Methods for Optimizing CRISPR-Cas9 Genome Editing Specificity.

[1]  Jin-Soo Kim,et al.  Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells , 2016, Nature Biotechnology.

[2]  Martin J. Aryee,et al.  Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells , 2016, Nature Biotechnology.

[3]  Eric S. Lander,et al.  C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector , 2016, Science.

[4]  Kira S. Makarova,et al.  Crystal Structure of Cpf1 in Complex with Guide RNA and Target DNA , 2016, Cell.

[5]  J. Keith Joung,et al.  731. High-Fidelity CRISPR-Cas9 Nucleases with No Detectable Genome-Wide Off-Target Effects , 2016 .

[6]  Ines Fonfara,et al.  The CRISPR-associated DNA-cleaving enzyme Cpf1 also processes precursor CRISPR RNA , 2016, Nature.

[7]  Jacob E Corn,et al.  Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA , 2016, Nature Biotechnology.

[8]  Maximilian Müller,et al.  Streptococcus thermophilus CRISPR-Cas9 Systems Enable Specific Editing of the Human Genome. , 2016, Molecular therapy : the journal of the American Society of Gene Therapy.

[9]  Jennifer A. Doudna,et al.  Structures of a CRISPR-Cas9 R-loop complex primed for DNA cleavage , 2016, Science.

[10]  George M. Church,et al.  In vivo gene editing in dystrophic mouse muscle and muscle stem cells , 2016, Science.

[11]  Jin-Soo Kim,et al.  Genome-wide target specificities of CRISPR-Cas9 nucleases revealed by multiplex Digenome-seq , 2016, Genome research.

[12]  Gang Bao,et al.  The Neisseria meningitidis CRISPR-Cas9 System Enables Specific Genome Editing in Mammalian Cells , 2016, Molecular therapy : the journal of the American Society of Gene Therapy.

[13]  Jennifer A. Doudna,et al.  Biology and Applications of CRISPR Systems: Harnessing Nature’s Toolbox for Genome Engineering , 2016, Cell.

[14]  M. Porteus,et al.  Genome Editing: A New Approach to Human Therapeutics. , 2016, Annual review of pharmacology and toxicology.

[15]  Wendell A. Lim,et al.  Expanding the CRISPR imaging toolset with Staphylococcus aureus Cas9 for simultaneous imaging of multiple genomic loci , 2016, Nucleic acids research.

[16]  J. Joung,et al.  High-fidelity CRISPR-Cas9 variants with undetectable genome-wide off-targets , 2015, Nature.

[17]  David A. Scott,et al.  Rationally engineered Cas9 nucleases with improved specificity , 2015, Science.

[18]  Meagan E. Sullender,et al.  Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9 , 2015, Nature Biotechnology.

[19]  Jennie Choi,et al.  Optimizing sgRNA structure to improve CRISPR-Cas9 knockout efficiency , 2015, Genome Biology.

[20]  J. Joung,et al.  Broadening the targeting range of Staphylococcus aureus CRISPR-Cas9 by modifying PAM recognition , 2015, Nature Biotechnology.

[21]  Morgan L. Maeder,et al.  Characterization of Staphylococcus aureus Cas9: a smaller Cas9 for all-in-one adeno-associated virus delivery and paired nickase applications , 2015, Genome Biology.

[22]  C. Bennett,et al.  Synthetic CRISPR RNA-Cas9–guided genome editing in human cells , 2015, Proceedings of the National Academy of Sciences.

[23]  R. Tjian,et al.  Dynamics of CRISPR-Cas9 genome interrogation in living cells , 2015, Science.

[24]  Lucas B. Harrington,et al.  Single-Stranded DNA Cleavage by Divergent CRISPR-Cas9 Enzymes. , 2015, Molecular cell.

[25]  M. Garber,et al.  DNA-binding domain fusions enhance the targeting range and precision of Cas9 , 2015, Nature Methods.

[26]  Mazhar Adli,et al.  Cas9-chromatin binding information enables more accurate CRISPR off-target prediction , 2015, Nucleic acids research.

[27]  Feng Zhang,et al.  Orthogonal gene knock out and activation with a catalytically active Cas9 nuclease , 2015, Nature Biotechnology.

[28]  Eugene V Koonin,et al.  Discovery and Functional Characterization of Diverse Class 2 CRISPR-Cas Systems. , 2015, Molecular cell.

[29]  Jennifer A. Doudna,et al.  Conformational control of DNA target cleavage by CRISPR–Cas9 , 2015, Nature.

[30]  A. Regev,et al.  Cpf1 Is a Single RNA-Guided Endonuclease of a Class 2 CRISPR-Cas System , 2015, Cell.

[31]  G. Church,et al.  Cas9 gRNA engineering for genome editing, activation and repression , 2015, Nature Methods.

[32]  Christopher M. Vockley,et al.  Genome-wide specificity of DNA binding, gene regulation, and chromatin remodeling by TALE- and CRISPR/Cas9-based transcriptional activators , 2015, Genome research.

[33]  Clifford A. Meyer,et al.  Sequence determinants of improved CRISPR sgRNA design , 2015, Genome research.

[34]  Yinqing Li,et al.  Crystal Structure of Staphylococcus aureus Cas9 , 2015, Cell.

[35]  G. Church,et al.  Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach , 2015, Nature Methods.

[36]  Unwanted mutations: Standards needed for gene-editing errors , 2015, Nature.

[37]  Israel Steinfeld,et al.  Chemically modified guide RNAs enhance CRISPR-Cas genome editing in human primary cells , 2015, Nature Biotechnology.

[38]  Manoj Kumar,et al.  CrisprGE: a central hub of CRISPR/Cas-based genome editing , 2015, Database J. Biol. Databases Curation.

[39]  Jennifer A. Doudna,et al.  A Cas9–guide RNA complex preorganized for target DNA recognition , 2015, Science.

[40]  Martin J. Aryee,et al.  Engineered CRISPR-Cas9 nucleases with altered PAM specificities , 2015, Nature.

[41]  JoungJ. Keith,et al.  Dimeric CRISPR RNA-Guided FokI-dCas9 Nucleases Directed by Truncated gRNAs for Highly Specific Genome Editing , 2015 .

[42]  Morgan L. Maeder,et al.  Delivery and Specificity of CRISPR-Cas9 Genome Editing Technologies for Human Gene Therapy. , 2015, Human gene therapy.

[43]  Jin-Soo Kim,et al.  Measuring and Reducing Off-Target Activities of Programmable Nucleases Including CRISPR-Cas9 , 2015, Molecules and cells.

[44]  R. Samulski,et al.  Adeno-associated virus at 50: a golden anniversary of discovery, research, and gene therapy success--a personal perspective. , 2015, Human gene therapy.

[45]  David R. Liu,et al.  Small Molecule-Triggered Cas9 Protein with Improved Genome-Editing Specificity , 2015, Nature chemical biology.

[46]  David A. Scott,et al.  In vivo genome editing using Staphylococcus aureus Cas9 , 2015, Nature.

[47]  Jong-il Kim,et al.  Digenome-seq: genome-wide profiling of CRISPR-Cas9 off-target effects in human cells , 2015, Nature Methods.

[48]  Hidde L Ploegh,et al.  Inhibition of non-homologous end joining increases the efficiency of CRISPR/Cas9-mediated precise [TM: inserted] genome editing , 2015, Nature Biotechnology.

[49]  C. Gersbach,et al.  A light-inducible CRISPR/Cas9 system for control of endogenous gene activation , 2015, Nature chemical biology.

[50]  Lei S. Qi,et al.  Small molecules enhance CRISPR genome editing in pluripotent stem cells. , 2015, Cell stem cell.

[51]  Manfred Schmidt,et al.  Mapping the precision of genome editing , 2015, Nature Biotechnology.

[52]  Xiaoling Wang,et al.  Unbiased detection of off-target cleavage by CRISPR-Cas9 and TALENs using integrase-defective lentiviral vectors , 2015, Nature Biotechnology.

[53]  Randall J. Platt,et al.  Therapeutic genome editing: prospects and challenges , 2015, Nature Medicine.

[54]  Alexandro E. Trevino,et al.  Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex , 2014, Nature.

[55]  N. Pollet,et al.  Comparison of T7E1 and Surveyor Mismatch Cleavage Assays to Detect Mutations Triggered by Engineered Nucleases , 2015, G3: Genes, Genomes, Genetics.

[56]  Martin J. Aryee,et al.  GUIDE-Seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases , 2014, Nature Biotechnology.

[57]  Richard L. Frock,et al.  Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases , 2014, Nature Biotechnology.

[58]  E. Lander,et al.  Development and Applications of CRISPR-Cas 9 for Genome Engineering , 2015 .

[59]  J. Joung,et al.  Dimeric CRISPR RNA-Guided FokI-dCas9 Nucleases Directed by Truncated gRNAs for Highly Specific Genome Editing. , 2015, Human gene therapy.

[60]  Eugene V Koonin,et al.  Annotation and Classification of CRISPR-Cas Systems. , 2015, Methods in molecular biology.

[61]  S. Wolfe,et al.  Creating and evaluating accurate CRISPR-Cas9 scalpels for genomic surgery , 2015, Nature Methods.

[62]  J. Keith Joung,et al.  Efficient Delivery of Genome-Editing Proteins In Vitro and In Vivo , 2014, Nature Biotechnology.

[63]  Steven Lin,et al.  Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery , 2014, eLife.

[64]  Meagan E. Sullender,et al.  Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation , 2014, Nature Biotechnology.

[65]  Gang Wang,et al.  Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells , 2014, Nature Communications.

[66]  A. Fire,et al.  Landscape of target:guide homology effects on Cas9-mediated cleavage , 2014, Nucleic acids research.

[67]  Chase L. Beisel,et al.  Guide RNA functional modules direct Cas9 activity and orthogonality. , 2014, Molecular cell.

[68]  George M. Church,et al.  Genome editing assessment using CRISPR Genome Analyzer (CRISPR-GA) , 2014, Bioinform..

[69]  Max A. Horlbeck,et al.  Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation , 2014, Cell.

[70]  L. Zhu,et al.  CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems , 2014, PloS one.

[71]  M. Jinek,et al.  Structural basis of PAM-dependent target DNA recognition by the Cas9 endonuclease , 2014, Nature.

[72]  Mazhar Adli,et al.  Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease , 2014, Nature Biotechnology.

[73]  Donald J. Zack,et al.  Expansion of the CRISPR-Cas9 genome targeting space through the use of H1 promoter-expressed guide–RNAs , 2014, Nature Communications.

[74]  Daesik Kim,et al.  Highly efficient RNA-guided genome editing in human cells via delivery of purified Cas9 ribonucleoproteins , 2014, Genome research.

[75]  David R. Liu,et al.  Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification , 2014, Nature Biotechnology.

[76]  E. Lander,et al.  Development and Applications of CRISPR-Cas9 for Genome Engineering , 2014, Cell.

[77]  L. Nissim,et al.  Multiplexed and programmable regulation of gene networks with an integrated RNA and CRISPR/Cas toolkit in human cells. , 2014, Molecular cell.

[78]  Martin J. Aryee,et al.  Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing , 2014, Nature Biotechnology.

[79]  Jeffry D. Sander,et al.  CRISPR-Cas systems for editing, regulating and targeting genomes , 2014, Nature Biotechnology.

[80]  David A. Scott,et al.  Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells , 2014, Nature Biotechnology.

[81]  V. Iyer,et al.  Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects , 2014, Nature Methods.

[82]  Feng Zhang,et al.  Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA , 2014, Cell.

[83]  Jennifer A. Doudna,et al.  DNA interrogation by the CRISPR RNA-guided endonuclease Cas9 , 2014, Nature.

[84]  J. Keith Joung,et al.  Improving CRISPR-Cas nuclease specificity using truncated guide RNAs , 2014, Nature Biotechnology.

[85]  Wei Zhang,et al.  Dynamic Imaging of Genomic Loci in Living Human Cells by an Optimized CRISPR/Cas System , 2014, Cell.

[86]  Neville E. Sanjana,et al.  Genome-Scale CRISPR-Cas9 Knockout Screening in Human Cells , 2014, Science.

[87]  S. Ha,et al.  Highly efficient gene knockout in mice and zebrafish with RNA-guided endonucleases , 2014, Genome research.

[88]  Kira S. Makarova,et al.  Phylogeny of Cas9 determines functional exchangeability of dual-RNA and Cas9 among orthologous type II CRISPR-Cas systems , 2013, Nucleic acids research.

[89]  Juan P Albar,et al.  The Minimal Information about a Proteomics Experiment (MIAPE) from the Proteomics Standards Initiative. , 2014, Methods in molecular biology.

[90]  Jin-Soo Kim,et al.  Analysis of off-target effects of CRISPR/Cas-derived RNA-guided endonucleases and nickases , 2014, Genome research.

[91]  Dana Carroll,et al.  Heritable Gene Knockout in Caenorhabditis elegans by Direct Injection of Cas9–sgRNA Ribonucleoproteins , 2013, Genetics.

[92]  David A. Scott,et al.  Genome engineering using the CRISPR-Cas9 system , 2013, Nature Protocols.

[93]  G. Church,et al.  Cas9 as a versatile tool for engineering biology , 2013, Nature Methods.

[94]  Eli J. Fine,et al.  DNA targeting specificity of RNA-guided Cas9 nucleases , 2013, Nature Biotechnology.

[95]  David A. Scott,et al.  Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity , 2013, Cell.

[96]  Nicholas E. Propson,et al.  Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis , 2013, Proceedings of the National Academy of Sciences.

[97]  David R. Liu,et al.  High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity , 2013, Nature Biotechnology.

[98]  G. Church,et al.  CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering , 2013, Nature Biotechnology.

[99]  Christopher M. Vockley,et al.  RNA-guided gene activation by CRISPR-Cas9-based transcription factors , 2013, Nature Methods.

[100]  Randall J. Platt,et al.  Optical Control of Mammalian Endogenous Transcription and Epigenetic States , 2013, Nature.

[101]  J. Keith Joung,et al.  High frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells , 2013, Nature Biotechnology.

[102]  S. Deventer,et al.  Mir‐142‐3p target sequences reduce transgene‐directed immunogenicity following intramuscular adeno‐associated virus 1 vector‐mediated gene delivery , 2013, The journal of gene medicine.

[103]  Emmanuelle Charpentier,et al.  The tracrRNA and Cas9 families of type II CRISPR-Cas immunity systems , 2013, RNA biology.

[104]  Feng Zhang,et al.  CRISPR-assisted editing of bacterial genomes , 2013, Nature Biotechnology.

[105]  Seung Woo Cho,et al.  Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease , 2013, Nature Biotechnology.

[106]  James E. DiCarlo,et al.  RNA-Guided Human Genome Engineering via Cas9 , 2013, Science.

[107]  Le Cong,et al.  Multiplex Genome Engineering Using CRISPR/Cas Systems , 2013, Science.

[108]  Bo Zhang,et al.  EENdb: a database and knowledge base of ZFNs and TALENs for endonuclease engineering , 2012, Nucleic Acids Res..

[109]  David G Hendrickson,et al.  Differential analysis of gene regulation at transcript resolution with RNA-seq , 2012, Nature Biotechnology.

[110]  Cole Trapnell,et al.  TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions , 2013, Genome Biology.

[111]  R. Barrangou,et al.  Cas9–crRNA ribonucleoprotein complex mediates specific DNA cleavage for adaptive immunity in bacteria , 2012, Proceedings of the National Academy of Sciences.

[112]  J. Doudna,et al.  A Programmable Dual-RNA–Guided DNA Endonuclease in Adaptive Bacterial Immunity , 2012, Science.

[113]  Philippe Horvath,et al.  The Streptococcus thermophilus CRISPR/Cas system provides immunity in Escherichia coli , 2011, Nucleic acids research.

[114]  Elo Leung,et al.  A TALE nuclease architecture for efficient genome editing , 2011, Nature Biotechnology.

[115]  J. Vogel,et al.  CRISPR RNA maturation by trans-encoded small RNA and host factor RNase III , 2011, Nature.

[116]  Chris F. Taylor,et al.  Data standards for Omics data: the basis of data sharing and reuse. , 2011, Methods in molecular biology.

[117]  Erin L. Doyle,et al.  Targeting DNA Double-Strand Breaks with TAL Effector Nucleases , 2010, Genetics.

[118]  Jeffrey C. Miller,et al.  A rapid and general assay for monitoring endogenous gene modification. , 2010, Methods in molecular biology.

[119]  Jens Boch,et al.  Breaking the Code of DNA Binding Specificity of TAL-Type III Effectors , 2009, Science.

[120]  Matthew J. Moscou,et al.  A Simple Cipher Governs DNA Recognition by TAL Effectors , 2009, Science.

[121]  V. Beneš,et al.  The MIQE guidelines: minimum information for publication of quantitative real-time PCR experiments. , 2009, Clinical chemistry.

[122]  Stan J. J. Brouns,et al.  Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes , 2008, Science.

[123]  J. Rabinowitz,et al.  Analysis of AAV serotypes 1-9 mediated gene expression and tropism in mice after systemic injection. , 2008, Molecular therapy : the journal of the American Society of Gene Therapy.

[124]  Thorsten Henrich,et al.  Minimum information specification for in situ hybridization and immunohistochemistry experiments (MISFISHIE) , 2008, Nature Biotechnology.

[125]  Lennart Martens,et al.  The minimum information about a proteomics experiment (MIAPE) , 2007, Nature Biotechnology.

[126]  Adam James Waite,et al.  An improved zinc-finger nuclease architecture for highly specific genome editing , 2007, Nature Biotechnology.

[127]  C. Carles,et al.  Selectivity and proofreading both contribute significantly to the fidelity of RNA polymerase III transcription , 2007, Proceedings of the National Academy of Sciences.

[128]  R. Barrangou,et al.  CRISPR Provides Acquired Resistance Against Viruses in Prokaryotes , 2007, Science.

[129]  Chris F. Taylor,et al.  Minimum Reporting Requirements for Proteomics: A MIAPE Primer , 2006, Proteomics.

[130]  James M. Wilson,et al.  Adeno-associated virus serotype 9 vectors transduce murine alveolar and nasal epithelia and can be readministered , 2006, Proceedings of the National Academy of Sciences.

[131]  Ronald C. Taylor,et al.  Development of the Minimum Information Specification for In Situ Hybridization and Immunohistochemistry Experiments (MISFISHIE). , 2006, Omics : a journal of integrative biology.

[132]  Jeffrey C. Miller,et al.  Highly efficient endogenous human gene correction using designed zinc-finger nucleases , 2005, Nature.

[133]  G. Vergnaud,et al.  CRISPR elements in Yersinia pestis acquire new repeats by preferential uptake of bacteriophage DNA, and provide additional tools for evolutionary studies. , 2005, Microbiology.

[134]  J. García-Martínez,et al.  Intervening Sequences of Regularly Spaced Prokaryotic Repeats Derive from Foreign Genetic Elements , 2005, Journal of Molecular Evolution.

[135]  L. Schouls,et al.  Identification of genes that are associated with DNA repeats in prokaryotes , 2002, Molecular microbiology.

[136]  Jason E. Stewart,et al.  Minimum information about a microarray experiment (MIAME)—toward standards for microarray data , 2001, Nature Genetics.

[137]  J. Mcarthur,et al.  Factors influencing the development of an anti-factor IX (FIX) immune response following administration of adeno-associated virus-FIX. , 2001, Blood.

[138]  Dana Carroll,et al.  Stimulation of Homologous Recombination through Targeted Cleavage by Chimeric Nucleases , 2001, Molecular and Cellular Biology.

[139]  L. Brieba,et al.  Misincorporation by wild-type and mutant T7 RNA polymerases: identification of interactions that reduce misincorporation rates by stabilizing the catalytically incompetent open conformation. , 2000, Biochemistry.

[140]  F. J. Mojica,et al.  Biological significance of a family of regularly spaced repeats in the genomes of Archaea, Bacteria and mitochondria , 2000, Molecular microbiology.