Proteomics data mining

@article{Wilkins2009ProteomicsDM,
  title={Proteomics data mining},
  author={Marc R. Wilkins},
  journal={Expert Review of Proteomics},
  year={2009},
  volume={6},
  pages={599 - 603}
}
  • M. Wilkins
  • Published 1 December 2009
  • Medicine
  • Expert Review of Proteomics
Marc Wilkins completed his undergraduate and doctoral studies at Macquarie University, Sydney, Australia. During his doctoral studies, he defined the concept of the proteome and coined the term. After postdoctoral studies in Geneva, Switzerland, during which he co-edited the first book on proteomics, he returned to Australia, where he cofounded the company Proteome Systems. More recently, Marc took a position as Professor of Systems Biology at the University of New South Wales. He has… Expand

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References

SHOWING 1-10 OF 10 REFERENCES
Hares and tortoises: The high‐ versus low‐throughput proteomic race
TLDR
This review finds that the understanding of the yeast proteome has been furthered more substantially by the slower “tortoise techniques” than the “high‐throughput hares”, and how electrophoretic separations can continue to support the field of proteomics is explored. Expand
Guidelines for the next 10 years of proteomics
TLDR
A minimal set of guidelines for proteomics research are described, which will serve as a set of criteria which editors of PROTEOMICS will use for assessment of future submissions to the Journal. Expand
Optimal replication and the importance of experimental design for gel-based quantitative proteomics.
TLDR
The ways to improve the quality of protein expression data from 2-DE gels are explored, and an approach for defining the number of samples required and thenumber of gels per sample is described. Expand
Two‐dimensional gel electrophoresis for proteome projects: The effects of protein hydrophobicity and copy number
TLDR
Investigation of the effects of protein hydrophobicity and cellular protein copy number on a protein's presence or absence on a two‐dimensional gel concluded that further developments of 2‐D electrophoresis techniques are desirable to enable the visualization and analysis of all proteins expressed by a cell or tissue. Expand
A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies*
TLDR
A new version (4.0) of the Human Protein Atlas has been developed in a genecentric manner with the inclusion of all human genes and splice variants predicted from genome efforts together with a visualization of each protein with characteristics such as predicted membrane regions, signal peptide, and protein domains and new plots showing the uniqueness of every fraction of eachprotein toward all other human proteins. Expand
Interactive three-dimensional visualization and contextual analysis of protein interaction networks.
TLDR
This study has adapted a 3-D network visualization platform, GEOMI, to allow the coanalysis of protein-protein interaction networks with proteomic parameters such as protein localization, abundance, physicochemical parameters, post-translational modifications, and gene ontology classification. Expand
Inter-individual variation in expression: a missing link in biomarker biology?
TLDR
It is argued that a consideration of genetics, in conjunction with proteomic biomarker discovery projects, should improve the proportion of biomarkers that can accurately classify patients. Expand
The Interactorium: Visualising proteins, complexes and interaction networks in a virtual 3‐D cell
TLDR
The Interactorium is a tool in which a Virtual Cell is used as the context for the seamless visualisation of the yeast protein interaction network, protein complexes and protein 3‐D structures and is a considerable advance over existing approaches. Expand
Dynamic Proteomics of Individual Cancer Cells in Response to a Drug
TLDR
A dynamic-proteomics approach is presented that measures the levels and locations of nearly 1000 different endogenously tagged proteins in individual living cells at high temporal resolution, and identifies proteins whose dynamics differ widely between cells, in a way that corresponds to the outcomes—cell death or survival. Expand
The limitations of two - dimensional gel electrophoresis for proteome projects , the effects of protein copy number and hydrophobicity
  • Electrophoresis
  • 1998