• Genome-scale modeling of photorespiratory pathway manipulation. (mpg.de)
  • Characterization of effects of genetic variants via genome-scale metabolic modelling. (mpg.de)
  • We focus on modeling and understanding resource allocation in large (sometimes genome-scale) metabolic models. (fu-berlin.de)
  • 2021. The KEGG pathway database consists of two sections: the metabolic pathway section and the regulatory pathway section. (opensourcebiology.eu)
  • However, the number of EFMs typically grows exponentially with the size of the metabolic network, leading to excessive computational demands, and unfortunately, a large fraction of these EFMs are not biologically feasible due to system constraints. (mdpi.com)
  • Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways. (mpg.de)
  • Metabolomics uses sophisticated analytical chemistry techniques, combined with software that provides computational methods, to reconstruct cellular pathways of interest. (ddw-online.com)
  • This thesis is a contribution to the field of systems biology, where mathematical and computational models are used to study large biological networks such as the metabolism or the signaling pathways of living organisms. (fu-berlin.de)
  • Animal models provide strong evidence that disruption of circadian pathways are associated with metabolic dysregulation and sleep-related pathologies, while high-fat feeding reveals disrupted circadian rhythms of feeding, activity, and sleep. (northwestern.edu)
  • This might lead to dangerous, long-lasting dysregulation of the miRNA pathways. (ldsfreedomforum.com)
  • Systems analysis of robustness in cellular networks. (mpg.de)
  • Elementary Flux Modes (EFMs) provide a rigorous basis to systematically characterize the steady state, cellular phenotypes, as well as metabolic network robustness and fragility. (mdpi.com)
  • A network property necessary for concentration robustness. (mpg.de)
  • Found insideA Focused, State-of-the-Art Overview of This Evolving FieldPresents Various Techniques for GlycoinformaticsThe development and use of informatics tools and databases for glycobiology and glycomics research have increased considerably in … In contrast, KEGG modules in the KEGG MODULE database are higher-resolution, localized wiring diagrams, representing tighter functional units within a pathway map, such as subpathways conserved among specific organism groups and molecular complexes. (opensourcebiology.eu)
  • In: European Training and Network Activity: Plant Genomics and Bioinformatics - Expression Micro Arrays and Beyong: a course book. (mpg.de)
  • Bill Andersen is chief technology officer at Knowledge Bus, Inc. The company is working with the European Media Laboratory Scientific Databases and Visualization Group in Heidelberg, Germany, on the creation of an ontology comprising knowledge of biochemical pathways. (nationalacademies.org)
  • To better understand the function of the altered genes, gene ontology and pathway analysis are performed. (bvsalud.org)
  • Two approaches for metabolic pathway analysis? (mpg.de)
  • Lymnaea provides a highly tractable model system that is well established in the learning and memory field for its uses in behavioral, electrophysiological, molecular and cellular network experimentation, allowing for both in vivo and in vitro approaches 14 . (nature.com)
  • Comparison of network-based pathway analysis methods. (mpg.de)
  • Her main research interest is identifying enzymes from secondary metabolite pathways with potential synthetic utility and developing methods based on these biocatalysts to enable access to biologically active target molecules. (grc.org)
  • Metabolic network structure determines key aspects of functionality and regulation. (mpg.de)
  • Modular Mathematical Modeling of Complex Regulatory Networks: Application to Cell Cycle Regulation in Saccharomyces Cerevisiae. (mpg.de)
  • Most of the biological processes were associated with cellular processes, biological regulation, metabolic processes, and developmental processes. (bvsalud.org)
  • Specifically, genetic programming automatically created a metabolic pathway involving four chemical reactions that consume glycerol and fatty acid as input, use ATP as a cofactor, and produce diacyl-glycerol as the final product. (upenn.edu)
  • The topology and sizing of the entire metabolic pathway was automatically created using only the time-domain concentration values of diacyl-glycerol (the final product). (upenn.edu)
  • Co-expression pan-network reveals genes involved in complex traits within maize pan-genome. (usda.gov)
  • Pathways that include all genes in gene_ids. (opensourcebiology.eu)
  • KEGG Pathway Painter (KPP) performs batch painting of all relevant pathways in KEGG according to uploaded lists of upregulated and downregulated genes. (opensourcebiology.eu)
  • In this chapter, we will go over how to identify disease-causing culprit genes from the raw microarray data, using various packages of R programming. (bvsalud.org)
  • Further, regulatory networks were constructed by the DEGs which are also co-expressed and the hub genes were identified. (bvsalud.org)
  • The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models. (mpg.de)
  • Structure discrimination of continuous models for biochemical reaction networks via finite state machines. (mpg.de)
  • One of the largest networks studied within systems biology is the metabolism, which comprises all the biochemical reactions happening inside a cell. (fu-berlin.de)
  • Until recently, such large metabolic networks have been studied mainly in isolation and under stationary conditions, without considering the environment dynamics or the enzymatic resources needed to catalyze all the biochemical reactions. (fu-berlin.de)
  • abstract = "Recent work has demonstrated that genetic programming is capable of automatically creating complex networks (e.g., analog electrical circuits, controllers) whose behaviour is modelled by linear and non-linear continuous-time differential equations and whose behaviour matches prespecified output values. (upenn.edu)
  • Genetic programming starts with observed time-domain concentrations of substances and automatically creates both the topology of the network of chemical reactions and the rates of each reaction of a network such that the behaviour of the automatically created network matches the observed time-domain data. (upenn.edu)
  • For example, cancer, the quintessential genetic disease, is being redefined by metabolic abnormalities, endowing tumours with the ability to outcompete normal cells in the tumour microenvironment. (ddw-online.com)
  • A dding fuel to the fire, there is early evidence that directing the metabolic programming of immune cells may improve the efficacy and durability of immunotherapies that are completely agnostic to cancer's genetic drivers. (ddw-online.com)
  • The savvy healthcare provider should therefore endeavour to understand both the genetic and metabolic drivers of a disease to really see the full picture (Figure 1). (ddw-online.com)
  • e.g. inflammation, genotoxicity, and This chapter focuses on issues as- ellers, growth factors, growth factor epigenetic alterations) and can have sociated with the understanding and receptors, signal transducers, and both genetic and epigenetic origins. (who.int)
  • 5. Vranová E, Coman D, Gruissem W. Network analysis of the MVA and MEP pathways for isoprenoid synthesis. (ac.ir)
  • Here we used a behaviorally and physiologically tractable animal model to investigate Aβ-induced memory loss and electrophysiological changes in the absence of neuronal death in a defined network underlying associative memory. (nature.com)
  • At this time it is possible that mRNA and adenoviral DNA vaccines could influence key miRNA's in the causal pathway to a primary arrhythmic cardiac death in the absence of clinical myocarditis. (ldsfreedomforum.com)
  • Her research topics include metabolic networks, bacterial signaling, and bioenergy production. (wikipedia.org)
  • Our lab conducts biomedical research directed to establish the metabolic strategies and host- pathogen relationship in bacterial pathogenic species, such as Chlamydia trachomatis , the most prevalent sexually transmitted disease in the world, and Vibrio cholerae , which produces severe gastrointestinal disease to millions of people in developing countries. (iit.edu)
  • After giving an overview of existing tools for the study of metabolic resource allocation, the thesis presents a new mathematical derivation of the widely used steady-state assumption for metabolic networks and shows how this can be used to provide upper bounds on dynamic resource allocation solutions. (fu-berlin.de)
  • Stoichiometric capacitance reveals the theoretical capabilities of metabolic networks. (mpg.de)
  • Virtually every area of life science research will benefit in some way from increased knowledge of the metabolic networks that underlie their relevant cellular processes. (ddw-online.com)
  • Mathematical Modeling of Complex Regulatory Networks. (mpg.de)
  • We end with a perspectives chapter which provides some preliminary results for using time courses from dynamic resource allocation models to infer the regulatory structures that implement these optimal behaviors. (fu-berlin.de)
  • Further chapters deal with epigenetics in relation to cancers, premature aging, longevity and the developmental origins of disease. (caister.com)
  • Dr Natchus has published of 50 peer-reviewed manuscripts and three book chapters, and he is a key author on over forty patents and patent applications, many of which have issued in the US other countries throughout the world. (grc.org)
  • FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. (mpg.de)
  • Effects of microcompartmentation on flux distribution and metabolic pools in Chlamydomonas reinhardtii chloroplasts. (mpg.de)
  • Comparable to a 'Trojan horse', it can be assumed that a whole series of metabolic events will be triggered as a positive feedback loop in any given gene network that is regulated by miRNAs. (ldsfreedomforum.com)
  • As cellular metabolic pathways follow the law of mass action, a substantial number of miRNAs targeted to numerous viral mRNAs should be produced. (ldsfreedomforum.com)
  • It is also possible that the host's miRNA machinery might be overwhelmed in the processing of miRNAs and diverted away from its normal cellular functions and molecular pathways. (ldsfreedomforum.com)
  • The first seven chapters describe the different biological mechanisms of the epigenetic machinery including: DNA methylation, histone tails, chromatin structure, nucleosome occupancy, Polycomb group proteins, siRNAs and miRNAs. (caister.com)
  • Of particular interest has been the role of habitual physical activity and related health behaviors in metabolic and hemodynamic factors contributing to the development of atherothrombotic vascular disease and diabetes mellitus. (cuanschutz.edu)
  • In the hands of skilled scientists, these tools are revealing changes in metabolic pathways that are providing new insights into disease progression. (ddw-online.com)
  • Measuring mitochondrial network morphology in mitochondrial disease. (brocku.ca)
  • Ketosis (hyperketonemia) is a prevalent metabolic disease of transition dairy cows that affects ~30-40% of the cows during early lactation. (uthscsa.edu)
  • Metabolic Dysfunction-Associated Liver Disease (MASLD) Steatotic liver disease is due to excessive accumulation of lipid in hepatocytes. (msdmanuals.com)
  • Metabolic dysfunction-associated liver disease (MASLD) includes simple fatty infiltration (a benign condition. (msdmanuals.com)
  • the entire network of chemical processes involved in maintaining life. (hindantibiotics.in)
  • Many of the mitochondrial phenomena we investigate exert effects on these processes and thus manifest as changes in mitochondrial network morphology. (brocku.ca)
  • Since leaving Procter and Gamble in 2001, Dr. Natchus lead the chemistry and development efforts in the area of metabolic disorders at Somatocor Pharmaceuticals and was the Vice President of R&D at Metastatix. (grc.org)
  • Modelling biological networks by action languages via answer set programming. (mpg.de)
  • The DEGs were further analysed for their gene ontologies (GO), pathway, protein-protein interactions and co-expression. (bvsalud.org)
  • DeMarini, and Chapter 20, by Rice and cell death determine the size protein in several signal ing path- and Herceg). (who.int)
  • In some recent metabolomics studies, data show that the number of metabolites altered in the plasma/serum or milk and metabolic pathways perturbed during ketosis are numerous. (uthscsa.edu)
  • 7 Discussion We have Configuring Forex programs feedback electric field control of seizure-like events in neuronal networks. (forexpand.com)
  • Loops are more frain identified if the transition network inferred with the DBN algorithm is translated into a cyclic graph in which nodes re- ferring to the same variable at consecutive time points are collapsed into a single node. (forexpand.com)
  • This chapter summarizes the main molecular mechanisms to C. albicans antifungal drug resistance, besides offering an overview of new antifungal agents and new antifungal targets to combat fungal infections. (intechopen.com)
  • mechanisms of carcinogenesis chapter 13. (who.int)
  • In 2020, Chris became the Chair of the National Cardiovascular Network for Wales (NCN), a partnership between Welsh Government and the British Heart Foundation. (swansea.ac.uk)
  • These highly regarded scientists, from academic medical centers around the country, offer a national and international mentoring network for our researchers, provide updates on research underway at other centers and medical institutions, and support senior faculty at the Ludeman Center in developing and implementing a robust research agenda. (cuanschutz.edu)
  • His group uses molecular and cellular tools combined with network theory to explore the links between calcium signaling, cellular behavior and the early events leading to the destruction of normal heart rhythm (arrhythmia). (swansea.ac.uk)
  • Combinatorial complexity of pathway analysis in metabolic networks. (mpg.de)
  • To facilitate this we developed the Mitochondrial Network Analysis (MiNA) toolset as a simple set of macros making use of existing ImageJ plug-ins that allows a semi-automated analysis of mitochondrial networks in cultured mammalian cells. (brocku.ca)
  • Integrating molecular markers into metabolic models improves genomic selection for Arabidopsis growth. (mpg.de)
  • These models are simplified representations of the studied biological systems and come in different granularities and abstraction levels, depending on the size of the networks and on the modeling formalisms. (fu-berlin.de)
  • These data are critical for the evaluation of network models of nervous-system function. (nationalacademies.org)
  • Fracture Healing in Diabetes Fracture repair entails recruitment of mesenchymal stem cells after which differentiation to chondrocytes that type cartilage (see Chapter 12). (dnahelix.com)
  • The book presents a collection of MATLAB-based chapters of various engineering background. (opensourcebiology.eu)
  • He authored more than 75 publications in journals indexed at Journal Citation Reports from ISI Web of Knowledge, two books, and 20 book chapters from international editors and has more than 150 communications in national and international meetings. (apaset.ac.cn)
  • To reduce morbidity and mortality as a result of uncontrolled hemorrhage, patients needing a massive transfusion, specifically addressed in detail later in this chapter, must be quickly identified so that immediate interventions can prevent the development of the lethal triad of coagulopathy, hypothermia, and acidosis. (medscape.com)
  • A health improvement database network study from the United Kingdom showed the next price of decrease extremity fractures in subjects with T1D, with danger persistently higher across all ages. (dnahelix.com)
  • Cell cycle gene expression networks discovered using systems biology: Significance in carcinogenesis. (genenetwork.org)
  • The following chapters cover the epigenetic systems of plants, the epigenetic profile of embryonic stem cells, cell differentiation, imprinting marks, and random X chromosome inactivation. (caister.com)
  • This chapter demonstrates that it is possible to automatically create (reverse engineer) a network of chemical reactions from observed time-domain data. (upenn.edu)
  • The metabolic pathway was created from 270 data points. (upenn.edu)
  • Learning multiple evolutionary pathways from cross-sectional data. (mpg.de)
  • The concentrations of substances participating in networks of chemical reactions are modelled by non-linear continuous-time differential equations. (upenn.edu)
  • encompasses all the sequences of chemical reactions that occur in the body Anabolic pathway Use small simpler compounds to build larger more complex compounds. (hindantibiotics.in)
  • Observability of plant metabolic networks is reflected in the correlation of metabolic profiles. (mpg.de)