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Search Results: 1 - 10 of 15065 matches for " systems biology "
All listed articles are free for downloading (OA Articles)
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Systems Biology: The take, input, vision, concerns and hopes  [PDF]
Graeme Tucker
Journal of Biomedical Science and Engineering (JBiSE) , 2009, DOI: 10.4236/jbise.2009.22014
Abstract: Systems Biology is a relatively new branch of biology that brings together an interdisciplinary team of scientist, computer engineers and mathematicians. Biomedicine can gain much from the input of Systems Biology. The object and aims of this article centre on clarification and direction for Systems Biology, notably in regard to human health and disease.
Extending cell cycle synchrony and deconvolving population effects in budding yeast through an analysis of volume growth with a structured Leslie model  [PDF]
Chris C. Stowers, Asmita M. Boczko
Journal of Biomedical Science and Engineering (JBiSE) , 2010, DOI: 10.4236/jbise.2010.310129
Abstract: Budding yeast are a fundamental organism at the center of systems biology research. Understanding the physiology and kinetics of their growth and division is fundamental to the design of models of gene regulation and the interpretation of experimental measurements. We have developed a Leslie model with structured volume and age classes to understand population growth and cell cycle synchrony in budding yeast. The model exhibits broad agreement with a variety of experimental data. The model is easily annotated with volume milestones and cell cycle phases and at least three distinct goals are realizable: 1) One can investigate how any single cell property manifests itself at the population level. 2) One can deconvolve observed population averages into individual cell signals structured by volume and age. 3) One can investigate controllability of the population dynamics. We focus on the latter question. Our model was initially designed to answer the question: Can continuous volume filtration extend synchrony? To date, most general experimental methods can produce an initially synchronous population whose synchrony decays rapidly over three or four cell cycles. Our model predicts that continuous volume filtration can extend this maintenance of synchrony by an order of magnitude. Our data inform the development of simple fluidic devices to extend synchrony in continuous culture at all scales from nanophysiometers to bioreactors.
A digital cmos sequential circuit model for bio-cellular adaptive immune response pathway using phagolysosomic digestion: a digital phagocytosis engine  [PDF]
Sayed Mohammad Rezaul Hasan
Journal of Biomedical Science and Engineering (JBiSE) , 2010, DOI: 10.4236/jbise.2010.35065
Abstract: Living systems have to constantly counter micro-or- ganisms which seek parasitic existence by extracting nutrition (amino acids) from the host. Phagocytosis is the ingestion of micro-creatures by certain cells of living systems for counter nutrition (breakdown of the micro-creature into basic components) as part of cellular adaptive immune response. These particular cells are called phagocytes, all of which are different types of white blood cells or their derivatives. Phagocytes are activated by certain components of the micro-creatures which act as an antigen, generating an- tibody secretion by the phagocyte. This paper develops a digital CMOS circuit model of phagocytosis: the immune response biochemical pathway of a pha- gocyte. A micro-sequenced model has been developed where the different stages in phagocytosis are modeled as different states clocked by circadian time intervals. The model converts the bio-chemical immune system digestive pathway into a cascade of CMOS multi-step logical transformations from micro-crea- ture ingestion to the secretion of indigestible residuals. This modeling technique leads to the understanding of cellular immune deficiency diseases of living systems in the form of logical (electrical) faults in a circuit.
Zooming (a little) out of the M-theory
Roberto Piergentili
Journal of Molecular Biochemistry , 2013,
Abstract:
Ontologies and Standards in Bioscience Research: For Machine or for Human
Huaiyu Mi
Frontiers in Physiology , 2011, DOI: 10.3389/fphys.2011.00005
Abstract: Ontologies and standards are very important parts of today’s bioscience research. With the rapid increase of biological knowledge, they provide mechanisms to better store and represent data in a controlled and structured way, so that scientists can share the data, and utilize a wide variety of software and tools to manage and analyze the data. Most of these standards are initially designed for computers to access large amounts of data that are difficult for human biologists to handle, and it is important to keep in mind that ultimately biologists are going to produce and interpret the data. While ontologies and standards must follow strict semantic rules that may not be familiar to biologists, effort must be spent to lower the learning barrier by involving biologists in the process of development, and by providing software and tool support. A standard will not succeed without support from the wider bioscience research community. Thus, it is crucial that these standards be designed not only for machines to read, but also to be scientifically accurate and intuitive to human biologists.
Systems Biology as an Integrated Platform for Bioinformatics, Systems Synthetic Biology, and Systems Metabolic Engineering
Bor-Sen Chen,Chia-Chou Wu
Cells , 2013, DOI: 10.3390/cells2040635
Abstract: Systems biology aims at achieving a system-level understanding of living organisms and applying this knowledge to various fields such as synthetic biology, metabolic engineering, and medicine. System-level understanding of living organisms can be derived from insight into: (i) system structure and the mechanism of biological networks such as gene regulation, protein interactions, signaling, and metabolic pathways; (ii) system dynamics of biological networks, which provides an understanding of stability, robustness, and transduction ability through system identification, and through system analysis methods; (iii) system control methods at different levels of biological networks, which provide an understanding of systematic mechanisms to robustly control system states, minimize malfunctions, and provide potential therapeutic targets in disease treatment; (iv) systematic design methods for the modification and construction of biological networks with desired behaviors, which provide system design principles and system simulations for synthetic biology designs and systems metabolic engineering. This review describes current developments in systems biology, systems synthetic biology, and systems metabolic engineering for engineering and biology researchers. We also discuss challenges and future prospects for systems biology and the concept of systems biology as an integrated platform for bioinformatics, systems synthetic biology, and systems metabolic engineering.
What is systems biology?
Rainer Breitling
Frontiers in Physiology , 2010, DOI: 10.3389/fphys.2010.00009
Abstract: Systems biology is increasingly popular, but to many biologists it remains unclear what this new discipline actually encompasses. This brief personal perspective starts by outlining the asthetic qualities that motivate systems biologists, discusses which activities do not belong to the core of systems biology, and finally explores the crucial link with synthetic biology. It concludes by attempting to define systems biology as the research endeavor that aims at providing the scientific foundation for successful synthetic biology.
Relevant Enzymes, Genes and Regulation Mechanisms in Biosynthesis Pathway of Stilbenes  [PDF]
Di LU, Wei ZHAO, Shujin ZHAO
Open Journal of Medicinal Chemistry (OJMC) , 2012, DOI: 10.4236/ojmc.2012.22003
Abstract: Stilbenes are natural phenolic compounds which function as antimicrobial phytoalexins in plants and affect human health as cardioprotective, antibaceteria, antioxidative and antineoplastic agents. In this review, the progresses of study on relevant enzymes, genes, and regulation mechanism in biosynthesis pathway of stilbenes are described. Here we introduce a holistic and systematic method of researching relevant enzymes, genes and other regulatory factors in biosynthesis pathway of stilbenes—Systems biology. The application of knowledge of relative enzymes, genes and regulation mechanisms in stilbenes biosynthesis in metabolic engineering which is used as a tool of improving the disease resistance of plants and health caring quality of crops is also discussed.
A Novel Analytical Method for Structural Characteristics of Gene Networks and its Application  [PDF]
Shudong Wang, Yuanyuan Zhang, Kaikai Li, Dazhi Meng
Computational Molecular Bioscience (CMB) , 2012, DOI: 10.4236/cmb.2012.23009
Abstract: Analyzing gene network structure is an important way to discover and understand some unknown relevant functions and regulatory mechanisms of organism at the molecular level. In this work, mutual information networks and Boolean logic networks are constructed using the methods of reverse modeling based on gene expression profiles in lung tissues with and without cancer. The comparison of these network structures shows that average degree, the proportion of non-isolated nodes, average betweenness and average coreness can distinguish the networks corresponding to the lung tissues with and without cancer. According to the difference of degree, betweenness and coreness of each gene in these networks, nine structural key genes are obtained. Seven of them which are related to lung cancer are supported by literatures. The remaining two genes AKT1 and RBL may have important roles in the formation, development and metastasis of lung cancer. Furthermore, the contrast of these logic networks suggests that the distributions of logic types are obviously different. The structural differences can help us to understand the mechanism of formation and development of lung cancer.
Bacterial Cells as Model Factories  [PDF]
Ichiro Matsumura
American Journal of Operations Research (AJOR) , 2013, DOI: 10.4236/ajor.2013.31A007
Abstract:

Bacteria, like industrial engineers, must manage processes that convert low value inputs into high value outputs. Bacteria are not intelligent, so they utilize self-organizing production systems to accelerate life-sustaining chemical processes. Here I explore two questions. First, can businesses apply the principles of self-organization? Second, can operations researchers contribute to our understanding of biological systems? I explain biochemical concepts in plain terms, illustrated with a few informative laboratory evolution experiments, and describe the organizing principles that underlie complex biological systems. I describe the new disciplines of synthetic biology and metabolic engineering, which offer opportunities for interdisciplinary collaboration between life scientists and operations researchers.

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