References

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Review

Research methods

     Bioinformatics

Medical application

Specific research

Review

Proteomics
Proteomics to study genes and genomes
 
Proteomics:new perspectives, new biomedical opportunities
 
Proteomics:translating genomics into products
 
A post-genomic challenge: learning to read patterns of protein synthesis
 
A Biological Atlas of Functional Maps
 

Proteomics- a technology-driven and technology-limited discovery science
Proteomics- new technologies and their applications
Experimentalism in proteomics
Modification-specific proteomics-systematic strategies for analysing post-translationally modified proteins 
Proteomics - the industrialization of protein chemistry
The human proteomics initiative
A post-genomic perspective
Convergent evolution with combinatorial peptides
Four years of post-genomic life with 6000 yeast genes
From the analysis of protein complexes to proteome-wide linkage maps
Guilt-by-association goes global
Lessons from metabolic engineering for functional genomics and drug discovery
Origin of multicellular eukaryotes – insights from proteome comparisons

Probing proteomes--seeing the whole picture
Protein interaction maps for model organisms
Relationship between Whole Proteome Aminoacid Composition and Static DNA Curvature
The end of the beginning for genomic medicine
Proteomics and genomics A selection of World Wide Web 
Proteomics and genomics Presidential preference, protein purpose
Proteomics- the next step after genomics
Selection and application of peptide-binding peptides 
The nature of the universal ancestor and the evolution of the proteome
Towards a truly integrative biology through the functional genomics of yeast
Use of protein-interaction maps to formulate biological questions

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Research methods

Gene products are where the biological action is
Advances in 2D gel techniques

Probing proteomes--seeing the whole picture?
2D or not 2D
Characterisation of bacterial proteomes by two-dimensional electrophoresis

Imaging mass spectrometry: A new technology for the analysis of protein expression in mammalian tissues
Evolution of ESI–mass spectrometry and Fourier transform ion cyclotron resonance or proteomics and other biological applications
Mass spectrometry - from genomics to proteomics
Trends in automation and mass spectrometry for proteomics
Measuring gene expression by quantitative proteome analysis
Functional genomics by mass spectrometry
Mass spectrometry and proteomics

Advances in mass spectrometry for proteome analysis

Trends in automation and mass spectrometry for proteomics

Using mass spectrometry for quantitative proteomics

Protein complexes and analysis of their assembly by mass spectrometry

Mass spectrometric identification of proteins and characterization of their post-translational modifications in proteome analysis


Protein-interaction mapping for functional proteomics
Two-hybrid analysis of genetic regulatory networks 

Yeast Two-Hybrid: State of the Art

Genome-wide protein interaction maps using two-hybrid systems
  

From the analysis of protein complexes to proteome-wide linkage maps  

Protein microarrays- prospects and problems
Protein microarrays for highly parallel detection and quantitation of specific proteins and antibodies in complex solutions
Chip-based microsystems for genomic and proteomic analysis
Protein and antibody arrays and their medical applications
Protein arrays- a high-throughput solution for proteomics research
Protein arrays and microarrays
Protein biochips for differential profiling

Large-scale functional analysis using peptide or protein arrays

Microarrays and cell cycle transcription in yeast

Gene expression profling: monitoring transcription and translation products using DNA microarrays and proteomics

Proteomic analysis
Experimentalism in proteomics
Measuring gene expression by quantitative proteome analysis
Chemical strategies for the global analysis of protein function
Genomic analysis of biochemical function

Chemical biology beyond binary codes

Profiling the specific reactivity of the proteome with non-directed activity-based probes

The use of recombinant antibodies in proteomics

Domain repertoires as a tool to derive protein recognition rules

A generic protein purification method for protein complex characterization and proteome exploration

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Bioinformatics

Database searching with mass-spectrometric information
Sequences and topology- Genome and proteome informatics
Identifying the proteome- software tools

Protein structure prediction

Making predictions about the proteome

Use of mass spectrometry-derived data to annotate nucleotide and protein sequence databases

Integration of genome data and protein structures: 
prediction of protein folds, protein interactions and ‘molecular phenotypes’ of single nucleotide polymorphisms

3D modelling of gene expression patterns

Databases and knowledge resources for proteomics research

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Medical application

Proteomics in Medicine
Genomes, Proteomes, and Medicine: Opportunities in Medical Science in the 21st Century  (Celera article)
Proteomics of the nervous system
Proteomics — the protein expression technology to study connective tissue biology
Antibacterial vaccine design using genomics and proteomics
Cardiovascular Proteomics
Genomics and medicine
Studying heart disease using the proteomic approach

Current status and perspectives of proteomics in aging research

Antibodies in diagnostics – from immunoassays to protein chips

Proteomics- a major new technology for the drug discovery process
Proteomics: New tools for a new era

Will genomics revolutionize antimicrobial drug discovery

Is the development of a new tuberculosis vaccine possible

The end of the beginning for genomic medicine

Recent patents in proteomics

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Specific research

Insights into a plasma membrane signature
Proteomic analysis of macrophage differentiation
Alternative splicing: increasing diversity in the proteomic world
Piecing together the significance of splicing
A comprehensive analysis of protein-protein interactions in Saccharomyces cerevisiae
A genomic perspective on plant transcription factors
A network of protein-protein interactions in yeast 
A yeast prion provides a mechanism for genetic variation and phenotypic diversity
Functional genomic analysis of C. elegans chromosome I by systematic RNA interference
 
Large-scale analysis of the yeast proteome by multidimensional protein identification technology
Parasite Proteomics
 
Protein folds- molecular systematics in three dimensions
Surfing the p53 network

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