Tomer Shlomi

..Here, we perform a rigorous comparative analysis and performance assessment among these different methods...

..The CDA presented is likely to serve as a new reference source for metabolic gene annotation...

..The rapid development of high-throughput technologies for measuring protein interactions calls for extending this fundamental operation to the level of pathways in protein networks...

..Overall, SR-FBA enables one to address a host of new questions concerning the interplay between regulation and metabolism...

..Our results establish a computational basis for the genome-wide study of normal and abnormal human metabolism in a tissue-specific manner...

..Pepitope can also be applied for inferring other types of protein-protein interactions beyond the immunological context, and as a general tool for aligning linear sequences to a 3D structure. AVAILABILITY: http://pepitope.tau.ac.il/..

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..PRINCE's predictions for these diseases highly match the known literature, suggesting several novel causal genes and protein complexes for further investigation...

..Considering the lack of high-throughput flux measurements, while high-throughput metabolomic and proteomic data are becoming readily available, we expect IOMA to significantly contribute to future research of cellular metabolism...

..Finally, potential selective treatments for specific cancers that depend on cancer type-specific downregulation of gene expression and somatic mutations are compiled...

..This paper examines the functional significance of regulatory network patterns via their biological annotation and evolutionary conservation...

..We further examine the capabilities of PepSurf for predicting other types of protein-protein interfaces. The performance of PepSurf is compared to other available epitope mapping programs...

..Further work is needed to identify metrics that characterize the complete trajectory from the initial to the final metabolic steady states after genetic perturbations...

..Availability and Implementation: http://imat.cs.tau.ac.il/...

..67 versus 0.59). The approach presented can be used to construct other human tissue-specific models, and be applied to other organisms...

..Here, we present metabolite dilution flux balance analysis, which addresses this problem, resulting in improved metabolic phenotype predictions...

..Similar results are obtained for other mammals. Taken together, these results demonstrate the role of codon bias in TE in humans, and pave the way for future studies of tissue-specific TE in multicellular organisms...

..We show how the resulting map of modules provides clues for the elucidation of function both at the level of individual genes and at the level of functional modules...

..This supports the possibility that there is less selective pressure to maintain genes that are relevant for only a small number of metabolic states...

..Our results demonstrate how multiple molecular interaction types can be integrated toward a global wiring diagram of the cell, and they provide insights into the evolutionary dynamics of protein complex regulation...

..However, these approaches offer only a static description of the properties of interest and offer moderate (albeit significant) correlations with pertinent experimental data...