Full-length transcript sequencing of human and mouse cerebral cortex identifies widespread isoform diversity and alternative splicing

A spatially resolved brain region- and cell type-specific isoform atlas of the postnatal mouse brain

(2021) Anoushka Joglekar et al.   Nature Communications

Interpretation of risk loci from genome-wide association studies of Alzheimer's disease

(2020) Shea J Andrews et al.   LANCET NEUROLOGY

The multiplex model of the genetics of Alzheimer’s disease

(2020) Rebecca Sims et al.   NATURE NEUROSCIENCE

Fusion transcripts in normal human cortex increase with age and show distinct genomic features for single cells and tissues

(2020) Bharati Mehani et al.   Scientific Reports

Transcriptional Signatures of Tau and Amyloid Neuropathology

(2020) Isabel Castanho et al.   Cell Reports

Transcript expression-aware annotation improves rare variant interpretation

(2020) Beryl B. Cummings et al.   NATURE

Incomplete annotation has a disproportionate impact on our understanding of Mendelian and complex neurogenetic disorders

(2020) David Zhang et al.   Science Advances

Intron retention and its impact on gene expression and protein diversity: A review and a practical guide

(2020) David F. Grabski et al.   Wiley Interdisciplinary Reviews-RNA

Gene regulation by long non-coding RNAs and its biological functions

(2020) Luisa Statello et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Analysis of Transcriptome and Epitranscriptome in Plants Using PacBio Iso-Seq and Nanopore-Based Direct RNA Sequencing

(2019) Liangzhen Zhao et al.   Frontiers in Genetics

Benefits and limitations of genome-wide association studies

(2019) Vivian Tam et al.   NATURE REVIEWS GENETICS

Reviving the Transcriptome Studies: An Insight Into the Emergence of Single-Molecule Transcriptome Sequencing

(2019) Bo Wang et al.   Frontiers in Genetics

Gene Fusions Derived by Transcriptional Readthrough are Driven by Segmental Duplication in Human

(2019) Ann M McCartney et al.   Genome Biology and Evolution

Alternative Splicing Regulatory Networks: Functions, Mechanisms, and Evolution

(2019) Jernej Ule et al.   MOLECULAR CELL

A tailored approach to fusion transcript identification increases diagnosis of rare inherited disease

(2019) Gavin R. Oliver et al.   PLoS One

The Expanding Landscape of Alternative Splicing Variation in Human Populations

(2018) Eddie Park et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Minimap2: pairwise alignment for nucleotide sequences

(2018) Heng Li   BIOINFORMATICS

Corrigendum: SQANTI: extensive characterization of long-read transcript sequences for quality control in full-length transcriptome identification and quantification

(2018) Manuel Tardaguila et al.   GENOME RESEARCH

Enhanced Global Post-translational Modification Discovery with MetaMorpheus

(2018) Stefan K. Solntsev et al.   JOURNAL OF PROTEOME RESEARCH

Common schizophrenia alleles are enriched in mutation-intolerant genes and in regions under strong background selection

(2018) Antonio F. Pardiñas et al.   NATURE GENETICS

Integrative transcriptome analyses of the aging brain implicate altered splicing in Alzheimer’s disease susceptibility

(2018) Towfique Raj et al.   NATURE GENETICS

Update of the FANTOM web resource: expansion to provide additional transcriptome atlases

(2018) Marina Lizio et al.   NUCLEIC ACIDS RESEARCH

Integrative functional genomic analysis of human brain development and neuropsychiatric risks

(2018) Mingfeng Li et al.   SCIENCE

Intron retention as a component of regulated gene expression programs

(2017) Aishwarya G. Jacob et al.   HUMAN GENETICS

The Activity-Induced Long Non-Coding RNA Meg3 Modulates AMPA Receptor Surface Expression in Primary Cortical Neurons

(2017) Men C. Tan et al.   Frontiers in Cellular Neuroscience

Genome-wide identification of splicing QTLs in the human brain and their enrichment among schizophrenia-associated loci

(2017) Atsushi Takata et al.   Nature Communications

Evaluation of the External RNA Controls Consortium (ERCC) reference material using a modified Latin square design

(2016) P. Scott Pine et al.   BMC BIOTECHNOLOGY

Widespread Expansion of Protein Interaction Capabilities by Alternative Splicing

(2016) Xinping Yang et al.   CELL

Genome-wide changes in lncRNA, splicing and regional gene expression patterns in autism

(2016) Neelroop N. Parikshak et al.   NATURE

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

Mechanism and regulation of the nonsense-mediated decay pathway

(2016) Nele Hug et al.   NUCLEIC ACIDS RESEARCH

Enrichr: a comprehensive gene set enrichment analysis web server 2016 update

(2016) Maxim V. Kuleshov et al.   NUCLEIC ACIDS RESEARCH

Unveiling the complexity of the maize transcriptome by single-molecule long-read sequencing

(2016) Bo Wang et al.   Nature Communications

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

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

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

(2015) Bushra Raj et al.   NEURON

The Genotype-Tissue Expression (GTEx) pilot analysis: Multitissue gene regulation in humans

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Widespread Polycistronic Transcripts in Fungi Revealed by Single-Molecule mRNA Sequencing

(2015) Sean P. Gordon et al.   PLoS One

Widespread intron retention in mammals functionally tunes transcriptomes

(2014) Ulrich Braunschweig et al.   GENOME RESEARCH

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Context-dependent control of alternative splicing by RNA-binding proteins

(2014) Xiang-Dong Fu et al.   NATURE REVIEWS GENETICS

The functional consequences of intron retention: Alternative splicing coupled to NMD as a regulator of gene expression

(2013) Ying Ge et al.   BIOESSAYS

Ribosome Profiling Provides Evidence that Large Noncoding RNAs Do Not Encode Proteins

(2013) Mitchell Guttman et al.   CELL

Widespread splicing changes in human brain development and aging

(2013) P. Mazin et al.   Molecular Systems Biology

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

CPAT: Coding-Potential Assessment Tool using an alignment-free logistic regression model

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

Systematically Differentiating Functions for Alternatively Spliced Isoforms through Integrating RNA-seq Data

(2013) Ridvan Eksi et al.   PLoS Computational Biology

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Coding vs non-coding: Translatability of short ORFs found in putative non-coding transcripts

(2011) Yuji Kageyama et al.   BIOCHIMIE

Analysis of alternative splicing associated with aging and neurodegeneration in the human brain

(2011) J. R. Tollervey et al.   GENOME RESEARCH

Total RNA sequencing reveals nascent transcription and widespread co-transcriptional splicing in the human brain

(2011) Adam Ameur et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Alternative splicing of mRNA in the molecular pathology of neurodegenerative diseases

(2011) James Dominic Mills et al.   NEUROBIOLOGY OF AGING

Review Article: Genetics of Alzheimer Disease

(2010) Lynn M. Bekris et al.   JOURNAL OF GERIATRIC PSYCHIATRY AND NEUROLOGY

Expression of Conjoined Genes: Another Mechanism for Gene Regulation in Eukaryotes

(2010) Tulika Prakash et al.   PLoS One

Erratum: Addendum: Deep surveying of alternative splicing complexity in the human transcriptome by high-throughput sequencing

(2009) Qun Pan et al.   NATURE GENETICS

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE