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Learning delayed influences of biological systems.

ABSTRACT: Boolean networks are widely used model to represent gene interactions and global dynamical behavior of gene regulatory networks. To understand the memory effect involved in some interactions between biological components, it is necessary to include delayed influences in the model. In this paper, we present a logical method to learn such models from sequences of gene expression data. This method analyzes each sequence one by one to iteratively construct a Boolean network that captures the dynamics of these observations. To illustrate the merits of this approach, we apply it to learning real data from bioinformatic literature. Using data from the yeast cell cycle, we give experimental results and show the scalability of the method. We show empirically that using this method we can handle millions of observations and successfully capture delayed influences of Boolean networks.

SUBMITTER: Ribeiro T

PROVIDER: S-EPMC4296389 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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Learning delayed influences of biological systems.

Ribeiro Tony T Magnin Morgan M Inoue Katsumi K Sakama Chiaki C

Frontiers in bioengineering and biotechnology 20150116

Boolean networks are widely used model to represent gene interactions and global dynamical behavior of gene regulatory networks. To understand the memory effect involved in some interactions between biological components, it is necessary to include delayed influences in the model. In this paper, we present a logical method to learn such models from sequences of gene expression data. This method analyzes each sequence one by one to iteratively construct a Boolean network that captures the dynamic ...[more]

PMID: 25642421

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Project description:Dengue virus (DENV) infects hundreds of millions of people annually, yet there is only a limited knowledge of the host immune response to dengue. Here, we used a systems biological approach to perform a detailed analysis of the innate immune response to DENV infection in the whole blood samples of acutely infected humans in Bangkok, Thailand. Transcriptomic analysis revealed that genes encoding pro-inflammatory mediators and type I IFN related proteins, were associated with high levels of virus during the first few days of infection. Individuals with low or negative viremia at the late stage of fever were enriched with genes associated with pathways involved in cell cycle, proliferation, cell metabolism and translational control. Meta-analysis showed significant enrichment in genes specific for innate cells (monocytes, macrophages and DCs) in the specimens with high VL and enrichment in genes specific for NK cells, CD4+ and CD8+ T cells as well as B cells in specimens with low VL. Furthermore, flow cytometric analysis revealed an expansion in the numbers of CD14+CD16+ monocytes and depletion of CD14dimCD16++ cells and BDCA-1+ myeloid DC in blood. Consistent with this, in a non-human primate model, infection with DENV boosted the numbers of CD14+CD16+ monocytes in the blood and in secondary lymphoid organs. In vitro, freshly isolated blood monocytes infected with DENV up regulated CD16 and mediated robust differentiation of resting B cells to CD27++CD38++ plasmablasts and IgG and IgM secretion. Taken together, these data provide a detailed picture of the innate response to dengue infection in humans, and highlight an unappreciated role for CD14+CD16+ monocytes in promoting the differentiation of plasmablasts and mediating antibody response to DENV. We analyzed whole blood samples from 28 dengue patients (DF n=18, DHF=10) hospitalized at the Siriraj Hospital in Bangkok, Thailand during the season of 2009 The specimens were acquired between days 2 and 9 after onset of symptoms (acute illness), and for 19 patients (DF n=13, DHF=6) also at the convalescence at 4 weeks or later after discharge. Additionally, blood was sampled from 9 healthy, non-infected donors to provide controls for transcriptomic and immunological analysis.

Project description:BackgroundThe distinction between autism and Asperger syndrome has been abandoned in the DSM-5. However, this clinical categorization largely overlaps with the presence or absence of a speech onset delay which is associated with clinical, cognitive, and neural differences. It is unknown whether these different speech development pathways and associated cognitive differences are involved in the heterogeneity of the restricted interests that characterize autistic adults.MethodThis study tested the hypothesis that speech onset delay, or conversely, early mastery of speech, orients the nature and verbal reporting of adult autistic interests. The occurrence of a priori defined descriptors for perceptual and thematic dimensions were determined, as well as the perceived function and benefits, in the response of autistic people to a semi-structured interview on their intense interests. The number of words, grammatical categories, and proportion of perceptual/thematic descriptors were computed and compared between groups by variance analyses. The participants comprised 40 autistic adults grouped according to the presence (N = 20) or absence (N = 20) of speech onset delay, as well as 20 non-autistic adults, also with intense interests, matched for non-verbal intelligence using Raven's Progressive Matrices.ResultsThe overall nature, function, and benefit of intense interests were similar across autistic subgroups, and between autistic and non-autistic groups. However, autistic participants with a history of speech onset delay used more perceptual than thematic descriptors when talking about their interests, whereas the opposite was true for autistic individuals without speech onset delay. This finding remained significant after controlling for linguistic differences observed between the two groups.ConclusionsVerbal reporting, but not the nature or positive function, of intense interests differed between adult autistic individuals depending on their speech acquisition history: oral reporting of intense interests was characterized by perceptual dominance for autistic individuals with delayed speech onset and thematic dominance for those without. This may contribute to the heterogeneous presentation observed among autistic adults of normal intelligence.

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Learning delayed influences of biological systems.

Publications

Learning delayed influences of biological systems.

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