A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons

Matt: Unix tools for alternative splicing analysis

(2018) André Gohr et al.   BIOINFORMATICS

High-Density Proximity Mapping Reveals the Subcellular Organization of mRNA-Associated Granules and Bodies

(2018) Ji-Young Youn et al.   MOLECULAR CELL

Autism-like phenotype and risk gene mRNA deadenylation by CPEB4 mis-splicing

(2018) Alberto Parras et al.   NATURE

Genome-wide CRISPR-Cas9 Interrogation of Splicing Networks Reveals a Mechanism for Recognition of Autism-Misregulated Neuronal Microexons

(2018) Thomas Gonatopoulos-Pournatzis et al.   MOLECULAR CELL

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

(2017) Javier Tapial et al.   GENOME RESEARCH

Gene duplication and neo-functionalization in the evolutionary and functional divergence of the metazoan copper transporters Ctr1 and Ctr2

(2017) Brandon L. Logeman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes

(2017) Demian Burguera et al.   Nature Communications

Data Independent Acquisition analysis in ProHits 4.0

(2016) Guomin Liu et al.   Journal of Proteomics

Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders

(2016) Mathieu Quesnel-Vallières et al.   MOLECULAR CELL

Large-scale remodeling of a repressed exon ribonucleoprotein to an exon definition complex active for splicing

(2016) Somsakul Pop Wongpalee et al.   eLife

Conserved functional antagonism of CELF and MBNL proteins controls stem cell-specific alternative splicing in planarians

(2016) Jordi Solana et al.   eLife

Essential roles for the splicing regulator nSR100/SRRM4 during nervous system development

(2015) Mathieu Quesnel-Vallières et al.   GENES & DEVELOPMENT

Proximity biotinylation and affinity purification are complementary approaches for the interactome mapping of chromatin-associated protein complexes

(2015) Jean-Philippe Lambert et al.   Journal of Proteomics

LSD1n is an H4K20 demethylase regulating memory formation via transcriptional elongation control

(2015) Jianxun Wang et al.   NATURE NEUROSCIENCE

An alternative splicing event amplifies evolutionary differences between vertebrates

(2015) S. Gueroussov et al.   SCIENCE

The alternative splicing factor Nova2 regulates vascular development and lumen formation

(2015) Costanza Giampietro et al.   Nature Communications

Identification of Ohnolog Genes Originating from Whole Genome Duplication in Early Vertebrates, Based on Synteny Comparison across Multiple Genomes

(2015) Param Priya Singh et al.   PLoS Computational Biology

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models

(2014) Travis J Wheeler et al.   BMC BIOINFORMATICS

A Highly Conserved Program of Neuronal Microexons Is Misregulated in Autistic Brains

(2014) Manuel Irimia et al.   CELL

Evolution of DNA Specificity in a Transcription Factor Family Produced a New Gene Regulatory Module

(2014) Alesia N. McKeown et al.   CELL

RBFOX and PTBP1 proteins regulate the alternative splicing of micro-exons in human brain transcripts

(2014) Yang I. Li et al.   GENOME RESEARCH

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

A Global Regulatory Mechanism for Activating an Exon Network Required for Neurogenesis

(2014) Bushra Raj et al.   MOLECULAR CELL

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

SAINTexpress: Improvements and additional features in Significance Analysis of INTeractome software

(2013) Guoci Teo et al.   Journal of Proteomics

MBNL proteins repress ES-cell-specific alternative splicing and reprogramming

(2013) Hong Han et al.   NATURE

Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

(2013) Adrian M. Altenhoff et al.   PLoS One

A Mutation in the Srrm4 Gene Causes Alternative Splicing Defects and Deafness in the Bronx Waltzer Mouse

(2012) Yoko Nakano et al.   PLoS Genetics

ProtTest 3: fast selection of best-fit models of protein evolution

(2011) Diego Darriba et al.   BIOINFORMATICS

Nervous systems of the sea anemone Nematostella vectensis are generated by ectoderm and endoderm and shaped by distinct mechanisms

(2011) N. Nakanishi et al.   DEVELOPMENT

iProphet: Multi-level Integrative Analysis of Shotgun Proteomic Data Improves Peptide and Protein Identification Rates and Error Estimates

(2011) David Shteynberg et al.   MOLECULAR & CELLULAR PROTEOMICS

Multi-domain conformational selection underlies pre-mRNA splicing regulation by U2AF

(2011) Cameron D. Mackereth et al.   NATURE

Generation of stable Drosophila cell lines using multicistronic vectors

(2011) Monika González et al.   Scientific Reports

Old gene duplication facilitates origin and diversification of an innovative communication system--twice

(2010) M. E. Arnegard et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

Genome-Wide Association between Branch Point Properties and Alternative Splicing

(2010) André Corvelo et al.   PLoS Computational Biology

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

(2009) M. D. Robinson et al.   BIOINFORMATICS

Regulation of Vertebrate Nervous System Alternative Splicing and Development by an SR-Related Protein

(2009) John A. Calarco et al.   CELL

Physical and genetic interactions of yeast Cwc21p, an ortholog of human SRm300/SRRM2, suggest a role at the catalytic center of the spliceosome

(2009) R. J. Grainger et al.   RNA

A systematic characterization of Cwc21, the yeast ortholog of the human spliceosomal protein SRm300

(2009) M. Khanna et al.   RNA

Altered Motor Activity of Alternative Splice Variants of the Mammalian Kinesin-3 Protein KIF1B

(2009) Masafumi Matsushita et al.   TRAFFIC

The amphioxus genome and the evolution of the chordate karyotype

(2008) Nicholas H. Putnam et al.   NATURE

Spliceosomal introns as tools for genomic and evolutionary analysis

(2008) M. Irimia et al.   NUCLEIC ACIDS RESEARCH