CRISPR/Cas9 genome editing in human pluripotent stem cells: Harnessing human genetics in a dish

Genome Editing of Lineage Determinants in Human Pluripotent Stem Cells Reveals Mechanisms of Pancreatic Development and Diabetes

(2016) Zengrong Zhu et al.   Cell Stem Cell

Functional genetic screens for enhancer elements in the human genome using CRISPR-Cas9

(2016) Gozde Korkmaz et al.   NATURE BIOTECHNOLOGY

Knock-in of large reporter genes in human cells via CRISPR/Cas9-induced homology-dependent and independent DNA repair

(2016) Xiangjun He et al.   NUCLEIC ACIDS RESEARCH

Generation and validation of PAX7 reporter lines from human iPS cells using CRISPR/Cas9 technology

(2016) Jianbo Wu et al.   Stem Cell Research

Generation and Characterization of a MYF5 Reporter Human iPS Cell Line Using CRISPR/Cas9 Mediated Homologous Recombination

(2016) Jianbo Wu et al.   Scientific Reports

Induction of site-specific chromosomal translocations in embryonic stem cells by CRISPR/Cas9

(2016) Junfeng Jiang et al.   Scientific Reports

WGE: a CRISPR database for genome engineering: Fig. 1.

(2015) Alex Hodgkins et al.   BIOINFORMATICS

Functional Correction of Large Factor VIII Gene Chromosomal Inversions in Hemophilia A Patient-Derived iPSCs Using CRISPR-Cas9

(2015) Chul-Yong Park et al.   Cell Stem Cell

Engineering Human Stem Cell Lines with Inducible Gene Knockout using CRISPR/Cas9

(2015) Yuejun Chen et al.   Cell Stem Cell

CRISPR-mediated genotypic and phenotypic correction of a chronic granulomatous disease mutation in human iPS cells

(2015) Rowan Flynn et al.   EXPERIMENTAL HEMATOLOGY

Inhibition of nonhomologous end joining to increase the specificity of CRISPR/Cas9 genome editing

(2015) Supriya V. Vartak et al.   FEBS Journal

Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex

(2015) Silvana Konermann et al.   NATURE

Kidney organoids from human iPS cells contain multiple lineages and model human nephrogenesis

(2015) Minoru Takasato 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

Inducible in vivo genome editing with CRISPR-Cas9

(2015) Lukas E Dow et al.   NATURE BIOTECHNOLOGY

Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains

(2015) Junwei Shi 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

Functional annotation of native enhancers with a Cas9–histone demethylase fusion

(2015) Nicola A Kearns et al.   NATURE METHODS

Unraveling CRISPR-Cas9 genome engineering parameters via a library-on-library approach

(2015) Raj Chari et al.   NATURE METHODS

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

High-throughput functional genomics using CRISPR–Cas9

(2015) Ophir Shalem et al.   NATURE REVIEWS GENETICS

Beyond editing: repurposing CRISPR–Cas9 for precision genome regulation and interrogation

(2015) Antonia A. Dominguez et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Cas9-chromatin binding information enables more accurate CRISPR off-target prediction

(2015) Ritambhara Singh et al.   NUCLEIC ACIDS RESEARCH

Human Induced Pluripotent Stem CellNEUROG2Dual Knockin Reporter Lines Generated by the CRISPR/Cas9 System

(2015) Shenglan Li et al.   STEM CELLS AND DEVELOPMENT

Efficient CRISPR-Cas9-Mediated Generation of Knockin Human Pluripotent Stem Cells Lacking Undesired Mutations at the Targeted Locus

(2015) Florian T. Merkle et al.   Cell Reports

Pharmacological inhibition of DNA-PK stimulates Cas9-mediated genome editing

(2015) Francis Robert et al.   Genome Medicine

Off-target Effects in CRISPR/Cas9-mediated Genome Engineering

(2015) Xiao-Hui Zhang et al.   Molecular Therapy-Nucleic Acids

A CRISPR/Cas-Mediated Selection-free Knockin Strategy in Human Embryonic Stem Cells

(2015) Zengrong Zhu et al.   Stem Cell Reports

A new age in functional genomics using CRISPR/Cas9 in arrayed library screening

(2015) Alexander Agrotis et al.   Frontiers in Genetics

Differentiation of human ESCs to retinal ganglion cells using a CRISPR engineered reporter cell line

(2015) Valentin M. Sluch et al.   Scientific Reports

CRISPRdirect: software for designing CRISPR/Cas guide RNA with reduced off-target sites

(2014) Yuki Naito et al.   BIOINFORMATICS

Generation of Functional Human Pancreatic β Cells In Vitro

(2014) Felicia W. Pagliuca et al.   CELL

A Protein-Tagging System for Signal Amplification in Gene Expression and Fluorescence Imaging

(2014) Marvin E. Tanenbaum et al.   CELL

Genome-Scale CRISPR-Mediated Control of Gene Repression and Activation

(2014) Luke A. Gilbert et al.   CELL

Genome-wide identification of CRISPR/Cas9 off-targets in human genome

(2014) Jinzhi Duan et al.   CELL RESEARCH

Targeted Gene Correction Minimally Impacts Whole-Genome Mutational Load in Human-Disease-Specific Induced Pluripotent Stem Cell Clones

(2014) Keiichiro Suzuki et al.   Cell Stem Cell

Low Incidence of Off-Target Mutations in Individual CRISPR-Cas9 and TALEN Targeted Human Stem Cell Clones Detected by Whole-Genome Sequencing

(2014) Adrian Veres et al.   Cell Stem 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

An iCRISPR Platform for Rapid, Multiplexable, and Inducible Genome Editing in Human Pluripotent Stem Cells

(2014) Federico González et al.   Cell Stem Cell

Seamless gene correction of β-thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 andpiggyBac

(2014) Fei Xie et al.   GENOME RESEARCH

53BP1, BRCA1, and the Choice between Recombination and End Joining at DNA Double-Strand Breaks

(2014) J. M. Daley et al.   MOLECULAR AND CELLULAR BIOLOGY

High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells

(2014) Yuexin Zhou et al.   NATURE

Human oocytes reprogram adult somatic nuclei of a type 1 diabetic to diploid pluripotent stem cells

(2014) Mitsutoshi Yamada et al.   NATURE

Saturation editing of genomic regions by multiplex homology-directed repair

(2014) Gregory M. Findlay et al.   NATURE

Programmable RNA recognition and cleavage by CRISPR/Cas9

(2014) Mitchell R. O’Connell et al.   NATURE

In vivo engineering of oncogenic chromosomal rearrangements with the CRISPR/Cas9 system

(2014) Danilo Maddalo et al.   NATURE

Improving CRISPR-Cas nuclease specificity using truncated guide RNAs

(2014) Yanfang Fu et al.   NATURE BIOTECHNOLOGY

CRISPR-Cas systems for editing, regulating and targeting genomes

(2014) Jeffry D Sander et al.   NATURE BIOTECHNOLOGY

Rational design of highly active sgRNAs for CRISPR-Cas9–mediated gene inactivation

(2014) John G Doench et al.   NATURE BIOTECHNOLOGY

Reversal of diabetes with insulin-producing cells derived in vitro from human pluripotent stem cells

(2014) Alireza Rezania et al.   NATURE BIOTECHNOLOGY

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

(2014) John P Guilinger 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

Efficient genome modification by CRISPR-Cas9 nickase with minimal off-target effects

(2014) Bin Shen et al.   NATURE METHODS

E-CRISP: fast CRISPR target site identification

(2014) Florian Heigwer et al.   NATURE METHODS

Generation of a vascularized and functional human liver from an iPSC-derived organ bud transplant

(2014) Takanori Takebe et al.   Nature Protocols

Pluripotent stem cells in regenerative medicine: challenges and recent progress

(2014) Viviane Tabar et al.   NATURE REVIEWS GENETICS

Unravelling the structural and mechanistic basis of CRISPR–Cas systems

(2014) John van der Oost et al.   NATURE REVIEWS MICROBIOLOGY

Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells

(2014) Susan M. Byrne 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

Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5Δ32 mutation confers resistance to HIV infection

(2014) Lin Ye et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Organogenesis in a dish: Modeling development and disease using organoid technologies

(2014) M. A. Lancaster et al.   SCIENCE

Targeted and genome-wide sequencing reveal single nucleotide variations impacting specificity of Cas9 in human stem cells

(2014) Luhan Yang et al.   Nature Communications

Engineering human tumour-associated chromosomal translocations with the RNA-guided CRISPR–Cas9 system

(2014) R. Torres et al.   Nature Communications

Targeted genomic rearrangements using CRISPR/Cas technology

(2014) Peter S. Choi et al.   Nature Communications

Multiplex genome engineering in human cells using all-in-one CRISPR/Cas9 vector system

(2014) Tetsushi Sakuma et al.   Scientific Reports

Specific Gene Repression by CRISPRi System Transferred through Bacterial Conjugation

(2014) Weiyue Ji et al.   ACS Synthetic Biology

Homologous recombination in human embryonic stem cells using CRISPR/Cas9 nickase and a long DNA donor template

(2014) Zhili Rong et al.   Protein & Cell

Enhanced homology-directed human genome engineering by controlled timing of CRISPR/Cas9 delivery

(2014) Steven Lin et al.   eLife

Molecular Mechanisms of RNA Interference

(2013) Ross C. Wilson et al.   Annual Review of Biophysics

Efficient isolation of specific genomic regions and identification of associated proteins by engineered DNA-binding molecule-mediated chromatin immunoprecipitation (enChIP) using CRISPR

(2013) Toshitsugu Fujita et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

One-Step Generation of Mice Carrying Mutations in Multiple Genes by CRISPR/Cas-Mediated Genome Engineering

(2013) Haoyi Wang et al.   CELL

Repurposing CRISPR as an RNA-Guided Platform for Sequence-Specific Control of Gene Expression

(2013) Lei S. Qi et al.   CELL

Double Nicking by RNA-Guided CRISPR Cas9 for Enhanced Genome Editing Specificity

(2013) F. Ann Ran et al.   CELL

CRISPR-Mediated Modular RNA-Guided Regulation of Transcription in Eukaryotes

(2013) Luke A. Gilbert et al.   CELL

Human Embryonic Stem Cells Derived by Somatic Cell Nuclear Transfer

(2013) Masahito Tachibana et al.   CELL

Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system

(2013) Albert W Cheng et al.   CELL RESEARCH

Genetic and Epigenetic Variations in iPSCs: Potential Causes and Implications for Application

(2013) Gaoyang Liang et al.   Cell Stem Cell

Enhanced Efficiency of Human Pluripotent Stem Cell Genome Editing through Replacing TALENs with CRISPRs

(2013) Qiurong Ding et al.   Cell Stem Cell

Human pluripotent stem cells: an emerging model in developmental biology

(2013) Z. Zhu et al.   DEVELOPMENT

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

(2013) S. W. Cho et al.   GENOME RESEARCH

Vascularized and functional human liver from an iPSC-derived organ bud transplant

(2013) Takanori Takebe et al.   NATURE

The zebrafish reference genome sequence and its relationship to the human genome

(2013) Kerstin Howe et al.   NATURE

Cerebral organoids model human brain development and microcephaly

(2013) Madeline A. Lancaster et al.   NATURE

Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library

(2013) Hiroko Koike-Yusa et al.   NATURE BIOTECHNOLOGY

DNA targeting specificity of RNA-guided Cas9 nucleases

(2013) Patrick D Hsu et al.   NATURE BIOTECHNOLOGY

Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease

(2013) Seung Woo Cho 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

Directed differentiation of human pluripotent cells to ureteric bud kidney progenitor-like cells

(2013) Yun Xia et al.   NATURE CELL BIOLOGY

Directing human embryonic stem cell differentiation towards a renal lineage generates a self-organizing kidney

(2013) M. Takasato et al.   NATURE CELL BIOLOGY

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

(2013) Pablo Perez-Pinera et al.   NATURE METHODS

CRISPR RNA–guided activation of endogenous human genes

(2013) Morgan L Maeder et al.   NATURE METHODS

CRISPR interference (CRISPRi) for sequence-specific control of gene expression

(2013) Matthew H Larson et al.   Nature Protocols

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

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

(2013) David Bikard et al.   NUCLEIC ACIDS RESEARCH

Optimization of scarless human stem cell genome editing

(2013) Luhan Yang et al.   NUCLEIC ACIDS RESEARCH

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

Noncoding Transcription at Enhancers: General Principles and Functional Models

(2012) Gioacchino Natoli et al.   Annual Review of Genetics

Self-Formation of Optic Cups and Storable Stratified Neural Retina from Human ESCs

(2012) Tokushige Nakano et al.   Cell Stem Cell

A TALEN Genome-Editing System for Generating Human Stem Cell-Based Disease Models

(2012) Qiurong Ding et al.   Cell Stem Cell

A t(1;11) translocation linked to schizophrenia and affective disorders gives rise to aberrant chimeric DISC1 transcripts that encode structurally altered, deleterious mitochondrial proteins

(2012) Jennifer E. Eykelenboom et al.   HUMAN MOLECULAR GENETICS

TALENs: a widely applicable technology for targeted genome editing

(2012) J. Keith Joung et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

(2012) M. Jinek et al.   SCIENCE

An Automated High Throughput Screening-Compatible Assay to Identify Regulators of Stem Cell Neural Differentiation

(2011) Laura Casalino et al.   MOLECULAR BIOTECHNOLOGY

Genetic engineering of human pluripotent cells using TALE nucleases

(2011) Dirk Hockemeyer et al.   NATURE BIOTECHNOLOGY

Harnessing the potential of induced pluripotent stem cells for regenerative medicine

(2011) Sean M. Wu et al.   NATURE CELL BIOLOGY

High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases

(2011) Fuqiang Chen et al.   NATURE METHODS

Regulation of Homologous Recombination in Eukaryotes

(2010) Wolf-Dietrich Heyer et al.   Annual Review of Genetics

2010: A Century of Drosophila Genetics Through the Prism of the white Gene

(2010) M. M. Green   GENETICS

Patient-specific induced pluripotent stem-cell-derived models of LEOPARD syndrome

(2010) Xonia Carvajal-Vergara et al.   NATURE

A genome-wide RNAi screen reveals determinants of human embryonic stem cell identity

(2010) Na-Yu Chia et al.   NATURE

Directed differentiation of human pluripotent stem cells into intestinal tissue in vitro

(2010) Jason R. Spence et al.   NATURE

Genome editing with engineered zinc finger nucleases

(2010) Fyodor D. Urnov et al.   NATURE REVIEWS GENETICS

Synthesis of high-quality libraries of long (150mer) oligonucleotides by a novel depurination controlled process

(2010) Emily M. LeProust et al.   NUCLEIC ACIDS RESEARCH

Novel regulators of stem cell fates identified by a multivariate phenotype screen of small compounds on human embryonic stem cell colonies

(2010) Ivana Barbaric et al.   Stem Cell Research

A high-throughput multiplexed screening assay for optimizing serum-free differentiation protocols of human embryonic stem cells

(2010) Joel T. Outten et al.   Stem Cell Research

A Small Molecule Primes Embryonic Stem Cells for Differentiation

(2009) Shoutian Zhu et al.   Cell Stem Cell

Gene Targeting of a Disease-Related Gene in Human Induced Pluripotent Stem and Embryonic Stem Cells

(2009) Jizhong Zou et al.   Cell Stem Cell

A Genome-Scale RNAi Screen for Oct4 Modulators Defines a Role of the Paf1 Complex for Embryonic Stem Cell Identity

(2009) Li Ding et al.   Cell Stem Cell

A genome-wide RNAi screen identifies a new transcriptional module required for self-renewal

(2009) G. Hu et al.   GENES & DEVELOPMENT

Disease-corrected haematopoietic progenitors from Fanconi anaemia induced pluripotent stem cells

(2009) Ángel Raya et al.   NATURE

Efficient targeting of expressed and silent genes in human ESCs and iPSCs using zinc-finger nucleases

(2009) Dirk Hockemeyer et al.   NATURE BIOTECHNOLOGY

Disease-Specific Induced Pluripotent Stem Cells

(2008) In-Hyun Park et al.   CELL

An RNAi Screen of Chromatin Proteins Identifies Tip60-p400 as a Regulator of Embryonic Stem Cell Identity

(2008) Thomas G. Fazzio et al.   CELL

High-Throughput Screening Assay for the Identification of Compounds Regulating Self-Renewal and Differentiation in Human Embryonic Stem Cells

(2008) Sabrina C. Desbordes et al.   Cell Stem Cell

Induced pluripotent stem cells from a spinal muscular atrophy patient

(2008) Allison D. Ebert et al.   NATURE

Pancreatic endoderm derived from human embryonic stem cells generates glucose-responsive insulin-secreting cells in vivo

(2008) Evert Kroon et al.   NATURE BIOTECHNOLOGY