(Q37685115)

22 August 2017

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title

Proteogenomics and systems biology: quest for the ultimate missing parts (English)

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22 August 2017

Jean Armengaud

1

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22 August 2017

1 February 2010

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Expert Review of Proteomics

22 August 2017

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22 August 2017

7

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22 August 2017

1

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22 August 2017

65-77

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Origins of systems biology in William Harvey's masterpiece on the movement of the heart and the blood in animals

22 August 2017

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

The end of "naive reductionism": rise of systems biology or renaissance of physiology?

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Fifteen years of microbial genomics: meeting the challenges and fulfilling the dream

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Deciphering structure and topology of conserved COG2042 orphan proteins

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Yeast two-hybrid, a powerful tool for systems biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Quantitative proteomics reveals regulation of dynamic components within TATA-binding protein (TBP) transcription complexes.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Activity-based protein profiling for the functional annotation of enzymes

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Reactome array: forging a link between metabolome and genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Applying mass spectrometry-based proteomics to genetics, genomics and network biology

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Distinguishing protein-coding and noncoding genes in the human genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Revisiting the missing protein-coding gene catalog of the domestic dog

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Numerous novel annotations of the human genome sequence supported by a 5'-end-enriched cDNA collection

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Ortho-proteogenomics: multiple proteomes investigation through orthology and a new MS-based protocol.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Inteins, introns, and homing endonucleases: recent revelations about the life cycle of parasitic genetic elements

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Protein-splicing intein: Genetic mobility, origin, and evolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Fractured genes: a novel genomic arrangement involving new split inteins and a new homing endonuclease family

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Exploring the prokaryotic virosphere

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

The virophage as a unique parasite of the giant mimivirus

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

The 1.2-megabase genome sequence of Mimivirus

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Proteogenomic mapping as a complementary method to perform genome annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

The complete genome and proteome of Mycoplasma mobile

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Proteogenomics: needs and roles to be filled by proteomics in genome annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Proteogenomic approaches for the molecular characterization of natural microbial communities

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Whole proteome analysis of post-translational modifications: applications of mass-spectrometry for proteogenomic annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

A proteome reference map and proteomic analysis of Bifidobacterium longum NCC2705.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Alliance of proteomics and genomics to unravel the specificities of Sahara bacterium Deinococcus deserti

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Global analysis of the Deinococcus radiodurans proteome by using accurate mass tags

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

LC-MS/MS based proteomic analysis and functional inference of hypothetical proteins in Desulfovibrio vulgaris

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Localization, annotation, and comparison of the Escherichia coli K-12 proteome under two states of growth.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

From the genome sequence to the proteome and back: evaluation of E. coli genome annotation with a 2-D gel-based proteomics approach

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Re-annotating the Mycoplasma pneumoniae genome sequence: adding value, function and reading frames.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Interrupted coding sequences in Mycobacterium smegmatis: authentic mutations or sequencing errors?

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Proteomics reveals open reading frames in Mycobacterium tuberculosis H37Rv not predicted by genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Global detection and characterization of hypothetical proteins in Shewanella oneidensis MR-1 using LC-MS based proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Confirmation of the expression of a large set of conserved hypothetical proteins in Shewanella oneidensis MR-1.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Phylogenomics and signature proteins for the alpha proteobacteria and its main groups

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Global profiling of Shewanella oneidensis MR-1: expression of hypothetical genes and improved functional annotations

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Validation of Shewanella oneidensis MR-1 small proteins by AMT tag-based proteome analysis

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Subproteomic tools to increase genome annotation complexity

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Analysis of the cytosolic proteome of Halobacterium salinarum and its implication for genome annotation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Global analysis of a "simple" proteome: Methanococcus jannaschii

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Genome-wide proteomics of Natronomonas pharaonis.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Genome analysis and genome-wide proteomics of Thermococcus gammatolerans, the most radioresistant organism known amongst the Archaea

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Linking genome and proteome by mass spectrometry: large-scale identification of yeast proteins from two dimensional gels

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Parallel identification of new genes in Saccharomyces cerevisiae

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Exploiting proteomic data for genome annotation and gene model validation in Aspergillus niger

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

In planta proteomics and proteogenomics of the biotrophic barley fungal pathogen Blumeria graminis f. sp. hordei

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

PepLine: a software pipeline for high-throughput direct mapping of tandem mass spectrometry data on genomic sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Analysis of the Plasmodium falciparum proteome by high-accuracy mass spectrometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

The proteome of Toxoplasma gondii: integration with the genome provides novel insights into gene expression and annotation

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Genome annotation of Anopheles gambiae using mass spectrometry-derived data.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Discovery and revision of Arabidopsis genes by proteogenomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Analysis of small human proteins reveals the translation of upstream open reading frames of mRNAs

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Improving gene annotation using peptide mass spectrometry

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Overview of the HUPO Plasma Proteome Project: results from the pilot phase with 35 collaborating laboratories and multiple analytical groups, generating a core dataset of 3020 proteins and a publicly-available database

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

The low molecular weight proteome of Halobacterium salinarum

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Chemistry meets proteomics: the use of chemical tagging reactions for MS-based proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Exploring proteomes and analyzing protein processing by mass spectrometric identification of sorted N-terminal peptides

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Improved recovery of proteome-informative, protein N-terminal peptides by combined fractional diagonal chromatography (COFRADIC).

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Targeted analysis of protein termini.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Identification and functional characterization of N-terminally acetylated proteins in Drosophila melanogaster

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Proteomics analyses reveal the evolutionary conservation and divergence of N-terminal acetyltransferases from yeast and humans

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Comparative genomics, minimal gene-sets and the last universal common ancestor

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Systems biology: Functional analysis of natural microbial consortia using community proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

A model for random sampling and estimation of relative protein abundance in shotgun proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Isotope dilution strategies for absolute quantitative proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Proteomic applications of protein quantification by isotope-dilution mass spectrometry.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Proteome-wide cellular protein concentrations of the human pathogen Leptospira interrogans

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Full dynamic range proteome analysis of S. cerevisiae by targeted proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Activity-based protein profiling: from enzyme chemistry to proteomic chemistry

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

The development and application of methods for activity-based protein profiling

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Revealing promiscuous drug-target interactions by chemical proteomics.

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Target profiling of small molecules by chemical proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Complete genome sequences of cellular life forms: glimpses of theoretical evolutionary genomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Towards completion of the Earth's proteome

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Complete genome sequence of the myxobacterium Sorangium cellulosum

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Modular approaches to expanding the functions of living matter

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Decoding biological principles using gene circuits

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Comparative bacterial proteomics: analysis of the core genome concept

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Complete chemical synthesis, assembly, and cloning of a Mycoplasma genitalium genome

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Genome transplantation in bacteria: changing one species to another

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Recent developments in ion-trap mass spectrometry and related technologies

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Mass spectrometry for proteomics

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

Proteomics by mass spectrometry: approaches, advances, and applications

21 January 2018

1 reference

https://api.crossref.org/works/10.1586%2FEPR.09.104

21 January 2018

Identifiers

DOI

10.1586/EPR.09.104

1 reference

22 August 2017

1 reference

PubMed ID

20121477