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BMC Systems Biology

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https://www.readbyqxmd.com/read/28222737/dynamic-genome-scale-metabolic-modeling-of-the-yeast-pichia-pastoris
#1
Francisco Saitua, Paulina Torres, José Ricardo Pérez-Correa, Eduardo Agosin
BACKGROUND: Pichia pastoris shows physiological advantages in producing recombinant proteins, compared to other commonly used cell factories. This yeast is mostly grown in dynamic cultivation systems, where the cell's environment is continuously changing and many variables influence process productivity. In this context, a model capable of explaining and predicting cell behavior for the rational design of bioprocesses is highly desirable. Currently, there are five genome-scale metabolic reconstructions of P...
February 21, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28219373/a-new-efficient-approach-to-fit-stochastic-models-on-the-basis-of-high-throughput-experimental-data-using-a-model-of-irf7-gene-expression-as-case-study
#2
Luis U Aguilera, Christoph Zimmer, Ursula Kummer
BACKGROUND: Mathematical models are used to gain an integrative understanding of biochemical processes and networks. Commonly the models are based on deterministic ordinary differential equations. When molecular counts are low, stochastic formalisms like Monte Carlo simulations are more appropriate and well established. However, compared to the wealth of computational methods used to fit and analyze deterministic models, there is only little available to quantify the exactness of the fit of stochastic models compared to experimental data or to analyze different aspects of the modeling results...
February 20, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28209199/making-life-difficult-for-clostridium-difficile-augmenting-the-pathogen-s-metabolic-model-with-transcriptomic-and-codon-usage-data-for-better-therapeutic-target-characterization
#3
Sara Saheb Kashaf, Claudio Angione, Pietro Lió
BACKGROUND: Clostridium difficile is a bacterium which can infect various animal species, including humans. Infection with this bacterium is a leading healthcare-associated illness. A better understanding of this organism and the relationship between its genotype and phenotype is essential to the search for an effective treatment. Genome-scale metabolic models contain all known biochemical reactions of a microorganism and can be used to investigate this relationship. RESULTS: We present icdf834, an updated metabolic network of C...
February 16, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28209158/gene-regulatory-network-underlying-the-immortalization-of-epithelial-cells
#4
Luis Fernando Méndez-López, Jose Davila-Velderrain, Elisa Domínguez-Hüttinger, Christian Enríquez-Olguín, Juan Carlos Martínez-García, Elena R Alvarez-Buylla
BACKGROUND: Tumorigenic transformation of human epithelial cells in vitro has been described experimentally as the potential result of spontaneous immortalization. This process is characterized by a series of cell-state transitions, in which normal epithelial cells acquire first a senescent state which is later surpassed to attain a mesenchymal stem-like phenotype with a potentially tumorigenic behavior. In this paper we aim to provide a system-level mechanistic explanation to the emergence of these cell types, and to the time-ordered transition patterns that are common to neoplasias of epithelial origin...
February 16, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28193218/a-combined-model-reduction-algorithm-for-controlled-biochemical-systems
#5
Thomas J Snowden, Piet H van der Graaf, Marcus J Tindall
BACKGROUND: Systems Biology continues to produce increasingly large models of complex biochemical reaction networks. In applications requiring, for example, parameter estimation, the use of agent-based modelling approaches, or real-time simulation, this growing model complexity can present a significant hurdle. Often, however, not all portions of a model are of equal interest in a given setting. In such situations methods of model reduction offer one possible approach for addressing the issue of complexity by seeking to eliminate those portions of a pathway that can be shown to have the least effect upon the properties of interest...
February 13, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28166778/markov-state-models-of-gene-regulatory-networks
#6
Brian K Chu, Margaret J Tse, Royce R Sato, Elizabeth L Read
BACKGROUND: Gene regulatory networks with dynamics characterized by multiple stable states underlie cell fate-decisions. Quantitative models that can link molecular-level knowledge of gene regulation to a global understanding of network dynamics have the potential to guide cell-reprogramming strategies. Networks are often modeled by the stochastic Chemical Master Equation, but methods for systematic identification of key properties of the global dynamics are currently lacking. RESULTS: The method identifies the number, phenotypes, and lifetimes of long-lived states for a set of common gene regulatory network models...
February 6, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28153012/kinetic-stability-analysis-of-protein-assembly-on-the-center-manifold-around-the-critical-point
#7
Tatsuaki Tsuruyama
BACKGROUND: Non-linear kinetic analysis is a useful method for illustration of the dynamic behavior of cellular biological systems. To date, center manifold theory (CMT) has not been sufficiently applied for stability analysis of biological systems. The aim of this study is to demonstrate the application of CMT to kinetic analysis of protein assembly and disassembly, and to propose a novel framework for nonlinear multi-parametric analysis. We propose a protein assembly model with nonlinear kinetics provided by the fluctuation in monomer concentrations during their diffusion...
February 2, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28137253/the-integration-of-weighted-human-gene-association-networks-based-on-link-prediction
#8
Jian Yang, Tinghong Yang, Duzhi Wu, Limei Lin, Fan Yang, Jing Zhao
BACKGROUND: Physical and functional interplays between genes or proteins have important biological meaning for cellular functions. Some efforts have been made to construct weighted gene association meta-networks by integrating multiple biological resources, where the weight indicates the confidence of the interaction. However, it is found that these existing human gene association networks share only quite limited overlapped interactions, suggesting their incompleteness and noise. RESULTS: Here we proposed a workflow to construct a weighted human gene association network using information of six existing networks, including two weighted specific PPI networks and four gene association meta-networks...
January 31, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28122561/jupoets-a-constrained-multiobjective-optimization-approach-to-estimate-biochemical-model-ensembles-in-the-julia-programming-language
#9
David M Bassen, Michael Vilkhovoy, Mason Minot, Jonathan T Butcher, Jeffrey D Varner
BACKGROUND: Ensemble modeling is a promising approach for obtaining robust predictions and coarse grained population behavior in deterministic mathematical models. Ensemble approaches address model uncertainty by using parameter or model families instead of single best-fit parameters or fixed model structures. Parameter ensembles can be selected based upon simulation error, along with other criteria such as diversity or steady-state performance. Simulations using parameter ensembles can estimate confidence intervals on model variables, and robustly constrain model predictions, despite having many poorly constrained parameters...
January 25, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28122551/sampling-based-bayesian-approaches-reveal-the-importance-of-quasi-bistable-behavior-in-cellular-decision-processes-on-the-example-of-the-mapk-signaling-pathway-in-pc-12-cell-lines
#10
Antje Jensch, Caterina Thomaseth, Nicole E Radde
BACKGROUND: Positive and negative feedback loops are ubiquitous motifs in biochemical signaling pathways. The mitogen-activated protein kinase (MAPK) pathway module is part of many distinct signaling networks and comprises several of these motifs, whose functioning depends on the cell line at hand and on the particular context. The maintainance of specificity of the response of the MAPK module to distinct stimuli has become a key paradigm especially in PC-12 cells, where the same module leads to different cell fates, depending on the stimulating growth factor...
January 25, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28103880/the-use-of-genome-scale-metabolic-network-reconstruction-to-predict-fluxes-and-equilibrium-composition-of-n-fixing-versus-c-fixing-cells-in-a-diazotrophic-cyanobacterium-trichodesmium-erythraeum
#11
Joseph J Gardner, Nanette R Boyle
BACKGROUND: Computational, genome based predictions of organism phenotypes has enhanced the ability to investigate the biological phenomena that help organisms survive and respond to their environments. In this study, we have created the first genome-scale metabolic network reconstruction of the nitrogen fixing cyanobacterium T. erythraeum and used genome-scale modeling approaches to investigate carbon and nitrogen fluxes as well as growth and equilibrium population composition. RESULTS: We created a genome-scale reconstruction of T...
January 19, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28103878/synthetic-circuits-that-process-multiple-light-and-chemical-signal-inputs
#12
Lizhong Liu, Wei Huang, Jian-Dong Huang
BACKGROUND: Multi-signal processing circuits are essential for rational design of sophisticated synthetic systems with good controllability and modularity, therefore, enable construction of high-level networks. Moreover, light-inducible systems provide fast and reversible means for spatiotemporal control of gene expression. RESULTS: Here, in HEK 293 cells, we present combinatory genetic circuits responding to light and chemical signals, simultaneously. We first constructed a dual input circuit converting different light intensities into varying of the sensitivity of the promoter to a chemical inducer (doxycycline)...
January 19, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28061857/coordinated-regulation-of-acid-resistance-in-escherichia-coli
#13
Patricia Aquino, Brent Honda, Suma Jaini, Anna Lyubetskaya, Krutika Hosur, Joanna G Chiu, Iriny Ekladious, Dongjian Hu, Lin Jin, Marianna K Sayeg, Arion I Stettner, Julia Wang, Brandon G Wong, Winnie S Wong, Stephen L Alexander, Cong Ba, Seth I Bensussen, David B Bernstein, Dana Braff, Susie Cha, Daniel I Cheng, Jang Hwan Cho, Kenny Chou, James Chuang, Daniel E Gastler, Daniel J Grasso, John S Greifenberger, Chen Guo, Anna K Hawes, Divya V Israni, Saloni R Jain, Jessica Kim, Junyu Lei, Hao Li, David Li, Qian Li, Christopher P Mancuso, Ning Mao, Salwa F Masud, Cari L Meisel, Jing Mi, Christine S Nykyforchyn, Minhee Park, Hannah M Peterson, Alfred K Ramirez, Daniel S Reynolds, Nae Gyune Rim, Jared C Saffie, Hang Su, Wendell R Su, Yaqing Su, Meng Sun, Meghan M Thommes, Tao Tu, Nitinun Varongchayakul, Tyler E Wagner, Benjamin H Weinberg, Rouhui Yang, Anastasia Yaroslavsky, Christine Yoon, Yanyu Zhao, Alicia J Zollinger, Anne M Stringer, John W Foster, Joseph Wade, Sahadaven Raman, Natasha Broude, Wilson W Wong, James E Galagan
BACKGROUND: Enteric Escherichia coli survives the highly acidic environment of the stomach through multiple acid resistance (AR) mechanisms. The most effective system, AR2, decarboxylates externally-derived glutamate to remove cytoplasmic protons and excrete GABA. The first described system, AR1, does not require an external amino acid. Its mechanism has not been determined. The regulation of the multiple AR systems and their coordination with broader cellular metabolism has not been fully explored...
January 6, 2017: BMC Systems Biology
https://www.readbyqxmd.com/read/28155727/an-improved-method-for-functional-similarity-analysis-of-genes-based-on-gene-ontology
#14
Zhen Tian, Chunyu Wang, Maozu Guo, Xiaoyan Liu, Zhixia Teng
BACKGROUND: Measures of gene functional similarity are essential tools for gene clustering, gene function prediction, evaluation of protein-protein interaction, disease gene prioritization and other applications. In recent years, many gene functional similarity methods have been proposed based on the semantic similarity of GO terms. However, these leading approaches may make errorprone judgments especially when they measure the specificity of GO terms as well as the IC of a term set. Therefore, how to estimate the gene functional similarity reliably is still a challenging problem...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28155725/moro-a-cytoscape-app-for-relationship-analysis-between-modularity-and-robustness-in-large-scale-biological-networks
#15
Cong-Doan Truong, Tien-Dzung Tran, Yung-Keun Kwon
BACKGROUND: Although there have been many studies revealing that dynamic robustness of a biological network is related to its modularity characteristics, no proper tool exists to investigate the relation between network dynamics and modularity. RESULTS: Accordingly, we developed a novel Cytoscape app called MORO, which can conveniently analyze the relationship between network modularity and robustness. We employed an existing algorithm to analyze the modularity of directed graphs and a Boolean network model for robustness calculation...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28155718/improved-protein-protein-interactions-prediction-via-weighted-sparse-representation-model-combining-continuous-wavelet-descriptor-and-pseaa-composition
#16
Yu-An Huang, Zhu-Hong You, Xing Chen, Gui-Ying Yan
BACKGROUND: Protein-protein interactions (PPIs) are essential to most biological processes. Since bioscience has entered into the era of genome and proteome, there is a growing demand for the knowledge about PPI network. High-throughput biological technologies can be used to identify new PPIs, but they are expensive, time-consuming, and tedious. Therefore, computational methods for predicting PPIs have an important role. For the past years, an increasing number of computational methods such as protein structure-based approaches have been proposed for predicting PPIs...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28155715/screening-lifespan-extending-drugs-in-caenorhabditis-elegans-via-label-propagation-on-drug-protein-networks
#17
Hui Liu, Mengmeng Guo, Ting Xue, Jihong Guan, Libo Luo, Ziheng Zhuang
BACKGROUND: One of the most challenging tasks in the exploration of anti-aging is to discover drugs that can promote longevity and delay the incidence of age-associated diseases of human. Up to date, a number of drugs, including some antioxidants, metabolites and synthetic compounds, have been found to effectively delay the aging of nematodes and insects. RESULTS: We proposed a label propagation algorithm on drug-protein network to infer drugs that can extend the lifespan of C...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28155714/pretata-predicting-tata-binding-proteins-with-novel-features-and-dimensionality-reduction-strategy
#18
Quan Zou, Shixiang Wan, Ying Ju, Jijun Tang, Xiangxiang Zeng
BACKGROUND: It is necessary and essential to discovery protein function from the novel primary sequences. Wet lab experimental procedures are not only time-consuming, but also costly, so predicting protein structure and function reliably based only on amino acid sequence has significant value. TATA-binding protein (TBP) is a kind of DNA binding protein, which plays a key role in the transcription regulation. Our study proposed an automatic approach for identifying TATA-binding proteins efficiently, accurately, and conveniently...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28155711/interspecies-gene-function-prediction-using-semantic-similarity
#19
Guoxian Yu, Wei Luo, Guangyuan Fu, Jun Wang
BACKGROUND: Gene Ontology (GO) is a collaborative project that maintains and develops controlled vocabulary (or terms) to describe the molecular function, biological roles and cellular location of gene products in a hierarchical ontology. GO also provides GO annotations that associate genes with GO terms. GO consortium independently and collaboratively annotate terms to gene products, mainly from model organisms (or species) they are interested in. Due to experiment ethics, research interests of biologists and resources limitations, homologous genes from different species currently are annotated with different terms...
December 23, 2016: BMC Systems Biology
https://www.readbyqxmd.com/read/28155709/the-extraction-of-drug-disease-correlations-based-on-module-distance-in-incomplete-human-interactome
#20
Liang Yu, Bingbo Wang, Xiaoke Ma, Lin Gao
BACKGROUND: Extracting drug-disease correlations is crucial in unveiling disease mechanisms, as well as discovering new indications of available drugs, or drug repositioning. Both the interactome and the knowledge of disease-associated and drug-associated genes remain incomplete. RESULTS: We present a new method to predict the associations between drugs and diseases. Our method is based on a module distance, which is originally proposed to calculate distances between modules in incomplete human interactome...
December 23, 2016: BMC Systems Biology
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