Whole-organism lineage tracing by combinatorial and cumulative genome editing

Emerging Imaging and Genomic Tools for Developmental Systems Biology

(2016) Zhe Liu et al.   DEVELOPMENTAL CELL

A CRISPR/Cas9 Vector System for Tissue-Specific Gene Disruption in Zebrafish

(2015) Julien Ablain et al.   DEVELOPMENTAL CELL

Multiplex Conditional Mutagenesis Using Transgenic Expression of Cas9 and sgRNAs

(2015) Linlin Yin et al.   GENETICS

Engineered CRISPR-Cas9 nucleases with altered PAM specificities

(2015) Benjamin P. Kleinstiver et al.   NATURE

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

Rationally engineered Cas9 nucleases with improved specificity

(2015) I. M. Slaymaker et al.   SCIENCE

Somatic mutation in single human neurons tracks developmental and transcriptional history

(2015) M. A. Lodato et al.   SCIENCE

Multiplex single-cell profiling of chromatin accessibility by combinatorial cellular indexing

(2015) D. A. Cusanovich et al.   SCIENCE

Multiplex Conditional Mutagenesis Using Transgenic Expression of Cas9 and sgRNAs

(2015) Linlin Yin et al.   GENETICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

CRISPR-Cas9 Knockin Mice for Genome Editing and Cancer Modeling

(2014) Randall J. Platt et al.   CELL

Genome sequencing of normal cells reveals developmental lineages and mutational processes

(2014) Sam Behjati et al.   NATURE

Improving CRISPR-Cas nuclease specificity using truncated guide RNAs

(2014) Yanfang Fu 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

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Efficient Mutagenesis by Cas9 Protein-Mediated Oligonucleotide Insertion and Large-Scale Assessment of Single-Guide RNAs

(2014) James A. Gagnon et al.   PLoS One

The new frontier of genome engineering with CRISPR-Cas9

(2014) J. A. Doudna et al.   SCIENCE

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Genomically encoded analog memory with precise in vivo DNA writing in living cell populations

(2014) F. Farzadfard et al.   SCIENCE

Lentiviral and targeted cellular barcoding reveals ongoing clonal dynamics of cell lines in vitro and in vivo

(2014) Shaina N Porter et al.   GENOME BIOLOGY

Zebrabow: multispectral cell labeling for cell tracing and lineage analysis in zebrafish

(2013) Y. Albert Pan et al.   DEVELOPMENT

Novel Blood Collection Method Allows Plasma Proteome Analysis from Single Zebrafish

(2013) Fatemeh Babaei et al.   JOURNAL OF PROTEOME RESEARCH

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Unravelling stem cell dynamics by lineage tracing

(2013) Cédric Blanpain et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Lineage Tracing

(2012) Kai Kretzschmar et al.   CELL

Clonally dominant cardiomyocytes direct heart morphogenesis

(2012) Vikas Gupta et al.   NATURE

FLASH: fast length adjustment of short reads to improve genome assemblies

(2011) T. Magoc et al.   BIOINFORMATICS

Universal patterns of stem cell fate in cycling adult tissues

(2011) A. M. Klein et al.   DEVELOPMENT

Tracking single hematopoietic stem cells in vivo using high-throughput sequencing in conjunction with viral genetic barcoding

(2011) Rong Lu et al.   NATURE BIOTECHNOLOGY

Decoding cell lineage from acquired mutations using arbitrary deep sequencing

(2011) Cheryl A Carlson et al.   NATURE METHODS

Intestinal Crypt Homeostasis Results from Neutral Competition between Symmetrically Dividing Lgr5 Stem Cells

(2010) Hugo J. Snippert et al.   CELL

Ubiquitous transgene expression and Cre-based recombination driven by the ubiquitin promoter in zebrafish

(2010) C. Mosimann et al.   DEVELOPMENT

The Rag GTPases Bind Raptor and Mediate Amino Acid Signaling to mTORC1

(2008) Y. Sancak et al.   SCIENCE