Resources for integrative systems biology: from data through databases to networks and dynamic system models

Ng, Aylwin; Bursteinas, Borisas; Gao, Qiong; Mollison, Ewan; Zvelebil, Marketa

doi:10.1093/bib/bbl036

Cited by 76 publications

(48 citation statements)

References 88 publications

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“…The limit for this and other approaches is the enormous amount of data these techniques can generate. According to Costas Mitsoupoulos (London, United Kingdom), bioinformatics is the appropriate tool to convert information into knowledge, and this was illustrated by studies on cross-talk between intracellular signaling pathways (Ng et al, 2006). Signaling network analysis involves building models of pathways of interest, annotating protein/gene information, identifying mutually exclusive interactions, and mapping mutations onto binding interfaces.…”

Section: Selection Of Appropriate Biomarkers Of Peripheral Inflammationmentioning

confidence: 99%

Identification and treatment of symptoms associated with inflammation in medically ill patients

Dantzer

Capuron

Irwin

et al. 2008

Psychoneuroendocrinology

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Medically ill patients present with a high prevalence of non-specific comorbid symptoms including pain, sleep disorders, fatigue and cognitive and mood alterations that is a leading cause of disability. However, despite major advances in the understanding of the immune-to-brain communication pathways that underlie the pathophysiology of these symptoms in inflammatory conditions, little has been done to translate this newly acquired knowledge to the clinics and to identify appropriate therapies. In a multidisciplinary effort to address this problem, clinicians and basic scientists with expertise in areas of inflammation, psychiatry, neurosciences and psychoneuroimmunology were brought together in a specialized meeting organized in Bordeaux, France, on May 28-29, 2007. These experts considered key questions in the field, in particular those related to identification and quantification of the predominant symptoms associated with inflammation, definition of systemic and central markers of inflammation, possible domains of intervention for controlling inflammation associated symptoms, and relevance of animal models of inflammation associated symptoms. This

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Section: Selection Of Appropriate Biomarkers Of Peripheral Inflammationmentioning

confidence: 99%

Identification and treatment of symptoms associated with inflammation in medically ill patients

Dantzer

Capuron

Irwin

et al. 2008

Psychoneuroendocrinology

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“…An increasingly large amount of data are made publicly available through a variety of web-based databases (Ng et al 2006;Armit 2007). Some commonly used databases are listed in Table 1.…”

Section: Public Data Repositories and Bioinformatic Toolsmentioning

confidence: 99%

Application of a systems approach to study developmental gene regulation

2012

Biophys Rev

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All cells in a multicellular organism contain the same genome, yet different cell types express different sets of genes. Recent advances in high throughput genomic technologies have opened up new opportunities to understand the gene regulatory network in diverse cell types in a genome-wide manner. Here, I discuss recent advances in experimental and computational approaches for the study of gene regulation in embryonic development from a systems perspective. This review is written for computational biologists who have an interest in studying developmental gene regulation through integrative analysis of gene expression, chromatin landscape, and signaling pathways. I highlight the utility of publicly available data and tools, as well as some common analysis approaches.

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“…In particular, several specific metabolic reactions can be missing in the commonly used metabolic pathway databases, thus affecting automatic reconstruction solely based on genome information (Pitkä nen et al, 2010;Ruppin et al, 2010). To overcome this situation, metabolite profiles and prior biochemical knowledge about the organisms of interest can be used to refine this mapping (Ng et al, 2006). More specifically, transport reactions or intracellular localization of enzymes, which represent key processes for investigating phenotypical changes under environmental constraints, are often missing or are only partially considered in public databases.…”

Section: Building the Metabolic Network From Omics Datamentioning

confidence: 99%

Toward Systems Biology in Brown Algae to Explore Acclimation and Adaptation to the Shore Environment

Tonon

Eveillard

Prigent

et al. 2011

OMICS: A Journal of Integrative Biology

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Brown algae belong to a phylogenetic lineage distantly related to land plants and animals. They are almost exclusively found in the intertidal zone, a harsh and frequently changing environment where organisms are submitted to marine and terrestrial constraints. In relation with their unique evolutionary history and their habitat, they feature several peculiarities, including at the level of their primary and secondary metabolism. The establishment of Ectocarpus siliculosus as a model organism for brown algae has represented a framework in which several omics techniques have been developed, in particular, to study the response of these organisms to abiotic stresses. With the recent publication of medium to high throughput profiling data, it is now possible to envision integrating observations at the cellular scale to apply systems biology approaches. As a first step, we propose a protocol focusing on integrating heterogeneous knowledge gained on brown algal metabolism. The resulting abstraction of the system will then help understanding how brown algae cope with changes in abiotic parameters within their unique habitat, and to decipher some of the mechanisms underlying their (1) acclimation and (2) adaptation, respectively consequences of (1) the behavior or (2) the topology of the system resulting from the integrative approach.

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Resources for integrative systems biology: from data through databases to networks and dynamic system models

Cited by 76 publications

References 88 publications

Identification and treatment of symptoms associated with inflammation in medically ill patients

Identification and treatment of symptoms associated with inflammation in medically ill patients

Application of a systems approach to study developmental gene regulation

Toward Systems Biology in Brown Algae to Explore Acclimation and Adaptation to the Shore Environment

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