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Metabolic Network Analysis Demystified [chapter]

Leonid Chindelevitch, Aviv Regev, Bonnie Berger
2011 Lecture Notes in Computer Science  
While the constraint-based approach to metabolic network analysis is over 15 years old, our work is, to our knowledge, the first time the theory of linear programming is used to reveal structural elements  ...  Metabolic networks are a representation of current knowledge about the metabolic reactions available to a given organism.  ...  While the constraint-based approach to metabolic network analysis is over 15 years old, our work is, to our knowledge, the first time the theory of linear programming is used to reveal structural elements  ... 
doi:10.1007/978-3-642-20036-6_3 fatcat:4pvllpz5bja6tg5kw4z6tyjzzy

Metabolic network structure and function in bacteria goes beyond conserved enzyme components

Jannell Bazurto, Diana Downs
2016 Microbial Cell  
At large, genome annotation and metabolic network reconstructions have demystified genomic content of nonculturable microorganisms and allowed researchers to explore the breadth of metabolisms in silico  ...  metabolic network structure.  ...  The following fundamental questions arose during the course of the aforementioned studies: i) are metabolic network structures dissected by mutational analysis biologically relevant?  ... 
doi:10.15698/mic2016.06.509 pmid:28357363 pmcid:PMC5348995 fatcat:rs4qf5o2obgafacde6zslqeaae

Data mining analysis of human gut microbiota links Fusobacterium spp. with colorectal cancer onset

Najla Kharrat, Laboratory of Molecular and Cellular Screening Processes, Centre of Biotechnologyof Sfax, Bioinformatics Group, P.O. Box: 1177, Sfax, 3018 Tunisia, Mourad Assidi, Muhammad Abu-Elmagd, Peter N. Pushparaj, Areej Alkhaldy, Leila Arfaoui, Muhammad Imran Naseer, Abdelfatteh El Omri, Safia Messaoudi, Abdelbaset Buhmeida, Ahmed Rebai
2019 Bioinformation  
Results from the analysis of publically available datasets showed that four species: Fusobacteium, Citrobacter, Microbacterium and Slaxkia have estimated non-null lower bounds of causal effects of CRC.  ...  Hence, we used a Bayesian Networks in combination with the IDA (Intervention calculus when the DAG is absent) to generate a graphical model that allows causal relationships to be inferred from observational  ...  For the two-independent analysis, the common hubs of the two networks were the two species Fusobacterium spp. and Slackia.  ... 
doi:10.6026/97320630015372 pmid:31312073 pmcid:PMC6614120 fatcat:5a4bhyqvv5ayfpp2nvtaxcugfe

HOX cluster and their cofactors showed an altered expression pattern in eutopic and ectopic endometriosis tissues

Fereshteh Esfandiari, Fereshteh Chitsazian, Masoumeh Golestan Jahromi, Raha Favaedi, Masood Bazrgar, Reza Aflatoonian, Parvaneh Afsharian, Abbas Aflatoonian, Maryam Shahhoseini
2021 Reproductive Biology and Endocrinology  
Therefore, demystifying the molecular mechanisms that underlie endometriosis is essential to develop advanced therapies for this disease.  ...  Pathway analysis revealed the involvement of differentially expressed genes in cancer that correlate with an association between endometriosis and cancer.  ...  Analysis of interference with other diseases Many DEGs in ectopic tissues play a role in developmental, neurological, and metabolic diseases.  ... 
doi:10.1186/s12958-021-00816-y pmid:34470627 pmcid:PMC8409001 fatcat:p2zndptr2zgpjphwnvmah6mjhe

13C-Metabolic Flux Analysis: An Accurate Approach to Demystify Microbial Metabolism for Biochemical Production

Weihua Guo, Jiayuan Sheng, Xueyang Feng
2015 Bioengineering  
In order to overcome this challenge, 13 C Metabolic Flux Analysis ( 13 C-MFA) has been continuously developed and widely applied to rigorously investigate cell metabolism and quantify the carbon flux distribution  ...  in central metabolic pathways.  ...  networks (Table 1) .  ... 
doi:10.3390/bioengineering3010003 pmid:28952565 pmcid:PMC5597161 fatcat:s2sfi7hgtrfm3c5dyqll6fv4qa

IL-6-induced upregulation of T-type Ca2+ currents and sensitization of DRG nociceptors is attenuated by MNK inhibition: translational research perspective

Saumya Pandey
2020 Journal of Neurophysiology  
TO THE EDITOR: Nociceptor hyperexcitability is emerging as a major public health challenge globally; precise dissection of cellular, molecular, and genetic regulatory networks is essential for demystifying  ...  neurophysiological basis of IL-6-induced upregulation of T-type Ca 2ϩ currents and sensitization of dorsal root ganglions (DRG) nociceptors in "at risk" susceptible populations of varying genetic and metabolic  ...  TO THE EDITOR: Nociceptor hyperexcitability is emerging as a major public health challenge globally; precise dissection of cellular, molecular, and genetic regulatory networks is essential for demystifying  ... 
doi:10.1152/jn.00372.2020 pmid:32663420 fatcat:hgodhewsm5dj3md367lwmvjavq

Integrating System Biology Tools to Decipher the Mechanisms of Action of Herbal Medicine

Benoit Leclerc
2018 MOJ Proteomics & Bioinformatics  
These metabolic perturbations participate in glycerophospholipid metabolism, sphingolipid metabolism and steroid hormone biosynthesis.  ...  Proteomics Analysis Fewer studies have looked over protein expression profiling to underlie the signaling pathways and regulatory networks following TCM treatment.  ... 
doi:10.15406/mojpb.2018.07.00210 fatcat:vrlvougl7bco7djx6wc3cw332q

The International Conference on Intelligent Biology and Medicine 2019 (ICIBM 2019): conference summary and innovations in genomics

Ewy Mathé, Chi Zhang, Kai Wang, Xia Ning, Yan Guo, Zhongming Zhao
2019 BMC Genomics  
These articles cover methods and applications for functional annotations of miRNA targeting, clonal evolution of bacterial cells, gene co-expression networks that describe a given phenotype, functional  ...  binding site analysis of RNA-binding proteins, normalization of genome architecture mapping data, sample predictions based on multiple NGS data types, and prediction of an individual's genetic admixture  ...  using Network-based Gene Set Analysis.  ... 
doi:10.1186/s12864-019-6326-5 pmid:31888451 pmcid:PMC6936133 fatcat:w3ghrdk2frffxcpurrkyvp7aue

Learning the LingoA Cell Biologist's Guide to Modeling and Bioinformatics, by HolmesRaquell M.; 2007; 203 pp.; John Wiley and Sons (Hoboken, NJ); ISBN-10:0471164208

Laurie J. Heyer
2008 CBE - Life Sciences Education  
Chapter 3 focuses on protein sequence analysis, in particular, the characterization of protein domains and families, and lists several important methods and databases.  ...  The algorithm and parameters are described in enough detail to demystify BLAST; the careful reader will know quite a bit about how to obtain and interpret desired results.  ...  Chapter 3 focuses on protein sequence analysis, in particular, the characterization of protein domains and families, and lists several important methods and databases.  ... 
doi:10.1187/cbe.08-06-0034 pmcid:PMC2527975 fatcat:vw37blinxvgtbom4e3x6akldou

Markov Chain Monte Carlo Algorithm based metabolic flux distribution analysis on Corynebacterium glutamicum

V. Kadirkamanathan, J. Yang, S. A. Billings, P. C. Wright
2006 Bioinformatics  
Motivation: Metabolic flux analysis via a 13 C tracer experiment has been achieved using a Monte Carlo method with the assumption of system noise as Gaussian noise.  ...  Results: In this paper, a stochastic generative model of the metabolic system is developed. Following this, the Markov Chain Monte Carlo (MCMC) approach is applied to flux distribution analysis.  ...  However, in order to demystify the intracellular metabolic network, the crucial issue is to discover the distributions of various types of internal entities.  ... 
doi:10.1093/bioinformatics/btl445 pmid:16940326 fatcat:bvk5stx3zbeathkd7t2rrszxyi

Cirrhosis, hyperammonemia and hepatic encephalopathy. Edited by S. Grisolia and V. Felipo, 148 pp. New York: Plenum Press, 1993. $59.50

Anastasios A. Mihas
1995 Hepatology  
The latter chapter includes a few paragraphs of information on modeling of prognosis and the use of decision analysis in clinical decisionmaking.  ...  The second chapter is a (very) brief overview of brain metabolism in hepatic encephalopathy and hyperammonemia.  ... 
doi:10.1002/hep.1840210143 fatcat:ejcmcrixt5gsjejrl2bng2j7su

Systems Biology Approaches and Applications in Obesity, Diabetes, and Cardiovascular Diseases

Qingying Meng, Ville-Petteri Mäkinen, Helen Luk, Xia Yang
2012 Current Cardiovascular Risk Reports  
Despite decades of intense research, a large part of the molecular pathogenesis behind complex metabolic diseases remains unknown.  ...  In this review, we summarize systems biology methodologies such as functional genomics, causality inference, data-driven biological network construction, and higher-level integrative analyses that can  ...  This module is termed macrophage-enriched metabolic network (MEMN).  ... 
doi:10.1007/s12170-012-0280-y pmid:23326608 pmcid:PMC3543610 fatcat:gjtf52f3ozgznpi4ozzjium6xq

Power of metabolomics in diagnosis and biomarker discovery of hepatocellular carcinoma

Xijun Wang, Aihua Zhang, Hui Sun
2013 Hepatology  
Metabolic profiles, which are affected by many physiological and pathological processes, may provide further insight into the metabolic consequences of this severe liver disease.  ...  This technique-driven review aims to demystify the metabolomics pathway, while also illustrating the potential of this technique, with recent examples of its application in  ...  Metabolomics analysis will allow the testing of global or targeted signaling networks to determine the on-target efficacy of combination therapies that inhibit signaling pathways in series or in parallel  ... 
doi:10.1002/hep.26130 pmid:23150189 fatcat:pf4eawt76rhtjhptospm24td4q

The future of molecular imaging in paradigm shift from reactive to proactive (P4) medicine

Majid Assadi, Iraj Nabipour
2014 Nuclear medicine communications  
Most significantly, the future of practice and research will require network-connected and interdisciplinary teams of image professionals, clinicians, specialists familiar with the integrated analysis  ...  There are several networks working in the context of an individual's body, such as genetic networks, molecular networks, cellular networks and organ networks, which must be considered to truly understand  ... 
doi:10.1097/mnm.0000000000000205 pmid:25211627 fatcat:sygc45l2kbcqvnqwjt5r7w6aey

Genome Wide Analysis Points towards Subtype-Specific Diseases in Different Genetic Forms of Amyotrophic Lateral Sclerosis

Banaja P. Dash, Marcel Naumann, Jared Sterneckert, Andreas Hermann
2020 International Journal of Molecular Sciences  
In contrast, SOD1 is mainly characterized by alterations in the metabolic pathways and alterations in the neuroactive-ligand–receptor interactions.  ...  In particular, pathway and interactome analysis preceded by GO enrichment analysis revealed a network enriched in pathways associated with synaptic/neuronal functions and metabolism, indicating metabolic  ...  Towards demystifying this puzzle, we made an attempt through our interactome analysis for ALS-associated protein FUS using STRING database [40] , engaging a PPI network employing 108 and 884 DEGs from  ... 
doi:10.3390/ijms21186938 pmid:32967368 pmcid:PMC7555318 fatcat:fqb23gikljelxphmft2ozcylna
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