Integrating transcriptomic and proteomic data for accurate assembly and annotation of genomes

Proteogenomic Discovery of a Small, Novel Protein in Yeast Reveals a Strategy for the Detection of Unannotated Short Open Reading Frames

(2015) Daniel Yagoub et al.   JOURNAL OF PROTEOME RESEARCH

Galaxy Integrated Omics: Web-based Standards-Compliant Workflows for Proteomics Informed by Transcriptomics

(2015) Jun Fan et al.   MOLECULAR & CELLULAR PROTEOMICS

An Analysis of the Sensitivity of Proteogenomic Mapping of Somatic Mutations and Novel Splicing Events in Cancer

(2015) Kelly V. Ruggles et al.   MOLECULAR & CELLULAR PROTEOMICS

A Scalable Approach for Protein False Discovery Rate Estimation in Large Proteomic Data Sets

(2015) Mikhail M. Savitski et al.   MOLECULAR & CELLULAR PROTEOMICS

Defining the transcriptomic landscape of Candida glabrata by RNA-Seq

(2015) Jörg Linde et al.   NUCLEIC ACIDS RESEARCH

Forty-Four Novel Protein-Coding Loci Discovered Using a Proteomics Informed by Transcriptomics (PIT) Approach in Rat Male Germ Cells1

(2014) Sophie Chocu et al.   BIOLOGY OF REPRODUCTION

Discovery of Novel Genes and Gene Isoforms by Integrating Transcriptomic and Proteomic Profiling from Mouse Liver

(2014) Peng Wu et al.   JOURNAL OF PROTEOME RESEARCH

Proteogenomics ofGammarus fossarumto Document the Reproductive System of Amphipods

(2014) Judith Trapp et al.   MOLECULAR & CELLULAR PROTEOMICS

Annotation of the Zebrafish Genome through an Integrated Transcriptomic and Proteomic Analysis

(2014) Dhanashree S. Kelkar et al.   MOLECULAR & CELLULAR PROTEOMICS

A draft map of the human proteome

(2014) Min-Sik Kim et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

An integrated approach for genome annotation of the eukaryotic thermophile Chaetomium thermophilum

(2014) Thomas Bock et al.   NUCLEIC ACIDS RESEARCH

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

(2014) Evgenia V. Kriventseva et al.   NUCLEIC ACIDS RESEARCH

Highly evolvable malaria vectors: The genomes of 16 Anopheles mosquitoes

(2014) D. E. Neafsey et al.   SCIENCE

L_RNA_scaffolder: scaffolding genomes with transcripts

(2013) Wei Xue et al.   BMC GENOMICS

Proteogenomic Database Construction Driven from Large Scale RNA-seq Data

(2013) Sunghee Woo et al.   JOURNAL OF PROTEOME RESEARCH

Peppy: Proteogenomic Search Software

(2013) Brian A. Risk et al.   JOURNAL OF PROTEOME RESEARCH

An Automated Proteogenomic Method Uses Mass Spectrometry to Reveal Novel Genes inZea mays

(2013) Natalie E. Castellana et al.   MOLECULAR & CELLULAR PROTEOMICS

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

(2013) Liguo Wang et al.   NUCLEIC ACIDS RESEARCH

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

Long noncoding RNAs are rarely translated in two human cell lines

(2012) B. Banfai et al.   GENOME RESEARCH

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Identification of novel transcripts in annotated genomes using RNA-Seq

(2011) A. Roberts et al.   BIOINFORMATICS

Assemblathon 1: A competitive assessment of de novo short read assembly methods

(2011) D. Earl et al.   GENOME RESEARCH

A proteogenomic analysis of Anopheles gambiae using high-resolution Fourier transform mass spectrometry

(2011) R. Chaerkady et al.   GENOME RESEARCH

GAGE: A critical evaluation of genome assemblies and assembly algorithms

(2011) S. L. Salzberg et al.   GENOME RESEARCH

Proteogenomic Analysis ofMycobacterium tuberculosisBy High Resolution Mass Spectrometry

(2011) Dhanashree S. Kelkar et al.   MOLECULAR & CELLULAR PROTEOMICS

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics

(2011) K. Megy et al.   NUCLEIC ACIDS RESEARCH

TopHat-Fusion: an algorithm for discovery of novel fusion transcripts

(2011) Daehwan Kim et al.   GENOME BIOLOGY

Scaffolding a Caenorhabditis nematode genome with RNA-seq

(2010) A. Mortazavi et al.   GENOME RESEARCH

Assembly of large genomes using second-generation sequencing

(2010) M. C. Schatz et al.   GENOME RESEARCH

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Leveraging skewed transcript abundance by RNA-Seq to increase the genomic depth of the tree of life

(2010) C. T. Hittinger et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteogenomics

(2010) Santosh Renuse et al.   PROTEOMICS

Integrative Analysis of the Caenorhabditis elegans Genome by the modENCODE Project

(2010) M. B. Gerstein et al.   SCIENCE

A perfect genome annotation is within reach with the proteomics and genomics alliance

(2009) Jean Armengaud   CURRENT OPINION IN MICROBIOLOGY

Use of shotgun proteomics for the identification, confirmation, and correction of C. elegans gene annotations

(2008) G. E. Merrihew et al.   GENOME RESEARCH

Comparative proteogenomics: Combining mass spectrometry and comparative genomics to analyze multiple genomes

(2008) N. Gupta et al.   GENOME RESEARCH

Annotating genomes with massive-scale RNA sequencing

(2008) France Denoeud et al.   GENOME BIOLOGY