Oncogenic translation directs spliceosome dynamics revealing an integral role for SF3A3 in breast cancer

Asymmetrically Segregated Mitochondria Provide Cellular Memory of Hematopoietic Stem Cell Replicative History and Drive HSC Attrition

(2020) Ashwini Hinge et al.   Cell Stem Cell

The SF3b complex: splicing and beyond

(2020) Chengfu Sun   CELLULAR AND MOLECULAR LIFE SCIENCES

Analyses of non-coding somatic drivers in 2,658 cancer whole genomes

(2020) Esther Rheinbay et al.   NATURE

Translational control of breast cancer plasticity

(2020) Michael Jewer et al.   Nature Communications

The splicing factor RBM25 controls MYC activity in acute myeloid leukemia

(2019) Ying Ge et al.   Nature Communications

Dynamics of breast-cancer relapse reveal late-recurring ER-positive genomic subgroups

(2019) Oscar M. Rueda et al.   NATURE

In vivo analysis of influenza A mRNA secondary structures identifies critical regulatory motifs

(2019) Lisa Marie Simon et al.   NUCLEIC ACIDS RESEARCH

The X-Linked DDX3X RNA Helicase Dictates Translation Reprogramming and Metastasis in Melanoma

(2019) Bengt Phung et al.   Cell Reports

A unified mechanism for intron and exon definition and back-splicing

(2019) Xueni Li et al.   NATURE

Whole-genome sequencing of triple-negative breast cancers in a population-based clinical study

(2019) Johan Staaf et al.   NATURE MEDICINE

Targeting mRNA processing as an anticancer strategy

(2019) Joana Desterro et al.   NATURE REVIEWS DRUG DISCOVERY

RNA2Drawer: geometrically strict drawing of nucleic acid structures with graphical structure editing and highlighting of complementary subsequences

(2019) Philip Z. Johnson et al.   RNA Biology

Drp1 Promotes KRas-Driven Metabolic Changes to Drive Pancreatic Tumor Growth

(2019) Sarbajeet Nagdas et al.   Cell Reports

Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution

(2019) Jernej Ule et al.   MOLECULAR CELL

Altered RNA Processing in Cancer Pathogenesis and Therapy

(2019) Esther A. Obeng et al.   Cancer Discovery

Cross comparison and prognostic assessment of breast cancer multigene signatures in a large population-based contemporary clinical series

(2019) Johan Vallon-Christersson et al.   Scientific Reports

Matt: Unix tools for alternative splicing analysis

(2018) André Gohr et al.   BIOINFORMATICS

Apoptotic Cell-Derived Extracellular Vesicles Promote Malignancy of Glioblastoma Via Intercellular Transfer of Splicing Factors

(2018) Marat S. Pavlyukov et al.   CANCER CELL

Pseudouridylation of tRNA-Derived Fragments Steers Translational Control in Stem Cells

(2018) Nicola Guzzi et al.   CELL

RNA Framework: an all-in-one toolkit for the analysis of RNA structures and post-transcriptional modifications

(2018) Danny Incarnato et al.   NUCLEIC ACIDS RESEARCH

Exploiting Metabolic Vulnerabilities of Cancer with Precision and Accuracy

(2018) Adam J. Wolpaw et al.   TRENDS IN CELL BIOLOGY

Mutually exclusive acetylation and ubiquitylation of the splicing factor SRSF5 control tumor growth

(2018) Yuhan Chen et al.   Nature Communications

Mitochondrial fission as a driver of stemness in tumor cells: mDIVI1 inhibits mitochondrial function, cell migration and cancer stem cell (CSC) signalling

(2018) Maria Peiris-Pagès et al.   Oncotarget

Steric interference from intrinsically disordered regions controls dynamin-related protein 1 self-assembly during mitochondrial fission

(2018) Bin Lu et al.   Scientific Reports

Dynamin-Related Protein 1 at the Crossroads of Cancer

(2018) Ana Rita Lima et al.   Genes

Structural basis of mitochondrial receptor binding and constriction by DRP1

(2018) Raghav Kalia et al.   NATURE

A widespread alternate form of cap-dependent mRNA translation initiation

(2018) Columba de la Parra et al.   Nature Communications

Single sample scoring of molecular phenotypes

(2018) Momeneh Foroutan et al.   BMC BIOINFORMATICS

The BioGRID interaction database: 2019 update

(2018) Rose Oughtred et al.   NUCLEIC ACIDS RESEARCH

Simplified CRISPR tools for efficient genome editing and streamlined protocols for their delivery into mammalian cells and mouse zygotes

(2017) Ashley M. Jacobi et al.   METHODS

Basal-A Triple-Negative Breast Cancer Cells Selectively Rely on RNA Splicing for Survival

(2017) Stefanie Chan et al.   MOLECULAR CANCER THERAPEUTICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

Functional 5′ UTR mRNA structures in eukaryotic translation regulation and how to find them

(2017) Kathrin Leppek et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Guanylate-binding protein 2 regulates Drp1-mediated mitochondrial fission to suppress breast cancer cell invasion

(2017) Juan Zhang et al.   Cell Death & Disease

An Integrated Systems Biology Approach Identifies TRIM25 as a Key Determinant of Breast Cancer Metastasis

(2017) Logan A. Walsh et al.   Cell Reports

Copy-number and gene dependency analysis reveals partial copy loss of wild-type SF3B1 as a novel cancer vulnerability

(2017) Brenton R Paolella et al.   eLife

FANTOM5 CAGE profiles of human and mouse samples

(2017) Shuhei Noguchi et al.   Scientific Data

QuPath: Open source software for digital pathology image analysis

(2017) Peter Bankhead et al.   Scientific Reports

Extracellular Vesicles in Cancer: Cell-to-Cell Mediators of Metastasis

(2016) Annette Becker et al.   CANCER CELL

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

(2016) Xinping Yang et al.   CELL

RNA Splicing Modulation Selectively Impairs Leukemia Stem Cell Maintenance in Secondary Human AML

(2016) Leslie A. Crews et al.   Cell Stem Cell

Therapeutic targeting of splicing in cancer

(2016) Stanley Chun-Wei Lee et al.   NATURE MEDICINE

DMS-MaPseq for genome-wide or targeted RNA structure probing in vivo

(2016) Meghan Zubradt et al.   NATURE METHODS

Splicing-factor alterations in cancers

(2016) Olga Anczuków et al.   RNA

The somatic mutation profiles of 2,433 breast cancers refines their genomic and transcriptomic landscapes

(2016) Bernard Pereira et al.   Nature Communications

The lncRNA SLNCR1 Mediates Melanoma Invasion through a Conserved SRA1-like Region

(2016) Karyn Schmidt et al.   Cell Reports

A MYC-Driven Change in Mitochondrial Dynamics Limits YAP/TAZ Function in Mammary Epithelial Cells and Breast Cancer

(2015) Björn von Eyss et al.   CANCER CELL

SRSF1-Regulated Alternative Splicing in Breast Cancer

(2015) Olga Anczuków et al.   MOLECULAR CELL

Genome-Wide Identification of Fas/CD95 Alternative Splicing Regulators Reveals Links with Iron Homeostasis

(2015) J. Ramón Tejedor et al.   MOLECULAR CELL

Functional Splicing Network Reveals Extensive Regulatory Potential of the Core Spliceosomal Machinery

(2015) Panagiotis Papasaikas et al.   MOLECULAR CELL

Mitochondrial Division Is Requisite to RAS-Induced Transformation and Targeted by Oncogenic MAPK Pathway Inhibitors

(2015) Madhavika N. Serasinghe et al.   MOLECULAR CELL

Erk2 Phosphorylation of Drp1 Promotes Mitochondrial Fission and MAPK-Driven Tumor Growth

(2015) Jennifer A. Kashatus et al.   MOLECULAR CELL

eIF3 targets cell-proliferation messenger RNAs for translational activation or repression

(2015) Amy S. Y. Lee et al.   NATURE

The spliceosome is a therapeutic vulnerability in MYC-driven cancer

(2015) Tiffany Y.-T. Hsu et al.   NATURE

MYC regulates the core pre-mRNA splicing machinery as an essential step in lymphomagenesis

(2015) Cheryl M. Koh et al.   NATURE

Aberrant RNA splicing in cancer; expression changes and driver mutations of splicing factor genes

(2015) A Sveen et al.   ONCOGENE

The Sweden Cancerome Analysis Network - Breast (SCAN-B) Initiative: a large-scale multicenter infrastructure towards implementation of breast cancer genomic analyses in the clinical routine

(2015) Lao H Saal et al.   Genome Medicine

The Molecular Signatures Database Hallmark Gene Set Collection

(2015) Arthur Liberzon et al.   Cell Systems

New Strategies for Triple-Negative Breast Cancer--Deciphering the Heterogeneity

(2014) I. A. Mayer et al.   CLINICAL CANCER RESEARCH

Cellular senescence and its effector programs

(2014) R. Salama et al.   GENES & DEVELOPMENT

Improved vectors and genome-wide libraries for CRISPR screening

(2014) Neville E Sanjana et al.   NATURE METHODS

A day in the life of the spliceosome

(2014) A. Gregory Matera et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

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

MYC and Mitochondrial Biogenesis

(2014) F. Morrish et al.   Cold Spring Harbor Perspectives in Medicine

Enrichr: interactive and collaborative HTML5 gene list enrichment analysis tool

(2013) Edward Y Chen et al.   BMC BIOINFORMATICS

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

Alterations in c-Myc phenotypes resulting from dynamin-related protein 1 (Drp1)-mediated mitochondrial fission

(2013) M Sarin et al.   Cell Death & Disease

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

MYC on the Path to Cancer

(2012) Chi V. Dang   CELL

MYC pathway activation in triple-negative breast cancer is synthetic lethal with CDK inhibition

(2012) Dai Horiuchi et al.   JOURNAL OF EXPERIMENTAL MEDICINE

Emerging roles of the spliceosomal machinery in myelodysplastic syndromes and other hematological disorders

(2012) V Visconte et al.   LEUKEMIA

The genomic and transcriptomic architecture of 2,000 breast tumours reveals novel subgroups

(2012) Christina Curtis et al.   NATURE

NIH Image to ImageJ: 25 years of image analysis

(2012) Caroline A Schneider et al.   NATURE METHODS

Mitochondrial dynamics regulates migration and invasion of breast cancer cells

(2012) J Zhao et al.   ONCOGENE

Differential GC Content between Exons and Introns Establishes Distinct Strategies of Splice-Site Recognition

(2012) Maayan Amit et al.   Cell Reports

Identification of human triple-negative breast cancer subtypes and preclinical models for selection of targeted therapies

(2011) Brian D. Lehmann et al.   JOURNAL OF CLINICAL INVESTIGATION

Functional consequences of developmentally regulated alternative splicing

(2011) Auinash Kalsotra et al.   NATURE REVIEWS GENETICS

Genetic Dissection of the Oncogenic mTOR Pathway Reveals Druggable Addiction to Translational Control via 4EBP-eIF4E

(2010) Andrew C. Hsieh et al.   CANCER CELL

Triple-negative breast cancer: Molecular features, pathogenesis, treatment and current lines of research

(2010) Ana Bosch et al.   CANCER TREATMENT REVIEWS

Deregulation of oncogene-induced senescence and p53 translational control in X-linked dyskeratosis congenita

(2010) Cristian Bellodi et al.   EMBO JOURNAL

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

Spliceosome Structure and Function

(2010) C. L. Will et al.   Cold Spring Harbor Perspectives in Biology

VARNA: Interactive drawing and editing of the RNA secondary structure

(2009) Kévin Darty et al.   BIOINFORMATICS

A Core MYC Gene Expression Signature Is Prominent in Basal-Like Breast Cancer but Only Partially Overlaps the Core Serum Response

(2009) Sanjay Chandriani et al.   PLoS One

Identification, analysis, and prediction of protein ubiquitination sites

(2009) Predrag Radivojac et al.   PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS

The Epithelial-Mesenchymal Transition Generates Cells with Properties of Stem Cells

(2008) Sendurai A. Mani et al.   CELL

Module Map of Stem Cell Genes Guides Creation of Epithelial Cancer Stem Cells

(2008) David J. Wong et al.   Cell Stem Cell