model based inference of transcriptional regulatory mechanisms from dna microarray data
Báo cáo hóa học: " Research Article Inference of Gene Regulatory Networks Based on a Universal Minimum Description Length" pot
... resubstitution error of the empirical-error-rule classifier and a function of the VC dimension of the model family [19] The resubstitution error directly measures the deviation of the model from the data and ... most suited for the amount of data In essence, the MDL principle balances error (deviation from the data) and model complexity by using a cost function consisting of a sum of entropies, one relative ... MDL principle dictates that, given a dataset and some class of possible models, one should choose the model providing the shortest possible encoding of the data In our case, the MDL principle...
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báo cáo khoa học: " Prediction of transcriptional regulatory elements for plant hormone responses based on microarray data" docx
... distance from the major TSS used in ppdb This table is the basis of Figure cis-element prediction Figure Data flow of our prediction The data sources of the analysis are microarray data, promoter ... information of RAFL cDNA clones [19,31] The Arabidopsis genome sequence and its gene models were obtained from TAIR [32] Preparation of RAR tables and promoter scanning Microarray data (Table ... report, we describe the development of an octamer -based prediction method using microarray data of phytohormone responses and all the predicted data by analysis of 622 hormone-responsive Arabidopsis...
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06 ON TAYLOR MODEL BASED INTEGRATION OF ODES
... by a Taylor model, or • when operations between Taylor models are executed Example 2.4 Addition of two univariate floating-point Taylor models For simplicity, we use Taylor models of order and ... success of the Taylor model based integration method depends on the successful reduction of the excess introduced in the shrink wrapping process The process of applying shrink wrapping to a Taylor model ... Taylor models U and V instead of a Taylor model vector The symbolic variables are denoted by a and b (instead of the vector x) Example 5.1 Absorption of the interval part into the symbolic part of...
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10 on taylor model based integration of ODEs neuer 2006
... On Taylor Model Based Integration of ODEs Interval Arithmetic and Taylor Models Verified Integration of ODEs Taylor Model Methods for ODEs Verified Integration of Linear ODEs Quadratic Model Problem ... On Taylor Model Based Integration of ODEs Interval Arithmetic and Taylor Models Verified Integration of ODEs Taylor Model Methods for ODEs Verified Integration of Linear ODEs Quadratic Model Problem ... On Taylor Model Based Integration of ODEs Interval Arithmetic and Taylor Models Verified Integration of ODEs Taylor Model Methods for ODEs Verified Integration of Linear ODEs Quadratic Model Problem...
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Báo cáo y học: " Model-based analysis of two-color arrays (MA2C)" ppsx
... Figure intensities of the control channel data from [12] as a function of position-specific GC counts Average7 Average intensities of the control channel data from [12] as a function of position-specific ... samples are from [12]: (a) raw data; (b) median adjusted data; (c) QQ normalized data; (d) Lowess normalized data; (e) MA2C (Simple) normalized data; (f) MA2C (Robust C = 2) normalized data Different ... the performance of different scoring functions, the triplicate H3 acetylation data at 38 bp spacing from [25] were analyzed using a window size of 1,000 bp and a p value cutoff of 10-3 Median...
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Báo cáo y học: " Gene expression profiling of Hfe-/- liver and duodenum in mouse strains with differing susceptibilities to iron loading: identification of transcriptional regulatory targets of Hfe and potential hemochromatosis modifiers" pdf
... these customized microarrays Our goal in the present study was to identify functional classes of genes and individual candidates that are involved in the perturbation of mechanisms of iron homeostasis ... facilitating the release of excess iron [21] Somewhat unexpectedly, we observed significant downregulation of the sideroflexin gene (Sfxn2) and upregulation of the mitoferrin gene (Slc25a37) and ... the mitochondrial import/traffic of iron and heme export Also worthy of mention are several strain-specific modifications of the messengers of some regulators of iron metabolism in Hfedeficient...
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Báo cáo y học: "Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans" doc
... the expression of a core set of regulatory genes The extreme sequence conservation of CNEs likely reflects the functional importance of these elements as components of the gene regulatory networks ... factors from two high-quality databases: DBD, a database of computationally predicted transcription factors through homology to known DNA- binding domains [29]; and wTF2.0, a compendium of computationally ... expressed in the pharynx based on microarray data [31] From this dataset, Weeder identified a motif very similar to the consensus binding site for PHA-4, the master specifier of pharyngeal cell identity...
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Báo cáo khoa học: "Efficient Inference of CRFs for Large-Scale Natural Language Data" docx
... introducing approximate inference methods based on reduction of the search spaces to be explored 3.1 Efficient Inference Algorithm Method The key idea of our proposed efficient inference method is ... 4.13 22.18 3.67 3.27 model (Sparse) All of our model variants were based on Sparse model For the hyper parameter , we empirically selected 0.001 for Method (this preserves 99% of probability density), ... set These two problems are closely related The size of the active set affects both the complexity of inference algorithm and the quality of the model Therefore, our goal for selecting δ and ω is...
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Báo cáo y học: "Derivation of genetic interaction networks from quantitative phenotype data" pdf
... total of 127 genes involved in the regulation of invasion were selected for study from searches of the YPD database [20] and gene-expression profiling experiments [21,22] 138 mutant alleles of these ... [10] Modes of genetic-interaction Processing of invasion-assay data Colony growth and invasion were quantified using Dapple [26], software originally designed for the analysis of DNA microarray ... and 1b, using the example of the epistasis of a deletion of the FLO11 gene, a major determinant of invasiveness, to a deletion of the SFL1 gene, encoding a repressor of FLO11 Note that the error-bounded...
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Báo cáo y học: "The Inferelator: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo" pptx
... combinations of perturbations? A significant body of work has been devoted to the modeling and learning of regulatory networks [1-3] In these studies regulatory interactions and dynamics are modeled ... varying degrees of detail and model flexibility and, accordingly, such models can be separated into general classes based on the level of detail with which they model individual regulatory interactions ... fitting the parameters of those models Learning and/or modeling of regulatory networks can be greatly aided by reducing the dimensionality of the search space before network inference Two ways to...
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Báo cáo y học: "A novel scheme to assess factors involved in the reproducibility of DNA-microarray data" pdf
... used to obtain DNA- microarray data of improved quality METHODS DNA- microarray experimental procedures DNA- microarrays were prepared from amplicons of 2108 genes in the genome of Lactococcus ... validation scheme and assess data quality of a number of validation experiments performed on amplicon -based DNA- microarrays of L lactis IL1403 For any laboratory in which DNA- microarray experiments ... CVs, ranging from 11 to 23 %, reported for a number of studies using cDNA derived from eukaryotic cell cultures hybridized on various DNA microarray platforms [20-22] For other DNAmicroarray experiments...
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Báo cáo hóa học: " Research Article On the Impact of Entropy Estimation on Transcriptional Regulatory Network Inference Based on Mutual Information" potx
... some state -of- the-art network inference algorithms Section contains the description of the synthetic data generator, the description of the real data setting, and the related discussions of the results ... best combination of inference algorithm and estimator Impact of the Estimator In case of complete datasets with no noise, the empirical and the Miller-Madow estimators Impact of the Inference Algorithm ... this as the Simonis list Table 4: Number of samples and bibliographic references of the yeast microarray data used for network inference Dataset 10 Number of samples 7 77 173 52 63 300 20 Origin...
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Báo cáo hóa học: " Research Article Information-Theoretic Inference of Large Transcriptional Regulatory Networks" pdf
... generated microarray datasets In spite of the evident limitations of using synthetic data, this makes possible a quantitative assessment of the accuracy, thanks to the availability of the true ... and the number of variables of the network are weakly negatively correlated This appears to be true independently of the inference method and of the MI estimator Accuracy of the inference methods ... Accuracy sensitivity to the number of variables The number of variables ranges from 100 to 1000 for the datasets RV1, RV2, RV3, RV4, and RV5, and from 100 to 500 for the datasets SV1, SV2, SV3, SV4,...
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LAKE EUTROPHICATION MODEL BASED ON THE IMPACT OF THE ZOOPLANKTON COMMUNITY ON PHYTOPLANKTON SUCCESSION
... features of biomanipulation's stability However, the rate process parameters of these models, especially for the dynamics of zooplankton and fish, were estimated on the basis of a limited amount of data ... ecological model is one of the most powerful tools to predict the long-term effects of biomanipulation Studies have tried to predict the effects of biomanipulation on the basis of lake ecological model ... Mathematical modelling of the ecosystem of Lough Neagh Ph D dissertation, Queens University, Belfast Suzuki, M., Sagehashi, M., and Sakoda, A., Modelling the structural dynamics of a shallow...
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Estimation of emissions of nonmethane organic compounds from a closed landfill site using a landfill gas emission model
... potential (m3/mg of waste), Mi = the mass of solid waste in the ith section of the landfill (mg), ti = the age of the ith section of the section of the landfill (years), t = the age of the landfill ... The number of Monte Carlo terms chosen was based on the level of uncertainty believed to exist in the values of the uncertain parameters In Figure 3, the range of values of the age of the studied ... Journal of Energy and Environment (IJEE), Volume 4, Issue 1, 2013, pp.85-92 Figure Graph of frequency against range of values of age of landfill (t) Figure represents range of values of the total...
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Tài liệu Báo cáo khoa học: Phenol hydroxylase from Acinetobacter radioresistens S13 Isolation and characterization of the regulatory component docx
... (from residue number 3) to the sequence of the corresponding component of PH from A calcoaceticus NCIB 8250 (11/11 identity) [3] and very similar to that of the corresponding component of PH from ... degree of identity between the N-terminal sequence of PHI and those of ferredoxin-like proteins belonging to other oxygenases On the contrary, the N-terminus of PHI is identical to that of MopN from ... that of P2 from Pseudomonas CF600, both regulatory components of PHs PHI has been found to be strictly necessary for the phenol to catechol conversion, Fig Effect of PHI on the flavin fluorescence of...
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Báo cáo khoa học: A new clan of CBM families based on bioinformatics of starch-binding domains from families CBM20 and CBM21 potx
... features of a real SBD [66] although it appears away from the other CBM20 modules of actinomycetes [25] With regard to the large cluster of SBDs from Bacillus CGTases, the positions of the modules from ... glucoamylases (four of them were from patents), one GH77 4-a-glucanotransferase, one genethonin-1 (from rat), five unknown proteins of animal origin (four from insect and one from fish), two carbohydrate ... phosphorylating enzyme from Arabidopsis thaliana, contains a CBM20 module near the N-terminal end of the protein The N-terminal location is also seen in the case of the majority of unknown proteins of eukaryotic...
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Báo cáo khoa học: "HAL-based Cascaded Model for Variable-Length Semantic Pattern Induction from Psychiatry Web Resources" pdf
... Lexical Database Cambridge, MA: MIT Press T Grenager, D Klein, and C D Manning 2005 Unsupervised Learning of Field Segmentation Models for Information Extraction In Proc of the 43th Annual Meeting of ... Named Entities from Large Corpora In Proc of the 42th Annual Meeting of the ACL, pages 415-422 W.Lehnert, C Cardie, D Fisher, J McCarthy, E Riloff, and S Soderland 1992 University of Massachusetts: ... representation of words as well as combinations of words The HAL model constructs a high-dimensional context space for the psychiatry web corpora Each word in the HAL space is represented as a vector of...
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Báo cáo khoa học: "Automatic Acquisition of Language Model based on Head-Dependent Relation between Words" pdf
... experimented with three language models, tri-gram model (TRI), bi-gram model (BI), and the proposed model (DEP) on a raw corpus extracted from KAIST corpus The raw corpus consists of 1,589 sentences with ... methods For the size of the model, we are planning to test the effects of excluding the dependency relations with near zero probabilities i ( B I model) (TRI model) (DEP model) ,r, fuJ 200 400 ... shows the training corpus entropies of the three models It is not surprising that DEP performs better than BI DEP can be thought of as a kind of linguistic bi-gram model in which long distance dependencies...
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Báo cáo Y học: An active site homology model of phenylalanine ammonia-lyase from Petroselinum crispum docx
... HUSAR adaptation of the program MAP [25] Homology modelling Model of PAL 64–531 monomer The sequence of PAL (Swiss-Prot: P24481) was submitted to SWISS -MODEL (Automated Protein Modelling Server) ... enzyme Fig Comparison of X-ray structure of HAL [7] and homology model structure of PAL Comparison of the schematic representation of (A) tetrameric and (B) monomeric structures of HAL (left) and ... resulted in the best fold of the 1–63 fragment Model of PAL 532–716 fragment Swiss -MODEL [26,27] has not found a template eligible for modelling the terminal fragment (532–716) of the PAL sequence...
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