Advances in genome editing technology and its promising application in evolutionary and ecological studies

Crystal Structure of Cas9 in Complex with Guide RNA and Target DNA

(2014) Hiroshi Nishimasu et al.   CELL

Generation of Gene-Modified Cynomolgus Monkey via Cas9/RNA-Mediated Gene Targeting in One-Cell Embryos

(2014) Yuyu Niu et al.   CELL

TALEN-Mediated Gene Mutagenesis in Rhesus and Cynomolgus Monkeys

(2014) Hailiang Liu et al.   Cell Stem Cell

Nuclease-mediated genome editing: At the front-line of functional genomics technology

(2014) Tetsushi Sakuma et al.   DEVELOPMENT GROWTH & DIFFERENTIATION

Genome-Wide Prediction of Highly Specific Guide RNA Spacers for CRISPR–Cas9-Mediated Genome Editing in Model Plants and Major Crops

(2014) Kabin Xie et al.   Molecular Plant

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

(2014) Yuexin Zhou et al.   NATURE

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

CRISPR-Cas systems for editing, regulating and targeting genomes

(2014) Jeffry D Sander 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

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

CRISPR/Cas9-Mediated Targeted Mutagenesis in the Liverwort Marchantia polymorpha L.

(2014) Shigeo S. Sugano et al.   PLANT AND CELL PHYSIOLOGY

sgRNAcas9: A Software Package for Designing CRISPR sgRNA and Evaluating Potential Off-Target Cleavage Sites

(2014) Shengsong Xie et al.   PLoS One

Origin and Spread of de Novo Genes in Drosophila melanogaster Populations

(2014) L. Zhao et al.   SCIENCE

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

(2013) Haoyi Wang 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

A Developmental Switch Coupled to the Evolution of Plasticity Acts through a Sulfatase

(2013) Erik J. Ragsdale et al.   CELL

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

(2013) Luke A. Gilbert et al.   CELL

The CRISPR/Cas System mediates efficient genome engineering in Bombyx mori

(2013) Yueqiang Wang et al.   CELL RESEARCH

Efficient Targeted Mutagenesis in Medaka Using Custom-Designed Transcription Activator-Like Effector Nucleases

(2013) S. Ansai et al.   GENETICS

Highly efficient CRISPR/Cas9-mediated knock-in in zebrafish by homology-independent DNA repair

(2013) T. O. Auer et al.   GENOME RESEARCH

Targeted Mutagenesis in Zea mays Using TALENs and the CRISPR/Cas System

(2013) Zhen Liang et al.   Journal of Genetics and Genomics

Site-Specific Gene Targeting Using Transcription Activator-Like Effector (TALE)-Based Nuclease inBrassica oleracea

(2013) Zijian Sun et al.   Journal of Integrative Plant Biology

Targeted DNA demethylation and activation of endogenous genes using programmable TALE-TET1 fusion proteins

(2013) Morgan L Maeder 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

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

(2013) Seung Woo Cho 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

Targeted genome modification of crop plants using a CRISPR-Cas system

(2013) Qiwei Shan et al.   NATURE BIOTECHNOLOGY

RNA-guided editing of bacterial genomes using CRISPR-Cas systems

(2013) Wenyan Jiang et al.   NATURE BIOTECHNOLOGY

Genomic analyses identify distinct patterns of selection in domesticated pigs and Tibetan wild boars

(2013) Mingzhou Li et al.   NATURE GENETICS

TALE-mediated modulation of transcriptional enhancers in vivo

(2013) Justin Crocker et al.   NATURE METHODS

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

Evolution of crop species: genetics of domestication and diversification

(2013) Rachel S. Meyer et al.   NATURE REVIEWS GENETICS

Demonstration of CRISPR/Cas9/sgRNA-mediated targeted gene modification in Arabidopsis, tobacco, sorghum and rice

(2013) Wenzhi Jiang et al.   NUCLEIC ACIDS RESEARCH

Plant genome editing made easy: targeted mutagenesis in model and crop plants using the CRISPR/Cas system

(2013) Khaoula Belhaj et al.   Plant Methods

TALEN-Based Gene Disruption in the Dengue Vector Aedes aegypti

(2013) Azadeh Aryan et al.   PLoS One

Targeted Mutagenesis in the Malaria Mosquito Using TALE Nucleases

(2013) Andrea L. Smidler et al.   PLoS One

Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system

(2013) Li-En Jao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Efficient nonmeiotic allele introgression in livestock using custom endonucleases

(2013) W. Tan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Stepwise Evolution of Essential Centromere Function in a Drosophila Neogene

(2013) B. D. Ross et al.   SCIENCE

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

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering

(2013) Thomas Gaj et al.   TRENDS IN BIOTECHNOLOGY

Live pigs produced from genome edited zygotes

(2013) Simon G. Lillico et al.   Scientific Reports

Generation of gene disruptions by transcription activator-like effector nucleases (TALENs) in Xenopus tropicalis embryos

(2013) Yong Lei et al.   Cell and Bioscience

Highly Efficient Targeted Mutagenesis of Drosophila with the CRISPR/Cas9 System

(2013) Andrew R. Bassett et al.   Cell Reports

RNA-Guided Genome Editing for Target Gene Mutations in Wheat

(2013) Santosh Kumar Upadhyay et al.   G3-Genes Genomes Genetics

Targeted Myostatin Gene Editing in Multiple Mammalian Species Directed by a Single Pair of TALE Nucleases

(2013) Li Xu et al.   Molecular Therapy-Nucleic Acids

Reshaping of global gene expression networks and sex-biased gene expression by integration of a young gene

(2012) Sidi Chen et al.   EMBO JOURNAL

Drosophila melanogaster p24 trafficking proteins have vital roles in development and reproduction

(2012) Sehresh Saleem et al.   MECHANISMS OF DEVELOPMENT

The oyster genome reveals stress adaptation and complexity of shell formation

(2012) Guofan Zhang et al.   NATURE

Modular regulatory principles of large non-coding RNAs

(2012) Mitchell Guttman et al.   NATURE

FLASH assembly of TALENs for high-throughput genome editing

(2012) Deepak Reyon et al.   NATURE BIOTECHNOLOGY

High-efficiency TALEN-based gene editing produces disease-resistant rice

(2012) Ting Li et al.   NATURE BIOTECHNOLOGY

A transcription activator-like effector toolbox for genome engineering

(2012) Neville E Sanjana et al.   Nature Protocols

Emerging roles of non-coding RNAs in brain evolution, development, plasticity and disease

(2012) Irfan A. Qureshi et al.   NATURE REVIEWS NEUROSCIENCE

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

De Novo Origin of Protein-Coding Genes in Murine Rodents

(2012) Daniel N. Murphy et al.   PLoS One

Efficient TALEN-mediated gene knockout in livestock

(2012) D. F. Carlson 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

Simple Methods for Generating and Detecting Locus-Specific Mutations Induced with TALENs in the Zebrafish Genome

(2012) Timothy J. Dahlem et al.   PLoS Genetics

Rapid Functional Divergence of a Newly Evolved Polyubiquitin Gene in Drosophila and Its Role in the Trade-off between Male Fecundity and Lifespan

(2011) Z. Zhan et al.   MOLECULAR BIOLOGY AND EVOLUTION

A high-resolution map of human evolutionary constraint using 29 mammals

(2011) Kerstin Lindblad-Toh et al.   NATURE

Genome sequencing reveals insights into physiology and longevity of the naked mole rat

(2011) Eun Bae Kim et al.   NATURE

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Modularly assembled designer TAL effector nucleases for targeted gene knockout and gene replacement in eukaryotes

(2011) Ting Li et al.   NUCLEIC ACIDS RESEARCH

TAL Effectors: Customizable Proteins for DNA Targeting

(2011) A. J. Bogdanove et al.   SCIENCE

De Novo Origin of Human Protein-Coding Genes

(2011) Dong-Dong Wu et al.   PLoS Genetics

A de novo originated gene depresses budding yeast mating pathway and is repressed by the protein encoded by its antisense strand

(2010) Dan Li et al.   CELL RESEARCH

Genome-wide analysis of a long-term evolution experiment with Drosophila

(2010) Molly K. Burke et al.   NATURE

A TALE nuclease architecture for efficient genome editing

(2010) Jeffrey C Miller et al.   NATURE BIOTECHNOLOGY

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

Preassembled zinc-finger arrays for rapid construction of ZFNs

(2010) Seokjoong Kim et al.   NATURE METHODS

Modular system for the construction of zinc-finger libraries and proteins

(2010) Beatriz Gonzalez et al.   Nature Protocols

Annotating non-coding regions of the genome

(2010) Roger P. Alexander et al.   NATURE REVIEWS GENETICS

Adaptive impact of the chimeric gene Quetzalcoatl in Drosophila melanogaster

(2010) R. L. Rogers et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic Comparison of the Ants Camponotus floridanus and Harpegnathos saltator

(2010) R. Bonasio et al.   SCIENCE

New Genes in Drosophila Quickly Become Essential

(2010) S. Chen et al.   SCIENCE

Adaptation genomics: the next generation

(2010) Jessica Stapley et al.   TRENDS IN ECOLOGY & EVOLUTION

A Young Drosophila Duplicate Gene Plays Essential Roles in Spermatogenesis by Regulating Several Y-Linked Male Fertility Genes

(2010) Yun Ding et al.   PLoS Genetics

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

Linkage and Association Mapping of Arabidopsis thaliana Flowering Time in Nature

(2010) Benjamin Brachi et al.   PLoS Genetics

Small silencing RNAs: an expanding universe

(2009) Megha Ghildiyal et al.   NATURE REVIEWS GENETICS

Complete Resequencing of 40 Genomes Reveals Domestication Events and Genes in Silkworm (Bombyx)

(2009) Q. Xia et al.   SCIENCE

On the origin of new genes in Drosophila

(2008) Q. Zhou et al.   GENOME RESEARCH

Candidate Genes and Adaptive Radiation: Insights from Transcriptional Adaptation to the Limnetic Niche among Coregonine Fishes (Coregonus spp., Salmonidae)

(2008) J. Jeukens et al.   MOLECULAR BIOLOGY AND EVOLUTION

The evolution of courtship behaviors through the origination of a new gene in Drosophila

(2008) H. Dai et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The complex origins of domesticated crops in the Fertile Crescent

(2008) Terence A. Brown et al.   TRENDS IN ECOLOGY & EVOLUTION