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

Glial and Neuronal Protein Tyrosine Phosphatase Alpha (PTPα) Regulate Oligodendrocyte Differentiation and Myelination

(2017) Yuda Shih et al.   JOURNAL OF MOLECULAR NEUROSCIENCE

High-Resolution Expression Map of the Arabidopsis Root Reveals Alternative Splicing and lincRNA Regulation

(2016) Song Li et al.   DEVELOPMENTAL CELL

Human Proteome Project Mass Spectrometry Data Interpretation Guidelines 2.1

(2016) Eric W. Deutsch et al.   JOURNAL OF PROTEOME RESEARCH

The ribosome-engaged landscape of alternative splicing

(2016) Robert J Weatheritt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

Cytoplasmic Rbfox1 Regulates the Expression of Synaptic and Autism-Related Genes

(2016) Ji-Ann Lee et al.   NEURON

The role of telomeres and telomerase reverse transcriptase isoforms in pluripotency induction and maintenance

(2016) Jonathan H. Teichroeb et al.   RNA Biology

A survey of the sorghum transcriptome using single-molecule long reads

(2016) Salah E. Abdel-Ghany et al.   Nature Communications

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

(2016) Bo Wang et al.   Nature Communications

The ribosome-engaged landscape of alternative splicing

(2016) Robert J Weatheritt et al.   NATURE STRUCTURAL & MOLECULAR BIOLOGY

cDNA Library Enrichment of Full Length Transcripts for SMRT Long Read Sequencing

(2016) Maria Cartolano et al.   PLoS One

Benchmarking of the Oxford Nanopore MinION sequencing for quantitative and qualitative assessment of cDNA populations

(2016) Spyros Oikonomopoulos et al.   Scientific Reports

Characterization of glucose-related metabolic pathways in differentiated rat oligodendrocyte lineage cells

(2015) Ana I. Amaral et al.   GLIA

Pladipus Enables Universal Distributed Computing in Proteomics Bioinformatics

(2015) Kenneth Verheggen et al.   JOURNAL OF PROTEOME RESEARCH

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

PeptideShaker enables reanalysis of MS-derived proteomics data sets

(2015) Marc Vaudel et al.   NATURE BIOTECHNOLOGY

Cell type– and brain region–resolved mouse brain proteome

(2015) Kirti Sharma et al.   NATURE NEUROSCIENCE

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

(2015) Bushra Raj et al.   NEURON

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

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

LoRDEC: accurate and efficient long read error correction

(2014) Leena Salmela et al.   BIOINFORMATICS

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

(2014) Manuel Irimia et al.   CELL

Increasing the Coding Potential of Genomes Through Alternative Splicing: The Case of PARK2 Gene

(2014) Valentina La Cognata et al.   CURRENT GENOMICS

A comprehensive survey of non-canonical splice sites in the human transcriptome

(2014) Guillermo E. Parada et al.   NUCLEIC ACIDS RESEARCH

CIP4 promotes lung adenocarcinoma metastasis and is associated with poor prognosis

(2014) P Truesdell et al.   ONCOGENE

Proteomic analysis of mouse astrocytes and their secretome by a combination of FASP and StageTip-based, high pH, reversed-phase fractionation

(2014) Dohyun Han et al.   PROTEOMICS

Using Genome Query Language to uncover genetic variation

(2013) Christos Kozanitis et al.   BIOINFORMATICS

Frac-seq reveals isoform-specific recruitment to polyribosomes

(2013) T. Sterne-Weiler et al.   GENOME RESEARCH

3' UTR-isoform choice has limited influence on the stability and translational efficiency of most mRNAs in mouse fibroblasts

(2013) N. Spies et al.   GENOME RESEARCH

Control of alternative splicing in immune responses: many regulators, many predictions, much still to learn

(2013) Nicole M. Martinez et al.   IMMUNOLOGICAL REVIEWS

A single-molecule long-read survey of the human transcriptome

(2013) Donald Sharon et al.   NATURE BIOTECHNOLOGY

Assessment of transcript reconstruction methods for RNA-seq

(2013) Tamara Steijger et al.   NATURE METHODS

Characterization of the human ESC transcriptome by hybrid sequencing

(2013) K. F. Au et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Accurate Identification and Analysis of Human mRNA Isoforms Using Deep Long Read Sequencing

(2013) Hagen Tilgner et al.   G3-Genes Genomes Genetics

Alternative RNA splicing and cancer

(2013) Sali Liu et al.   Wiley Interdisciplinary Reviews-RNA

STAR: ultrafast universal RNA-seq aligner

(2012) Alexander Dobin et al.   BIOINFORMATICS

Primer-BLAST: A tool to design target-specific primers for polymerase chain reaction

(2012) Jian Ye et al.   BMC BIOINFORMATICS

Pacific biosciences sequencing technology for genotyping and variation discovery in human data

(2012) Mauricio O Carneiro et al.   BMC GENOMICS

iReckon: Simultaneous isoform discovery and abundance estimation from RNA-seq data

(2012) A. M. Mezlini et al.   GENOME RESEARCH

Sequencing the unsequenceable: Expanded CGG-repeat alleles of the fragile X gene

(2012) E. W. Loomis et al.   GENOME RESEARCH

CUG-BP, Elav-like family (CELF)-mediated alternative splicing regulation in the brain during health and disease

(2012) Andrea N. Ladd   MOLECULAR AND CELLULAR NEUROSCIENCE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

APPRIS: annotation of principal and alternative splice isoforms

(2012) Jose Manuel Rodriguez et al.   NUCLEIC ACIDS RESEARCH

Perceptions and Experiences of Research Participants on Gender-Based Violence Community Based Survey: Implications for Ethical Guidelines

(2012) Yandisa Sikweyiya et al.   PLoS One

The importance of identifying alternative splicing in vertebrate genome annotation

(2012) Adam Frankish et al.   Database-The Journal of Biological Databases and Curation

The Human Pancreatic Islet Transcriptome: Expression of Candidate Genes for Type 1 Diabetes and the Impact of Pro-Inflammatory Cytokines

(2012) Décio L. Eizirik et al.   PLoS Genetics

SpliceGrapher: detecting patterns of alternative splicing from RNA-Seq data in the context of gene models and EST data

(2012) Mark F Rogers et al.   GENOME BIOLOGY

RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome

(2011) Bo Li et al.   BMC BIOINFORMATICS

The Origins, Evolution, and Functional Potential of Alternative Splicing in Vertebrates

(2011) J. M. Mudge et al.   MOLECULAR BIOLOGY AND EVOLUTION

SearchGUI: An open-source graphical user interface for simultaneous OMSSA and X!Tandem searches

(2011) Marc Vaudel et al.   PROTEOMICS

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

(2010) T. Lu et al.   GENOME RESEARCH

Apparent Non-Canonical Trans-Splicing Is Generated by Reverse Transcriptase In Vitro

(2010) Jonathan Houseley et al.   PLoS One

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

Spectral Probabilities and Generating Functions of Tandem Mass Spectra: A Strike against Decoy Databases

(2008) Sangtae Kim et al.   JOURNAL OF PROTEOME RESEARCH

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

High-throughput functional annotation and data mining with the Blast2GO suite

(2008) S. Gotz et al.   NUCLEIC ACIDS RESEARCH

Cross-kingdom patterns of alternative splicing and splice recognition

(2008) Abigail M McGuire et al.   GENOME BIOLOGY