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Modeling complexity: cognitive constraints and computational model-building in integrative systems biology

Modern integrative systems biology defines itself by the complexity of the problems it takes on through computational modeling and simulation. However in integrative systems biology computers do not

Systems biology of the IMIDIA biobank from organ donors and pancreatectomised patients defines a novel transcriptomic signature of islets from individuals with type 2 diabetes

secretion in beta cells, and ARG2 and PPP1R1A, which promoted insulin secretion. Systems biology approaches identified HNF1A, PDX1 and REST as drivers of gene co-expression modules correlated with impaired ... Gene expression profiles OD modules PPP modules OD traits Intersection TF network NFATC2 TSC22D1 SOCS2 LMO4 EDN1 PTPRK NFKBIZ ƒFig. 5 Systems biology analysis predicted the key transcription

Formal reasoning about systems biology using theorem proving

System biology provides the basis to understand the behavioral properties of complex biological organisms at different levels of abstraction. Traditionally, analysing systems biology based models of ... provide a complete understanding of the behavior of such diseases, mainly due to the complex interactions of molecules connected through a chain of reactions. Systems biology [1] overcomes these limitations

Precision medicine driven by cancer systems biology

Molecular insights from genome and systems biology are influencing how cancer is diagnosed and treated. We critically evaluate big data challenges in precision medicine. The melanoma research ... inhibitors have the Cancer systems biology; Melanoma; Subtype; Cancer metabolism; Oncometabolite; Epigenomics; CSD; SCNA; Driver; Big data; Precision medicine; Personalized medicine; Neoantigen; Immunotherapy

Systems biology of the modified branched Entner-Doudoroff pathway in Sulfolobus solfataricus

deletion and perturbations? We employed a systems biology approach to answer these questions and to gain further knowledge on the emergent properties of this biological system. Specifically, we applied ... npED branch. Consequently, this experiment is not possible in the wet lab. However, using a systems biology approach, we can test in silico how the system behaves when the npED branch is inactive and the

The Physics behind Systems Biology

Systems Biology is a young and rapidly evolving research field, which combines experimental techniques and mathematical modeling in order to achieve a mechanistic understanding of processes ... , it may not be the best strategy in a search for design principles of biological systems and the fundamental laws underlying Biology. Physics has a long tradition of characterizing and understanding

Systems biology of seeds: deciphering the molecular mechanisms of seed storage, dormancy and onset of germination

70% of the world’s caloric intake in the form of food and animal feed produced through sustainable agriculture, which contributes to food and nutritional security. Seed systems biology remains an ... covered in this special issue of Plant Cell Reports highlight recent advances made in the area of seed biology that cover various systems biology applications such as gene regulatory networks, metabolomics

Systems and synthetic biology approaches in understanding biological oscillators

. Elucidating their fundamental mechanisms is of great significance to diseases, and yet challenging, due to the complexity and diversity of these oscillators. Results Approaches in quantitative systems biology ... regulators. Here, we will review major progress that has been made in understanding biological oscillators using these approaches. The quantitative systems biology approach allows for identification of the

The systems biology format converter

Background Interoperability between formats is a recurring problem in systems biology research. Many tools have been developed to convert computational models from one format to another. However ... developers. The source code and documentation of the framework are freely available from the project web site. Converter; Format; Systems biology; SBML Background Computational representations of pathways

Parameter estimation in large-scale systems biology models: a parallel and self-adaptive cooperative strategy

Background The development of large-scale kinetic models is one of the current key issues in computational systems biology and bioinformatics. Here we consider the problem of parameter estimation in ... ; Parallelization - Computational simulation and optimization are key topics in systems biology and bioinformatics, playing a central role in mathematical approaches considering the reverse engineering of

Osmoregulation in the Halophilic Bacterium Halomonas elongata: A Case Study for Integrative Systems Biology

Trk-type transport systems TrkH and TrkI [13]. With increasing K+-glutamate levels, ectoine synthesis is switched on. The compatible solute ectoine is critical for the biology of H. elongata as shown by

Allogenic adipose-derived stem cell therapy overcomes ischemia-induced microvessel rarefaction in the myocardium: systems biology study

interactome. Allogenic adipose-derived stem cells; Conditioned media; Angiogenesis; Myocardial infarction; Proteomics; Systems biology - Background Advances in pharmacological therapy and interventional ... reservoir of functionally active stem cells is reduced in obese patients . FASEB J . 2012 ; 26 : 4327 - 36 . 8. Ferrer-Lorente R , Bejar MT , Tous M , Vilahur G , Badimon L. Systems biology approach to

A Comprehensive Systems Biology Approach to Studying Zika Virus

glycosylation, particularly of ASN154, may have major biological implications for ZIKV disease. Taken together, the systems biology perspective of ZIKV indicates: a.) The recently emergent Asian/American N ... comprehensive approaches to facilitate control and ultimately treatment and prevention strategies. Here we present a systems biology analysis of ZIKV examining diversity in its sequence and glycosylation patterns

FAIRDOMHub: a repository and collaboration environment for sharing systems biology research

The FAIRDOMHub is a repository for publishing FAIR (Findable, Accessible, Interoperable and Reusable) Data, Operating procedures and Models (https://fairdomhub.org/) for the Systems Biology community ... storing and sharing systems biology research assets. It enables researchers to organize, share and publish data, models and protocols, interlink them in the context of the systems biology investigations

The 7th National Conference on Bioinformatics and Systems Biology of China

Synthetic & Systems Biology, TNLIST; Department of Automation, Tsinghua University , Beijing 100084 , China 2 MOE Key Laboratory of Bioinformatics, School of Life Sciences, Tsinghua University , Beijing ... , San Francisco, talked about cellular aging in the view of system biology. Prof. Jingdong Han of PICB, Shanghai Institute of Biological Sciences, CAS, introduced a systems approach to reverse engineer

Systems biology of the structural proteome

biological studies. In recent years, genome-scale reconstructions have been extended to include protein structural information, which has opened up new vistas in systems biology research and empowered ... , MD 20894 , USA 5 Department of Systems Biology, Harvard Medical School , Boston, MA 02115 , USA 6 National Center for Biotechnology Information, National Library of Medicine, National Institutes of

Copy number variability in Parkinson’s disease: assembling the puzzle through a systems biology approach

frequent copy number changes in familiar PD genes and provide a “systems biology” overview of rare individual rearrangements that could functionally act on commonly deregulated molecular pathways. Assessing ... need to assess the collective effect of common and rare variants that together may converge on PD pathology. In this context, the “systems biology” approach represents a worthwhile instrument to analyze

Copy Number Variations in Amyotrophic Lateral Sclerosis: Piecing the Mosaic Tiles Together through a Systems Biology Approach

approach that is inadequate for uncovering the genetic architectures of complex traits like ALS. The emergent paradigm of “systems biology” may offer a new perspective to better interpret the wide spectrum ... -assisted diagnosis and more effective and personalized treatments. Amyotrophic lateral sclerosis (ALS); Copy number variations (CNVs); Systems biology; Genomics - * Sebastiano Cavallaro Amyotrophic

Systems Biology for Biologists

you! Systems biology, at its core, is not a set of computational and mathematical techniques; these are merely tools, incredibly useful, but secondary. The heart of systems biology is simple: explaining ... system. For this, the training and intuition of a biologist is irreplaceable. Are There Any Systems Biology Success Stories? Why, yes, indeed there are. Successful mathematical modeling of biology has a

Cell-Based Systems Biology Analysis of Human AS03-Adjuvanted H5N1 Avian Influenza Vaccine Responses: A Phase I Randomized Controlled Trial

randomized twenty adults aged 18–49 to receive two doses of either AS03-adjuvanted (n = 10) or unadjuvanted (n = 10) H5N1 vaccine 28 days apart. We used a systems biology approach to characterize and correlate ... global molecular signatures of gene, protein, metabolite, and lipid expression [23±28]. We recently reported the use of a systems biology approach to study the immune responses in six individual immune