Discovery and Mass Spectrometric Analysis of Novel Splice-junction Peptides Using RNA-Seq

Proteoform: a single term describing protein complexity

(2013) Lloyd M Smith et al.   NATURE METHODS

Chimeras taking shape: Potential functions of proteins encoded by chimeric RNA transcripts

(2012) M. Frenkel-Morgenstern et al.   GENOME RESEARCH

GENCODE: The reference human genome annotation for The ENCODE Project

(2012) J. Harrow et al.   GENOME RESEARCH

Addressing Statistical Biases in Nucleotide-Derived Protein Databases for Proteogenomic Search Strategies

(2012) Paul Blakeley et al.   JOURNAL OF PROTEOME RESEARCH

Comparative Proteomics Reveals a Significant Bias Toward Alternative Protein Isoforms with Conserved Structure and Function

(2012) I. Ezkurdia et al.   MOLECULAR BIOLOGY AND EVOLUTION

De novo derivation of proteomes from transcriptomes for transcript and protein identification

(2012) Vanessa C Evans et al.   NATURE METHODS

Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case

(2012) Gloria Lopez-Casado et al.   PROTEOMICS

Alternative Splicing of RNA Triplets Is Often Regulated and Accelerates Proteome Evolution

(2012) Robert K. Bradley et al.   PLOS BIOLOGY

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

(2011) Bo Li et al.   BMC BIOINFORMATICS

Assessing the contribution of alternative splicing to proteome diversity in Arabidopsis thaliana using proteomics data

(2011) Edouard I Severing et al.   BMC PLANT BIOLOGY

De novo assembly and validation of planaria transcriptome by massive parallel sequencing and shotgun proteomics

(2011) C. Adamidi et al.   GENOME RESEARCH

Shotgun proteomics aids discovery of novel protein-coding genes, alternative splicing, and "resurrected" pseudogenes in the mouse genome

(2011) M. Brosch et al.   GENOME RESEARCH

Synthetic spike-in standards for RNA-seq experiments

(2011) L. Jiang et al.   GENOME RESEARCH

The discovery of novel protein-coding features in mouse genome based on mass spectrometry data

(2011) Xiao-Bin Xing et al.   GENOMICS

IsoformResolver: A Peptide-Centric Algorithm for Protein Inference

(2011) Karen Meyer-Arendt et al.   JOURNAL OF PROTEOME RESEARCH

Protein Identification Using Customized Protein Sequence Databases Derived from RNA-Seq Data

(2011) Xiaojing Wang et al.   JOURNAL OF PROTEOME RESEARCH

The quantitative proteome of a human cell line

(2011) M. Beck et al.   Molecular Systems Biology

Computational methods for transcriptome annotation and quantification using RNA-seq

(2011) Manuel Garber et al.   NATURE METHODS

Coding potential of the products of alternative splicing in human

(2011) Guido Leoni et al.   GENOME BIOLOGY

PEPPI: a peptidomic database of human protein isoforms for proteomics experiments

(2010) Ao Zhou et al.   BMC BIOINFORMATICS

Prediction of novel miRNAs and associated target genes in Glycine max

(2010) Trupti Joshi et al.   BMC BIOINFORMATICS

Proteomic Characterization of Novel Alternative Splice Variant Proteins in Human Epidermal Growth Factor Receptor 2/neu–Induced Breast Cancers

(2010) Rajasree Menon et al.   CANCER RESEARCH

Detection of Alternative Splice Variants at the Proteome Level inAspergillus flavus

(2010) Kung-Yen Chang et al.   JOURNAL OF PROTEOME RESEARCH

Proteogenomics to discover the full coding content of genomes: A computational perspective

(2010) Natalie Castellana et al.   Journal of Proteomics

A survey of computational methods and error rate estimation procedures for peptide and protein identification in shotgun proteomics

(2010) Alexey I. Nesvizhskii   Journal of Proteomics

Template Proteogenomics: Sequencing Whole Proteins Using an Imperfect Database

(2010) Natalie E. Castellana et al.   MOLECULAR & CELLULAR PROTEOMICS

Analysis and design of RNA sequencing experiments for identifying isoform regulation

(2010) Yarden Katz et al.   NATURE METHODS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

NCBI GEO: archive for functional genomics data sets--10 years on

(2010) T. Barrett et al.   NUCLEIC ACIDS RESEARCH

An Integrated Mass-Spectrometry Pipeline Identifies Novel Protein Coding-Regions in the Human Genome

(2010) Danny A. Bitton et al.   PLoS One

Investigating protein isoforms via proteomics: A feasibility study

(2010) Paul Blakeley et al.   PROTEOMICS

Computational analysis of unassigned high-quality MS/MS spectra in proteomic data sets

(2010) Kang Ning et al.   PROTEOMICS

TopHat: discovering splice junctions with RNA-Seq

(2009) Cole Trapnell et al.   BIOINFORMATICS

Universal sample preparation method for proteome analysis

(2009) Jacek R Wiśniewski et al.   NATURE METHODS

Stochastic noise in splicing machinery

(2009) Eugene Melamud et al.   NUCLEIC ACIDS RESEARCH

High-Throughput Proteomics Detection of Novel Splice Isoforms in Human Platelets

(2009) Karen A. Power et al.   PLoS One

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

(2009) Ben Langmead et al.   GENOME BIOLOGY

A compatible exon-exon junction database for the identification of exon skipping events using tandem mass spectrum data

(2008) Fan Mo et al.   BMC BIOINFORMATICS

Identification of Novel Alternative Splice Isoforms of Circulating Proteins in a Mouse Model of Human Pancreatic Cancer

(2008) R. Menon et al.   CANCER RESEARCH

Alternative isoform regulation in human tissue transcriptomes

(2008) Eric T. Wang et al.   NATURE

Genome-wide analysis of transcript isoform variation in humans

(2008) Tony Kwan et al.   NATURE GENETICS

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

(2008) Qun Pan et al.   NATURE GENETICS

Discovery and revision of Arabidopsis genes by proteogenomics

(2008) N. E. Castellana et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread and subtle: alternative splicing at short-distance tandem sites

(2008) Michael Hiller et al.   TRENDS IN GENETICS

Proteomics studies confirm the presence of alternative protein isoforms on a large scale

(2008) Michael L Tress et al.   GENOME BIOLOGY

Posterior Error Probabilities and False Discovery Rates: Two Sides of the Same Coin

(2007) Lukas Käll et al.   JOURNAL OF PROTEOME RESEARCH

Statistical Validation of Peptide Identifications in Large-Scale Proteomics Using the Target-Decoy Database Search Strategy and Flexible Mixture Modeling

(2007) Hyungwon Choi et al.   JOURNAL OF PROTEOME RESEARCH