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Developments in mass spectrometry for the analysis of complex protein mixtures
- Brief. Func. Genomic. Proteomic
, 2006
"... of complex protein mixtures ..."
PepAssem, a Peptide Assembly Algorithm for a Complex Protein Mixture
"... Analysis of a complex protein mixture is one of the main topics in proteomics. While the traditional 2D-PAGE method separates proteins first and then identifies each spot, an alternative method was proposed which cleavages the whole protein mixture with an enzyme like trypsin, separates the resulted ..."
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Analysis of a complex protein mixture is one of the main topics in proteomics. While the traditional 2D-PAGE method separates proteins first and then identifies each spot, an alternative method was proposed which cleavages the whole protein mixture with an enzyme like trypsin, separates
Stable isotope labeling by amino acids in cell culture, SILAC, as a simple and accurate approach to expression proteomics
- Mol. Cell. Proteomics
, 2002
"... The abbreviations used are: SILAC: Stable isotope labeling by amino acids in cell culture, 2DE: two dimensional (isoelectric focusing/SDS-PAGE) gel electrophoresis: ICATTM: isotope-coded affinity tag; MS: mass spectrometry; MALDI-TOF: matrix assisted laser desorption ionization-time of flight; PMF: ..."
Abstract
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Cited by 595 (23 self)
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have shown great promise for the simultaneous and automated identification and quantitation of complex protein mixtures. Here we describe a method, termed SILAC for Stable Isotope Labeling by Amino acids in Cell culture, for the in vivo incorporation of specific amino acids into all mammalian proteins
Mixtures of Probabilistic Principal Component Analysers
, 1998
"... Principal component analysis (PCA) is one of the most popular techniques for processing, compressing and visualising data, although its effectiveness is limited by its global linearity. While nonlinear variants of PCA have been proposed, an alternative paradigm is to capture data complexity by a com ..."
Abstract
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Cited by 532 (6 self)
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Principal component analysis (PCA) is one of the most popular techniques for processing, compressing and visualising data, although its effectiveness is limited by its global linearity. While nonlinear variants of PCA have been proposed, an alternative paradigm is to capture data complexity by a
Fractionation of Complex Protein Mixture by Virtual Three-Dimensional Liquid Chromatography Based on Combined pH and Salt Steps
, 2008
"... The complexity and diversity of biological samples in proteomics require intensive fractionation ahead of mass spectrometry identification. This work developed a chromatographic method called virtual three-dimensional chromatography to fractionate complex protein mixtures. By alternate elution with ..."
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The complexity and diversity of biological samples in proteomics require intensive fractionation ahead of mass spectrometry identification. This work developed a chromatographic method called virtual three-dimensional chromatography to fractionate complex protein mixtures. By alternate elution
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
- Proc Int Conf Intell Syst Mol Biol
, 1994
"... Abstract The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expect~tiou ma.,dmization to fit a two-component finite mixture model to the set of sequences. Multiple motifs are found by fitting a mixture model to th ..."
Abstract
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Cited by 947 (5 self)
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Abstract The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expect~tiou ma.,dmization to fit a two-component finite mixture model to the set of sequences. Multiple motifs are found by fitting a mixture model
The SWISS-MODEL Workspace: A web-based environment for protein structure homology modelling
- BIOINFORMATICS
, 2005
"... Motivation: Homology models of proteins are of great interest for planning and analyzing biological experiments when no experimental three-dimensional structures are available. Building homology models requires specialized programs and up-to-date sequence and structural databases. Integrating all re ..."
Abstract
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Cited by 575 (5 self)
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dedicated to protein structure homology modelling. It assists and guides the user in building protein homology models at different levels of complexity. A personal working environment is provided for each user where several modelling projects can be carried out in parallel. Protein sequence and structure
The KEGG resource for deciphering the genome
- Nucleic Acids Res
, 2004
"... A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behavior from genomic information. Toward this end we have been developing a knowledg ..."
Abstract
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Cited by 513 (24 self)
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A grand challenge in the post-genomic era is a complete computer representation of the cell and the organism, which will enable computational prediction of higher-level complexity of cellular processes and organism behavior from genomic information. Toward this end we have been developing a
Using Bayesian networks to analyze expression data
- Journal of Computational Biology
, 2000
"... DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a “snapshot ” of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key biologica ..."
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Cited by 1088 (17 self)
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DNA hybridization arrays simultaneously measure the expression level for thousands of genes. These measurements provide a “snapshot ” of transcription levels within the cell. A major challenge in computational biology is to uncover, from such measurements, gene/protein interactions and key
Rho GTPases and the actin cytoskeleton
- Science
, 1998
"... The actin cytoskeleton mediates a variety of essential biological functions in all eukaryotic cells. In addition to providing a structural framework around which cell shape and polarity are defined, its dynamic properties provide the driving force for cells to move and to divide. Understanding the b ..."
Abstract
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Cited by 615 (4 self)
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their interaction with multiple target proteins, they ensure coordinated control of other cellular activities such as gene transcription and adhesion. The story begins back in the early 1990s with the analysis of Rho, then a newly described member of the Ras superfamily of small guanosine triphosphatases (GTPases
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