ystematic assessment of protein interaction data using graph topology approaches

... Jin Chen 2006 Systematic Assessment of Protein Interaction Data using Graph Topology Approaches by Jin Chen, B.Eng Dissertation Presented to the Faculty of the School of Computing of the National ... of Singapore in Partial Fulﬁllment of the Requirements for the Degree of DOCTOR OF PHILOSOPHY National University of Singapore October 2006 Systematic Assessment of Protein Interaction Data using ... of Singapore October 2006 vi Systematic Assessment of Protein Interaction Data using Graph Topology Approaches Publication No Jin Chen, PhD National University of Singapore, 2006 Supervisor:...

Báo cáo hóa học: " Research Article Extraction of Protein Interaction Data: A Comparative Analysis of Methods in Use" potx

... completeness of information obtained from abstracts in comparison to the full-length articles as a measure of reliability of abstracts as sources of protein interaction data METHODS Selection of articles ... (proprietary protein interactions maps database from Jubilant Biosys Ltd.) was used IMaps is a manually curated database with more than 200 000 protein- protein, proteinRNA, protein- small molecule, and protein- DNA ... wrongly annotated as serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member and PI 4-phosphate 5-kinase as prolactininduced protein intensive Therefore, manual...

Báo cáo y học: "Coverage and error models of protein-protein interaction data by directed graph analysis" pptx

... represented by a directed graph Measured protein interaction data are represented by a directed graph The graph shows the interaction data between four selected proteins from the report by Krogan and ... cell For the Y2 H system, analyses conducted separately by Walhout and coworkers [31], Mrowka and colleagues [19], and Aloy and Russell [32] have reported on this type of artifact and have discussed ... in this direction Protein interaction data We investigated 12 publicly available datasets for S cerevisiae, of which seven were assayed by Y2 H and five were assayed by AP-MS We obtained [1-6,10]...

Báo cáo y học: "Making the most of high-throughput protein-interaction data" ppsx

... represent the grouping of objects They have two distinct types of nodes, and edges only connect a node of one type to a node of the other For example, the proteins of a biological system could be the ... question of whether or not they interact can be answered as either yes or no The aim of making a measurement is to record the true, typically unknown, value of a physical quantity, but in practice there ... to estimate the size of the prey populations for the datasets in [7] and [8] Their estimates are about double those of the number of viable prey Representation as graphs Graph theory offers a convenient...

Báo cáo y học: "Making the most of high-throughput protein-interaction data" potx

... aspects of the control of signaling by protein phosphorylation The abundance of high-quality data confirms that quantitative MS is here to stay and is already making key contributions to most areas ... responsible for the binding and extends the scope of the classic yeast two-hybrid experiment, which is only able to detect whether two fulllength proteins interact Probably the most spectacular ... DNA and identifies the combinatorial co-regulation of certain genes Walhout reported the development of an in vivo yeast one-hybrid system for the high-throughput identification of interactions...

Báo cáo Y học: Exploration of the diaphorase activity of neutrophil NADPH oxidase Critical assessment of the interaction of iodonitrotetrazolium with the oxidase redox components doc

... system [13], either by measurement of the rate of production of O2– or the rate of O2 uptake INT diaphorase activity was assayed by the rate of reduction of INT into formazan in the presence of ... The quantity of neutrophil membranes used in the oxygraphic assays was 10 · that used in the photometric assay For measurement of the Km of activated oxidase for O2, the O2 concentration of the ... preliminary experiment, we found that benzylimidazole and bipyridyl inhibited not only the production of O2– assayed by the SOD-sensitive reduction of cytochrome c, but also the reduction of INT with the...

Báo cáo hóa học: "Robust Fusion of Irregularly Sampled Data Using Adaptive Normalized Convolution" pot

... the adaptive NC is presented for fusion of shifted image sequences, the algorithm is applicable to any problem of fusion of irregularly sampled signals Not only useful in fusion of irregularly sampled ... analysis The eﬀectiveness of robust fusion using adaptive NC has been demonstrated through the application of superresolution reconstruction of LR image sequences In SR fusion, adaptive NC outperforms ... DISCUSSIONS We propose a solution for fusion of irregularly sampled images using adaptive normalized convolution The method performs a robust polynomial ﬁt over an adaptive neighborhood Each sample...

Báo cáo sinh học: "Metabolite-based clustering and visualization of mass spectrometry data using one-dimensional self-organizing map" ppt

... Figure Visualization of one-dimensional self-organizing map after clustering Visualization of one-dimensional self-organizing map after clustering 1D-SOM matrix after metabolite-based clustering ... metabolite-based clustering and visualization of large sets of metabolic marker candidates based on self-organizing maps (SOMs) Unlike applications of the classical two-dimensional SOMs, we are proposing one-dimensional ... condition The identification of metabolites was verified by exact mass measurement and coelution with authentic standards Data processing The raw mass spectrometry data of all samples were processed...

Báo cáo y học: "Spectral counting assessment of protein dynamic range in cerebrospinal fluid following depletion with plasma-designed immunoaffinity columns" doc

... peptide/ protein profiling Proteomics 2007, 7:3470-80 doi:10.1186/1559-0275-8-6 Cite this article as: Borg et al.: Spectral counting assessment of protein dynamic range in cerebrospinal fluid following ... manual inspection of the protein list not identified in samples subjected to IgY14 depletion indicates that 13 proteins (out of 24) were removed by IgY14 column (isoforms of haptoglobulin, fibrinogen, ... Angiotensinogen; ALB, albumin; APOA2, Apolipoprotein A-II; B2 M, Beta-2microglobulin; CST3, Cystatin-C; DKK3, Dickkopf-related protein- 3; GC, Vitamin-D-binding protein; HPX, Hemopexin; IGFBP6, Insulin-like...

... replicated 10 times Simulated rather than real data were used because a negative diagnosis, even based on the absence of bacteria in cell culture, is not a guarantee of health and the opposite has ... that the mixed HMM provides a good t to the data sets simulated in this study The advantages of the HMM over other approaches are the prediction of health or disease status, the reduction of ... by EADGENE (European Animal Disease Genomics Network of Excellence for Animal Health and Food Safety) REFERENCES [1] Altman R.M., Mixed hidden Markov model: an extension of the hidden Markov model...

STATISTICAL ANALYSIS OF CLINICAL TRIAL DATA USING MONTE CARLO METHODS

... his installation of Stan in Linux server I also thank other colleagues of mine for their encouragement v Baoguang Han STATISTICAL ANALYSIS OF CLINICAL TRIAL DATA USING MONTE CARLO METHODS In medical ... METHODS In medical research, data analysis often requires complex statistical methods where no closed-form solutions are available Under such circumstances, Monte Carlo (MC) methods have found many ... Table 2.3 NSABP B-14 data analysis based on general models 29 Table 2.4 NSABP B-22 data analysis using restricted models 34 Table 2.5 NSABP B-22 data analysis using general models ...

Computational methods for identifying conserved protein complexes between species from protein interaction data

... thesis A survey on computational methods for identifying conserved protein complexes between species: in this survey, computational methods for identifying conserved protein complexes are grouped ... present a definition for the problem of identifying conserved protein complexes between species from protein interaction data We then review the existing computational methods for this problem and ... 2.2 – The computational pipeline for identifying conserved protein complexes 2.2.4 Result evaluation for conserved protein complexes Detected conserved protein complexes need a benchmark dataset...

Computational methods for identifying conserved protein complexes between species from protein interaction data

USING THE ANALYTIC HIERARCHY PROCESS APPROACH FOR ASSESSMENT OF THE STRENGTH OF UNIVERSITY-INDUSTRY-GRI COOPERATION IN VIETNAM

... identify the strength of the individual linkage by determining the relative importance of the linkage types The goal is at the top of the model 4.4.2 The Actors Like the AHP model formulated for overall ... involvement in the process of technological assessment The objective of this study is to apply the Analytic Hierarchy Process (AHP) for assessing the strength of University-Industry-GRI cooperation ... At the bottom of the model, the alternatives of individual linkage hierarchy are the existing linkage types This level will determine the rank of linkage type The hierarchy developed for individual...

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