Cellular barcoding: lineage tracing, screening and beyond

Neural lineage tracing in the mammalian brain

(2018) Jian Ma et al.   CURRENT OPINION IN NEUROBIOLOGY

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Clonal analysis of lineage fate in native haematopoiesis

(2018) Alejo E. Rodriguez-Fraticelli et al.   NATURE

Simultaneous single-cell profiling of lineages and cell types in the vertebrate brain

(2018) Bushra Raj et al.   NATURE BIOTECHNOLOGY

Simultaneous lineage tracing and cell-type identification using CRISPR–Cas9-induced genetic scars

(2018) Bastiaan Spanjaard et al.   NATURE BIOTECHNOLOGY

On the design of CRISPR-based single-cell molecular screens

(2018) Andrew J Hill et al.   NATURE METHODS

Single-cell mapping of gene expression landscapes and lineage in the zebrafish embryo

(2018) Daniel E. Wagner et al.   SCIENCE

The logic of single-cell projections from visual cortex

(2018) Yunyun Han et al.   NATURE

UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy

(2017) Tom Smith et al.   GENOME RESEARCH

Multiplexed Engineering and Analysis of Combinatorial Enhancer Activity in Single Cells

(2017) Shiqi Xie et al.   MOLECULAR CELL

In situ genotyping of a pooled strain library after characterizing complex phenotypes

(2017) Michael J Lawson et al.   Molecular Systems Biology

Synthetic recording and in situ readout of lineage information in single cells

(2017) Kirsten L. Frieda et al.   NATURE

Polylox barcoding reveals haematopoietic stem cell fates realized in vivo

(2017) Weike Pei et al.   NATURE

High-throughput, image-based screening of pooled genetic-variant libraries

(2017) George Emanuel et al.   NATURE METHODS

Pooled CRISPR screening with single-cell transcriptome readout

(2017) Paul Datlinger et al.   NATURE METHODS

Building a lineage from single cells: genetic techniques for cell lineage tracking

(2017) Mollie B. Woodworth et al.   NATURE REVIEWS GENETICS

Using high-throughput barcode sequencing to efficiently map connectomes

(2017) Ian D. Peikon et al.   NUCLEIC ACIDS RESEARCH

Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

(2017) Xiaoyin Chen et al.   NUCLEIC ACIDS RESEARCH

Quantitative Analysis of Synthetic Cell Lineage Tracing Using Nuclease Barcoding

(2017) Stephanie Tzouanas Schmidt et al.   ACS Synthetic Biology

Examining Sources of Error in PCR by Single-Molecule Sequencing

(2017) Vladimir Potapov et al.   PLoS One

Illumina error profiles: resolving fine-scale variation in metagenomic sequencing data

(2016) Melanie Schirmer et al.   BMC BIOINFORMATICS

Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq

(2016) Diego Adhemar Jaitin et al.   CELL

Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens

(2016) Atray Dixit et al.   CELL

A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response

(2016) Britt Adamson et al.   CELL

Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage

(2016) Alexis C. Komor et al.   NATURE

High-throughput identification of genotype-specific cancer vulnerabilities in mixtures of barcoded tumor cell lines

(2016) Channing Yu et al.   NATURE BIOTECHNOLOGY

Rapidly evolving homing CRISPR barcodes

(2016) Reza Kalhor et al.   NATURE METHODS

High-Throughput Mapping of Single-Neuron Projections by Sequencing of Barcoded RNA

(2016) Justus M. Kebschull et al.   NEURON

Whole-organism lineage tracing by combinatorial and cumulative genome editing

(2016) Aaron McKenna et al.   SCIENCE

Continuous genetic recording with self-targeting CRISPR-Cas in human cells

(2016) S. D. Perli et al.   SCIENCE

A model of breast cancer heterogeneity reveals vascular mimicry as a driver of metastasis

(2015) Elvin Wagenblast et al.   NATURE

Quantitative evolutionary dynamics using high-resolution lineage tracking

(2015) Sasha F. Levy et al.   NATURE

Studying clonal dynamics in response to cancer therapy using high-complexity barcoding

(2015) Hyo-eun C Bhang et al.   NATURE MEDICINE

Cell Lineage Analysis in Human Brain Using Endogenous Retroelements

(2015) Gilad D. Evrony et al.   NEURON

Insight into biases and sequencing errors for amplicon sequencing with the Illumina MiSeq platform

(2015) Melanie Schirmer et al.   NUCLEIC ACIDS RESEARCH

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

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

Neural Networks of the Mouse Neocortex

(2014) Brian Zingg et al.   CELL

The Yeast Deletion Collection: A Decade of Functional Genomics

(2014) Guri Giaever et al.   GENETICS

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

(2014) Yuexin Zhou et al.   NATURE

Clonal dynamics of native haematopoiesis

(2014) Jianlong Sun et al.   NATURE

A mesoscale connectome of the mouse brain

(2014) Seung Wook Oh et al.   NATURE

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

Single-cell in situ RNA profiling by sequential hybridization

(2014) Eric Lubeck et al.   NATURE METHODS

Multiplex Cell and Lineage Tracking with Combinatorial Labels

(2014) Karine Loulier et al.   NEURON

In vivo generation of DNA sequence diversity for cellular barcoding

(2014) Ian D. Peikon et al.   NUCLEIC ACIDS RESEARCH

Regulation of anti-sense transcription by Mot1p and NC2 via removal of TATA-binding protein (TBP) from the 3′-end of genes

(2014) Maria J.E. Koster et al.   NUCLEIC ACIDS RESEARCH

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Diverse and heritable lineage imprinting of early haematopoietic progenitors

(2013) Shalin H. Naik et al.   NATURE

In situ sequencing for RNA analysis in preserved tissue and cells

(2013) Rongqin Ke et al.   NATURE METHODS

Improved tools for the Brainbow toolbox

(2013) Dawen Cai et al.   NATURE METHODS

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

Statistical Analysis of Molecular Signal Recording

(2013) Joshua I. Glaser et al.   PLoS Computational Biology

Lineage Tracing

(2012) Kai Kretzschmar et al.   CELL

Digital RNA sequencing minimizes sequence-dependent bias and amplification noise with optimized single-molecule barcodes

(2012) K. Shiroguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing the Connectome

(2012) Anthony M. Zador et al.   PLOS BIOLOGY

Sensory maps in the olfactory cortex defined by long-range viral tracing of single neurons

(2011) Sulagna Ghosh et al.   NATURE

Wiring specificity in the direction-selectivity circuit of the retina

(2011) Kevin L. Briggman et al.   NATURE

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

(2011) Rong Lu et al.   NATURE BIOTECHNOLOGY

Counting absolute numbers of molecules using unique molecular identifiers

(2011) Teemu Kivioja et al.   NATURE METHODS

A method for counting PCR template molecules with application to next-generation sequencing

(2011) J. A. Casbon et al.   NUCLEIC ACIDS RESEARCH

Counting individual DNA molecules by the stochastic attachment of diverse labels

(2011) G. K. Fu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detection and quantification of rare mutations with massively parallel sequencing

(2011) I. Kinde et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cellular barcoding tool for clonal analysis in the hematopoietic system

(2010) A. Gerrits et al.   BLOOD

Viral Mutation Rates

(2010) R. Sanjuan et al.   JOURNAL OF VIROLOGY

Quantitative phenotyping via deep barcode sequencing

(2009) A. M. Smith et al.   GENOME RESEARCH

Recruitment of Antigen-Specific CD8+ T Cells in Response to Infection Is Markedly Efficient

(2009) J. W. J. van Heijst et al.   SCIENCE

Dissecting T cell lineage relationships by cellular barcoding

(2008) Koen Schepers et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Identification of genetic variants using bar-coded multiplexed sequencing

(2008) David W Craig et al.   NATURE METHODS

Profiling Essential Genes in Human Mammary Cells by Multiplex RNAi Screening

(2008) J. M. Silva et al.   SCIENCE

DNA barcoding for ecologists

(2008) Alice Valentini et al.   TRENDS IN ECOLOGY & EVOLUTION