Parallel genetics of regulatory sequences using scalable genome editing in vivo

High-accuracy long-read amplicon sequences using unique molecular identifiers with Nanopore or PacBio sequencing

(2021) Søren M. Karst et al.   NATURE METHODS

Dissection of the Fgf8 regulatory landscape by in vivo CRISPR-editing reveals extensive intra- and inter-enhancer redundancy

(2021) A. Hörnblad et al.   Nature Communications

Targeted, random mutagenesis of plant genes with dual cytosine and adenine base editors

(2020) Chao Li et al.   NATURE BIOTECHNOLOGY

Comprehensive In Vivo Interrogation Reveals Phenotypic Impact of Human Enhancer Variants

(2020) Evgeny Z. Kvon et al.   CELL

A structural variation reference for medical and population genetics

(2020) Ryan L. Collins et al.   NATURE

An engineered ScCas9 with broad PAM range and high specificity and activity

(2020) Pranam Chatterjee et al.   NATURE BIOTECHNOLOGY

Unconstrained genome targeting with near-PAMless engineered CRISPR-Cas9 variants

(2020) Russell T. Walton et al.   SCIENCE

Efficient Transgenesis in Caenorhabditis elegans Using Flp Recombinase-Mediated Cassette Exchange

(2020) Michael L. Nonet   GENETICS

Genome editing with CRISPR–Cas nucleases, base editors, transposases and prime editors

(2020) Andrew V. Anzalone et al.   NATURE BIOTECHNOLOGY

Dense and pleiotropic regulatory information in a developmental enhancer

(2020) Timothy Fuqua et al.   NATURE

Genetics in Light of Transcriptional Adaptation

(2020) Zacharias Kontarakis et al.   TRENDS IN GENETICS

Engineering rules that minimize germline silencing of transgenes in simple extrachromosomal arrays in C. elegans

(2020) Mohammed D. Aljohani et al.   Nature Communications

Mutational Landscape of Spontaneous Base Substitutions and Small Indels in Experimental Caenorhabditis elegans Populations of Differing Size

(2019) Anke Konrad et al.   GENETICS

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Large dataset enables prediction of repair after CRISPR–Cas9 editing in primary T cells

(2019) Ryan T. Leenay et al.   NATURE BIOTECHNOLOGY

Synthetic evolution

(2019) Anna J. Simon et al.   NATURE BIOTECHNOLOGY

Rational targeting of a NuRD subcomplex guided by comprehensive in situ mutagenesis

(2019) Falak Sher et al.   NATURE GENETICS

Massively parallel profiling and predictive modeling of the outcomes of CRISPR/Cas9-mediated double-strand break repair

(2019) Wei Chen et al.   NUCLEIC ACIDS RESEARCH

Templated Insertions: A Smoking Gun for Polymerase Theta-Mediated End Joining

(2019) Joost Schimmel et al.   TRENDS IN GENETICS

The Caenorhabditis elegans Transgenic Toolbox

(2019) Jeremy Nance et al.   GENETICS

Context-specific regulation of cell survival by a miRNA-controlled BIM rheostat

(2019) Verena Labi et al.   GENES & DEVELOPMENT

Search-and-replace genome editing without double-strand breaks or donor DNA

(2019) Andrew V. Anzalone et al.   NATURE

Biological plasticity rescues target activity in CRISPR knock outs

(2019) Arne H. Smits et al.   NATURE METHODS

De novo identification of essential protein domains from CRISPR-Cas9 tiling-sgRNA knockout screens

(2019) Wei He et al.   Nature Communications

Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor

(2019) Haiqi Chen et al.   NATURE BIOTECHNOLOGY

Sequence, Structure, and Context Preferences of Human RNA Binding Proteins

(2018) Daniel Dominguez et al.   MOLECULAR CELL

Precise and Predictable CRISPR Chromosomal Rearrangements Reveal Principles of Cas9-Mediated Nucleotide Insertion

(2018) Jia Shou et al.   MOLECULAR CELL

Repair of double-strand breaks induced by CRISPR–Cas9 leads to large deletions and complex rearrangements

(2018) Michael Kosicki et al.   NATURE BIOTECHNOLOGY

An interplay of miRNA abundance and target site architecture determines miRNA activity and specificity

(2018) Giovanna Brancati et al.   NUCLEIC ACIDS RESEARCH

Single-cell profiling of the developing mouse brain and spinal cord with split-pool barcoding

(2018) Alexander B. Rosenberg et al.   SCIENCE

Functional Genetic Variants Revealed by Massively Parallel Precise Genome Editing

(2018) Eilon Sharon et al.   CELL

Large deletions induced by Cas9 cleavage

(2018) Fatwa Adikusuma et al.   NATURE

Spatiotemporal m(i)RNA Architecture and 3′ UTR Regulation in the C. elegans Germline

(2018) Asija Diag et al.   DEVELOPMENTAL CELL

Target-Specific Precision of CRISPR-Mediated Genome Editing

(2018) Anob M. Chakrabarti et al.   MOLECULAR CELL

Predictable and precise template-free CRISPR editing of pathogenic variants

(2018) Max W. Shen et al.   NATURE

Predicting the mutations generated by repair of Cas9-induced double-strand breaks

(2018) Felicity Allen et al.   NATURE BIOTECHNOLOGY

Chromatin accessibility dynamics across C. elegans development and ageing

(2018) Jürgen Jänes et al.   eLife

PiGx: reproducible genomics analysis pipelines with GNU Guix

(2018) Ricardo Wurmus et al.   GigaScience

LIN41 Post-transcriptionally Silences mRNAs by Two Distinct and Position-Dependent Mechanisms

(2017) Florian Aeschimann et al.   MOLECULAR CELL

A Massively Parallel Reporter Assay of 3′ UTR Sequences Identifies In Vivo Rules for mRNA Degradation

(2017) Michal Rabani et al.   MOLECULAR CELL

Comprehensive single-cell transcriptional profiling of a multicellular organism

(2017) Junyue Cao et al.   SCIENCE

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

A tissue-specific protein purification approach in Caenorhabditis elegans identifies novel interaction partners of DLG-1/Discs large

(2016) Selma Waaijers et al.   BMC BIOLOGY

Ever-Changing Landscapes: Transcriptional Enhancers in Development and Evolution

(2016) Hannah K. Long et al.   CELL

Massively Parallel Genetics

(2016) Jay Shendure et al.   GENETICS

Pairing beyond the Seed Supports MicroRNA Targeting Specificity

(2016) James P. Broughton et al.   MOLECULAR CELL

Applications of CRISPR technologies in research and beyond

(2016) Rodolphe Barrangou et al.   NATURE BIOTECHNOLOGY

Targeted AID-mediated mutagenesis (TAM) enables efficient genomic diversification in mammalian cells

(2016) Yunqing Ma et al.   NATURE METHODS

RESA identifies mRNA-regulatory sequences at high resolution

(2016) Valeria Yartseva et al.   NATURE METHODS

Directed evolution using dCas9-targeted somatic hypermutation in mammalian cells

(2016) Gaelen T Hess et al.   NATURE METHODS

The power of multiplexed functional analysis of genetic variants

(2016) Molly Gasperini et al.   Nature Protocols

Massively Parallel Genetics

(2016) Jay Shendure et al.   GENETICS

The auxin-inducible degradation (AID) system enables versatile conditional protein depletion in C. elegans

(2015) L. Zhang et al.   DEVELOPMENT

The let-7 microRNA Directs Vulval Development through a Single Target

(2015) Matyas Ecsedi et al.   DEVELOPMENTAL CELL

Dramatic Enhancement of Genome Editing by CRISPR/Cas9 Through Improved Guide RNA Design

(2015) Behnom Farboud et al.   GENETICS

Streamlined Genome Engineering with a Self-Excising Drug Selection Cassette

(2015) Daniel J. Dickinson et al.   GENETICS

BCL11A enhancer dissection by Cas9-mediated in situ saturating mutagenesis

(2015) Matthew C. Canver et al.   NATURE

Discovery of cancer drug targets by CRISPR-Cas9 screening of protein domains

(2015) Junwei Shi et al.   NATURE BIOTECHNOLOGY

Functional footprinting of regulatory DNA

(2015) Jeff Vierstra et al.   NATURE METHODS

Specificity and nonspecificity in RNA–protein interactions

(2015) Eckhard Jankowsky et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Functional relevance of “seed” and “non-seed” sequences in microRNA-mediated promotion ofC. elegansdevelopmental progression

(2015) Huibin Zhang et al.   RNA

Suboptimization of developmental enhancers

(2015) E. K. Farley et al.   SCIENCE

Polymerase Θ is a key driver of genome evolution and of CRISPR/Cas9-mediated mutagenesis

(2015) Robin van Schendel et al.   Nature Communications

Dramatic Enhancement of Genome Editing by CRISPR/Cas9 Through Improved Guide RNA Design

(2015) Behnom Farboud et al.   GENETICS

Streamlined Genome Engineering with a Self-Excising Drug Selection Cassette

(2015) Daniel J. Dickinson et al.   GENETICS

FLP/FRT and Cre/lox recombination technology in C. elegans

(2014) E. Jane Albert Hubbard   METHODS

Saturation editing of genomic regions by multiplex homology-directed repair

(2014) Gregory M. Findlay et al.   NATURE

Random and targeted transgene insertion in Caenorhabditis elegans using a modified Mos1 transposon

(2014) Christian Frøkjær-Jensen et al.   NATURE METHODS

E-CRISP: fast CRISPR target site identification

(2014) Florian Heigwer et al.   NATURE METHODS

In pursuit of design principles of regulatory sequences

(2014) Michal Levo et al.   NATURE REVIEWS GENETICS

Illumina TruSeq Synthetic Long-Reads Empower De Novo Assembly and Resolve Complex, Highly-Repetitive Transposable Elements

(2014) Rajiv C. McCoy et al.   PLoS One

CRISPR/Cas9-Targeted Mutagenesis in Caenorhabditis elegans

(2013) Selma Waaijers et al.   GENETICS

Heritable genome editing in C. elegans via a CRISPR-Cas9 system

(2013) Ari E Friedland et al.   NATURE METHODS

Efficient and Rapid C. elegans Transgenesis by Bombardment and Hygromycin B Selection

(2013) Inja Radman et al.   PLoS One

Software for Computing and Annotating Genomic Ranges

(2013) Michael Lawrence et al.   PLoS Computational Biology

Functional Genomic Analysis of the let-7 Regulatory Network in Caenorhabditis elegans

(2013) Shaun E. Hunter et al.   PLoS Genetics

Snakemake--a scalable bioinformatics workflow engine

(2012) J. Koster et al.   BIOINFORMATICS

Beyond genotype to phenotype: why the phenotype of an individual cannot always be predicted from their genome sequence and the environment that they experience

(2012) Alejandro Burga et al.   FEBS Journal

Improved Mos1-mediated transgenesis in C. elegans

(2012) Christian Frøkjær-Jensen et al.   NATURE METHODS

Genomic approaches towards finding cis-regulatory modules in animals

(2012) Ross C. Hardison et al.   NATURE REVIEWS GENETICS

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

Gene regulatory networks and the role of robustness and stochasticity in the control of gene expression

(2011) L. T. MacNeil et al.   GENOME RESEARCH

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence

(2011) Patricia J. Wittkopp et al.   NATURE REVIEWS GENETICS

Enzymatic assembly of DNA molecules up to several hundred kilobases

(2009) Daniel G Gibson et al.   NATURE METHODS

Single-copy insertion of transgenes in Caenorhabditis elegans

(2008) Christian Frøkjær-Jensen et al.   NATURE GENETICS