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Titlebook: Systems Biology and Computational Proteomics; Joint RECOMB 2006 Sa Trey Ideker,Vineet Bafna Conference proceedings 2007 Springer-Verlag Ber

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A Computational Approach for the Identification of Site-Specific Protein Glycosylations Through Ionroteins from liquid chromatography ion-trap-based mass spectrometry (LC/MS) data. This method was implemented in a software tool and tested on several model glycoproteins. The results demonstrate the potential of our computational approach in automating the high throughput identification of glycoproteins.
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Markov Additive Chains and Applications to Fragment Statistics for Peptide Mass Fingerprinting,ently, much attention has been given to the question of how to evaluate the significance of identifications; results have been developed mostly from a combinatorial perspective. In particular, existing methods generally do not capture the fact that the same amino acid can have different masses becau
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A Context-Specific Network of Protein-DNA and Protein-Protein Interactions Reveals New Regulatory Mding the concerted regulation of proteins involved in complex formation. In this work, we use a Bayesian evidence integration framework to assemble an integrated network, including both protein-DNA and protein-protein interactions, in a specific cellular context(human B cells). We then use it to stu
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Identification and Evaluation of Functional Modules in Gene Co-expression Networks,thod to construct gene co-expression networks from microarray data, and then propose an efficient spectral clustering algorithm to identify natural communities, which are relatively densely connected sub-graphs, in the network. To assess the effectiveness of our approach and its advantage over exist
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