RNA isoform screens uncover the essentiality and tumor-suppressor activity of ultraconserved poison exons

Quality and quantity control of gene expression by nonsense-mediated mRNA decay

(2019) Tatsuaki Kurosaki et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Spliceosomal disruption of the non-canonical BAF complex in cancer

(2019) Daichi Inoue et al.   NATURE

Ultraconserved Enhancers Are Required for Normal Development

(2018) Diane E. Dickel et al.   CELL

Transcriptome Engineering with RNA-Targeting Type VI-D CRISPR Effectors

(2018) Silvana Konermann et al.   CELL

Most human introns are recognized via multiple and tissue-specific branchpoints

(2018) Jose Mario Bello Pineda et al.   GENES & DEVELOPMENT

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

(2018) Michael Kosicki et al.   NATURE BIOTECHNOLOGY

CRISPR–Cas9 genome editing induces a p53-mediated DNA damage response

(2018) Emma Haapaniemi et al.   NATURE MEDICINE

Alternative-splicing defects in cancer: Splicing regulators and their downstream targets, guiding the way to novel cancer therapeutics

(2018) Laura M. Urbanski et al.   Wiley Interdisciplinary Reviews-RNA

Correction of diverse muscular dystrophy mutations in human engineered heart muscle by single-site genome editing

(2018) Chengzu Long et al.   Science Advances

Genetic Modulation of RNA Splicing with a CRISPR-Guided Cytidine Deaminase

(2018) Juanjuan Yuan et al.   MOLECULAR CELL

Genome-wide screening for functional long noncoding RNAs in human cells by Cas9 targeting of splice sites

(2018) Ying Liu et al.   NATURE BIOTECHNOLOGY

Aurora kinase A drives the evolution of resistance to third-generation EGFR inhibitors in lung cancer

(2018) Khyati N. Shah et al.   NATURE MEDICINE

FDA-Approved Oligonucleotide Therapies in 2017

(2017) Cy A. Stein et al.   MOLECULAR THERAPY

Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells

(2017) Robin M Meyers et al.   NATURE GENETICS

A tiling-deletion-based genetic screen for cis-regulatory element identification in mammalian cells

(2017) Yarui Diao et al.   NATURE METHODS

Am I ready for CRISPR? A user's guide to genetic screens

(2017) John G. Doench   NATURE REVIEWS GENETICS

Alternative splicing as a regulator of development and tissue identity

(2017) Francisco E. Baralle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Single-cut genome editing restores dystrophin expression in a new mouse model of muscular dystrophy

(2017) Leonela Amoasii et al.   Science Translational Medicine

Genome-scale deletion screening of human long non-coding RNAs using a paired-guide RNA CRISPR–Cas9 library

(2016) Shiyou Zhu et al.   NATURE BIOTECHNOLOGY

Transcriptome-wide identification of NMD-targeted human mRNAs reveals extensive redundancy between SMG6- and SMG7-mediated degradation pathways

(2016) Martino Colombo et al.   RNA

Cancer-associated SF3B1 mutations affect alternative splicing by promoting alternative branchpoint usage

(2016) Samar Alsafadi et al.   Nature Communications

CRISPR Screens Provide a Comprehensive Assessment of Cancer Vulnerabilities but Generate False-Positive Hits for Highly Amplified Genomic Regions

(2016) D. M. Munoz et al.   Cancer Discovery

Genomic Copy Number Dictates a Gene-Independent Cell Response to CRISPR/Cas9 Targeting

(2016) A. J. Aguirre et al.   Cancer Discovery

Precise gene deletion and replacement using the CRISPR/Cas9 system in human cells

(2016) Qiupeng Zheng et al.   BIOTECHNIQUES

Genome-wide CRISPR Screen in a Mouse Model of Tumor Growth and Metastasis

(2015) Sidi Chen et al.   CELL

High-Resolution CRISPR Screens Reveal Fitness Genes and Genotype-Specific Cancer Liabilities

(2015) Traver Hart et al.   CELL

Intron retention is a widespread mechanism of tumor-suppressor inactivation

(2015) Hyunchul Jung et al.   NATURE GENETICS

Orchestrating high-throughput genomic analysis with Bioconductor

(2015) Wolfgang Huber et al.   NATURE METHODS

RNA mis-splicing in disease

(2015) Marina M. Scotti et al.   NATURE REVIEWS GENETICS

Epigenetic factor EPC1 is a master regulator of DNA damage response by interacting with E2F1 to silence death and activate metastasis-related gene signatures

(2015) Yajie Wang et al.   NUCLEIC ACIDS RESEARCH

Systematic discovery of regulated and conserved alternative exons in the mammalian brain reveals NMD modulating chromatin regulators

(2015) Qinghong Yan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread intron retention diversifies most cancer transcriptomes

(2015) Heidi Dvinge et al.   Genome Medicine

Functional analysis of limb transcriptional enhancers in the mouse

(2014) Mark J. Nolte et al.   EVOLUTION & DEVELOPMENT

Nuclear localization of MBNL1: splicing-mediated autoregulation and repression of repeat-derived aberrant proteins

(2014) Yoshihiro Kino et al.   HUMAN MOLECULAR GENETICS

Whole Transcriptome Sequencing Reveals Extensive Unspliced mRNA in Metastatic Castration-Resistant Prostate Cancer

(2014) Adam G. Sowalsky et al.   MOLECULAR CANCER RESEARCH

Comprehensive molecular profiling of lung adenocarcinoma

(2014) Eric A. Collisson et al.   NATURE

Sample processing obscures cancer-specific alterations in leukemic transcriptomes

(2014) Heidi Dvinge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Flexible Mouse-On-Mouse Immunohistochemical Staining Technique Adaptable to Biotin-Free Reagents, Immunofluorescence, and Multiple Antibody Staining

(2013) Tracy Goodpaster et al.   JOURNAL OF HISTOCHEMISTRY & CYTOCHEMISTRY

Enhancers of Polycomb EPC1 and EPC2 sustain the oncogenic potential of MLL leukemia stem cells

(2013) X Huang et al.   LEUKEMIA

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line

(2013) Andrew Adey et al.   NATURE

The splicing factor SRSF1 regulates apoptosis and proliferation to promote mammary epithelial cell transformation

(2012) Olga Anczuków et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Muscleblind-like 2-Mediated Alternative Splicing in the Developing Brain and Dysregulation in Myotonic Dystrophy

(2012) Konstantinos Charizanis et al.   NEURON

The UCSC Genome Browser database: extensions and updates 2013

(2012) Laurence R. Meyer et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2013

(2012) Paul Flicek et al.   NUCLEIC ACIDS RESEARCH

Splicing Factor hnRNP A2/B1 Regulates Tumor Suppressor Gene Splicing and Is an Oncogenic Driver in Glioblastoma

(2011) R. Golan-Gerstl et al.   CANCER RESEARCH

Optimization of Dosing for EGFR-Mutant Non-Small Cell Lung Cancer with Evolutionary Cancer Modeling

(2011) J. Chmielecki et al.   Science Translational Medicine

A Chromatin-Mediated Reversible Drug-Tolerant State in Cancer Cell Subpopulations

(2010) Sreenath V. Sharma et al.   CELL

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Widespread Shortening of 3′UTRs by Alternative Cleavage and Polyadenylation Activates Oncogenes in Cancer Cells

(2009) Christine Mayr et al.   CELL

Regulation of Multiple Core Spliceosomal Proteins by Alternative Splicing-Coupled Nonsense-Mediated mRNA Decay

(2008) A. L. Saltzman et al.   MOLECULAR AND CELLULAR BIOLOGY

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2008) Qun Pan et al.   NATURE GENETICS