Transcriptional recording by CRISPR spacer acquisition from RNA

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

Integrative omics for health and disease

(2018) Konrad J. Karczewski et al.   NATURE REVIEWS GENETICS

Rewritable multi-event analog recording in bacterial and mammalian cells

(2018) Weixin Tang et al.   SCIENCE

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

(2017) Kirsten L. Frieda et al.   NATURE

CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria

(2017) Seth L. Shipman et al.   NATURE

Multiplex recording of cellular events over time on CRISPR biological tape

(2017) Ravi U. Sheth et al.   SCIENCE

On the Origin of Reverse Transcriptase-Using CRISPR-Cas Systems and Their Hyperdiverse, Enigmatic Spacer Repertoires

(2017) Sukrit Silas et al.   mBio

Type III CRISPR-Cas systems can provide redundancy to counteract viral escape from type I systems

(2017) Sukrit Silas et al.   eLife

Adaptation in CRISPR-Cas Systems

(2016) Samuel H. Sternberg et al.   MOLECULAR CELL

Rapidly evolving homing CRISPR barcodes

(2016) Reza Kalhor et al.   NATURE METHODS

CRISPR–Cas adaptation: insights into the mechanism of action

(2016) Gil Amitai et al.   NATURE REVIEWS MICROBIOLOGY

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

Molecular recordings by directed CRISPR spacer acquisition

(2016) Seth L. Shipman et al.   SCIENCE

Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase-Cas1 fusion protein

(2016) S. Silas et al.   SCIENCE

CRISPR adaptation biases explain preference for acquisition of foreign DNA

(2015) Asaf Levy et al.   NATURE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Unravelling the structural and mechanistic basis of CRISPR–Cas systems

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

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

(2014) F. Farzadfard et al.   SCIENCE

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Inter-viral conflicts that exploit host CRISPR immune systems ofSulfolobus

(2013) Susanne Erdmann et al.   MOLECULAR MICROBIOLOGY

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

RNA snap ™: a rapid, quantitative and inexpensive, method for isolating total RNA from bacteria

(2012) Mark B. Stead et al.   NUCLEIC ACIDS RESEARCH

Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli

(2012) Ido Yosef et al.   NUCLEIC ACIDS RESEARCH

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

(2012) M. Jinek et al.   SCIENCE

HMMER web server: interactive sequence similarity searching

(2011) R. D. Finn et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data

(2010) Thomas J Hardcastle et al.   BMC BIOINFORMATICS

The CRISPR/Cas bacterial immune system cleaves bacteriophage and plasmid DNA

(2010) Josiane E. Garneau et al.   NATURE

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

CRISPR interference: RNA-directed adaptive immunity in bacteria and archaea

(2010) Luciano A. Marraffini et al.   NATURE REVIEWS GENETICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

BioNumbers—the database of key numbers in molecular and cell biology

(2009) Ron Milo et al.   NUCLEIC ACIDS RESEARCH

Golden Gate Shuffling: A One-Pot DNA Shuffling Method Based on Type IIs Restriction Enzymes

(2009) Carola Engler et al.   PLoS One

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS