In situ readout of DNA barcodes and single base edits facilitated by in vitro transcription

Allele-specific RNA imaging shows that allelic imbalances can arise in tissues through transcriptional bursting

(2019) Orsolya Symmons et al.   PLoS Genetics

Transcriptome-scale super-resolved imaging in tissues by RNA seqFISH+

(2019) Chee-Huat Linus Eng et al.   NATURE

Molecular recording of mammalian embryogenesis

(2019) Michelle M. Chan et al.   NATURE

Constitutive splicing and economies of scale in gene expression

(2019) Fangyuan Ding et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

DNA Microscopy: Optics-free Spatio-genetic Imaging by a Stand-Alone Chemical Reaction

(2019) Joshua A. Weinstein et al.   CELL

High-fidelity amplified FISH for the detection and allelic discrimination of single mRNA molecules

(2019) Salvatore A. E. Marras et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Single-Nucleotide-Resolution Computing and Memory in Living Cells

(2019) Fahim Farzadfard et al.   MOLECULAR CELL

Optical Pooled Screens in Human Cells

(2019) David Feldman et al.   CELL

Dynamics and Spatial Genomics of the Nascent Transcriptome by Intron seqFISH

(2018) Sheel Shah et al.   CELL

Third-generationin situhybridization chain reaction: multiplexed, quantitative, sensitive, versatile, robust

(2018) Harry M. T. Choi et al.   DEVELOPMENT

Whole-organism clone tracing using single-cell sequencing

(2018) Anna Alemany et al.   NATURE

Base editing with a Cpf1–cytidine deaminase fusion

(2018) Xiaosa Li et al.   NATURE BIOTECHNOLOGY

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

Rewritable multi-event analog recording in bacterial and mammalian cells

(2018) Weixin Tang et al.   SCIENCE

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

(2018) Xiao Wang et al.   SCIENCE

Prediction of off-target activities for the end-to-end design of CRISPR guide RNAs

(2018) Jennifer Listgarten et al.   Nature Biomedical Engineering

An APOBEC3A-Cas9 base editor with minimized bystander and off-target activities

(2018) Jason M Gehrke et al.   NATURE BIOTECHNOLOGY

Emerging applications for DNA writers and molecular recorders

(2018) Fahim Farzadfard et al.   SCIENCE

Developmental barcoding of whole mouse via homing CRISPR

(2018) Reza Kalhor et al.   SCIENCE

Single-cell mapping of lineage and identity in direct reprogramming

(2018) Brent A. Biddy et al.   NATURE

ClampFISH detects individual nucleic acid molecules using click chemistry–based amplification

(2018) Sara H Rouhanifard et al.   NATURE BIOTECHNOLOGY

Cellular barcoding: lineage tracing, screening and beyond

(2018) Justus M. Kebschull et al.   NATURE METHODS

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

Programmable base editing of A•T to G•C in genomic DNA without DNA cleavage

(2017) Nicole M. Gaudelli et al.   NATURE

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

(2017) George Emanuel et al.   NATURE METHODS

seqFISH Accurately Detects Transcripts in Single Cells and Reveals Robust Spatial Organization in the Hippocampus

(2017) Sheel Shah et al.   NEURON

Efficient in situ barcode sequencing using padlock probe-based BaristaSeq

(2017) Xiaoyin Chen et al.   NUCLEIC ACIDS RESEARCH

Massively parallel digital transcriptional profiling of single cells

(2017) Grace X. Y. Zheng et al.   Nature Communications

Improved base excision repair inhibition and bacteriophage Mu Gam protein yields C:G-to-T:A base editors with higher efficiency and product purity

(2017) Alexis C. Komor et al.   Science Advances

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

(2016) Atray Dixit et al.   CELL

Mapping a multiplexed zoo of mRNA expression

(2016) Harry M. T. Choi et al.   DEVELOPMENT

Single-molecule RNA detection at depth by hybridization chain reaction and tissue hydrogel embedding and clearing

(2016) Sheel Shah et al.   DEVELOPMENT

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

(2016) Alexis C. Komor et al.   NATURE

Optimized sgRNA design to maximize activity and minimize off-target effects of CRISPR-Cas9

(2016) John G Doench 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

Microscopy-Based High-Content Screening

(2015) Michael Boutros et al.   CELL

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

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

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

Continuously tunable nucleic acid hybridization probes

(2015) Lucia R Wu et al.   NATURE METHODS

Spatially resolved, highly multiplexed RNA profiling in single cells

(2015) K. H. Chen et al.   SCIENCE

A Barcoding Strategy Enabling Higher-Throughput Library Screening by Microscopy

(2015) Robert Chen et al.   ACS Synthetic Biology

Exquisite Sequence Selectivity with Small Conditional RNAs

(2014) Jonathan B. Sternberg et al.   NANO LETTERS

Highly Multiplexed Subcellular RNA Sequencing in Situ

(2014) J. H. Lee et al.   SCIENCE

Selective Nucleic Acid Capture with Shielded Covalent Probes

(2013) Jeffrey R. Vieregg et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

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

Visualizing SNVs to quantify allele-specific expression in single cells

(2013) Marshall J Levesque et al.   NATURE METHODS

Multiplex Genome Engineering Using CRISPR/Cas Systems

(2013) L. Cong et al.   SCIENCE

Fiji: an open-source platform for biological-image analysis

(2012) Johannes Schindelin et al.   NATURE METHODS

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

(2011) Rong Lu et al.   NATURE BIOTECHNOLOGY

Programmable in situ amplification for multiplexed imaging of mRNA expression

(2010) Harry M T Choi et al.   NATURE BIOTECHNOLOGY

Imaging individual mRNA molecules using multiple singly labeled probes

(2008) Arjun Raj et al.   NATURE METHODS