Recent advances in the reconstruction of metabolic models and integration of omics data

Saha, Rajib; Chowdhury, Anupam; Maranas, Costas D.

doi:10.1016/j.copbio.2014.02.011

Cited by 116 publications

(87 citation statements)

References 76 publications

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“…Being a member of the genus Brassicaceae, A. thaliana is a host of Xcc. Other genome-scale reconstructions are available for maize [239] and barley [240], a host of X. translucens pv. translucens [241,242], and it is likely that more plant models will become available with the increasing number of genomes being sequenced.…”

Section: Environmental Systems Biology As a Perspective For Analysis mentioning

confidence: 99%

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

et al. 2017

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Bacteria of the genus Xanthomonas are a major group of plant pathogens. They are hazardous to important crops and closely related to human pathogens. Being collectively a major focus of molecular phytopathology, an increasing number of diverse and intricate mechanisms are emerging by which they communicate, interfere with host signalling and keep competition at bay. Interestingly, they are also biotechnologically relevant polysaccharide producers. Systems biotechnology techniques have revealed their central metabolism and a growing number of remarkable features. Traditional analyses of Xanthomonas metabolism missed the Embden-Meyerhof-Parnas pathway (glycolysis) as being a route by which energy and molecular building blocks are derived from glucose. As a consequence of the emerging full picture of their metabolism process, xanthomonads were discovered to have three alternative catabolic pathways and they use an unusual and reversible phosphofructokinase as a key enzyme. In this review, we summarize the synthetic and systems biology methods and the bioinformatics tools applied to reconstruct their metabolic network and reveal the dynamic fluxes within their complex carbohydrate metabolism. This is based on insights from omics disciplines; in particular, genomics, transcriptomics, proteomics and metabolomics. Analysis of high-throughput omics data facilitates the reconstruction of organism-specific large-and genome-scale metabolic networks. Reconstructed metabolic networks are fundamental to the formulation of metabolic models that facilitate the simulation of actual metabolic activities under specific environmental conditions. SYSTEMS BIOLOGYIn recent years, systems and synthetic biology have substantially increased our understanding of many processes in life sciences at molecular and cellular levels [1][2][3]. Systems biology intends to understand the cell from a system-wide perspective. For over 100 years, life sciences have aimed at elucidating the details of molecular processes in organisms. In systems biology, scientists have started to inter-relate this data on a large scale in order to analyse the interactions of all elements [4,5], and thus initiate the decoding of entire systems, aiming at their quantitative understanding. This became possible with the development of high-throughput techniques associated with diverse computational methods and the availability of faster computing. Fundamental highthroughput methods are now routinely available in the fields of genomics, transcriptomics, metabolomics and proteomics, while additional specialized branches of omics disciplines have been developed, such as lipidomics [6][7][8], glycomics [9][10][11] and 13 C fluxomics [12,13].

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Section: Environmental Systems Biology As a Perspective For Analysis mentioning

confidence: 99%

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

et al. 2017

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“…Omics experiments are more and more commonly explored in contemporary plant research [1][2][3]. Taking RNAseq as example, transcriptomics results can provide a comprehensive overview on the differences between sample groups in different conditions or at different times.…”

Section: Introductionmentioning

confidence: 99%

Predicted Arabidopsis Interactome Resource-A Network Modeling Method of Integration and Analysis for the Omics Data

Yao¹,

Chen

Wang

2017

Proceedings of the 2017 International Conference on Applied Mathematics, Modeling and Simulation (AMMS 2017)

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Abstract-The Predicted Arabidopsis Interactome Resource (PAIR) is an online database of the functional interactions between Arabidopsis genes. PAIR is inferred by integrating six types of evidence each of which suggests a different aspect of functional associations between Arabidopsis genes and therefore enables extended analysis on the potential functional impacts of the observed omics changes at the physiological level.

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“…As this field requires database processing and analyzing interactive systems, such as genetic circuits, cells, biochemical pathways, and metabolism, modeling is actively used through so-called computational biology (Kitano, 2002b). Metabolic reconstruction, recently receiving high attention, is an example of domain that intensively uses computational modeling (Saha et al, 2014). Metabolic reconstruction is an organism-specific process based on high-throughput genome-scale and "-omics" data to investigate generally from rats, have been studied using mathematical models to elucidate the functions and mechanisms of corresponding cells and organs in human (Finegood et al, 1995;Heethaar et al, 1973;Pandit et al, 2001).…”

Section: Introductionmentioning

confidence: 99%

A novel approach in analyzing agriculture and food systems: Review of modeling and its applications

Kim¹,

Cho²,

Lee³

2016

Korean Journal of Agricultural Science

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For the past decades, advances in computational devices have propelled mathematical modeling to become an effective tool for solving the black box of complex biological systems because of its prominent analytical power and comprehensive insight. Nevertheless, modeling is still limitedly used in the fields of agriculture and food which generally concentrate on producing experimental data rather than processing them. This study, hence, intends to introduce modeling in terms of its procedure types of structure, formulation, analyses, and software, with reviews of current notable studies from micro to macro scales so as to propose the modeling technique as a novel approach in discerning conundrums in agriculture and food systems. We expect this review to provide an eligible source for researchers who are willing to apply modeling techniques into the unexplored fields related to bio-systems that comprehensively include biology, nutrition, agriculture, food, animal science, and ecology.

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Recent advances in the reconstruction of metabolic models and integration of omics data

Cited by 116 publications

References 76 publications

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

Systems and synthetic biology perspective of the versatile plant-pathogenic and polysaccharide-producing bacterium Xanthomonas campestris

Predicted Arabidopsis Interactome Resource-A Network Modeling Method of Integration and Analysis for the Omics Data

A novel approach in analyzing agriculture and food systems: Review of modeling and its applications

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