Role of a Web-based Software Platform for Systems Biology

Turenne, Nicolas

doi:10.4172/jcsb.1000101e

Cited by 10 publications

(8 citation statements)

References 99 publications

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“…Study of proteins along with mRNA transcripts is referred as proteomics and transcriptomics, respectively [59]. For transcriptomics studies, there are numerous databases comprising microarray data: NASCArrays, ArrayExpress, Genevestigator, Stanford Microarray Database, and the Gene Expression Omnibus, which are freely available [61].…”

Section: Proteomics and Transcriptomicsmentioning

confidence: 99%

Bioinformatics: A Way Forward to Explore “Plant Omics”

Rahman¹,

Shaheen²,

Rahman³

et al. 2016

Bioinformatics - Updated Features and Applications

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"ioinformatics, a computer-assisted science aiming at managing a huge volume of genomic data, is an emerging discipline that combines the power of computers, mathematical algorithms, and statistical concepts to solve multiple genetic/biological puzzles. This science has progressed parallel to the evolution of genome-sequencing tools, for example, the next-generation sequencing technologies, that resulted in arranging and analyzing the genome-sequencing information of large genomes. Synergism of plant omics and bioinformatics set a firm foundation for deducing ancestral karyotype of multiple plant families, predicting genes, etc. Second, the huge genomic data can be assembled to acquire maximum information from a voluminous omics data. The science of bioinformatics is handicapped due to lack of appropriate computational procedures in assembling sequencing reads of the homologs occurring in complex genomes like cotton n = x = , wheat n = x = , etc., and shortage of multidisciplinary-oriented trained manpower. In addition, the rapid expansion of sequencing data restricts the potential of acquisitioning, storing, distributing, and analyzing the genomic information. In future, inventions of high-tech computational tools and skills together with improved biological expertise would provide better insight into the genomes, and this information would be helpful in sustaining crop productivities on this planet.

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Section: Proteomics and Transcriptomicsmentioning

confidence: 99%

Bioinformatics: A Way Forward to Explore “Plant Omics”

Rahman¹,

Shaheen²,

Rahman³

et al. 2016

Bioinformatics - Updated Features and Applications

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show abstract

“…A Data warehouse retrieves data from multiple resources, translates the formats and puts them in one database. The examples of data warehouses include: Atlas, BioMart, Biowarehouse, Columba, SYSTOMONAS, BioDwH, vINedb, Booly, GNCPro (Turenne 2011). The XML is a general-purpose markup language that helps in sharing data across heterogeneous systems.…”

Section: Integration Of Multiple 'Omics' Datamentioning

confidence: 99%

Plant systems biology: insights, advances and challenges

Sheth

Thaker

2014

Planta

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Plants dwelling at the base of biological food chain are of fundamental significance in providing solutions to some of the most daunting ecological and environmental problems faced by our planet. The reductionist views of molecular biology provide only a partial understanding to the phenotypic knowledge of plants. Systems biology offers a comprehensive view of plant systems, by employing a holistic approach integrating the molecular data at various hierarchical levels. In this review, we discuss the basics of systems biology including the various 'omics' approaches and their integration, the modeling aspects and the tools needed for the plant systems research. A particular emphasis is given to the recent analytical advances, updated published examples of plant systems biology studies and the future trends.

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“…Short interfering RNAs (siRNAs) can be used to suppress gene expression and have a lot of potential applications in therapy, yet how to design an effective siRNA is still under consideration [43]. Virtual screening by molecular docking has become a largely used approach to lead discovery in the pharmaceutical industry when a high-resolution structure of the biological target of interest is available [44,58]. Quantification of the metabolic network of an organism offers insights into possible ways of developing mutant strain for better productivity of an extra-cellular metabolite.…”

Section: Application To Biosciencementioning

confidence: 99%

“…The primary platforms in use are mass spectrometry and microarrays which associate tools to process data flows [1]. If we look at the bibliography, history started with database building and microarray processing; both terms 'systems biology' and 'platform' in bioinformatics occur with the emergence of large databases of high-throughput data and pathways availability [2]. The Metabolome represents the collection of all metabolites in a biological organism, which are the end products of its gene expression.…”

Section: Introductionmentioning

confidence: 99%

Metabolomics and its Value in Today?s Era

Tripathy¹,

Nanda²

2011

J Comput Sci Syst Biol

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Metabolomics is the newly emerging field of 'omics' research.Its Comprehensive and simultaneous systematic determination of metabolite levels in the metabolome and their changes over time.This review outlines how metabolomics is emerging in today's life. It presents metabolomics methodology and focuses on the current and potential applications of metabolomics in different diseases with particular attention to its use as a biomarker in diagnosis, prognosis, and therapeutic evaluation. We think this review will appeal to both translational researchers and clinicians as it reviews up-to-date evidence on the utility of metabolomics, an often poorly understood topic. The report also highlights the use of metabolomics in maximizing and sustaining revenues post-marketing and in the development of clinical diagnostics.

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Role of a Web-based Software Platform for Systems Biology

Cited by 10 publications

References 99 publications

Bioinformatics: A Way Forward to Explore “Plant Omics”

Bioinformatics: A Way Forward to Explore “Plant Omics”

Plant systems biology: insights, advances and challenges

Metabolomics and its Value in Today?s Era

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