标题
Review of CRISPR/Cas9 sgRNA Design Tools
作者
关键词
CRISPR, CRISPR/Cas9, SgRNA design, On-target efficiency, Off-target detection
出版物
Interdisciplinary Sciences-Computational Life Sciences
Volume 10, Issue 2, Pages 455-465
出版商
Springer Nature
发表日期
2018-04-11
DOI
10.1007/s12539-018-0298-z
参考文献
相关参考文献
注意：仅列出部分参考文献，下载原文获取全部文献信息。- GuideScan software for improved single and paired CRISPR guide RNA design
- (2017) Alexendar R Perez 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
- Refined sgRNA efficacy prediction improves large- and small-scale CRISPR–Cas9 applications
- (2017) Maurice Labuhn et al. NUCLEIC ACIDS RESEARCH
- In Silico Meets In Vivo : Towards Computational CRISPR-Based sgRNA Design
- (2017) Guo-hui Chuai et al. TRENDS IN BIOTECHNOLOGY
- sgRNA Scorer 2.0: A Species-Independent Model To Predict CRISPR/Cas9 Activity
- (2017) Raj Chari et al. ACS Synthetic Biology
- A machine learning approach for predicting CRISPR-Cas9 cleavage efficiencies and patterns underlying its mechanism of action
- (2017) Shiran Abadi et al. PLoS Computational Biology
- Scalable Design of Paired CRISPR Guide RNAs for Genomic Deletion
- (2017) Carlos Pulido-Quetglas et al. PLoS Computational Biology
- In Silico Analysis of nsSNPs of Carp TLR22 Gene Affecting its Binding Ability with Poly I:C
- (2017) Vemulawada Chakrapani et al. Interdisciplinary Sciences-Computational Life Sciences
- Insight into a Transcriptional Adaptor Zinc Finger Encoded by a Putative Protein in the White Spot Syndrome Virus Genome
- (2017) Malathi Shekar et al. Interdisciplinary Sciences-Computational Life Sciences
- Comprehensive Analysis of MILE Gene Expression Data Set Advances Discovery of Leukaemia Type and Subtype Biomarkers
- (2017) Wojciech Labaj et al. Interdisciplinary Sciences-Computational Life Sciences
- Correction: CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool
- (2017) Manuel Stemmer et al. PLoS One
- CRISPR-FOCUS: A web server for designing focused CRISPR screening experiments
- (2017) Qingyi Cao et al. PLoS One
- CRISPRpred: A flexible and efficient tool for sgRNAs on-target activity prediction in CRISPR/Cas9 systems
- (2017) Md. Khaledur Rahman et al. PLoS One
- CRISPR-DO for genome-wide CRISPR design and optimization
- (2016) Jian Ma et al. BIOINFORMATICS
- CRISPR/Cas9 advances engineering of microbial cell factories
- (2016) Tadas Jakočiūnas et al. METABOLIC ENGINEERING
- Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
- (2016) John G Doench et al. NATURE BIOTECHNOLOGY
- Breaking-Cas—interactive design of guide RNAs for CRISPR-Cas experiments for ENSEMBL genomes
- (2016) Juan C. Oliveros et al. NUCLEIC ACIDS RESEARCH
- CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering
- (2016) Kornel Labun et al. NUCLEIC ACIDS RESEARCH
- Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting
- (2016) A. J. Aguirre et al. Cancer Discovery
- CT-Finder: A Web Service for CRISPR Optimal Target Prediction and Visualization
- (2016) Houxiang Zhu et al. Scientific Reports
- A CRISPR Dropout Screen Identifies Genetic Vulnerabilities and Therapeutic Targets in Acute Myeloid Leukemia
- (2016) Konstantinos Tzelepis et al. Cell Reports
- Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation
- (2016) Max A Horlbeck et al. eLife
- Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis
- (2015) Sidi Chen et al. CELL
- Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System
- (2015) Bernd Zetsche et al. CELL
- Dramatic Enhancement of Genome Editing by CRISPR/Cas9 Through Improved Guide RNA Design
- (2015) Behnom Farboud et al. GENETICS
- Sequence determinants of improved CRISPR sgRNA design
- (2015) Han Xu et al. GENOME RESEARCH
- Cas9 specifies functional viral targets during CRISPR–Cas adaptation
- (2015) Robert Heler et al. NATURE
- Flexible guide-RNA design for CRISPR applications using Protospacer Workbench
- (2015) Cameron Ross MacPherson et al. NATURE BIOTECHNOLOGY
- CRISPRscan: designing highly efficient sgRNAs for CRISPR-Cas9 targeting in vivo
- (2015) Miguel A Moreno-Mateos et al. NATURE METHODS
- Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach
- (2015) Raj Chari et al. NATURE METHODS
- CRISPR-CAS9 D10A nickase target-specific fluorescent labeling of double strand DNA for whole genome mapping and structural variation analysis
- (2015) Jennifer McCaffrey et al. NUCLEIC ACIDS RESEARCH
- Cas9-chromatin binding information enables more accurate CRISPR off-target prediction
- (2015) Ritambhara Singh et al. NUCLEIC ACIDS RESEARCH
- Identification and characterization of essential genes in the human genome
- (2015) T. Wang et al. SCIENCE
- Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi
- (2015) Benjamin E. Housden et al. Science Signaling
- PAM multiplicity marks genomic target sites as inhibitory to CRISPR-Cas9 editing
- (2015) Abba Malina et al. Nature Communications
- Dramatic Enhancement of Genome Editing by CRISPR/Cas9 Through Improved Guide RNA Design
- (2015) Behnom Farboud et al. GENETICS
- Identification of potential drug targets for tuberous sclerosis complex by synthetic screens combining CRISPR-based knockouts with RNAi
- (2015) Benjamin E. Housden et al. Science Signaling
- A quick guide to CRISPR sgRNA design tools
- (2015) Vincent A Brazelton et al. GM Crops & Food-Biotechnology in Agriculture and the Food Chain
- CRISPR MultiTargeter: A Web Tool to Find Common and Unique CRISPR Single Guide RNA Targets in a Set of Similar Sequences
- (2015) Sergey V. Prykhozhij et al. PLoS One
- CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites
- (2014) Yuki Naito et al. BIOINFORMATICS
- GT-Scan: identifying unique genomic targets
- (2014) A. O'Brien et al. BIOINFORMATICS
- Cas-OFFinder: a fast and versatile algorithm that searches for potential off-target sites of Cas9 RNA-guided endonucleases
- (2014) S. Bae et al. BIOINFORMATICS
- Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation
- (2014) Luke A. Gilbert et al. CELL
- Whole-Genome Sequencing Analysis Reveals High Specificity of CRISPR/Cas9 and TALEN-Based Genome Editing in Human iPSCs
- (2014) Cory Smith et al. Cell Stem Cell
- Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells
- (2014) Xuebing Wu et al. NATURE BIOTECHNOLOGY
- Improving CRISPR-Cas nuclease specificity using truncated guide RNAs
- (2014) Yanfang Fu et al. NATURE BIOTECHNOLOGY
- Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing
- (2014) Shengdar Q Tsai et al. NATURE BIOTECHNOLOGY
- Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease
- (2014) Cem Kuscu et al. NATURE BIOTECHNOLOGY
- Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation
- (2014) John G Doench et al. NATURE BIOTECHNOLOGY
- GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases
- (2014) Shengdar Q Tsai et al. NATURE BIOTECHNOLOGY
- E-CRISP: fast CRISPR target site identification
- (2014) Florian Heigwer et al. NATURE METHODS
- CRISPR/Cas9 systems have off-target activity with insertions or deletions between target DNA and guide RNA sequences
- (2014) Y. Lin et al. NUCLEIC ACIDS RESEARCH
- CHOPCHOP: a CRISPR/Cas9 and TALEN web tool for genome editing
- (2014) Tessa G. Montague et al. NUCLEIC ACIDS RESEARCH
- sgRNAcas9: A Software Package for Designing CRISPR sgRNA and Evaluating Potential Off-Target Cleavage Sites
- (2014) Shengsong Xie et al. PLoS One
- CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems
- (2014) Lihua J. Zhu et al. PLoS One
- TALEN and CRISPR/Cas9-mediated genome editing in the early-branching metazoan Nematostella vectensis
- (2014) Aissam Ikmi et al. Nature Communications
- Enhanced Specificity and Efficiency of the CRISPR/Cas9 System with Optimized sgRNA Parameters in Drosophila
- (2014) Xingjie Ren et al. Cell Reports
- Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression
- (2013) Lei S. Qi et al. CELL
- One-Step Generation of Mice Carrying Reporter and Conditional Alleles by CRISPR/Cas-Mediated Genome Engineering
- (2013) Hui Yang et al. CELL
- Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity
- (2013) F. Ann Ran et al. CELL
- Enhanced Efficiency of Human Pluripotent Stem Cell Genome Editing through Replacing TALENs with CRISPRs
- (2013) Qiurong Ding et al. Cell Stem Cell
- Genome Engineering of Drosophila with the CRISPR RNA-Guided Cas9 Nuclease
- (2013) Scott J. Gratz et al. GENETICS
- Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
- (2013) M. S. Enuameh et al. GENOME RESEARCH
- Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases
- (2013) S. W. Cho et al. GENOME RESEARCH
- Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library
- (2013) Hiroko Koike-Yusa et al. NATURE BIOTECHNOLOGY
- CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering
- (2013) Prashant Mali et al. NATURE BIOTECHNOLOGY
- DNA targeting specificity of RNA-guided Cas9 nucleases
- (2013) Patrick D Hsu et al. NATURE BIOTECHNOLOGY
- Efficient genome editing in zebrafish using a CRISPR-Cas system
- (2013) Woong Y Hwang et al. NATURE BIOTECHNOLOGY
- High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity
- (2013) Vikram Pattanayak et al. NATURE BIOTECHNOLOGY
- High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells
- (2013) Yanfang Fu et al. NATURE BIOTECHNOLOGY
- Heritable gene targeting in the mouse and rat using a CRISPR-Cas system
- (2013) Dali Li et al. NATURE BIOTECHNOLOGY
- RNA-guided editing of bacterial genomes using CRISPR-Cas systems
- (2013) Wenyan Jiang et al. NATURE BIOTECHNOLOGY
- Heritable genome editing in C. elegans via a CRISPR-Cas9 system
- (2013) Ari E Friedland et al. NATURE METHODS
- CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity
- (2013) Thomas J. Cradick et al. NUCLEIC ACIDS RESEARCH
- Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems
- (2013) Ines Fonfara et al. NUCLEIC ACIDS RESEARCH
- Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis
- (2013) Z. Hou et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- CRISPR-Cas
- (2013) Eugene V. Koonin et al. RNA Biology
- RNA-Guided Human Genome Engineering via Cas9
- (2013) P. Mali et al. SCIENCE
- 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
- RNA-programmed genome editing in human cells
- (2013) Martin Jinek et al. eLife
- Exploring the DNA-recognition potential of homeodomains
- (2012) S. W. Chu et al. GENOME RESEARCH
- A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity
- (2012) M. Jinek et al. SCIENCE
- CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III
- (2011) Elitza Deltcheva et al. NATURE
- TAL Effectors: Customizable Proteins for DNA Targeting
- (2011) A. J. Bogdanove et al. SCIENCE
- A TALE nuclease architecture for efficient genome editing
- (2010) Jeffrey C Miller et al. NATURE BIOTECHNOLOGY
- Genome editing with engineered zinc finger nucleases
- (2010) Fyodor D. Urnov et al. NATURE REVIEWS GENETICS
- Zinc finger protein-dependent and -independent contributions to the in vivo off-target activity of zinc finger nucleases
- (2010) Ankit Gupta et al. NUCLEIC ACIDS RESEARCH
- CRISPR/Cas, the Immune System of Bacteria and Archaea
- (2010) P. Horvath et al. SCIENCE
- Fast and accurate short read alignment with Burrows-Wheeler transform
- (2009) H. Li et al. BIOINFORMATICS
- Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors
- (2009) J. Boch et al. SCIENCE
- A Simple Cipher Governs DNA Recognition by TAL Effectors
- (2009) M. J. Moscou et al. SCIENCE
- Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
- (2009) Ben Langmead et al. GENOME BIOLOGY
- Targeted gene inactivation in zebrafish using engineered zinc-finger nucleases
- (2008) Xiangdong Meng et al. NATURE BIOTECHNOLOGY
Add your recorded webinar
Do you already have a recorded webinar? Grow your audience and get more views by easily listing your recording on Peeref.
Upload NowAsk a Question. Answer a Question.
Quickly pose questions to the entire community. Debate answers and get clarity on the most important issues facing researchers.
Get Started