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BMC Systems Biology

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https://www.readbyqxmd.com/read/28420402/sser-species-specific-essential-reactions-database
#1
Abraham A Labena, Yuan-Nong Ye, Chuan Dong, Fa-Z Zhang, Feng-Biao Guo
BACKGROUND: Essential reactions are vital components of cellular networks. They are the foundations of synthetic biology and are potential candidate targets for antimetabolic drug design. Especially if a single reaction is catalyzed by multiple enzymes, then inhibiting the reaction would be a better option than targeting the enzymes or the corresponding enzyme-encoding gene. The existing databases such as BRENDA, BiGG, KEGG, Bio-models, Biosilico, and many others offer useful and comprehensive information on biochemical reactions...
April 19, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28412970/membrane-potential-independent-transport-of-nh3-in-the-absence-of-ammonium-permeases-in-saccharomyces-cerevisiae
#2
Hugo F Cueto-Rojas, Nicholas Milne, Ward van Helmond, Mervin M Pieterse, Antonius J A van Maris, Jean-Marc Daran, S Aljoscha Wahl
BACKGROUND: Microbial production of nitrogen containing compounds requires a high uptake flux and assimilation of the N-source (commonly ammonium), which is generally coupled with ATP consumption and negatively influences the product yield. In the industrial workhorse Saccharomyces cerevisiae, ammonium (NH4(+)) uptake is facilitated by ammonium permeases (Mep1, Mep2 and Mep3), which transport the NH4(+) ion, resulting in ATP expenditure to maintain the intracellular charge balance and pH by proton export using the plasma membrane-bound H(+)-ATPase...
April 17, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28407804/mathematical-model-of-tgf-%C3%AE-signalling-feedback-coupling-is-consistent-with-signal-switching
#3
Shabnam Khatibi, Hong-Jian Zhu, John Wagner, Chin Wee Tan, Jonathan H Manton, Antony W Burgess
BACKGROUND: Transforming growth factor β (TGF-β) signalling regulates the development of embryos and tissue homeostasis in adults. In conjunction with other oncogenic changes, long-term perturbation of TGF-β signalling is associated with cancer metastasis. Although TGF-β signalling can be complex, many of the signalling components are well defined, so it is possible to develop mathematical models of TGF-β signalling using reduction and scaling methods. The parameterization of our TGF-β signalling model is consistent with experimental data...
April 13, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28403906/an-additional-k-means-clustering-step-improves-the-biological-features-of-wgcna-gene-co-expression-networks
#4
Juan A Botía, Jana Vandrovcova, Paola Forabosco, Sebastian Guelfi, Karishma D'Sa, John Hardy, Cathryn M Lewis, Mina Ryten, Michael E Weale
BACKGROUND: Weighted Gene Co-expression Network Analysis (WGCNA) is a widely used R software package for the generation of gene co-expression networks (GCN). WGCNA generates both a GCN and a derived partitioning of clusters of genes (modules). We propose k-means clustering as an additional processing step to conventional WGCNA, which we have implemented in the R package km2gcn (k-means to gene co-expression network, https://github.com/juanbot/km2gcn ). RESULTS: We assessed our method on networks created from UKBEC data (10 different human brain tissues), on networks created from GTEx data (42 human tissues, including 13 brain tissues), and on simulated networks derived from GTEx data...
April 12, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28395655/sbpipe-a-collection-of-pipelines-for-automating-repetitive-simulation-and-analysis-tasks
#5
Piero Dalle Pezze, Nicolas Le Novère
BACKGROUND: The rapid growth of the number of mathematical models in Systems Biology fostered the development of many tools to simulate and analyse them. The reliability and precision of these tasks often depend on multiple repetitions and they can be optimised if executed as pipelines. In addition, new formal analyses can be performed on these repeat sequences, revealing important insights about the accuracy of model predictions. RESULTS: Here we introduce SBpipe, an open source software tool for automating repetitive tasks in model building and simulation...
April 10, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28381275/quantitative-evaluation-and-reversion-analysis-of-the-attractor-landscapes-of-an-intracellular-regulatory-network-for-colorectal-cancer
#6
Yunseong Kim, Sea Choi, Dongkwan Shin, Kwang-Hyun Cho
BACKGROUND: Cancer reversion, converting the phenotypes of a cancer cell into those of a normal cell, has been sporadically observed throughout history. However, no systematic analysis has been attempted so far. RESULTS: To investigate this from a systems biological perspective, we have constructed a logical network model of colorectal tumorigenesis by integrating key regulatory molecules and their interactions from previous experimental data. We identified molecular targets that can reverse cancerous cellular states to a normal state by systematically perturbing each molecular activity in the network and evaluating the resulting changes of the attractor landscape with respect to uncontrolled proliferation, EMT, and stemness...
April 5, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28376924/period-doubling-cascades-of-limit-cycles-in-cardiac-action-potential-models-as-precursors-to-chaotic-early-afterdepolarizations
#7
Philipp Kügler, M A K Bulelzai, André H Erhardt
BACKGROUND: Early afterdepolarizations (EADs) are pathological voltage oscillations during the repolarization phase of cardiac action potentials (APs). EADs are caused by drugs, oxidative stress or ion channel disease, and they are considered as potential precursors to cardiac arrhythmias in recent attempts to redefine the cardiac drug safety paradigm. The irregular behaviour of EADs observed in experiments has been previously attributed to chaotic EAD dynamics under periodic pacing, made possible by a homoclinic bifurcation in the fast subsystem of the deterministic AP system of differential equations...
April 4, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28376810/rewiring-of-the-inferred-protein-interactome-during-blood-development-studied-with-the-tool-ppicompare
#8
Thorsten Will, Volkhard Helms
BACKGROUND: Differential analysis of cellular conditions is a key approach towards understanding the consequences and driving causes behind biological processes such as developmental transitions or diseases. The progress of whole-genome expression profiling enabled to conveniently capture the state of a cell's transcriptome and to detect the characteristic features that distinguish cells in specific conditions. In contrast, mapping the physical protein interactome for many samples is experimentally infeasible at the moment...
April 4, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28376782/image-analysis-driven-single-cell-analytics-for-systems-microbiology
#9
Athanasios D Balomenos, Panagiotis Tsakanikas, Zafiro Aspridou, Anastasia P Tampakaki, Konstantinos P Koutsoumanis, Elias S Manolakos
BACKGROUND: Time-lapse microscopy is an essential tool for capturing and correlating bacterial morphology and gene expression dynamics at single-cell resolution. However state-of-the-art computational methods are limited in terms of the complexity of cell movies that they can analyze and lack of automation. The proposed Bacterial image analysis driven Single Cell Analytics (BaSCA) computational pipeline addresses these limitations thus enabling high throughput systems microbiology. RESULTS: BaSCA can segment and track multiple bacterial colonies and single-cells, as they grow and divide over time (cell segmentation and lineage tree construction) to give rise to dense communities with thousands of interacting cells in the field of view...
April 4, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28347313/estimating-genome-wide-regulatory-activity-from-multi-omics-data-sets-using-mathematical-optimization
#10
Saskia Trescher, Jannes Münchmeyer, Ulf Leser
BACKGROUND: Gene regulation is one of the most important cellular processes, indispensable for the adaptability of organisms and closely interlinked with several classes of pathogenesis and their progression. Elucidation of regulatory mechanisms can be approached by a multitude of experimental methods, yet integration of the resulting heterogeneous, large, and noisy data sets into comprehensive and tissue or disease-specific cellular models requires rigorous computational methods. Recently, several algorithms have been proposed which model genome-wide gene regulation as sets of (linear) equations over the activity and relationships of transcription factors, genes and other factors...
March 27, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28340582/optimisation-of-an-exemplar-oculomotor-model-using-multi-objective-genetic-algorithms-executed-on-a-gpu-cpu-combination
#11
Eleftherios Avramidis, Ozgur E Akman
BACKGROUND: Parameter optimisation is a critical step in the construction of computational biology models. In eye movement research, computational models are increasingly important to understanding the mechanistic basis of normal and abnormal behaviour. In this study, we considered an existing neurobiological model of fast eye movements (saccades), capable of generating realistic simulations of: (i) normal horizontal saccades; and (ii) infantile nystagmus - pathological ocular oscillations that can be subdivided into different waveform classes...
March 24, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28302111/quantifying-the-roles-of-random-motility-and-directed-motility-using-advection-diffusion-theory-for-a-3t3-fibroblast-cell-migration-assay-stimulated-with-an-electric-field
#12
Matthew J Simpson, Kai-Yin Lo, Yung-Shin Sun
BACKGROUND: Directed cell migration can be driven by a range of external stimuli, such as spatial gradients of: chemical signals (chemotaxis); adhesion sites (haptotaxis); or temperature (thermotaxis). Continuum models of cell migration typically include a diffusion term to capture the undirected component of cell motility and an advection term to capture the directed component of cell motility. However, there is no consensus in the literature about the form that the advection term takes...
March 17, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28298210/delineating-functional-principles-of-the-bow-tie-structure-of-a-kinase-phosphatase-network-in-the-budding-yeast
#13
Diala Abd-Rabbo, Stephen W Michnick
BACKGROUND: Kinases and phosphatases (KP) form complex self-regulating networks essential for cellular signal processing. In spite of having a wealth of data about interactions among KPs and their substrates, we have very limited models of the structures of the directed networks they form and consequently our ability to formulate hypotheses about how their structure determines the flow of information in these networks is restricted. RESULTS: We assembled and studied the largest bona fide kinase-phosphatase network (KP-Net) known to date for the yeast Saccharomyces cerevisiae...
March 16, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28298218/systematic-identification-of-an-integrative-network-module-during-senescence-from-time-series-gene-expression
#14
Chihyun Park, So Jeong Yun, Sung Jin Ryu, Soyoung Lee, Young-Sam Lee, Youngmi Yoon, Sang Chul Park
BACKGROUND: Cellular senescence irreversibly arrests growth of human diploid cells. In addition, recent studies have indicated that senescence is a multi-step evolving process related to important complex biological processes. Most studies analyzed only the genes and their functions representing each senescence phase without considering gene-level interactions and continuously perturbed genes. It is necessary to reveal the genotypic mechanism inferred by affected genes and their interaction underlying the senescence process...
March 15, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28298216/network-reconstruction-of-the-mouse-secretory-pathway-applied-on-cho-cell-transcriptome-data
#15
Anne Mathilde Lund, Christian Schrøder Kaas, Julian Brandl, Lasse Ebdrup Pedersen, Helene Faustrup Kildegaard, Claus Kristensen, Mikael Rørdam Andersen
BACKGROUND: Protein secretion is one of the most important processes in eukaryotes. It is based on a highly complex machinery involving numerous proteins in several cellular compartments. The elucidation of the cell biology of the secretory machinery is of great importance, as it drives protein expression for biopharmaceutical industry, a 140 billion USD global market. However, the complexity of secretory process is difficult to describe using a simple reductionist approach, and therefore a promising avenue is to employ the tools of systems biology...
March 15, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28361714/finding-low-conductance-sets-with-dense-interactions-flcd-for-better-protein-complex-prediction
#16
Yijie Wang, Xiaoning Qian
BACKGROUND: Intuitively, proteins in the same protein complexes should highly interact with each other but rarely interact with the other proteins in protein-protein interaction (PPI) networks. Surprisingly, many existing computational algorithms do not directly detect protein complexes based on both of these topological properties. Most of them, depending on mathematical definitions of either "modularity" or "conductance", have their own limitations: Modularity has the inherent resolution problem ignoring small protein complexes; and conductance characterizes the separability of complexes but fails to capture the interaction density within complexes...
March 14, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28361711/receptor-guided-3d-qsar-studies-molecular-dynamics-simulation-and-free-energy-calculations-of-btk-kinase-inhibitors
#17
Pavithra K Balasubramanian, Anand Balupuri, Hee-Young Kang, Seung Joo Cho
BACKGROUND: Bruton tyrosine kinase (Btk) plays an important role in B-cell development, differentiation, and signaling. It is also found be in involved in male immunodeficiency disease such as X-linked agammaglobulinemia (XLA). Btk is considered as a potential therapeutic target for treating autoimmune diseases and hematological malignancies. RESULTS: In this work, a combined molecular modeling study was performed on a series of thieno [3,2-c] pyridine-4-amine derivatives as Btk inhibitors...
March 14, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28361708/sequoia-significance-enhanced-network-querying-through-context-sensitive-random-walk-and-minimization-of-network-conductance
#18
Hyundoo Jeong, Byung-Jun Yoon
BACKGROUND: Network querying algorithms provide computational means to identify conserved network modules in large-scale biological networks that are similar to known functional modules, such as pathways or molecular complexes. Two main challenges for network querying algorithms are the high computational complexity of detecting potential isomorphism between the query and the target graphs and ensuring the biological significance of the query results. RESULTS: In this paper, we propose SEQUOIA, a novel network querying algorithm that effectively addresses these issues by utilizing a context-sensitive random walk (CSRW) model for network comparison and minimizing the network conductance of potential matches in the target network...
March 14, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28361705/snp-by-snp-by-environment-interaction-network-of-alcoholism
#19
Amin Zollanvari, Gil Alterovitz
BACKGROUND: Alcoholism has a strong genetic component. Twin studies have demonstrated the heritability of a large proportion of phenotypic variance of alcoholism ranging from 50-80%. The search for genetic variants associated with this complex behavior has epitomized sequence-based studies for nearly a decade. The limited success of genome-wide association studies (GWAS), possibly precipitated by the polygenic nature of complex traits and behaviors, however, has demonstrated the need for novel, multivariate models capable of quantitatively capturing interactions between a host of genetic variants and their association with non-genetic factors...
March 14, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28361702/a-sequence-based-method-to-predict-the-impact-of-regulatory-variants-using-random-forest
#20
Qiao Liu, Mingxin Gan, Rui Jiang
BACKGROUND: Most disease-associated variants identified by genome-wide association studies (GWAS) exist in noncoding regions. In spite of the common agreement that such variants may disrupt biological functions of their hosting regulatory elements, it remains a great challenge to characterize the risk of a genetic variant within the implicated genome sequence. Therefore, it is essential to develop an effective computational model that is not only capable of predicting the potential risk of a genetic variant but also valid in interpreting how the function of the genome is affected with the occurrence of the variant...
March 14, 2017: BMC Systems Biology
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