*  Cancer systems biology - Wikipedia
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 ...
  https://en.wikipedia.org/wiki/Cancer_systems_biology
*  Computational Systems Biology: German/Russian Network of Computational Systems Biology
Hofestädt, R., and Kolchanov, N. eds. (2010). Computational Systems Biology: German/Russian Network of Computational Systems Biology. Medizinische Informatik und Bioinformatik ...
  https://pub.uni-bielefeld.de/publication/2376605
*  Systems Biology of Apoptosis - beck-shop.de
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 ...
  http://m.beck-shop.de/item/3130343934313432
*  A systems biology perspective on the role of WRKY transcription factors in drought responses in plants | SpringerLink
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. ...
  https://link.springer.com/article/10.1007/s00425-013-1985-y
*  Systems biology perspectives on calcium signaling and DNA repair
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 ...
  https://edoc.hu-berlin.de/handle/18452/16382
*  Metabolomics for Investigating Disease Process
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 ...
  http://www.tifr.res.in/~dcs/index.php?option=com_content&view=article&id=71&Itemid=173
*  A systems biology analysis of the unique and overlapping transcriptional responses to caloric restriction and dietary...
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 ...
  https://www.pubfacts.com/detail/24571921/A-systems-biology-analysis-of-the-unique-and-overlapping-transcriptional-responses-to-caloric-restri
*  The genetic control of growth rate: a systems biology study in yeast | BMC Systems Biology | Full Text
Appropriate control of the rate of cell growth is central to the long-term survival of species, particularly microorganisms. A fast growth rate is a competitive advantage when environmental conditions are favourable, while slow growth or even quiescence may allow survival under stress conditions such as rapid changes in the physicochemical environment, starvation, or exposure to toxins. Thus most organisms have evolved stringent controls over the rate of cell growth, and any disruption of these controls has severe consequences; an obvious example being the development of cancer as a result of uncontrolled cell division.. Our genome-scale approach to the investigation of growth rate control in the model eukaryote cell, S. cerevisiae, is based on the concepts of Metabolic Control Analysis (MCA; [1]). MCA defines the extent of control exerted over the flux through a pathway by its components. In our context, flux is the growth rate of cells, pathway components are the gene products, and control ...
  https://bmcsystbiol.biomedcentral.com/articles/10.1186/1752-0509-6-4
*  npj Systems Biology and Applications
... 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.
  http://www.nature.com/npjsba/?error=cookies_not_supported&code=006fcf5d-c492-4e3d-b55a-0dd9d7039674
*  npj Systems Biology and Applications
... 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.
  http://www.nature.com/npjsba/?error=cookies_not_supported&code=4abc74f4-d105-44ba-b9f6-6c048a9acb1f
*  Manchester Centre for Integrative Systems Biology
Current research interests: Metabolomics. Rick's 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 ...
  http://www.mcisb.org/people/dunn/
*  Developing optimal input design strategies in cancer systems biology with applications to microfluidic device engineering | BMC...
Our understanding of molecular basis of complex diseases is being dramatically changed by systems investigation supported by the most advanced tools and techniques developed by the scientific community. In particular, cancer investigation has greatly benefited by systems level approaches since tumor development and progression are believed to be among those system trajectories that arise from abnormal working states. The work by Hornberg and colleagues [1] pointed out the relevance of Systems Biology approaches in the study of dynamics leading to cancer. Epidermal Growth Factor Receptor (EGFR) pathway is one of those biochemical reaction networks believed to play a central role in cancer development. As a matter of fact EGFR and receptors in the same family (ErbB2, ErbB3 and ErbB4) mediate cell to cell interactions both in organogenesis and in adult tissues [2]. The 40-year long study of this pathway led to associate overexpression of the ...
  https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-10-S12-S4
*  Andreas Dräger | Systems Biology Research Group
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 ...
  http://sbrg.ucsd.edu/Researchers/Draeger
*  M barkeri | Systems Biology Research Group
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:. ...
  http://sbrg.ucsd.edu/InSilicoOrganisms/Mbarkeri
*  Byung-Kwan Cho | Systems Biology Research Group
Cho, B.K., Zengler, K., Knight, E.M., Park, Y.S., Qiu, Y., Barrett, C.L., Lovley, D., and Palsson, B.O. (2009). "Genome-wide analysis of protein-DNA interactions in bacteria.", Microbial Systems Biology, in press.. Seo, J.H., Lee, G.S., Kim, J., Cho, B.K., Joo, K., Lee, J., and Kim, B.G. (2009). "Automatic protein structure prediction system enabling rapid and accurate model building for enzyme screening." Enzyme Microb. Technol., accepted.. Lewis, N.E., Cho, B.K., Knight, E.M., and Palsson, B.O. (2009). Gene Expression Profiling Data and Insight into the Use of Genome-scale In Silico Models of Escherichia coli for Analysis: Providing Context for Content. J. Bacteriol., 191:3437-3444.. Park, S.H., Park, H.Y., Cho, B.K., Yang, Y.H., Sohng, J.K., Lee, H.C., Liou, K., and Kim, B.G. (2009). Reconstitution of Antibiotics Glycosylation by Domain Exchanged Chimeric Glycosyltransferase. J Mol. Catalysis B: Enzymatic, accepted.. Hwang, J.Y., Park, J., Seo, J.H., Cha, M., Cho, B.K., ...
  http://sbrg.ucsd.edu/Researchers/Previous/BKCho
*  A Phase 1 Systems Biology Study to Investigate Immune Correlates of the Response to an Experimental Hepatitis B Vaccine ...
This trial is investigating the immune correlates of the response to V 270 [HEPLISAV; Dynavax Technologies] in healthy, older adult subjects.
  http://adisinsight.springer.com/trials/700239482
*  Na/K pump regulation of cardiac repolarization: insights from a systems biology approach. - Oxford Neuroscience
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 ...
  https://www.neuroscience.ox.ac.uk/publications/401270
*  Ines Thiele | Systems Biology Research Group
Genome-Scale reconstruction of the transcriptional and translational machinery in Escherichia coli: A knowledge-database and its mathematical formulation", 1st Bioinfo Expo, San Diego, February 2009, Ines Thiele, Neema Jamshidi, Ronan M.T. Fleming, and Bernhard Ø. Palsson. "Genome-Scale reconstruction of the transcriptional and tr anslational machinery in Escherichia coli: A knowledge-database and its mathematical formulation", 16th Annual International Conference on Microbial Genomes, Lake Arrowhead, September 2008, Ines Thiele, Neema Jamshidi, Ronan M.T. Fleming, and Bernhard Ø. Palsson. "From Network to Function: Systematic annotation of gene function using metabolic network reconstructions.", Workshop on the Biological Annotation of Novel Proteins, San Diego, March 2008, Ines Thiele and Bernhard Ø. Palsson.. "Genome-Scale reconstruction of the transcriptional and translational machinery in Escherichia coli: A knowledge-database and its mathematical formulation", ICSB 2007, Long Beach, ...
  http://sbrg.ucsd.edu/Researchers/Previous/Thiele
*  Computational Systems Biology
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. ...
  http://www.ucl.ac.uk/prospective-students/study-abroad-ucl/summer-school/modules/computational-systems-biology
*  Computational and Systems Biology of Cancer
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 ...
  http://www.aacr.org/Meetings/Pages/MeetingDetail.aspx?EventItemID=29
*  Systems biology analysis of hepatitis C virus infection reveals the role of copy number increases in regions of chromosome 1q...
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 ...
  http://kth.diva-portal.org/smash/record.jsf?pid=diva2:931712
*  The Metabolic Impact of a NADH-producing Glucose-6-phosphate Dehydrogenase in Escherichia coli. | Systems Biology Research Group
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 ...
  http://systemsbiology.ucsd.edu/node/979
*  Dae-Hee Lee | Systems Biology Research Group
Dae-Hee Lee, Adam M. Feist and Bernhard O. Palsson, 2010, Cumulative number of cell divisions in Escherichia coli as a meaningful time-scale for laboratory adaptive evolution, (submitted to AEM).. Dae-Hee Lee, Nathan E. Lewis and Bernhard O. Palsson, 2010, Optimal metabolic states on unnatural substrates form through laboratory adaptive evolution, (in preparation).. Dae-Hee Lee, Ye-Ji Lee, Yeon-Woo Ryu, and Jin-Ho Seo, 2010, "Molecular cloning and biochemical characterization of a novel erythrose reductase from Candida magnoliae JH110", Microbial Cell Factories 9: 43.. Dae-Hee Lee and Bernhard O. Palsson, 2010, "Adaptive evolution of Escherichia coli K-12 MG1655 on a non-native carbon source, L-1,2-Propanediol", Applied and Environmental Microbiology 76(3):4158-4168.. Dae-Hee Lee, Sung-Gun Kim, Dae-Hyuk Kweon and Jin-Ho Seo, 2009, "Folding machineries displayed on a cation-exchanger for the concerted refolding of cysteine- or proline-rich protein", BMC Biotechnology 9:27.. Dae-Hee Lee, ...
  http://sbrg.ucsd.edu/Researchers/Previous/DHLee
*  Publications | Systems Biology Research Group
Conrad TM, Frazier M, Joyce AR, Cho B-K, Knight EM, Lewis NE, Landick R, Palsson BØ. 2010. RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media.. Proceedings of the National Academy of Sciences of the United States of America. 107(47):20500-5. ...
  http://sbrg.ucsd.edu/Publications
*  Wendy Shieu | Systems Biology Research Group
Hi, I am currently completing my Masters through the 5-year M.S./B.S. program at UCSD. I obtained my undergraduate degree at UCSD in Bioengineering with an emphasis in Biotechnology in June 2009. I am collaborating with Yu and Karsten on studying the transcription factors of Geobacter. When I'm not at lab, I'm probably doing wushu!. ...
  http://sbrg.ucsd.edu/Researchers/Previous/Shieu