A comprehensive overview of computational resources to aid in precision genome editing with engineered nucleases
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Title
A comprehensive overview of computational resources to aid in precision genome editing with engineered nucleases
Authors
Keywords
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Journal
BRIEFINGS IN BIOINFORMATICS
Volume -, Issue -, Pages bbw052
Publisher
Oxford University Press (OUP)
Online
2016-07-04
DOI
10.1093/bib/bbw052
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Note: Only part of the references are listed.- Death receptor-based enrichment of Cas9-expressing cells
- (2016) C. Liesche et al. BMC BIOTECHNOLOGY
- c-Myc and viral cofactor Kaposin B co-operate to elicit angiogenesis through modulating miRNome traits of endothelial cells
- (2016) Hsin-Chuan Chang et al. BMC Systems Biology
- High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects
- (2016) Benjamin P. Kleinstiver et al. NATURE
- Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9
- (2016) John G Doench et al. NATURE BIOTECHNOLOGY
- Selection-free gene repair after adenoviral vector transduction of designer nucleases: rescue of dystrophin synthesis in DMD muscle cell populations
- (2016) Ignazio Maggio et al. NUCLEIC ACIDS RESEARCH
- Quantitative proteomics identify DAB2 as a cardiac developmental regulator that inhibits WNT/β-catenin signaling
- (2016) Peter Hofsteen et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- 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
- One-step generation of triple gene-targeted pigs using CRISPR/Cas9 system
- (2016) Xianlong Wang et al. Scientific Reports
- In situ genetic correction of F8 intron 22 inversion in hemophilia A patient-specific iPSCs
- (2016) Yong Wu et al. Scientific Reports
- Mammalian cells lacking either the cotranslational or posttranslocational oligosaccharyltransferase complex display substrate-dependent defects in asparagine linked glycosylation
- (2016) Natalia A. Cherepanova et al. Scientific Reports
- Plasmodium falciparum PfSET7: enzymatic characterization and cellular localization of a novel protein methyltransferase in sporozoite, liver and erythrocytic stage parasites
- (2016) Patty B. Chen et al. Scientific Reports
- RETRACTED ARTICLE: Robust method for TALEN-edited correction of pF508del in patient-specific induced pluripotent stem cells
- (2016) María Vicenta Camarasa et al. Stem Cell Research & Therapy
- Improved Genome Editing Efficiency and Flexibility Using Modified Oligonucleotides with TALEN and CRISPR-Cas9 Nucleases
- (2016) Jean-Baptiste Renaud et al. Cell Reports
- Correction of the auditory phenotype in C57BL/6N mice via CRISPR/Cas9-mediated homology directed repair
- (2016) Joffrey Mianné et al. Genome Medicine
- antaRNA: ant colony-based RNA sequence design
- (2015) Robert Kleinkauf et al. BIOINFORMATICS
- ScreenBEAM: a novel meta-analysis algorithm for functional genomics screens via Bayesian hierarchical modeling
- (2015) Jiyang Yu et al. BIOINFORMATICS
- Logical transformation of genome-scale metabolic models for gene level applications and analysis
- (2015) Cheng Zhang et al. BIOINFORMATICS
- Cas-Designer: a web-based tool for choice of CRISPR-Cas9 target sites
- (2015) Jeongbin Park et al. BIOINFORMATICS
- CRISPR-ERA: a comprehensive design tool for CRISPR-mediated gene editing, repression and activation: Fig. 1.
- (2015) Honglei Liu et al. BIOINFORMATICS
- caRpools: an R package for exploratory data analysis and documentation of pooled CRISPR/Cas9 screens
- (2015) Jan Winter et al. BIOINFORMATICS
- WGE: a CRISPR database for genome engineering: Fig. 1.
- (2015) Alex Hodgkins et al. BIOINFORMATICS
- “Off-Spotter”: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs
- (2015) Venetia Pliatsika et al. Biology Direct
- Targeted genome editing in primate embryos
- (2015) Xiangyu Guo et al. CELL RESEARCH
- Lymphoid Regeneration from Gene-Corrected SCID-X1 Subject-Derived iPSCs
- (2015) Tushar Menon et al. Cell Stem Cell
- Current and future delivery systems for engineered nucleases: ZFN, TALEN and RGEN
- (2015) Qurrat Ul Ain et al. JOURNAL OF CONTROLLED RELEASE
- Pseudo nucleotide composition or PseKNC: an effective formulation for analyzing genomic sequences
- (2015) Wei Chen et al. Molecular BioSystems
- repRNA: a web server for generating various feature vectors of RNA sequences
- (2015) Bin Liu et al. MOLECULAR GENETICS AND GENOMICS
- Correction of Dystrophin Expression in Cells From Duchenne Muscular Dystrophy Patients Through Genomic Excision of Exon 51 by Zinc Finger Nucleases
- (2015) David G Ousterout et al. MOLECULAR THERAPY
- Integrase-mediated spacer acquisition during CRISPR–Cas adaptive immunity
- (2015) James K. Nuñez et al. NATURE
- Engineered CRISPR-Cas9 nucleases with altered PAM specificities
- (2015) Benjamin P. Kleinstiver et al. NATURE
- Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex
- (2015) Silvana Konermann et al. NATURE
- In vivo genome editing using Staphylococcus aureus Cas9
- (2015) F. Ann Ran et al. NATURE
- Increasing the efficiency of precise genome editing with CRISPR-Cas9 by inhibition of nonhomologous end joining
- (2015) Takeshi Maruyama et al. NATURE BIOTECHNOLOGY
- Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells
- (2015) Ayal Hendel et al. NATURE BIOTECHNOLOGY
- Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers
- (2015) Isaac B Hilton et al. NATURE BIOTECHNOLOGY
- Therapeutic genome editing: prospects and challenges
- (2015) David Benjamin Turitz Cox et al. NATURE MEDICINE
- DNA-binding-domain fusions enhance the targeting range and precision of Cas9
- (2015) Mehmet Fatih Bolukbasi et al. NATURE METHODS
- Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach
- (2015) Raj Chari et al. NATURE METHODS
- Nuclear domain ‘knock-in’ screen for the evaluation and identification of small molecule enhancers of CRISPR-based genome editing
- (2015) Jordan Pinder et al. NUCLEIC ACIDS RESEARCH
- Cas9-chromatin binding information enables more accurate CRISPR off-target prediction
- (2015) Ritambhara Singh et al. NUCLEIC ACIDS RESEARCH
- GBM Derived Gangliosides Induce T Cell Apoptosis through Activation of the Caspase Cascade Involving Both the Extrinsic and the Intrinsic Pathway
- (2015) Barun Mahata et al. PLoS One
- Efficient fdCas9 Synthetic Endonuclease with Improved Specificity for Precise Genome Engineering
- (2015) Mustapha Aouida et al. PLoS One
- Glycosylation inhibition reduces cholesterol accumulation in NPC1 protein-deficient cells
- (2015) Jian Li et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- Outbred genome sequencing and CRISPR/Cas9 gene editing in butterflies
- (2015) Xueyan Li et al. Nature Communications
- MYC Drives Pten/Trp53-Deficient Proliferation and Metastasis due to IL6 Secretion and AKT Suppression via PHLPP2
- (2015) D. G. Nowak et al. Cancer Discovery
- CrisprGE: a central hub of CRISPR/Cas-based genome editing
- (2015) Karambir Kaur et al. Database-The Journal of Biological Databases and Curation
- Both TALENs and CRISPR/Cas9 directly target the HBB IVS2–654 (C > T) mutation in β-thalassemia-derived iPSCs
- (2015) Peng Xu et al. Scientific Reports
- CRISPR/Cas9-based generation of knockdown mice by intronic insertion of artificial microRNA using longer single-stranded DNA
- (2015) Hiromi Miura et al. Scientific Reports
- GONAD: Genome-editing via Oviductal Nucleic Acids Delivery system: a novel microinjection independent genome engineering method in mice
- (2015) Gou Takahashi et al. Scientific Reports
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- Activation of Type I and III Interferon Response by Mitochondrial and Peroxisomal MAVS and Inhibition by Hepatitis C Virus
- (2015) Silke Bender et al. PLoS Pathogens
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- (2015) Bijal A. Parikh et al. PLoS One
- CCTop: An Intuitive, Flexible and Reliable CRISPR/Cas9 Target Prediction Tool
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- (2015) Valentin M. Sluch et al. Scientific Reports
- PseKNC: A flexible web server for generating pseudo K-tuple nucleotide composition
- (2014) Wei Chen et al. ANALYTICAL BIOCHEMISTRY
- CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites
- (2014) Yuki Naito et al. BIOINFORMATICS
- Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA)
- (2014) M. Guell et al. BIOINFORMATICS
- GT-Scan: identifying unique genomic targets
- (2014) A. O'Brien et al. BIOINFORMATICS
- PyBamView: a browser-based application for viewing short read alignments
- (2014) Melissa Gymrek BIOINFORMATICS
- Insights into structural variations and genome rearrangements in prokaryotic genomes
- (2014) Vinita Periwal et al. BIOINFORMATICS
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- (2014) A. Xiao et al. BIOINFORMATICS
- repDNA: a Python package to generate various modes of feature vectors for DNA sequences by incorporating user-defined physicochemical properties and sequence-order effects
- (2014) Bin Liu 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
- Accelerating genome editing in CHO cells using CRISPR Cas9 and CRISPy, a web-based target finding tool
- (2014) Carlotta Ronda et al. BIOTECHNOLOGY AND BIOENGINEERING
- Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation
- (2014) Luke A. Gilbert et al. CELL
- TALEN-Mediated Gene Mutagenesis in Rhesus and Cynomolgus Monkeys
- (2014) Hailiang Liu et al. Cell Stem Cell
- Highly Specific and Efficient CRISPR/Cas9-Catalyzed Homology-Directed Repair inDrosophila
- (2014) Scott J. Gratz et al. GENETICS
- Targeted genome editing in Aedes aegypti using TALENs
- (2014) Azadeh Aryan et al. METHODS
- CRISPR-P: A Web Tool for Synthetic Single-Guide RNA Design of CRISPR-System in Plants
- (2014) Yang Lei et al. Molecular Plant
- Improving CRISPR-Cas nuclease specificity using truncated guide RNAs
- (2014) Yanfang Fu et al. NATURE BIOTECHNOLOGY
- Simultaneous editing of three homoeoalleles in hexaploid bread wheat confers heritable resistance to powdery mildew
- (2014) Yanpeng Wang et al. NATURE BIOTECHNOLOGY
- Microhomology-based choice of Cas9 nuclease target sites
- (2014) Sangsu Bae et al. NATURE METHODS
- E-CRISP: fast CRISPR target site identification
- (2014) Florian Heigwer et al. NATURE METHODS
- Isolation of single-base genome-edited human iPS cells without antibiotic selection
- (2014) Yuichiro Miyaoka et al. NATURE METHODS
- A guide to genome engineering with programmable nucleases
- (2014) Hyongbum Kim et al. NATURE REVIEWS GENETICS
- Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity
- (2014) James K Nuñez et al. NATURE STRUCTURAL & MOLECULAR BIOLOGY
- Gene Editing of CCR5 in Autologous CD4 T Cells of Persons Infected with HIV
- (2014) Pablo Tebas et al. NEW ENGLAND JOURNAL OF MEDICINE
- An online bioinformatics tool predicts zinc finger and TALE nuclease off-target cleavage
- (2014) Eli J. Fine et al. NUCLEIC ACIDS RESEARCH
- SAPTA: a new design tool for improving TALE nuclease activity
- (2014) Yanni 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
- Easy quantitative assessment of genome editing by sequence trace decomposition
- (2014) Eva K. Brinkman et al. NUCLEIC ACIDS RESEARCH
- Multigene Knockout Utilizing Off-Target Mutations of the CRISPR/Cas9 System in Rice
- (2014) Masaki Endo et al. PLANT AND CELL PHYSIOLOGY
- A Modified TALEN-Based Strategy for Rapidly and Efficiently Generating Knockout Mice for Kidney Development Studies
- (2014) Yunhong Liu et al. PLoS One
- 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
- Generation of GGTA1 biallelic knockout pigs via zinc-finger nucleases and somatic cell nuclear transfer
- (2014) Lei Bao et al. Science China-Life Sciences
- Somatic mutations in DROSHA and DICER1 impair microRNA biogenesis through distinct mechanisms in Wilms tumours
- (2014) Dinesh Rakheja et al. Nature Communications
- Transcription activator-like effector nuclease-mediated transduction of exogenous gene into IL2RG locus
- (2014) Yohei Matsubara et al. Scientific Reports
- Efficient bi-allelic gene knockout and site-specific knock-in mediated by TALENs in pigs
- (2014) Jing Yao et al. Scientific Reports
- COSMID: A Web-based Tool for Identifying and Validating CRISPR/Cas Off-target Sites
- (2014) Thomas J Cradick et al. Molecular Therapy-Nucleic Acids
- TALENoffer: genome-wide TALEN off-target prediction
- (2013) Jan Grau et al. BIOINFORMATICS
- Expanding the scope of site-specific recombinases for genetic and metabolic engineering
- (2013) Thomas Gaj et al. BIOTECHNOLOGY AND BIOENGINEERING
- Mojo Hand, a TALEN design tool for genome editing applications
- (2013) Kevin L Neff et al. BMC BIOINFORMATICS
- The Ecdysone receptor constrains wingless expression to pattern cell cycle across the Drosophila wing margin in a cyclin B-dependent manner
- (2013) Naomi C Mitchell et al. BMC DEVELOPMENTAL BIOLOGY
- A modified TALEN-based system for robust generation of knock-out human pluripotent stem cell lines and disease models
- (2013) Stefan Frank et al. BMC GENOMICS
- Using GBrowse 2.0 to visualize and share next-generation sequence data
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- Gene targeting technologies in rats: Zinc finger nucleases, transcription activator-like effector nucleases, and clustered regularly interspaced short palindromic repeats
- (2013) Tomoji Mashimo DEVELOPMENT GROWTH & DIFFERENTIATION
- Breaking through an epigenetic wall
- (2013) Karla Juárez-Moreno et al. Epigenetics
- Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases
- (2013) S. W. Cho et al. GENOME RESEARCH
- Genomic Editing of the HIV-1 Coreceptor CCR5 in Adult Hematopoietic Stem and Progenitor Cells Using Zinc Finger Nucleases
- (2013) Lijing Li et al. MOLECULAR THERAPY
- Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins
- (2013) Morgan L Maeder et al. NATURE BIOTECHNOLOGY
- DNA targeting specificity of RNA-guided Cas9 nucleases
- (2013) Patrick D Hsu et al. NATURE BIOTECHNOLOGY
- A library of TAL effector nucleases spanning the human genome
- (2013) Yongsub Kim et al. NATURE BIOTECHNOLOGY
- Cas9 as a versatile tool for engineering biology
- (2013) Prashant Mali et al. NATURE METHODS
- Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish
- (2013) An Xiao et al. NUCLEIC ACIDS RESEARCH
- E-TALEN: a web tool to design TALENs for genome engineering
- (2013) Florian Heigwer et al. NUCLEIC ACIDS RESEARCH
- Zinc-finger-nucleases mediate specific and efficient excision of HIV-1 proviral DNA from infected and latently infected human T cells
- (2013) Xiying Qu et al. NUCLEIC ACIDS RESEARCH
- CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems
- (2013) Sita J. Lange et al. NUCLEIC ACIDS RESEARCH
- ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering
- (2013) Thomas Gaj et al. TRENDS IN BIOTECHNOLOGY
- A Guide RNA Sequence Design Platform for the CRISPR/Cas9 System for Model Organism Genomes
- (2013) Ming Ma et al. Biomed Research International
- A brief introduction to web-based genome browsers
- (2012) J. Wang et al. BRIEFINGS IN BIOINFORMATICS
- Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration
- (2012) H. Thorvaldsdottir et al. BRIEFINGS IN BIOINFORMATICS
- Engineered zinc finger nickases induce homology-directed repair with reduced mutagenic effects
- (2012) Cherie L. Ramirez et al. NUCLEIC ACIDS RESEARCH
- EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering
- (2012) An Xiao et al. NUCLEIC ACIDS RESEARCH
- TAL Effector-Nucleotide Targeter (TALE-NT) 2.0: tools for TAL effector design and target prediction
- (2012) Erin L. Doyle et al. NUCLEIC ACIDS RESEARCH
- Cas9-crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria
- (2012) G. Gasiunas et al. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
- The Crystal Structure of TAL Effector PthXo1 Bound to Its DNA Target
- (2012) A. N.-S. Mak et al. SCIENCE
- A Programmable Dual-RNA-Guided DNA Endonuclease in Adaptive Bacterial Immunity
- (2012) M. Jinek et al. SCIENCE
- ZFN-Site searches genomes for zinc finger nuclease target sites and off-target sites
- (2011) Thomas J Cradick et al. BMC BIOINFORMATICS
- ZFNGenome: A comprehensive resource for locating zinc finger nuclease target sites in model organisms
- (2011) Deepak Reyon et al. BMC GENOMICS
- Genome Engineering With Zinc-Finger Nucleases
- (2011) Dana Carroll GENETICS
- Generating gene knockout rats by homologous recombination in embryonic stem cells
- (2011) Chang Tong et al. Nature Protocols
- Evolution and classification of the CRISPR–Cas systems
- (2011) Kira S. Makarova et al. NATURE REVIEWS MICROBIOLOGY
- Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting
- (2011) Tomas Cermak et al. NUCLEIC ACIDS RESEARCH
- The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA
- (2010) Josiane E. Garneau et al. NATURE
- Human hematopoietic stem/progenitor cells modified by zinc-finger nucleases targeted to CCR5 control HIV-1 in vivo
- (2010) Nathalia Holt et al. NATURE BIOTECHNOLOGY
- ZiFiT (Zinc Finger Targeter): an updated zinc finger engineering tool
- (2010) J. D. Sander et al. NUCLEIC ACIDS RESEARCH
- ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data
- (2010) K. Wang et al. NUCLEIC ACIDS RESEARCH
- CRISPR/Cas, the Immune System of Bacteria and Archaea
- (2010) P. Horvath et al. SCIENCE
- ZifBASE: a database of zinc finger proteins and associated resources
- (2009) Mannu Jayakanthan et al. BMC GENOMICS
- A Simple Cipher Governs DNA Recognition by TAL Effectors
- (2009) M. J. Moscou et al. SCIENCE
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