Systematic exploration of dynamic splicing networks reveals conserved multistage regulators of neurogenesis

Differential contribution of transcriptomic regulatory layers in the definition of neuronal identity

(2021) Kevin C. H. Ha et al.   Nature Communications

Complexity and graded regulation of neuronal cell-type–specific alternative splicing revealed by single-cell RNA sequencing

(2021) Huijuan Feng et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Integrated analysis of multimodal single-cell data

(2021) Yuhan Hao et al.   CELL

Molecular architecture of the developing mouse brain

(2021) Gioele La Manno et al.   NATURE

Differential abundance testing on single-cell data using k-nearest neighbor graphs

(2021) Emma Dann et al.   NATURE BIOTECHNOLOGY

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

(2020) James D. Thomas et al.   NATURE GENETICS

Genetic interaction mapping and exon-resolution functional genomics with a hybrid Cas9–Cas12a platform

(2020) Thomas Gonatopoulos-Pournatzis et al.   NATURE BIOTECHNOLOGY

A single-cell and single-nucleus RNA-Seq toolbox for fresh and frozen human tumors

(2020) Michal Slyper et al.   NATURE MEDICINE

The changing mouse embryo transcriptome at whole tissue and single-cell resolution

(2020) Peng He et al.   NATURE

Alternative Splicing of Cdh23 Exon 68 Is Regulated by RBM24, RBM38, and PTBP1

(2020) Nana Li et al.   NEURAL PLASTICITY

Cancer-Associated Substitutions in RNA Recognition Motifs of PUF60 and U2AF65 Reveal Residues Required for Correct Folding and 3′ Splice-Site Selection

(2020) Jana Kralovicova et al.   Cancers

Co-expression analysis reveals interpretable gene modules controlled by trans-acting genetic variants

(2020) Liis Kolberg et al.   eLife

QUAKING Regulates Microexon Alternative Splicing of the Rho GTPase Pathway and Controls Microglia Homeostasis

(2020) Jeesan Lee et al.   Cell Reports

The single-cell transcriptional landscape of mammalian organogenesis

(2019) Junyue Cao et al.   NATURE

Comprehensive Integration of Single-Cell Data

(2019) Tim Stuart et al.   CELL

Landscape of ribosome-engaged transcript isoforms reveals extensive neuronal-cell-class-specific alternative splicing programs

(2019) Elisabetta Furlanis et al.   NATURE NEUROSCIENCE

CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons

(2019) Ruilin Tian et al.   NEURON

Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution

(2019) Jernej Ule et al.   MOLECULAR CELL

Fast, sensitive and accurate integration of single-cell data with Harmony

(2019) Ilya Korsunsky et al.   NATURE METHODS

Structural basis for mRNA recognition by human RBM38

(2019) Kaiyue Qian et al.   BIOCHEMICAL JOURNAL

Regulation of Neuronal Differentiation, Function, and Plasticity by Alternative Splicing

(2018) Elisabetta Furlanis et al.   Annual Review of Cell and Developmental Biology

Neuron-specific alternative splicing of transcriptional machineries: Implications for neurodevelopmental disorders

(2018) Robert S. Porter et al.   MOLECULAR AND CELLULAR NEUROSCIENCE

Integrating single-cell transcriptomic data across different conditions, technologies, and species

(2018) Andrew Butler et al.   NATURE BIOTECHNOLOGY

PUF60-activated exons uncover altered 3′ splice-site selection by germline missense mutations in a single RRM

(2018) Jana Královičová et al.   NUCLEIC ACIDS RESEARCH

Precise temporal regulation of alternative splicing during neural development

(2018) Sebastien M. Weyn-Vanhentenryck et al.   Nature Communications

Efficient and Accurate Quantitative Profiling of Alternative Splicing Patterns of Any Complexity on a Laptop

(2018) Timothy Sterne-Weiler et al.   MOLECULAR CELL

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

STRING v11: protein–protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets

(2018) Damian Szklarczyk et al.   NUCLEIC ACIDS RESEARCH

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

Multilayered Control of Alternative Splicing Regulatory Networks by Transcription Factors

(2017) Hong Han et al.   MOLECULAR CELL

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

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

(2016) Xinping Yang et al.   CELL

Dominant variants in the splicing factor PUF60 cause a recognizable syndrome with intellectual disability, heart defects and short stature

(2016) Salima El Chehadeh et al.   EUROPEAN JOURNAL OF HUMAN GENETICS

Data Independent Acquisition analysis in ProHits 4.0

(2016) Guomin Liu et al.   Journal of Proteomics

Robust transcriptome-wide discovery of RNA-binding protein binding sites with enhanced CLIP (eCLIP)

(2016) Eric L Van Nostrand et al.   NATURE METHODS

The neurogenetics of alternative splicing

(2016) Celine K. Vuong et al.   NATURE REVIEWS NEUROSCIENCE

Dissecting the multicellular ecosystem of metastatic melanoma by single-cell RNA-seq

(2016) I. Tirosh et al.   SCIENCE

Developmental regulation of RNA processing by Rbfox proteins

(2016) John G. Conboy   Wiley Interdisciplinary Reviews-RNA

Reconstruction of composite regulator-target splicing networks from high-throughput transcriptome data

(2015) Panagiotis Papasaikas et al.   BMC GENOMICS

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

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

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

Spatial reconstruction of single-cell gene expression data

(2015) Rahul Satija et al.   NATURE BIOTECHNOLOGY

MSPLIT-DIA: sensitive peptide identification for data-independent acquisition

(2015) Jian Wang et al.   NATURE METHODS

Trajectories of cell-cycle progression from fixed cell populations

(2015) Gabriele Gut et al.   NATURE METHODS

Alternative Splicing in the Mammalian Nervous System: Recent Insights into Mechanisms and Functional Roles

(2015) Bushra Raj et al.   NEURON

An alternative splicing event amplifies evolutionary differences between vertebrates

(2015) S. Gueroussov et al.   SCIENCE

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

(2014) Manuel Irimia et al.   CELL

RBM24 Is a Major Regulator of Muscle-Specific Alternative Splicing

(2014) Jiwen Yang et al.   DEVELOPMENTAL CELL

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

An RNA-Sequencing Transcriptome and Splicing Database of Glia, Neurons, and Vascular Cells of the Cerebral Cortex

(2014) Y. Zhang et al.   JOURNAL OF NEUROSCIENCE

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

(2014) Bushra Raj et al.   MOLECULAR CELL

SCRIB and PUF60 Are Primary Drivers of the Multisystemic Phenotypes of the 8q24.3 Copy-Number Variant

(2013) Andrew Dauber et al.   AMERICAN JOURNAL OF HUMAN GENETICS

GSVA: gene set variation analysis for microarray and RNA-Seq data

(2013) Sonja Hänzelmann et al.   BMC BIOINFORMATICS

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

(2013) Guoci Teo et al.   Journal of Proteomics

iCLIP: Protein–RNA interactions at nucleotide resolution

(2013) Ina Huppertz et al.   METHODS

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

(2013) Hong Han et al.   NATURE

A compendium of RNA-binding motifs for decoding gene regulation

(2013) Debashish Ray et al.   NATURE

The RNA Binding Protein RBM38 (RNPC1) Regulates Splicing during Late Erythroid Differentiation

(2013) Laurie A. Heinicke et al.   PLoS One

Site identification in high-throughput RNA–protein interaction data

(2012) Philip J. Uren et al.   BIOINFORMATICS

Alternative splicing: decoding an expansive regulatory layer

(2012) Manuel Irimia et al.   CURRENT OPINION IN CELL 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

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

(2012) Davis J. McCarthy et al.   NUCLEIC ACIDS RESEARCH

An Alternative Splicing Switch Regulates Embryonic Stem Cell Pluripotency and Reprogramming

(2011) Mathieu Gabut et al.   CELL

Translational repression of p53 by RNPC1, a p53 target overexpressed in lymphomas

(2011) J. Zhang et al.   GENES & 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

The importance of CELF control: molecular and biological roles of the CUG-BP, Elav-like family of RNA-binding proteins

(2011) Twishasri Dasgupta et al.   Wiley Interdisciplinary Reviews-RNA

Quantitative Characterization of the Interactions amongc-mycTranscriptional Regulators FUSE, FBP, and FIR

(2010) Hsin-hao Hsiao et al.   BIOCHEMISTRY

An Alternative Splicing Network Links Cell-Cycle Control to Apoptosis

(2010) Michael J. Moore et al.   CELL

The Generating Function of CID, ETD, and CID/ETD Pairs of Tandem Mass Spectra: Applications to Database Search

(2010) Sangtae Kim et al.   MOLECULAR & CELLULAR PROTEOMICS

Molecular basis of FIR-mediated c-myc transcriptional control

(2010) Cyprian D Cukier et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

RNPC1 modulates the RNA-binding activity of, and cooperates with, HuR to regulate p21 mRNA stability

(2010) S. J. Cho et al.   NUCLEIC ACIDS RESEARCH

A guided tour of the Trans-Proteomic Pipeline

(2010) Eric W. Deutsch et al.   PROTEOMICS

Next generation software for functional trend analysis

(2009) G. F. Berriz et al.   BIOINFORMATICS

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

A conserved peptide motif in Raver2 mediates its interaction with the polypyrimidine tract-binding protein

(2009) Berenike Henneberg et al.   EXPERIMENTAL CELL RESEARCH

RNA processing and its regulation: global insights into biological networks

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

Optimizing data intensive GPGPU computations for DNA sequence alignment

(2009) Cole Trapnell et al.   PARALLEL COMPUTING

Ultrafast and memory-efficient alignment of short DNA sequences to the human genome

(2009) Ben Langmead et al.   GENOME BIOLOGY

Dimerization and Protein Binding Specificity of the U2AF Homology Motif of the Splicing Factor Puf60

(2008) Lorenzo Corsini et al.   JOURNAL OF BIOLOGICAL CHEMISTRY