Computational comparison of common event-based differential splicing tools: practical considerations for laboratory researchers

Glucocorticoid Resistant Pediatric Acute Lymphoblastic Leukemia Samples Display Altered Splicing Profile and Vulnerability to Spliceosome Modulation

(2020) Rocco Sciarrillo et al.   Cancers

Association of altered folylpolyglutamate synthetase pre-mRNA splicing with methotrexate unresponsiveness in early rheumatoid arthritis

(2020) Ittai B Muller et al.   RHEUMATOLOGY

Systematic evaluation of differential splicing tools for RNA-seq studies

(2019) Arfa Mehmood et al.   BRIEFINGS IN BIOINFORMATICS

Splicing modulation as novel therapeutic strategy against diffuse malignant peritoneal mesothelioma

(2018) Rocco Sciarrillo et al.   EBioMedicine

Aberrant RNA Splicing in Cancer and Drug Resistance

(2018) Bi-Dar Wang et al.   Cancers

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Alternative splicing as a regulator of development and tissue identity

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

The association of aberrant folylpolyglutamate synthetase splicing with ex vivo methotrexate resistance and clinical outcome in childhood acute lymphoblastic leukemia

(2016) A. Wojtuszkiewicz et al.   HAEMATOLOGICA

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

The association of aberrant folylpolyglutamate synthetase splicing with ex vivo methotrexate resistance and clinical outcome in childhood acute lymphoblastic leukemia

(2016) A. Wojtuszkiewicz et al.   HAEMATOLOGICA

Using RNA-sequencing to Detect Novel Splice Variants Related to Drug Resistance in In Vitro Cancer Models

(2016) Rocco Sciarrillo et al.   Jove-Journal of Visualized Experiments

Alternative splicing as a biomarker and potential target for drug discovery

(2015) Kai-qin Le et al.   ACTA PHARMACOLOGICA SINICA

Mechanisms and Regulation of Alternative Pre-mRNA Splicing

(2015) Yeon Lee et al.   Annual Review of Biochemistry

Folylpolyglutamate synthetase splicing alterations in acute lymphoblastic leukemia are provoked by methotrexate and other chemotherapeutics and mediate chemoresistance

(2015) Anna Wojtuszkiewicz et al.   INTERNATIONAL JOURNAL OF CANCER

Methotrexate resistance in relation to treatment outcome in childhood acute lymphoblastic leukemia

(2015) Anna Wojtuszkiewicz et al.   Journal of Hematology & Oncology

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Comparisons of computational methods for differential alternative splicing detection using RNA-seq in plant systems

(2014) Ruolin Liu et al.   BMC BIOINFORMATICS

Pre-mRNA splicing in cancer: the relevance in oncogenesis, treatment and drug resistance

(2014) Anna Wojtuszkiewicz et al.   Expert Opinion on Drug Metabolism & Toxicology

rMATS: Robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

(2014) Shihao Shen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Modelling and simulating generic RNA-Seq experiments with the flux simulator

(2012) Thasso Griebel et al.   NUCLEIC ACIDS RESEARCH

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

Aberrant splicing of folylpolyglutamate synthetase as a novel mechanism of antifolate resistance in leukemia

(2009) M. Stark et al.   BLOOD

RNA processing and its regulation: global insights into biological networks

(2009) Donny D. Licatalosi et al.   NATURE REVIEWS GENETICS

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