Integrating transcriptome and proteome profiling: Strategies and applications

An Atlas of the Human Kinome Reveals the Mutational Landscape Underlying Dysregulated Phosphorylation Cascades in Cancer

(2016) Aleksandra Olow et al.   CANCER RESEARCH

Targeting irradiation-induced mitogen-activated protein kinase activation in vitro and in an ex vivo model for human head and neck cancer

(2016) Annette Affolter et al.   HEAD AND NECK-JOURNAL FOR THE SCIENCES AND SPECIALTIES OF THE HEAD AND NECK

Human Proteomic Variation Revealed by Combining RNA-Seq Proteogenomics and Global Post-Translational Modification (G-PTM) Search Strategy

(2016) Anthony J. Cesnik et al.   JOURNAL OF PROTEOME RESEARCH

Tissue-specific Proteogenomic Analysis ofPlutella xylostellaLarval Midgut Using a Multialgorithm Pipeline

(2016) Xun Zhu et al.   MOLECULAR & CELLULAR PROTEOMICS

ZLM-7 exhibits anti-angiogenic effects via impaired endothelial cell function and blockade of VEGF/VEGFR-2 signaling

(2016) Min Su et al.   Oncotarget

An update on transcriptional and post-translational regulation of brain voltage-gated sodium channels

(2015) Donatus O. Onwuli et al.   AMINO ACIDS

MSProGene: integrative proteogenomics beyond six-frames and single nucleotide polymorphisms

(2015) Franziska Zickmann et al.   BIOINFORMATICS

A machine learning heuristic to identify biologically relevant and minimal biomarker panels from omics data

(2015) Anna L Swan et al.   BMC GENOMICS

Transcriptome and venom proteome of the box jellyfish Chironex fleckeri

(2015) Diane L Brinkman et al.   BMC GENOMICS

Solution to Statistical Challenges in Proteomics Is More Statistics, Not Less

(2015) Oliver Serang et al.   JOURNAL OF PROTEOME RESEARCH

Probing the Missing Human Proteome: A Computational Perspective

(2015) Dhirendra Kumar et al.   JOURNAL OF PROTEOME RESEARCH

Comprehensive Characterization of Glycosylation and Hydroxylation of Basement Membrane Collagen IV by High-Resolution Mass Spectrometry

(2015) Trayambak Basak et al.   JOURNAL OF PROTEOME RESEARCH

Integrative Proteomics and Targeted Transcriptomics Analyses in Cardiac Endothelial Cells Unravel Mechanisms of Long-Term Radiation-Induced Vascular Dysfunction

(2015) Omid Azimzadeh et al.   JOURNAL OF PROTEOME RESEARCH

PPLine: An Automated Pipeline for SNP, SAP, and Splice Variant Detection in the Context of Proteogenomics

(2015) George Sergeevich Krasnov et al.   JOURNAL OF PROTEOME RESEARCH

PGTools: A Software Suite for Proteogenomic Data Analysis and Visualization

(2015) Shivashankar H. Nagaraj et al.   JOURNAL OF PROTEOME RESEARCH

Integrated Transcriptomic-Proteomic Analysis Using a Proteogenomic Workflow Refines Rat Genome Annotation

(2015) Dhirendra Kumar 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

Integrated Metabolomics, Transcriptomics and Proteomics Identifies Metabolic Pathways Affected byAnaplasma phagocytophilumInfection in Tick Cells

(2015) Margarita Villar et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomics of rare taxonomic phyla: A prospective treasure trove of protein coding genes

(2015) Dhirendra Kumar et al.   PROTEOMICS

DNMT1 is essential for mammary and cancer stem cell maintenance and tumorigenesis

(2015) Rajneesh Pathania et al.   Nature Communications

Expression profiling of lymph nodes in tuberculosis patients reveal inflammatory milieu at site of infection

(2015) Abhijit Maji et al.   Scientific Reports

Proteome- and Transcriptome-Driven Reconstruction of the Human Myocyte Metabolic Network and Its Use for Identification of Markers for Diabetes

(2015) Leif Väremo et al.   Cell Reports

Integrated Transcriptome and Proteome Analyses Reveal Organ-Specific Proteome Deterioration in Old Rats

(2015) Alessandro Ori et al.   Cell Systems

Using Galaxy-P to leverage RNA-Seq for the discovery of novel protein variations

(2014) Gloria M Sheynkman et al.   BMC GENOMICS

Integrative Analysis of Transcriptomics, Proteomics, and Metabolomics Data of White Adipose and Liver Tissue of High-Fat Diet and Rosiglitazone-Treated Insulin-Resistant Mice Identified Pathway Alterations and Molecular Hubs

(2014) David Meierhofer et al.   JOURNAL OF PROTEOME RESEARCH

Analyzing the First Drafts of the Human Proteome

(2014) Iakes Ezkurdia et al.   JOURNAL OF PROTEOME RESEARCH

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

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Mass-spectrometry-based draft of the human proteome

(2014) Mathias Wilhelm et al.   NATURE

ProteomeXchange provides globally coordinated proteomics data submission and dissemination

(2014) Juan A Vizcaíno et al.   NATURE BIOTECHNOLOGY

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Ribosome profiling: new views of translation, from single codons to genome scale

(2014) Nicholas T. Ingolia   NATURE REVIEWS GENETICS

PROTEOFORMER: deep proteome coverage through ribosome profiling and MS integration

(2014) Jeroen Crappé et al.   NUCLEIC ACIDS RESEARCH

A proteogenomics approach integrating proteomics and ribosome profiling increases the efficiency of protein identification and enables the discovery of alternative translation start sites

(2014) Alexander Koch et al.   PROTEOMICS

Discovery of rare protein-coding genes in model methylotrophMethylobacterium extorquensAM1

(2014) Dhirendra Kumar et al.   PROTEOMICS

Absolute quantitation of post-translational modifications

(2014) Ruchi Chaube   Frontiers in Chemistry

customProDB: an R package to generate customized protein databases from RNA-Seq data for proteomics search

(2013) Xiaojing Wang et al.   BIOINFORMATICS

3Omics: a web-based systems biology tool for analysis, integration and visualization of human transcriptomic, proteomic and metabolomic data

(2013) Tien-Chueh Kuo et al.   BMC Systems Biology

Combined proteome and transcriptome analyses for the discovery of urinary biomarkers for urothelial carcinoma

(2013) N J Shimwell et al.   BRITISH JOURNAL OF CANCER

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

Deep Proteome Coverage Based on Ribosome Profiling Aids Mass Spectrometry-based Protein and Peptide Discovery and Provides Evidence of Alternative Translation Products and Near-cognate Translation Initiation Events*

(2013) Gerben Menschaert et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomic Analysis ofBradyrhizobium japonicumUSDA110 Using Genosuite, an Automated Multi-algorithmic Pipeline

(2013) Dhirendra Kumar et al.   MOLECULAR & CELLULAR PROTEOMICS

The Genotype-Tissue Expression (GTEx) project

(2013) John Lonsdale et al.   NATURE GENETICS

Large-scale discovery of conopeptides and conoproteins in the injectable venom of a fish-hunting cone snail using a combined proteomic and transcriptomic approach

(2012) Aude Violette et al.   Journal of Proteomics

Integrated Proteomic, Transcriptomic, and Biological Network Analysis of Breast Carcinoma Reveals Molecular Features of Tumorigenesis and Clinical Relapse

(2012) Marcin Imielinski et al.   MOLECULAR & CELLULAR PROTEOMICS

Deep Venomics Reveals the Mechanism for Expanded Peptide Diversity in Cone Snail Venom

(2012) Sébastien Dutertre et al.   MOLECULAR & CELLULAR PROTEOMICS

Prediction and Characterization of Missing Proteomic Data inDesulfovibrio vulgaris

(2011) Feng Li et al.   COMPARATIVE AND FUNCTIONAL GENOMICS

MassWiz: A Novel Scoring Algorithm with Target-Decoy Based Analysis Pipeline for Tandem Mass Spectrometry

(2011) Amit Kumar Yadav et al.   JOURNAL OF PROTEOME RESEARCH

Proteogenomic Analysis ofMycobacterium tuberculosisBy High Resolution Mass Spectrometry

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

A Face in the Crowd: Recognizing Peptides Through Database Search

(2011) Jimmy K. Eng et al.   MOLECULAR & CELLULAR PROTEOMICS

Global quantification of mammalian gene expression control

(2011) Björn Schwanhäusser et al.   NATURE

A Systematic Analysis of Eluted Fraction of Plasma Post Immunoaffinity Depletion: Implications in Biomarker Discovery

(2011) Amit Kumar Yadav et al.   PLoS One

Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database

(2011) George A. Khoury et al.   Scientific Reports

Integrated network analysis of transcriptomic and proteomic data in psoriasis

(2010) Eleonora Piruzian et al.   BMC Systems Biology

Linking transcriptomic and proteomic data on the level of protein interaction networks

(2010) Paul Perco et al.   ELECTROPHORESIS

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

(2010) Natalie Castellana et al.   Journal of Proteomics

Expansion of the eukaryotic proteome by alternative splicing

(2010) Timothy W. Nilsen et al.   NATURE

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

An integrated proteomics and transcriptomics reference data set provides new insights into the Bradyrhizobium japonicum bacteroid metabolism in soybean root nodules

(2010) Nathanaël Delmotte et al.   PROTEOMICS

Proteogenomics

(2010) Santosh Renuse et al.   PROTEOMICS

Integrative analysis of transcriptomic and proteomic data of Desulfovibrio vulgaris: a non-linear model to predict abundance of undetected proteins

(2009) Wandaliz Torres-García et al.   BIOINFORMATICS

Correlation of mRNA and protein in complex biological samples

(2009) Tobias Maier et al.   FEBS LETTERS

Mapping identifiers for the integration of genomic datasets with the R/Bioconductor package biomaRt

(2009) Steffen Durinck et al.   Nature Protocols

The Proteomics Identifications database: 2010 update

(2009) Juan Antonio Vizcaíno et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Analysis in Vivo of Translation with Nucleotide Resolution Using Ribosome Profiling

(2009) N. T. Ingolia et al.   SCIENCE

Investigating the correspondence between transcriptomic and proteomic expression profiles using coupled cluster models

(2008) Simon Rogers et al.   BIOINFORMATICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

A combined transcriptome and proteome survey of malaria parasite liver stages

(2008) A. S. Tarun et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE