An “Omics” based survey of human colon cancer

Nambiar, Prashant R.; Gupta, Rishi; Misra, Vikas

doi:10.1016/j.mrfmmm.2010.07.008

Cited by 65 publications

(51 citation statements)

References 83 publications

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“…Thus, the metabolome in a living system is highly dynamic, and global metabolite profiles can be considered a summary manifestation of all the other upstream omics profiles. 12 Metabolomics may be able to detect the subtle changes of metabolic pathways and the deviation from homeostasis before the recognition of phenotypic changes. 13 To build knowledge about the mechanisms underlying the pathology of human colitis, various experimental animal models have been developed.…”

mentioning

confidence: 99%

GCMS-based metabolomic study in mice with colitis induced by dextran sulfate sodium

Shiomi

Nishiumi

Ooi

et al. 2011

Inflammatory Bowel Diseases

101

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mentioning

confidence: 99%

GCMS-based metabolomic study in mice with colitis induced by dextran sulfate sodium

Shiomi

Nishiumi

Ooi

et al. 2011

Inflammatory Bowel Diseases

101

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show abstract

“…Metabolomics, the newest "omic" technology, presents the ability to detect slight changes in the metabolic pathways and alteration in the homeostasis even before any phenotypical sign is detectable (Nambiar, Gupta, & Misra, 2010). Metabolomics allows the comprehensive study of the metabolites (small molecules, generally less than 1500 Da) in a biological system (cell, biofluid, tissue, or organism) at a time under given conditions (Fiehn, 2001).…”

Section: Metabolomics and Neurodegenerative Disordersmentioning

confidence: 99%

Recent Advances and Applications of Metabolomics to Investigate Neurodegenerative Diseases

Ibáñez¹,

Cifuentes²,

Simó³

2015

International Review of Neurobiology

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“…New advancements in high-throughput -omic technologies mean that ever more robust quantitative data is increasingly available at genomic, transcriptomic, proteomic and metabolomic scales [38], although the curation and exploitation of these rapidly expanding data sets introduces further difficulties (see [39], for review). These data do not in themselves constitute knowledge, and systems biology models are required to integrate component knowledge into a holistic representation [38].…”

Section: Modelling Challengesmentioning

confidence: 99%

Engineering Simulations for Cancer Systems Biology

Bown¹,

Andrews²,

Deeni³

et al. 2012

CDT

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Abstract:Computer simulation can be used to inform in vivo and in vitro experimentation, enabling rapid, low-cost hypothesis generation and directing experimental design in order to test those hypotheses. In this way, in silico models become a scientific instrument for investigation, and so should be developed to high standards, be carefully calibrated and their findings presented in such that they may be reproduced. Here, we outline a framework that supports developing simulations as scientific instruments, and we select cancer systems biology as an exemplar domain, with a particular focus on cellular signalling models. We consider the challenges of lack of data, incomplete knowledge and modelling in the context of a rapidly changing knowledge base. Our framework comprises a process to clearly separate scientific and engineering concerns in model and simulation development, and an argumentation approach to documenting models for rigorous way of recording assumptions and knowledge gaps. We propose interactive, dynamic visualisation tools to enable the biological community to interact with cellular signalling models directly for experimental design. There is a mismatch in scale between these cellular models and tissue structures that are affected by tumours, and bridging this gap requires substantial computational resource. We present concurrent programming as a technology to link scales without losing important details through model simplification. We discuss the value of combining this technology, interactive visualisation, argumentation and model separation to support development of multi-scale models that represent biologically plausible cells arranged in biologically plausible structures that model cell behaviour, interactions and response to therapeutic interventions.

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An “Omics” based survey of human colon cancer

Cited by 65 publications

References 83 publications

GCMS-based metabolomic study in mice with colitis induced by dextran sulfate sodium

GCMS-based metabolomic study in mice with colitis induced by dextran sulfate sodium

Recent Advances and Applications of Metabolomics to Investigate Neurodegenerative Diseases

Engineering Simulations for Cancer Systems Biology

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