Cancer systems biology encompasses the application of systems biology approaches to cancer research, in order to study the disease as a complex adaptive system with emerging properties at multiple biological scales. Cancer systems biology represents the application of systems biology approaches to the analysis of how the intracellular networks of normal cells are perturbed during carcinogenesis to develop effective predictive models that can assist scientists and clinicians in the validations of new therapies and drugs. Tumours are characterized by genomic and epigenetic instability that alters the functions of many different molecules and networks in a single cell as well as altering the interactions with the local environment. Cancer systems biology approaches, therefore, are based on the use of computational and mathematical methods to decipher the complexity in tumorigenesis as well as cancer heterogeneity. Cancer systems biology encompasses concrete applications of systems biology ...
Hofestädt, R., and Kolchanov, N. eds. (2010). Computational Systems Biology: German/Russian Network of Computational Systems Biology. Medizinische Informatik und Bioinformatik ...
Systems Biology of Apoptosis summarizes all current achievements in this emerging field. Apoptosis is a process common to all multicellular organisms. Apoptosis leads to the elimination of cells via a complex but highly defined cellular programme. Defects in the regulation of apoptosis result in serious diseases such as cancer, autoimmunity, AIDS and neurodegeneration. Recently, a substantial step forward in understanding the complex apoptotic pathways has been made by utilising systems biology approaches. Systems biology combines rigorous mathematical modelling with experimental approaches in a closed loop cycle for advancing our knowledge about complex biological processes. In this book, the editor describes the contemporary systems biology studies devoted to apoptotic signaling and focuses on the question how systems biology helps to understand life/death decisions made in the cell and to develop new approaches to rational treatment strategies ...
The term systems biology is now widely used and there is not one common definition of it. In reality, there are uncountable ways of understanding, explaining and applying systems biology. Concepts as represented in review articles by Hornberg et al. [7] or Bruggeman and Westerhoff [8] nicely describe what could be considered as common understanding of systems biology. In order to make clear how I understand systems biology I suggest one definition of systems biology as follows:. While traditional, reductionistic approaches investigated the property of one or of a few components (i.e. molecules) or their interaction with one or a few other molecules at the time, systems biology investigates the emergent properties of the system under investigation (e.g. organelles, cells, organs, organisms or eco systems) when multiple entities interact in networks. To do so, systems biology requires highly interdisciplinary approaches involving expertise from physics, mathematics, graph network theory and ...
Aging is a major risk factor for chronic diseases, which in turn can provide information about the aging of a biological system. This publication serves as an introduction to systems biology and its ...
2013) Delivering intellectual physical download computational systems biology inference and modelling 2016 in Russian events: a weight mass of Scottish Natural Heritage National Nature Reserves. International Research in Geographical and Environmental Education, multiperiod), 4-22. The Canadian Environmental Literacy Project( CELP).
Computational Systems Biology Lecture 2: Enzymes 1 Images from: David L. Nelson, Lehninger Principles of Biochemistry, IV Edition, Freeman ed. or under creative commons license (search for images at
Information regarding the different downstream target genes of WRKY TFs that regulate abiotic stress-induced responses is limited. Advances have, however, been made in a dehydration tolerance signaling pathway in the resurrection plant Boea hygrometrica (Wang et al. 2009). An important downstream target gene, Galactinol synthase 1 (BhGolS1), which plays a role in drought and cold tolerance (Teruaki et al. 2002) was found to be dehydration and ABA inducible. The BhGolS1 promoter contains four W boxes and chromatin immunoprecipitation showed that it is bound in vivo by the early dehydration and ABA-inducible BhWRKY1 TF (Wang et al. 2009). These observations provide direct insights into the role of a dehydration-inducible WRKY TF that interacts with a downstream target gene that plays an important role in drought responses. Recently, convincing evidence has been presented to show that AtWRKY8 functions antagonistically with its interacting partner VQ9 to modulate salinity tolerance (Hu et al. ...
The first part of this thesis focuses on the mechanisms of hormone induced Ca2+ oscillations and how these depend on fluctuations in the concentration of the Ca2+-releasing messenger, inositol 1,4,5-trisphosphate (IP3). We were able to show that IP3 oscillations greatly enhances the ability to frequency encode the hormone stimulus by Ca2+ oscillations. Two mechanisms for the generation of IP3-oscillations have been investigated, we could show that Ca2+-activation of phospholipase C is the most probable mechanism. To better understand the role of IP3-oscillations a detailed model for the phosphoinositide pathway has been developed. The model illustrates the importance of futile (de)phosphorylation cycles for regenerating phosphatidylinositol-4,5-bisphophat during stimulation, an essential property to support long-lasting Ca2+ signals. The second part of the thesis is devoted to nucleotide excision repair (NER). It is a versatile DNA repair mechanism that can remove lesions such as UV light ...
NMR spectroscopy is widely regarded as a technique that is unbiased, non-invasive and requires minimal sample preparation. These characteristics make this technique an ideal one to monitor the biological systems. In addition, NMR spectroscopy can also provide global snapshot and dynamics of complex biological systems such as cell, tissue or even an organism. This finds utility in the recently developed systems biological approaches that take holistic view of the complex biological networks rather than the conventional reductionism. Within the Biochemistry and Systems Biology group, Our lab focuses on one such complex problem that is the host-parasite interaction during infection by malarial parasite. Malaria is considered to be one of the major killers in large part of the world. We believe, systems biological approaches may provide us specific insights to the mechanism of disease progression, since this involves the joint biological network of host and the parasite. Therefore, understanding the ...
TY - JOUR. T1 - Global gene expression and systems biology analysis of bovine monocyte-derived macrophages in response to in vitro challenge with mycobacterium bovis. AU - Magee, David A.. AU - Taraktsoglou, Maria. AU - Killick, Kate E.. AU - Nalpas, Nicolas C.. AU - Browne, John A.. AU - Park, Stephen D.E.. AU - Conlon, Kevin M.. AU - Lynn, David. AU - Hokamp, Karsten. AU - Gordon, Stephen V.. AU - Gormley, Eamonn. AU - MacHugh, David E.. PY - 2012/2/22. Y1 - 2012/2/22. N2 - Background: Mycobacterium bovis, the causative agent of bovine tuberculosis, is a major cause of mortality in global cattle populations. Macrophages are among the first cell types to encounter M. bovis following exposure and the response elicited by these cells is pivotal in determining the outcome of infection. Here, a functional genomics approach was undertaken to investigate global gene expression profiles in bovine monocyte-derived macrophages (MDM) purified from seven age-matched non-related females, in response to in ...
Dietary methionine restriction (MR) and calorie restriction (CR) each improve metabolic health and extend life span. We used comprehensive transcriptome profiling and systems biology analysis to interrogate the unique and overlapping molecular responses in rats provided these dietary regimens for 20 mo after weaning. Microarray analysis was conducted on inguinal white adipose (IWAT), brown adipose tissue (BAT), liver, and skeletal muscle. Compared to controls, CR-induced transcriptomic responses (absolute fold change ≥1.5 and P≤0.05) were comparable in IWAT, BAT, and liver (~800 genes). MR-induced effects were largely restricted to IWAT and liver (~2400 genes). Pathway enrichment and gene-coexpression analyses showed that induction of fatty acid synthesis in IWAT was common to CR and MR, whereas immunity and proinflammatory signaling pathways were specifically down-regulated in MR-treated IWAT and liver (FDR≤0.07-0.3). BAT demonstrated consistent down-regulation of PPAR-signaling under CR ...
Osteosarcoma (OS) is the most common malignant bone tumor in children and adolescents. The survival rate of patients with metastatic disease remains very dismal. Nevertheless, metastasis is a complex process and a single-level analysis is not likely to identify its key biological determinants. In this study, we used a systems biology approach to identify common metastatic pathways that are jointly supported by both mRNA and protein expression data in two distinct human metastatic OS models. mRNA expression microarray and N-linked glycoproteomic analyses were performed on two commonly used isogenic pairs of human metastatic OS cell lines, namely HOS/143B and SaOS-2/LM7. Pathway analysis of the differentially regulated genes and glycoproteins separately revealed pathways associated to metastasis including cell cycle regulation, immune response, and epithelial-to-mesenchymal-transition. However, no common significant pathway was found at both genomic and proteomic levels between the two metastatic models,
We outline a computationally inferred model of the regulatory network of Populus leaves, and show how treating genes as interacting, rather than individual, entities identifies new regulators compared to traditional genomics analysis. Although systems biology models should be used with care considering the complexity of regulatory programs and the limitations of current genomics data, methods describing interactions can provide hypotheses about the underlying cause of emergent properties and are needed if we are to identify target genes other than those constituting the "low hanging fruit" of genomic analysis.. ...
... is a new open-access, online only multi- and interdisciplinary journal dedicated to publishing the finest research on the Systems Biology and related research to that System Biological approach is applied.
... is a new open-access, online only multi- and interdisciplinary journal dedicated to publishing the finest research on the Systems Biology and related research to that System Biological approach is applied.
Current research interests: Metabolomics. Ricks research goals focus on the systems biology investigations of microbial and mammalian systems, specifically the application of metabolomics to these disciplines and the development of analytical instrumentation and methodologies to fulfill these goals. Metabolomics is focussed on the holistic and data-driven investigation of the quantitative collection of low molecular weight organic and inorganic compounds present in biological systems. This collection of endogenous and exogenous metabolites is defined as the metabolome. Endogenous metabolites can be biochemically synthesized or catabolised within the system and exogenous metabolites are acquired from the external environment (for example, food nutrients and drugs) or from co-habiting species (for example, gut microbiome). A range of experimental strategies are employed to investigate the metabolome including metabolic profiling (untargeted analysis), targeted analysis and metabolite ...
Mechanistic models are becoming more and more popular in Systems Biology; identification and control of models underlying biochemical pathways of interest in oncology is a primary goal in this field. Unfortunately the scarce availability of data still limits our understanding of the intrinsic characteristics of complex pathologies like cancer: acquiring information for a system understanding of complex reaction networks is time consuming and expensive. Stimulus response experiments (SRE) have been used to gain a deeper insight into the details of biochemical mechanisms underlying cell life and functioning. Optimisation of the input time-profile, however, still remains a major area of research due to the complexity of the problem and its relevance for the task of information retrieval in systems biology-related experiments. We have addressed the problem of quantifying the information associated to an experiment using the Fisher Information Matrix and we have proposed an optimal experimental design
Ali Ebrahim, Eivind Almaas, Eugen Bauer, Aarash Bordbar, Anthony P. Burgard, Roger L. Chang, Andreas Dräger, Iman Famili, Adam M. Feist, Ronan M. T. Fleming, Stephen S. Fong, Vassily Hatzimanikatis, Markus J. Herrgard, Allen Holder, Michael Hucka, Daniel Hyduke, Neema Jamshidi, Sang Yup Lee, Nicolas Le Novère, Joshua A. Lerman, Nathan E. Lewis, Ding Ma, Radhakrishnan Mahadevan, Costas Maranas, Harish Nagarajan, Ali Navid, Jens Nielsen, Lars K. Nielsen, Juan Nogales, Alberto Noronha, Csaba Pal, Bernhard O. Palsson, Jason A. Papin, Kiran R. Patil, Nathan D. Price, Jennifer L. Reed, Michael Saunders, Ryan S. Senger, Nikolaus Sonnenschein, Yuekai Sun, and Ines Thiele. Do Genome-scale Models Need Exact Solvers or Clearer Standards? Molecular Systems Biology, 11(10), October 2015. [ DOI , link , pdf ...
There has been one iteration of the M. barkeri reconstruction and model published in Molecular Systems Biology in early 2006.. We have the following information available:. ...
Systems Biology: Neurobiology - University of Toronto. The new Department of Cell and Systems Biology at the University of Toronto invites applications for a tenure track faculty position to be appointed at the Assistant Professor level in the field of Systems Biology - Neurobiology to begin July 1, 2008.. We particularly encourage candidates to apply who have demonstrated excellence in addressing fundamental questions in neurobiology using high-throughput approaches or gene/protein network analyses with bioinformatics, genomic, proteomic, electrophysiological, or imaging tools. Our vision is to advance Systems-wide analyses in Neurobiology which complement existing strengths in the department (www.csb.utoronto.ca).. Candidates should have at least two years of research experience beyond their doctoral degree. In addition to pursuing a vigorous, internationally recognized research program, the successful candidate will contribute to undergraduate and graduate teaching in the molecular life ...
Learning, knowledge, research, insight: welcome to the world of UBC Library, the second-largest academic research library in Canada.
Plant carbohydrate metabolism comprises numerous metabolite interconversions, some of which form cycles of metabolite degradation and re-synthesis and are thus referred to as futile cycles. In this study, we present a systems biology approach to analyse any possible regulatory principle that operates such futile cycles based on experimental data for sucrose (Scr) cycling in photosynthetically active leaves of the model plant Arabidopsis thaliana. Kinetic parameters of enzymatic steps in Scr cycling were identified by fitting model simulations to experimental data. A statistical analysis of the kinetic parameters and calculated flux rates allowed for estimation of the variability and supported the predictability of the model. A principal component analysis of the parameter results revealed the identifiability of the model parameters. We investigated the stability properties of Scr cycling and found that feedback inhibition of enzymes catalysing metabolite interconversions at different steps of the cycle
Although gene discovery in neuropsychiatric disorders, including autism spectrum disorder, intellectual disability, epilepsy, schizophrenia, and Tourette disorder, has accelerated, resulting in a large number of molecular clues, it has proven difficult to generate specific hypotheses without the cor …
The sodium-potassium pump is widely recognized as the principal mechanism for active ion transport across the cellular membrane of cardiac tissue, being responsible for the creation and maintenance of the transarcolemmal sodium and potassium gradients, crucial for cardiac cell electrophysiology. Importantly, sodium-potassium pump activity is impaired in a number of major diseased conditions, including ischemia and heart failure. However, its subtle ways of action on cardiac electrophysiology, both directly through its electrogenic nature and indirectly via the regulation of cell homeostasis, make it hard to predict the electrophysiological consequences of reduced sodium-potassium pump activity in cardiac repolarization. In this review, we discuss how recent studies adopting the systems biology approach, through the integration of experimental and modeling methodologies, have identified the sodium-potassium pump as one of the most important ionic mechanisms in regulating key properties of cardiac
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Systems Biology Approaches to Alzheimers Disease Using Non-mammalian Laboratory Animals (R01) RFA-AG-17-057. NIA
Growth is a fundamental process of life. Growth requirements are well-characterized experimentally for many microbes; however, we lack a unified model for cellular growth. Such a model must be predictive of events at the molecular scale and capable of explaining the high-level behavior of the cell as a whole. Here, we construct an ME-Model for Escherichia coli-a genome-scale model that seamlessly integrates metabolic and gene product expression pathways. The model computes ∼80% of the functional proteome (by mass), which is used by the cell to support growth under a given condition. Metabolism and gene expression are interdependent processes that affect and constrain each other. We formalize these constraints and apply the principle of growth optimization to enable the accurate prediction of multi-scale phenotypes, ranging from coarse-grained (growth rate, nutrient uptake, by-product secretion) to fine-grained (metabolic fluxes, gene expression levels). Our results unify many existing ...
All biological interactions, whether they take place on a molecular, organism or ecosystem scale, are part of complex dynamical systems. Understanding the behaviour of these systems lies at the heart of many key challenges in biological research. In this module you will have the opportunity to develop and investigate mathematical models of biological systems. You will learn techniques to construct, implement and analyse interaction networks using the Python programming language. Research in the field of Systems Biology is highly interdisciplinary. It often involves biologists working with colleagues from the fields of physics, engineering, mathematics and computer science. Consequently this module encourages participation from any interested science or engineering student. ...
Systems Biology is the application of computational modelling and simulation to complex systems in biology. Examples include biochemical pathways, metabolic processes, protein complexes and information processing, genetic networks, self-organising systems, neuronal networks and cell-cell communication. This course will focus on the level of molecular and genetic systems and simulations ...
Linux For Linux, its zip file should be extracted into your $HOME/.taverna-1.6.2/lib folder. Your Taverna runme.sh script should then be edited with the text highlighted in bold as follows: (..) # Load customised properties if they exist if [ -f "$TAVERNA_HOME/custom.sh" ] ; then source "$TAVERNA_HOME/custom.sh" fi #Set to $TAVERNA_HOME/lib for shared installation LIB_PATH="$HOME/.taverna-1.6.2/lib" LD_LIBRARY_PATH="$LIB_PATH" export LD_LIBRARY_PATH ARGS="-Djava.library.path=$LIB_PATH" java $ARGS -jar "$TAVERNA_HOME/taverna-bootstrap-1.6.2.0.jar" [email protected] MacOS X For those people using MacOS X, the libsbml native libraries should be placed in the same directory where your Taverna application bundle resides. So for example, if your Taverna application bundle is in /Applications/Taverna-1.6.2/Taverna.app then the libxerces-c.27.dylib, libsbml.dylib and libsbmlj.jnilib files should be placed there. In constrast, the libsbml jar file should be placed in Tavernas lib folder which is found at ...
Congratulations to Dr. Cecilia Lo and Dr. Michael Tsang on their recently funded NIH administrative supplement, Assaying Heterotaxy Patient Genes in a Cilia Motility and Left-Right Patterning. This project will examine whether expression of the RCV can rescue the HTX phenotype elicited by MO gene knockdown in the zebrafish embryo.
Prepare for the conference with access to impactful genomics and systems biology articles, published across the AACR journals.. The field of cancer systems biology has emerged to address the increasing challenge of cancer as a complex, multifactorial disease using sophisticated model-based approaches, ranging from relatively coarse genome-wide regulatory and signaling networks to detailed kinetic models of key pathways. These networks and pathways are responsible for implementing cancer-relevant mechanisms and for processing aberrant signals from the spectrum of somatic mutations and heritable variants that contribute to tumor initiation, progression, and drug sensitivity. The ability to assemble and interrogate such cancer models is the direct result of the availability of large sample-matched collections of molecular profiles from thousands of human malignancies, as made available by large consortia, such as TCGA, ICG, and TARGET, among others. This AACR Special Conference complements and ...
Hepatitis C virus (HCV) infection is a worldwide healthcare problem; however, traditional treatment methods have failed to cure all patients, and HCV has developed resistance to new drugs. Systems biology-based analyses could play an important role in the holistic analysis of the impact of HCV on hepatocellular metabolism. Here, we integrated HCV assembly reactions with a genome-scale hepatocyte metabolic model to identify metabolic targets for HCV assembly and metabolic alterations that occur between different HCV progression states (cirrhosis, dysplastic nodule, and early and advanced hepatocellular carcinoma (HCC)) and healthy liver tissue. We found that diacylglycerolipids were essential for HCV assembly. In addition, the metabolism of keratan sulfate and chondroitin sulfate was significantly changed in the cirrhosis stage, whereas the metabolism of acyl-carnitine was significantly changed in the dysplastic nodule and early HCC stages. Our results explained the role of the upregulated ...
In Escherichia coli (E. coli), the oxidative branch of the pentose phosphate pathway (oxPPP) is one of the major sources of NADPH when glucose is the sole carbon nutrient. However, unbalanced NADPH production causes growth impairment as observed in a strain lacking phosphoglucoisomerase (Δpgi). In this work, we studied the metabolic response of this bacterium to the replacement of its glucose-6-phosphate dehydrogenase (G6PDH) by a NADH-producing variant. The homologous enzyme from Leuconostoc mesenteroides was studied by molecular dynamics and site-directed mutagenesis to obtain the NAD-preferring LmG6PDHR46E,Q47E. Through homologous recombination, the zwf loci (encoding for G6PDH) in the chromosomes of wild type (wt) and Δpgi E. coli strains were replaced by DNA encoding for LmG6PDHR46E,Q47E. Contrary to the predictions of a Robustness Analysis performed by flux balances simulation, the replacements caused a substantial effect on the growth rates, increasing 59% in the Δpgi strain, while ...
Biomolecular nuclear magnetic resonance spectroscopy (NMR) is a very versatile technique that can be used to determine the three dimensional structures of proteins, DNA, RNA, oligosaccharides and small molecules. It can also be used to study conformational changes, intermolecular interactions (both strong and weak), and molecular motion on many timescales in solution. NMR is widely used in metabolomics studies. (and enquiries for this type of application should be directed to Glasgow Polyomics) Solution state NMR complements the other techniques, such as circular dichroism and X-ray crystallography, available in the facility.. Generally, biomacromolecular NMR samples should be prepared with highly purified material, often isotopically labelled with 15N, 13C and even 2H, but NMR has been used e.g. to study proteins in living cells, and ligand-receptor interactions where the receptor comprises an un-purified membrane preparation.. Some guidance on typical sample requirements are given below, but ...
Walter Kolch is Director of Systems Biology Ireland at University College Dublin. A leading international proponent of precision medicine, Kolch originally trained as a clinician, subsequently working in the pharmaceutical industry, research institutes, and academia. He is internationally recognised for his cutting-edge research using systems approaches to understand signalling networks, and is ranked 3rd in the world in precision medicine, 8th in personalised medicine, and amongst the worlds top 50 in proteomics, systems biology, and signal transduction (Google Scholar). Through his leading involvement in pan-European strategic initiatives including Coordinating Action Systems Medicine, Infrastructure for Systems Biology Europe, and the ELIXIR research infrastructure for life science information, Kolch has played a central role in the development of precision medicine policy and funding at both national and international level.. Kolch has designed, developed and coordinated innovative systems ...
Dr. Aprison designs and produces a portfolio of education and training programs for high school students, teachers, undergraduates, graduate students, post-doctoral fellows, and faculty. He has partnerships with scholars at the University of Chicago, Northwestern University, the Field Museum, the Museum of Science & Industry, Chicago-area K-12 schools, the Collegiate Scholars Program, Urban Teacher Education Program, Research in the Biological Sciences, and Post-Baccalaureate Research Education Program. As a Senior Lecturer in the Biological Sciences Collegiate Division of the College, Dr. Aprison produces courses and lectures. They include classes for Systems Biology & Disease (MD-Ph.D. students), Systems & Networks in Cancer (grad students), Synthetic Biology & Regulation of Genes (undergrad students), and Topics in Immunology, Cancer, and Systems Biology (MD-Ph.D. students), and a system biology Journal Club and grant writing course (M.D. Ph. D. students.. Dr. Aprison works on campus-wide ...
Presented by the UCSD Institute for Genomic Medicine, The Genetics Training Program, The Bioinformatics and Systems Biology Program, and The San Diego Center for Systems Biology. View current schedule here: http://genomic.weebly.com/. When available, abstracts are posted on the Google calendar.. ...
Complex diseases such as cancer, arthritis, diabetes, endometriosis, Alzheimers, and many others, all involve interactions of tissue cells with immune system cells via molecular communication processes, and resulting disease consequently arises from dysregulated signaling network activities governing pathological cell behaviors. We are employing combined experimental and computational systems biology approaches to understand these communication and signaling processes at multiple scales, integrating across multiple intracellular pathways, multiple extracellular factors, and multiple cell types, with emphasis on in vivo studies in animal models and human subjects. This talk will present an overview of our paradigmatic concept, technical approaches, and example applications.. ...
Translating in vitro biological data into actionable information related to human health holds the potential to improve disease treatment and risk assessment of chemical exposures. While genomics has identified regulatory pathways at the cellular level, translation to the organism level requires a multiscale approach accounting for intra-cellular regulation, inter-cellular interaction, and tissue/organ-level effects. Tissue-level effects can now be probed in vitro thanks to recently developed systems of three-dimensional (3D), multicellular, "organotypic" cell cultures, which mimic functional responses of living tissue. However, there remains a knowledge gap regarding interactions across different biological scales, complicating accurate prediction of health outcomes from molecular/genomic data and tissue responses. Systems biology aims at mathematical modeling of complex, non-linear biological systems. We propose to apply a systems biology approach to achieve a computational representation of ...
Led by Dr. Andrei Ivanov, The ECBDC Computational Chemical Biology and Systems Pharmacology (CCBSP) team utilizes state-of-the-art bioinformatics, computational modeling, and systems biology approaches to study and regulate the molecular connectivity between the biological pathways to facilitated target discovery and therapeutic development ...
Postdoctoral Fellowship in Malaria Immunity Systems Biology. The focus of the postdoctoral fellowship is to evaluate the development of protection against human malaria using a systems biology approach in a collaborative project between the Williamson Laboratory at the Uniformed Services University of the Health Sciences, The University of Maryland, and the Center for Human Immunology at the National Institutes of Health.. Immunophenotyping, transcriptional profiling and Ig repertoire analysis will be used to assess the maturation of the humoral and cellular immune response through repetitive controlled human malaria infections. The results will be compared with clinical outcomes to identify specific responses that correlate with protection and the information used to develop new vaccine strategies.. ...
We employed a top‐down systems biological approach to identify regulation principles in the transcription factor network downstream of the RAS/MAPK pathway. To uncover elements of the network, we integrated perturbation of transcription factor expression by RNA interference, expression profiling of target genes and computational modelling. At the phenotypic level, siRNA‐mediated silencing of the transcription factors generated reproducible effects on morphology, growth and anchorage independence of ovarian epithelial cells. Since the relationship of the different regulators could not be interpreted intuitively, we introduced a modification of MRA, which has been established for the construction of genetic networks (Kholodenko et al, 2002; Santos et al, 2007). Local response coefficients illustrating the mutual impact of single transcription factor perturbations on other network components were derived from the model. The simulations predicted three central hubs (RelA, Gfi1 and Otx1), which ...
The aim of the present meeting will be to promote scientific networking among researchers working in the field of Systems Biology applied to immune mediated kidney diseases. Comparing the results derived from OMICS technologies applied to patients and animal models, the scientific sessions will provide an unique overview on immune-mediated renal diseases, shedding light on genomic and environmental factors influencing gene expression signatures, cellular signalling, metabolic pathways, hormonal and cytokine imbalance, new targets for treatment ...
The review examines the new approaches in modern systems biology, in terms of their use for a deeper understanding of the physiological adaptation of a healthy human in extreme environments. Human physiology under extreme conditions of life, or environmental physiology, and systems biology are natural partners. The similarities and differences between the object and methods in systems biology, the OMICs (proteomics, transcriptomics, metabolomics) disciplines, and other related sciences have been studied. The latest data on environmental human physiology obtained using systems biology methods are discussed. The independent achievements of systems biology in studying the adaptation of a healthy human to physical activity, including human presence at high altitude, to the effects of hypoxia and oxidative stress have been noted. A reasonable conclusion is drawn that the application of the methods and approaches used in systems biology to study the molecular pattern of the adaptive mechanisms that develop in
Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology. The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating ...
Feedback loops, which are ubiquitous in engineered systems, play a fundamental role in most biological processes. The survival of any organism strictly depends on its ability to sense and react to changes in its environment. Like electrical and mechanical control systems, cells have the molecular gear necessary to sense, compute and actuate. What are the theoretical and experimental tools available to understand the regulatory circuitry in biochemical systems? This course will provide students with an organized overview of research work between control theory and molecular biology. The first part of the class will be dedicated to modeling, identification and control-theoretic methods for the analysis of biological networks, following a systems biology perspective. The second part of the class will instead focus on design principles, and the challenges related to constructing biological pathways. Can we build modular and robust networks satisfying performance specifications? This fascinating ...
The exponential development of highly advanced scientific and medical research technologies throughout the past 30 years has arrived to the point where the high number of characterized molecular agents related to pathogenesis cannot be readily integrated or processed by conventional analytical approaches. Indeed, the realization that several moieties are signatures of disease has partly led to the increment of complex diseases being characterized. Scientists and clinicians can now investigate and analyse any individual dysregulations occurring within the genomic, transcriptomic, miRnomic, proteomic, and metabolomic levels thanks to currently available advanced technologies. However, there are drawbacks within this scientific brave new age in that only isolated molecular levels are individually investigated for their influence in affecting any particular health condition. Since their conception in 1992, systems biology/medicine focuses mainly on the perturbations of overall pathway kinetics for the
The University of Manchesters distance learning course, Bioinformatics for Systems Biology (http://octette.cs.man.ac.uk/bioinformatics/modules/systemsbiology.html) covers the use of networks for the integration and visualisation of biological data. It could be taken as a single course, or with one or more of our other Masters level courses in Digital Biology. Our other online courses include : Mathematics for metabolic modelling Bioinformatics for transcriptomics Computational Systems Biology Bioinformatics for Systems Biology covers: * the use of models in biology * structure and use of public pathway and interaction databases * reconstruction of biological networks from experimental data * network statistics * integration of transcriptome data with a network * advanced topics The final section will prepare participants for our advanced course in Computational Systems Biology. You will find links to all of our online courses here : ...
Shown above is a summary of the physiology of a neuro-muscular junction in a newly introduced visual language called Systems Biology Graphical Notation (SB