

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Gene order and chromosome dynamics coordinate spatiotemporal gene expression during the bacterial growth cycle

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Physical limits of cells and proteomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Structural basis for CRISPR RNA-guided DNA recognition by Cascade

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Thermodynamic contributions of single internal rA·dA, rC·dC, rG·dG and rU·dT mismatches in RNA/DNA duplexes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Automated design of synthetic ribosome binding sites to control protein expression

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Dynamics and stability of individual base pairs in two homologous RNA-DNA hybrids

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Superhelical destabilization in regulatory regions of stress response genes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Ribosome kinetics and aa-tRNA competition determine rate and fidelity of peptide synthesis

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Transcriptional regulation by the numbers: models.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Conformational fluctuations of DNA helix

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

crRNA and tracrRNA guide Cas9-mediated DNA interference in Streptococcus thermophilus

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Transcriptional inhibition by DNA torsional stress.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

Heritable gene targeting in the mouse and rat using a CRISPR-Cas system.

3 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004724

The effect of base sequence on the stability of RNA and DNA single base bulges.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004724

E-CRISP: fast CRISPR target site identification

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004724

The ribosome binding site calculator.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PCBI.1004724

Effective gene targeting in rabbits using RNA-guided Cas9 nucleases.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4732943

The superhelical density of nuclear DNA from human cells

27 November 2018

1 reference

12 December 2020

Torque transfer coefficient in DNA under torsional stress

1 reference

12 December 2020

Thermodynamic parameters to predict stability of RNA/DNA hybrid duplexes

1 reference

12 December 2020

Thermodynamics-structure relationship of single mismatches in RNA/DNA duplexes

1 reference

12 December 2020

Temperature dependence of thermodynamic properties for DNA/DNA and RNA/DNA duplex formation

1 reference

12 December 2020

10.1371/JOURNAL.PCBI.1004724

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DOI

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/pgkbehg7bvcqdkerckvymng43e

30 July 2022

journals/ploscb/FarasatS16

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

release_pgkbehg7bvcqdkerckvymng43e

28 January 2021

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/pgkbehg7bvcqdkerckvymng43e

30 July 2022

OpenCitations bibliographic resource ID

2334308

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

https://api.fatcat.wiki/v0/release/pgkbehg7bvcqdkerckvymng43e

30 July 2022

https://api.fatcat.wiki/v0/release/pgkbehg7bvcqdkerckvymng43e

PubMed publication ID

1 reference

30 July 2022