Connecting Proteomics to Next‐Generation Sequencing: Proteogenomics and Its Current Applications in Biology

Probing the colorectal cancer proteome for biomarkers: Current status and perspectives

(2018) Pey Yee Lee et al.   Journal of Proteomics

Splicing of platelet resident pre-mRNAs upon activation by physiological stimuli results in functionally relevant proteome modifications

(2018) Giovanni Nassa et al.   Scientific Reports

Proteogenomic studies on cancer drug resistance: towards biomarker discovery and target identification

(2017) Shuyue Fu et al.   Expert Review of Proteomics

An integrative strategy to identify the entire protein coding potential of prokaryotic genomes by proteogenomics

(2017) Ulrich Omasits et al.   GENOME RESEARCH

Next Generation Proteomic Pipeline for Chromosome-Based Proteomic Research Using NeXtProt and GENCODE Databases

(2017) Heeyoun Hwang et al.   JOURNAL OF PROTEOME RESEARCH

Progress on the HUPO Draft Human Proteome: 2017 Metrics of the Human Proteome Project

(2017) Gilbert S. Omenn et al.   JOURNAL OF PROTEOME RESEARCH

Integrating Next-Generation Genomic Sequencing and Mass Spectrometry To Estimate Allele-Specific Protein Abundance in Human Brain

(2017) Thomas S. Wingo et al.   JOURNAL OF PROTEOME RESEARCH

Unveiling alterative splice diversity from human oligodendrocyte proteome data

(2017) Raphael Tavares et al.   Journal of Proteomics

Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify

(2017) Malgorzata A. Komor et al.   MOLECULAR & CELLULAR PROTEOMICS

Methods, Tools and Current Perspectives in Proteogenomics

(2017) Kelly V. Ruggles et al.   MOLECULAR & CELLULAR PROTEOMICS

Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings

(2017) Fu-Yuan Zhu et al.   PLANT JOURNAL

Proteogenomic Re-Annotation of Coccidioides posadasii Strain Silveira

(2017) Natalie M. Mitchell et al.   PROTEOMICS

Proteogenomic Insights into the Intestinal Parasite Blastocystis sp. Subtype 4 Isolate WR1

(2017) Jean Armengaud et al.   PROTEOMICS

Plant Proteogenomics: Improvements to the Grapevine Genome Annotation

(2017) Brett Chapman et al.   PROTEOMICS

Detecting protein variants by mass spectrometry: a comprehensive study in cancer cell-lines

(2017) Javier A. Alfaro et al.   Genome Medicine

Fast, Quantitative and Variant Enabled Mapping of Peptides to Genomes

(2017) Christoph N. Schlaffner et al.   Cell Systems

Reannotation of Yersinia pestis Strain 91001 Based on Omics Data

(2016) Y. Mao et al.   AMERICAN JOURNAL OF TROPICAL MEDICINE AND HYGIENE

Progress in Top-Down Proteomics and the Analysis of Proteoforms

(2016) Timothy K. Toby et al.   Annual Review of Analytical Chemistry

Proteogenomics: Integrating Next-Generation Sequencing and Mass Spectrometry to Characterize Human Proteomic Variation

(2016) Gloria M. Sheynkman et al.   Annual Review of Analytical Chemistry

PGA: an R/Bioconductor package for identification of novel peptides using a customized database derived from RNA-Seq

(2016) Bo Wen et al.   BMC BIOINFORMATICS

Evaluating the effect of database inflation in proteogenomic search on sensitive and reliable peptide identification

(2016) Honglan Li et al.   BMC GENOMICS

Proteogenomics: Opportunities and Caveats

(2016) L. Dimitrakopoulos et al.   CLINICAL CHEMISTRY

Reconciling proteomics with next generation sequencing

(2016) Teck Yew Low et al.   CURRENT OPINION IN CHEMICAL BIOLOGY

Clinical implications of recent advances in proteogenomics

(2016) Marie Locard-Paulet et al.   Expert Review of Proteomics

Integrated Proteomic Pipeline Using Multiple Search Engines for a Proteogenomic Study with a Controlled Protein False Discovery Rate

(2016) Gun Wook Park et al.   JOURNAL OF PROTEOME RESEARCH

Toward an Upgraded Honey Bee (Apis mellifera L.) Genome Annotation Using Proteogenomics

(2016) Alison McAfee et al.   JOURNAL OF PROTEOME RESEARCH

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

Proteogenomic-based discovery of minor histocompatibility antigens with suitable features for immunotherapy of hematologic cancers

(2016) D P Granados et al.   LEUKEMIA

Proteogenomics connects somatic mutations to signalling in breast cancer

(2016) Philipp Mertins et al.   NATURE

Proteogenomics ofCandida tropicalis—An Opportunistic Pathogen with Importance for Global Health

(2016) Keshava K. Datta et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Comprehensive Annotation of the Parastagonospora nodorum Reference Genome Using Next-Generation Genomics, Transcriptomics and Proteogenomics

(2016) Robert A. Syme et al.   PLoS One

Exome-based proteogenomics of HEK-293 human cell line: Coding genomic variants identified at the level of shotgun proteome

(2016) Anna A. Lobas et al.   PROTEOMICS

Transcriptome- Assisted Label-Free Quantitative Proteomics Analysis Reveals Novel Insights into Piper nigrum—Phytophthora capsici Phytopathosystem

(2016) Chidambareswaren Mahadevan et al.   Frontiers in Plant Science

Plasma Proteome Profiling to Assess Human Health and Disease

(2016) Philipp E. Geyer et al.   Cell Systems

Well-characterized sequence features of eukaryote genomes and implications for ab initio gene prediction

(2016) Ying Huang et al.   Computational and Structural Biotechnology Journal

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

(2015) Franziska Zickmann et al.   BIOINFORMATICS

A note on the false discovery rate of novel peptides in proteogenomics

(2015) Kun Zhang et al.   BIOINFORMATICS

Integrated proteo-genomic approach for early diagnosis and prognosis of cancer

(2015) Hem D. Shukla et al.   CANCER LETTERS

PGx: Putting Peptides to BED

(2015) Manor Askenazi et al.   JOURNAL OF PROTEOME RESEARCH

NextSearch: A Search Engine for Mass Spectrometry Data against a Compact Nucleotide Exon Graph

(2015) Hyunwoo Kim et al.   JOURNAL OF PROTEOME RESEARCH

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

Proteogenomic Study beyond Chromosome 9: New Insight into Expressed Variant Proteome and Transcriptome in Human Lung Adenocarcinoma Tissues

(2015) Yong-In Kim et al.   JOURNAL OF PROTEOME RESEARCH

SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra

(2015) Mikhail Kolmogorov 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

Quantitative proteogenomics of human pathogens using DIA-MS

(2015) Lars Malmström et al.   Journal of Proteomics

Discovery by proteogenomics and characterization of an RF-amide neuropeptide from cone snail venom

(2015) Samuel D. Robinson et al.   Journal of Proteomics

proBAMsuite, a Bioinformatics Framework for Genome-Based Representation and Analysis of Proteomics Data

(2015) Xiaojing Wang et al.   MOLECULAR & CELLULAR PROTEOMICS

Improving genome annotation of enterotoxigenicEscherichia coliTW10598 by a label-free quantitative MS/MS approach

(2015) Veronika Kuchařová Pettersen et al.   PROTEOMICS

Experimental Validation of Bacillus anthracis A16R Proteogenomics

(2015) Zhiqi Gao et al.   Scientific Reports

Comparative Analysis of Genomics and Proteomics in Bacillus thuringiensis 4.0718

(2015) Jie Rang et al.   PLoS One

Tumor antigens as proteogenomic biomarkers in invasive ductal carcinomas

(2014) Lars Olsen et al.   BMC Medical Genomics

Database Construction and Peptide Identification Strategies for Proteogenomic Studies on Sequenced Genomes

(2014) Celine Hernandez et al.   CURRENT TOPICS IN MEDICINAL CHEMISTRY

Identification and Characterization of Proteins Encoded by Chromosome 12 as Part of Chromosome-centric Human Proteome Project

(2014) Srikanth Srinivas Manda et al.   JOURNAL OF PROTEOME RESEARCH

Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework

(2014) Pratik D. Jagtap et al.   JOURNAL OF PROTEOME RESEARCH

Functional Annotation of Proteome Encoded by Human Chromosome 22

(2014) Sneha M. Pinto et al.   JOURNAL OF PROTEOME RESEARCH

Proteogenomic characterization of human colon and rectal cancer

(2014) Bing Zhang et al.   NATURE

Onco-proteogenomics: cancer proteomics joins forces with genomics

(2014) Javier A Alfaro et al.   NATURE METHODS

Proteogenomics: concepts, applications and computational strategies

(2014) Alexey I Nesvizhskii   NATURE METHODS

Integration of mass spectrometry and RNA-Seq data to confirm human ab initio predicted genes and lncRNAs

(2014) Han Sun et al.   PROTEOMICS

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

Proteogenomic strategies for identification of aberrant cancer peptides using large-scale next-generation sequencing data

(2014) Sunghee Woo et al.   PROTEOMICS

Compact variant-rich customized sequence database and a fast and sensitive database search for efficient proteogenomic analyses

(2014) Heejin Park et al.   PROTEOMICS

ProteoAnnotator - Open source proteogenomics annotation software supporting PSI standards

(2014) Fawaz Ghali et al.   PROTEOMICS

Construction and assessment of individualized proteogenomic databases for large-scale analysis of nonsynonymous single nucleotide variants

(2014) Karsten Krug et al.   PROTEOMICS

Linking cancer genome to proteome: NCI's investment into proteogenomics

(2014) Robert C. Rivers et al.   PROTEOMICS

Tools to Covisualize and Coanalyze Proteomic Data with Genomes and Transcriptomes: Validation of Genes and Alternative mRNA Splicing

(2013) Chi Nam Ignatius Pang et al.   JOURNAL OF PROTEOME RESEARCH

Proteogenomic Database Construction Driven from Large Scale RNA-seq Data

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

Quantitative and Qualitative Proteome Characteristics Extracted from In-Depth Integrated Genomics and Proteomics Analysis

(2013) Teck Yew Low et al.   Cell Reports

Needles in stacks of needles: finding disease-causal variants in a wealth of genomic data

(2011) Gregory M. Cooper et al.   NATURE REVIEWS GENETICS

Next-generation transcriptome assembly

(2011) Jeffrey A. Martin et al.   NATURE REVIEWS GENETICS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS