Pathogenic impact of transcript isoform switching in 1,209 cancer samples covering 27 cancer types using an isoform-specific interaction network

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

(2020) Esther Rheinbay et al.   NATURE

Genomic basis for RNA alterations in cancer

(2020) Claudia Calabrese et al.   NATURE

Pan-cancer analysis of whole genomes

(2020)   NATURE

Pathway and network analysis of more than 2500 whole cancer genomes

(2020) Matthew A. Reyna et al.   Nature Communications

Systematic Multiomics Analysis of Alterations in C1QBP mRNA Expression and Relevance for Clinical Outcomes in Cancers

(2019) Subbroto Saha et al.   Journal of Clinical Medicine

Limitations of alignment-free tools in total RNA-seq quantification

(2018) Douglas C. Wu et al.   BMC GENOMICS

Nonsense-mediated mRNA Decay and Cancer

(2018) Maximilian W Popp et al.   CURRENT OPINION IN GENETICS & DEVELOPMENT

The Krebs Cycle Connection: Reciprocal Influence Between Alternative Splicing Programs and Cell Metabolism

(2018) Giuseppe Biamonti et al.   Frontiers in Oncology

Single-cell isoform RNA sequencing characterizes isoforms in thousands of cerebellar cells

(2018) Ishaan Gupta et al.   NATURE BIOTECHNOLOGY

An Emerging Role for Tubulin Isotypes in Modulating Cancer Biology and Chemotherapy Resistance

(2017) Amelia L. Parker et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The Landscape of Isoform Switches in Human Cancers

(2017) Kristoffer Vitting-Seerup et al.   MOLECULAR CANCER RESEARCH

Detecting alternatively spliced transcript isoforms from single-molecule long-read sequences without a reference genome

(2017) Xiaoxian Liu et al.   Molecular Ecology Resources

Impact of Alternative Splicing on the Human Proteome

(2017) Yansheng Liu et al.   Cell Reports

The Functional Impact of Alternative Splicing in Cancer

(2017) Héctor Climente-González et al.   Cell Reports

Stochastic principles governing alternative splicing of RNA

(2017) Jianfei Hu et al.   PLoS Computational Biology

Identifying HIPK1 as Target of miR-22-3p Enhancing Recombinant Protein Production From HEK 293 Cell by Using Microarray and HTP siRNA Screen

(2017) Sarah Inwood et al.   Biotechnology Journal

Splicing of Nascent RNA Coincides with Intron Exit from RNA Polymerase II

(2016) Fernando Carrillo Oesterreich et al.   CELL

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

(2016) Xinping Yang et al.   CELL

Predicting Protein–Protein Interactions from the Molecular to the Proteome Level

(2016) Ozlem Keskin et al.   CHEMICAL REVIEWS

Role of ribosomal protein mutations in tumor development (Review)

(2016) KAVEH M. GOUDARZI et al.   INTERNATIONAL JOURNAL OF ONCOLOGY

Coupling of RNA Polymerase II Transcription Elongation with Pre-mRNA Splicing

(2016) Tassa Saldi et al.   JOURNAL OF MOLECULAR BIOLOGY

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Structure of human MDM2 complexed with RPL11 reveals the molecular basis of p53 activation

(2015) Jiangge Zheng et al.   GENES & DEVELOPMENT

Most Highly Expressed Protein-Coding Genes Have a Single Dominant Isoform

(2015) Iakes Ezkurdia et al.   JOURNAL OF PROTEOME RESEARCH

Comprehensive transcriptome analysis using synthetic long-read sequencing reveals molecular co-association of distant splicing events

(2015) Hagen Tilgner et al.   NATURE BIOTECHNOLOGY

Identification of common genetic variants controlling transcript isoform variation in human whole blood

(2015) Xiaoling Zhang et al.   NATURE GENETICS

Detection of recurrent alternative splicing switches in tumor samples reveals novel signatures of cancer

(2015) Endre Sebestyén et al.   NUCLEIC ACIDS RESEARCH

Identification of recurrent regulated alternative splicing events across human solid tumors

(2015) Miri Danan-Gotthold et al.   NUCLEIC ACIDS RESEARCH

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

(2015) A Sveen et al.   ONCOGENE

Structural Insights into WD-Repeat 48 Activation of Ubiquitin-Specific Protease 46

(2015) Jianping Yin et al.   STRUCTURE

Tandem-repeat protein domains across the tree of life

(2015) Kristin K. Jernigan et al.   PeerJ

Correcting for the study bias associated with protein–protein interaction measurements reveals differences between protein degree distributions from different cancer types

(2015) Martin H. Schaefer et al.   Frontiers in Genetics

Identification of an Exon 4-Deletion Variant of Epidermal Growth Factor Receptor with Increased Metastasis-Promoting Capacity

(2015) Hai Wang et al.   NEOPLASIA

The role of mRNA splicing in prostate cancer

(2014) AnnaV Lapuk et al.   ASIAN JOURNAL OF ANDROLOGY

Analyzing the First Drafts of the Human Proteome

(2014) Iakes Ezkurdia et al.   JOURNAL OF PROTEOME RESEARCH

Targeting RAS–ERK signalling in cancer: promises and challenges

(2014) Ahmed A. Samatar et al.   NATURE REVIEWS DRUG DISCOVERY

SWISS-MODEL: modelling protein tertiary and quaternary structure using evolutionary information

(2014) Marco Biasini et al.   NUCLEIC ACIDS RESEARCH

STRING v10: protein–protein interaction networks, integrated over the tree of life

(2014) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

Protein interaction network of alternatively spliced isoforms from brain links genetic risk factors for autism

(2014) Roser Corominas et al.   Nature Communications

Phosphatase: PP2A structural importance, regulation and its aberrant expression in cancer

(2013) Parthasarathy Seshacharyulu et al.   CANCER LETTERS

Interactome Analysis Reveals that C1QBP (complement component 1, q subcomponent binding protein) Is Associated with Cancer Cell Chemotaxis and Metastasis

(2013) Xiaofang Zhang et al.   MOLECULAR & CELLULAR PROTEOMICS

The Cancer Genome Atlas Pan-Cancer analysis project

(2013) John N Weinstein et al.   NATURE GENETICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

3did: a catalog of domain-based interactions of known three-dimensional structure

(2013) Roberto Mosca et al.   NUCLEIC ACIDS RESEARCH

Hallmarks of alternative splicing in cancer

(2013) S Oltean et al.   ONCOGENE

Spliced MDM2 isoforms promote mutant p53 accumulation and gain-of-function in tumorigenesis

(2013) Tongsen Zheng et al.   Nature Communications

Transcriptome analysis of human tissues and cell lines reveals one dominant transcript per gene

(2013) Mar Gonzàlez-Porta et al.   GENOME BIOLOGY

Function of alternative splicing

(2012) Olga Kelemen et al.   GENE

Tissue-Specific Alternative Splicing Remodels Protein-Protein Interaction Networks

(2012) Jonathan D. Ellis et al.   MOLECULAR CELL

Tissue-Specific Splicing of Disordered Segments that Embed Binding Motifs Rewires Protein Interaction Networks

(2012) Marija Buljan et al.   MOLECULAR CELL

The deubiquitination enzyme USP46 functions as a tumor suppressor by controlling PHLPP-dependent attenuation of Akt signaling in colon cancer

(2012) X Li et al.   ONCOGENE

NPPC/NPR2 signaling is essential for oocyte meiotic arrest and cumulus oophorus formation during follicular development in the mouse ovary

(2012) Chiyo Kiyosu et al.   REPRODUCTION

Structural Probing of a Protein Phosphatase 2A Network by Chemical Cross-Linking and Mass Spectrometry

(2012) F. Herzog et al.   SCIENCE

Xwalk: computing and visualizing distances in cross-linking experiments

(2011) Abdullah Kahraman et al.   BIOINFORMATICS

Interactome Networks and Human Disease

(2011) Marc Vidal et al.   CELL

Epigenetics in Alternative Pre-mRNA Splicing

(2011) Reini F. Luco et al.   CELL

Cell-surface Receptor for Complement Component C1q (gC1qR) Is a Key Regulator for Lamellipodia Formation and Cancer Metastasis

(2011) Ki-Bum Kim et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

RAF inhibitor resistance is mediated by dimerization of aberrantly spliced BRAF(V600E)

(2011) Poulikos I. Poulikakos et al.   NATURE

The Pfam protein families database

(2011) M. Punta et al.   NUCLEIC ACIDS RESEARCH

Mutant p53 Gain-of-Function in Cancer

(2009) M. Oren et al.   Cold Spring Harbor Perspectives in Biology

Differential Isoform Expression and Interaction with the P32 Regulatory Protein Controls the Subcellular Localization of the Splicing Factor U2AF26

(2008) Florian Heyd et al.   JOURNAL OF BIOLOGICAL CHEMISTRY