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1. Full Text High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells
by Fu, Yanfang and Foden, Jennifer A and Khayter, Cyd and Maeder, Morgan L and Reyon, Deepak and Joung, J Keith and Sander, Jeffry D
Nature Biotechnology, ISSN 1087-0156, 09/2013, Volume 31, Issue 9, pp. 822 - 826
Clustered, regularly interspaced, short palindromic repeat (CRISPR) RNA-guided nucleases (RGNs) have rapidly emerged as a facile and efficient platform for... 
BACTERIA | ENDONUCLEASE | ARCHAEA | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | SYSTEMS | GENERATION | MICE | ZINC-FINGER NUCLEASES | Genetic Engineering - methods | Endonucleases - genetics | CRISPR-Associated Proteins - genetics | Base Sequence | Humans | HEK293 Cells | K562 Cells | Mutagenesis - genetics | Molecular Sequence Data | Physiological aspects | Nucleases | Research | Mutagenesis | Gene expression | Enzymes | Cellular biology | Ribonucleic acid--RNA | Index Medicus
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2. Full Text Improving CRISPR-Cas nuclease specificity using truncated guide RNAs
by Fu, Yanfang and Sander, Jeffry D and Reyon, Deepak and Cascio, Vincent M and Joung, J Keith
Nature Biotechnology, ISSN 1087-0156, 2014, Volume 32, Issue 3, pp. 279 - 284
Clustered, regularly interspaced, short palindromic repeat (CRISPR) RNA-guided nucleases (RGNs) are highly efficient genome editing tools(1-3).... 
ZINC-FINGER TARGETER | TRANSCRIPTION FACTORS | HUMAN GENOME | NICKING | ZIFIT | NICKASES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | HUMAN-CELLS | GENES | SYSTEMS | TOOL | Genetic research | Nucleases | Genetic engineering | Research | RNA | Methods | Enzymes | Mutation | Ribonucleic acid--RNA | Genomics | Index Medicus
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3. Full Text Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing
by Tsai, Shengdar Q and Wyvekens, Nicolas and Khayter, Cyd and Foden, Jennifer A and Thapar, Vishal and Reyon, Deepak and Goodwin, Mathew J and Aryee, Martin J and Joung, J. Keith
Nature Biotechnology, ISSN 1087-0156, 2014, Volume 32, Issue 6, pp. 569 - 576
  Monomeric CRISPR-Cas9 nucleases are widely used for targeted genome editing but can induce unwanted off-target mutations with high frequencies. Here we... 
Genetic research | Nucleases | Genetic aspects | Genetic engineering | Zinc finger proteins | Research | Biotechnology | Enzymes | Mutation | Genomics | Index Medicus
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4. Full Text FLASH assembly of TALENs for high-throughput genome editing
by Reyon, Deepak and Tsai, Shengdar Q and Khgayter, Cyd and Foden, Jennifer A and Sander, Jeffry D and Joung, J Keith
Nature Biotechnology, ISSN 1087-0156, 05/2012, Volume 30, Issue 5, pp. 460 - 465
Engineered transcription activator-like effector nucleases (TALENs) have shown promise as facile and broadly applicable genome editing tools. However, no... 
EFFECTORS | CELLS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | KNOCKOUT | PROTEINS | ZINC-FINGER NUCLEASES | DNA-BINDING SPECIFICITY | Gene Targeting - methods | Green Fluorescent Proteins - metabolism | Automation | Computational Biology - methods | Endonucleases - genetics | Biotinylation | DNA Restriction Enzymes - genetics | Epigenesis, Genetic | Humans | Molecular Sequence Data | Genetic Techniques | Sequence Homology, Nucleic Acid | Sequence Analysis, DNA - instrumentation | Neoplasms - genetics | Base Sequence | Transcription, Genetic | Mutation | Genome, Human | Sequence Analysis, DNA - methods | Physiological aspects | Nucleases | DNA binding proteins | Research | Genetic transcription | Proteins | Genomics | Binding sites | Biomedical engineering | Index Medicus
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5. Full Text Efficient genome editing in zebrafish using a CRISPR-Cas system
by Hwang, Woong Y and Fu, Yanfang and Reyon, Deepak and Maeder, Morgan L and Tsai, Shengdar Q and Sander, Jeffry D and Peterson, Randall T and Yeh, J-R Joanna and Joung, J Keith
Nature Biotechnology, ISSN 1087-0156, 03/2013, Volume 31, Issue 3, pp. 227 - 229
In bacteria, foreign nucleic acids are silenced by clustered, regularly interspaced, short palindromic repeats (CRISPR) CRISPR-associated (Gas) systems.... 
IMMUNITY | BACTERIA | TALENS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ZINC-FINGER NUCLEASES | PROKARYOTES | Endonucleases - genetics | RNA, Guide - genetics | RNA Editing | Molecular Sequence Data | Zebrafish - genetics | DNA - genetics | Animals | Genetic Engineering | Base Sequence | CRISPR-Cas Systems | Embryo, Nonmammalian | Mutation | Genome | Nucleic Acid Conformation | DNA Cleavage | Inverted Repeat Sequences | Physiological aspects | Genetic aspects | Restriction enzymes, DNA | Restriction-modification system | Zebra fish | Biotechnology | Zebrafish | Genetic engineering | Mutagenesis | Ribonucleic acid--RNA | Index Medicus
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6. Full Text Locus-specific editing of histone modifications at endogenous enhancers
by Mendenhall, Eric M and Williamson, Kaylyn E and Reyon, Deepak and Zou, James Y and Ram, Oren and Joung, J Keith and Bernstein, Bradley E
Nature Biotechnology, ISSN 1087-0156, 12/2013, Volume 31, Issue 12, pp. 1133 - 1136
Mammalian gene regulation is dependent on tissue-specific enhancers that can act across large distances to influence transcriptional activity(1-3). Mapping... 
ELEMENTS | CELLS | TAL EFFECTORS | CHROMATIN | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | DNA | DEMETHYLATION | TRANSCRIPTION | REGIONS | GENE-EXPRESSION | GENOME | Histones - genetics | Polymorphism, Single Nucleotide - genetics | Mutagenesis, Site-Directed - methods | Enhancer Elements, Genetic - genetics | Chromatin - genetics | Promoter Regions, Genetic - genetics | Regulatory Elements, Transcriptional - genetics | Physiological aspects | Histones | Genetic aspects | Research | Genetic regulation | Proteins | Chromatin | Cellular biology | Gene expression | Index Medicus
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7. Full Text Targeted gene disruption in somatic zebrafish cells using engineered TALENs
by Sander, Jeffry D and Cade, Lindsay and Khayter, Cyd and Reyon, Deepak and Peterson, Randall T and Joung, J Keith and Yeh, Jing-Ruey J
Nature Biotechnology, ISSN 1087-0156, 08/2011, Volume 29, Issue 8, pp. 697 - 698
EFFECTORS | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | ZINC-FINGER NUCLEASES | Combinatorial Chemistry Techniques - methods | Transcription Factors - metabolism | Mutagenesis, Site-Directed - methods | Genetic Engineering | Transcription Factors - genetics | Humans | Nucleases | Usage | Zebra fish | Physiological aspects | Genetic engineering | Genetic aspects | Research | Zinc finger proteins | Index Medicus
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8. Full Text Heritable and Precise Zebrafish Genome Editing Using a CRISPR-Cas System
by Hwang, Woong Y and Fu, Yanfang and Reyon, Deepak and Maeder, Morgan L and Kaini, Prakriti and Sander, Jeffry D and Joung, J. Keith and Peterson, Randall T and Yeh, Jing-Ruey Joanna
PLoS ONE, ISSN 1932-6203, 07/2013, Volume 8, Issue 7, pp. e68708 - e68708
We have previously reported a simple and customizable CRISPR (clustered regularly interspaced short palindromic repeats) RNA-guided Cas9 nuclease (RGN) system... 
CELLS | MUTAGENESIS | BACTERIA | ENDONUCLEASE | ARCHAEA | TALENS | MULTIDISCIPLINARY SCIENCES | TARGETED GENE DISRUPTION | ZINC-FINGER NUCLEASES | Oligonucleotides - genetics | CRISPR-Associated Proteins - chemistry | Oligonucleotides - chemistry | CRISPR-Associated Proteins - genetics | Molecular Sequence Data | Mutation Rate | INDEL Mutation | Zebrafish - genetics | Sequence Alignment | Animals | Genetic Engineering | Base Sequence | CRISPR-Cas Systems | Germ-Line Mutation | Mutagenesis, Insertional | Genome | Animal genetics | Nucleases | RNA | Oligodeoxynucleotides | Genomics | Genetic aspects | DNA binding proteins | Nucleotide sequencing | DNA sequencing | CRISPR | Medical research | Nucleotide sequence | Base pairs | Genes | Oligonucleotides | Zebrafish | Genomes | Biology | Ribonucleic acid--RNA | Medical schools | Medicine | Pathology | Engineering | Hospitals | Mutagenesis | DNA methylation | Mutation | Nuclease | Deoxyribonucleic acid--DNA | Cancer | Index Medicus | Ribonucleic acid | Deoxyribonucleic acid | DNA
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9. Full Text Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins
by Maeder, Morgan L and Angstman, James F and Richardson, Marcy E and Linder, Samantha J and Cascio, Vincent M and Tsai, Shengdar Q and Ho, Quan H and Sander, Jeffry D and Reyon, Deepak and Bernstein, Bradley E and Costello, Joseph F and Wilkinson, Miles F and Joung, J. Keith
Nature Biotechnology, ISSN 1087-0156, 12/2013, Volume 31, Issue 12, pp. 1137 - 1142
Genome-wide studies have defined cell type-specific patterns of DNA methylation(1) that are important for regulating gene expression in both normal... 
CELLS | 5-METHYLCYTOSINE | SEQUENCES | METHYLTRANSFERASES | BIOTECHNOLOGY & APPLIED MICROBIOLOGY | IN-VIVO | MAMMALIAN DEVELOPMENT | TET PROTEINS | CYTOSINE METHYLATION | 5-CARBOXYLCYTOSINE | 5-FORMYLCYTOSINE | Mixed Function Oxygenases | Gene Targeting - methods | Humans | Recombinant Fusion Proteins - genetics | Proto-Oncogene Proteins - genetics | Up-Regulation - genetics | DNA Methylation - genetics | Transcription Factors - genetics | DNA-Binding Proteins - genetics | Promoter Regions, Genetic - genetics | Usage | Genomics | Physiological aspects | Genetic aspects | Research | Methylation | Gene fusion | Methods | Proteins | DNA methylation | Cellular biology | Gene expression | Index Medicus
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10. Full Text Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells
by Liao, Jing and Karnik, Rahul and Gu, Hongcang and Ziller, Michael J and Clement, Kendell and Tsankov, Alexander M and Akopian, Veronika and Gifford, Casey A and Donaghey, Julie and Galonska, Christina and Pop, Ramona and Reyon, Deepak and Tsai, Shengdar Q and Mallard, William and Joung, J Keith and Rinn, John L and Gnirke, Andreas and Meissner, Alexander
Nature Genetics, ISSN 1061-4036, 05/2015, Volume 47, Issue 5, pp. 469 - 478
DNA methylation is a key epigenetic modification involved in regulating gene expression and maintaining genomic integrity. Here we inactivated all three... 
HUMAN GENOME | DNA METHYLATION | EPIGENETIC MEMORY | GENETICS & HEREDITY | SELF-RENEWAL | MAMMALIAN DEVELOPMENT | SOMATIC TISSUE | HUMAN CANCER-CELLS | CPG METHYLATION | DE-NOVO METHYLATION | REGULATORY REGIONS | Catalytic Domain | Gene Expression | Cell Proliferation | Cell Survival | DNA (Cytosine-5-)-Methyltransferase 1 | Coculture Techniques | Epigenesis, Genetic | Humans | Cells, Cultured | Embryonic Stem Cells - enzymology | Gene Knockout Techniques | Embryonic Stem Cells - physiology | DNA (Cytosine-5-)-Methyltransferases - genetics | DNA Methylation | Animals | Base Sequence | CpG Islands | Cell Differentiation | Mice | Apoptosis | Genetic aspects | Methyltransferases | Embryonic stem cells | Gene expression | Properties | Health aspects | Studies | DNA methylation | Mutation | Stem cells | Index Medicus
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11. Full Text Broad specificity profiling of TALENs results in engineered nucleases with improved DNA-cleavage specificity
by Guilinger, John P and Pattanayak, Vikram and Reyon, Deepak and Tsai, Shengdar Q and Sander, Jeffry D and Joung, J Keith and Liu, David R
Nature Methods, ISSN 1548-7091, 2014, Volume 11, Issue 4, pp. 429 - 435
Although transcription activator-like effector nucleases (TALENs) can be designed to cleave chosen DNA sequences, TALENs have activity against related... 
SYSTEM | DISEASE | BIOCHEMICAL RESEARCH METHODS | ZFNS | EFFECTOR NUCLEASES | KNOCKOUT | ZINC-FINGER NUCLEASES | GENOME | REVEALS | Cell Line | Deoxyribonucleases - genetics | Gene Targeting | Protein Engineering - methods | Base Sequence | Humans | Protein Binding | Substrate Specificity - physiology | DNA - metabolism | Binding Sites | Deoxyribonucleases - metabolism | Physiological aspects | Nucleases | Genetic transcription | Research | DNA binding proteins | Genetic engineering | Deoxyribonucleic acid--DNA | Cells | Index Medicus
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12. Full Text Toddler: An embryonic signal that promotes cell movement via apelin receptors
by Pauli, Andrea and Norris, Megan L and Valen, Eivind and Chew, Guo-Liang and Gagnon, James A and Zimmerman, Steven and Mitchell, Andrew and Ma, Jiao and Dubrulle, Julien and Reyon, Deepak and Tsai, Shengdar Q and Joung, J. Keith and Saghatelian, Alan and Schier, Alexander F
Science, ISSN 0036-8075, 2014, Volume 343, Issue 6172, pp. 746 - 746
It has been assumed that most, if not all, signals regulating early development have been identified. Contrary to this expectation, we identified 28 candidate... 
MIGRATION | CARDIOVASCULAR DEVELOPMENT | APJ RECEPTOR | STEM-CELLS | PROTEIN | ZEBRAFISH GASTRULATION | MULTIDISCIPLINARY SCIENCES | IN-VIVO | BLOOD-VESSELS | DROSOPHILA GASTRULATION | DEFICIENT MICE | Amino Acid Sequence | <