Genetic compensation triggered by mutant mRNA degradation

Hif-1α regulates macrophage-endothelial interactions during blood vessel development in zebrafish

(2017) Claudia Gerri et al.   Nature Communications

Genetic compensation: A phenomenon in search of mechanisms

(2017) Mohamed A. El-Brolosy et al.   PLoS Genetics

Small RNA-directed epigenetic programming of embryonic stem cell cardiac differentiation

(2017) Hossein Ghanbarian et al.   Scientific Reports

Regulation of Vegf signaling by natural and synthetic ligands

(2016) A. Rossi et al.   BLOOD

Analysis of protein-coding genetic variation in 60,706 humans

(2016) Monkol Lek et al.   NATURE

CHOPCHOP v2: a web tool for the next generation of CRISPR genome engineering

(2016) Kornel Labun et al.   NUCLEIC ACIDS RESEARCH

In vivo modulation of endothelial polarization by Apelin receptor signalling

(2016) Hyouk-Bum Kwon et al.   Nature Communications

Interrogating the degradation pathways of unstable mRNAs with XRN1-resistant sequences

(2016) Volker Boehm et al.   Nature Communications

Kindlin-2 cooperates with talin to activate integrins and induces cell spreading by directly binding paxillin

(2016) Marina Theodosiou et al.   eLife

Genetic compensation induced by deleterious mutations but not gene knockdowns

(2015) Andrea Rossi et al.   NATURE

Identification of a large set of rare complete human knockouts

(2015) Patrick Sulem et al.   NATURE GENETICS

Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements

(2015) Pratiksha I Thakore et al.   NATURE METHODS

Tip cell-specific requirement for an atypical Gpr124- and Reck-dependent Wnt/β-catenin pathway during brain angiogenesis

(2015) Benoit Vanhollebeke et al.   eLife

Kablammo: an interactive, web-based BLAST results visualizer

(2014) J. A. Wintersinger et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Identification and Characterization of Small Molecules That Inhibit Nonsense-Mediated RNA Decay and Suppress Nonsense p53 Mutations

(2014) L. Martin et al.   CANCER RESEARCH

Early-Onset Stroke and Vasculopathy Associated with Mutations in ADA2

(2014) Qing Zhou et al.   NEW ENGLAND JOURNAL OF MEDICINE

deepTools: a flexible platform for exploring deep-sequencing data

(2014) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

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

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

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

(2013) Y. Liao et al.   BIOINFORMATICS

Gene Expression Is Circular: Factors for mRNA Degradation Also Foster mRNA Synthesis

(2013) Gal Haimovich et al.   CELL

Kraken: A set of tools for quality control and analysis of high-throughput sequence data

(2013) Matthew P.A. Davis et al.   METHODS

Genome-wide Consequences of Deleting Any Single Gene

(2013) Xinchen Teng et al.   MOLECULAR CELL

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

(2013) Ronnie Blecher-Gonen et al.   Nature Protocols

Genome engineering using the CRISPR-Cas9 system

(2013) F Ann Ran et al.   Nature Protocols

TAL Effector Specificity for base 0 of the DNA Target Is Altered in a Complex, Effector- and Assay-Dependent Manner by Substitutions for the Tryptophan in Cryptic Repeat –1

(2013) Erin L. Doyle et al.   PLoS One

Assessing the Disease-Liability of Mutations in CFTR

(2013) C. Ferec et al.   Cold Spring Harbor Perspectives in Medicine

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Comparative dynamic transcriptome analysis (cDTA) reveals mutual feedback between mRNA synthesis and degradation

(2012) M. Sun et al.   GENOME RESEARCH

Inhibition of natural antisense transcripts in vivo results in gene-specific transcriptional upregulation

(2012) Farzaneh Modarresi et al.   NATURE BIOTECHNOLOGY

Identification of Cytoplasmic Capping Targets Reveals a Role for Cap Homeostasis in Translation and mRNA Stability

(2012) Chandrama Mukherjee et al.   Cell Reports

Metabolic labeling of RNA uncovers principles of RNA production and degradation dynamics in mammalian cells

(2011) Michal Rabani et al.   NATURE BIOTECHNOLOGY

Integrative genomics viewer

(2011) James T Robinson et al.   NATURE BIOTECHNOLOGY

Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting

(2011) Tomas Cermak et al.   NUCLEIC ACIDS RESEARCH

KOBAS 2.0: a web server for annotation and identification of enriched pathways and diseases

(2011) Chen Xie et al.   NUCLEIC ACIDS RESEARCH

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

Major role for mRNA stability in shaping the kinetics of gene induction

(2010) Ran Elkon et al.   BMC GENOMICS

Cranial vasculature in zebrafish forms by angioblast cluster-derived angiogenesis

(2010) Kira Proulx et al.   DEVELOPMENTAL BIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

H3 lysine 4 di- and tri-methylation deposited by cryptic transcription attenuates promoter activation

(2009) Marina Pinskaya et al.   EMBO JOURNAL

The stability of mRNA influences the temporal order of the induction of genes encoding inflammatory molecules

(2009) Shengli Hao et al.   NATURE IMMUNOLOGY

A cryptic unstable transcript mediates transcriptional trans-silencing of the Ty1 retrotransposon in S. cerevisiae

(2008) J. Berretta et al.   GENES & DEVELOPMENT