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Thursday, July 16, 2020 | History

2 edition of Integration, analysis and presentation of yeast phenomics data found in the catalog.

Integration, analysis and presentation of yeast phenomics data

Luciano Fernandez-Ricaud

Integration, analysis and presentation of yeast phenomics data

by Luciano Fernandez-Ricaud

  • 228 Want to read
  • 35 Currently reading

Published by Department of Cell and Molecular Biology, Microbiology, Göteborg University in Göteborg .
Written in English

    Subjects:
  • Saccharomyces cerevisiae,
  • Yeasts,
  • Phenotype

  • Edition Notes

    StatementLuciano Fernandez-Ricaud.
    Classifications
    LC ClassificationsQK623.S23 F47 2007
    The Physical Object
    Pagination1 v. (various pagings) :
    ID Numbers
    Open LibraryOL24072241M
    ISBN 109789162871611
    LC Control Number2007440825

    One unique aspect of HTP data is that phenomics platforms often produce large-scale data with high spatial and temporal resolution for capturing dynamic growth, development, and stress responses.   Compressed yeast contains about 70 percent water and 30 percent yeast solids. Of the yeast solids, about 50 percent is protein, 40 percent is carbohy- drate, and the rest is fat and ash. The sol- ids content can vary from about 27 to 33 percent, depending on how it is filtered. The higher the yeast solids, the higher the activity.

    Integration of Macromolecular Complex Data into the Saccharomyces Genome Database. Database (Oxford). Jan 1; doi: /database/baz PMID Howe DG, Blake JA, Bradford YM, Bult CJ, Calvi BR, Engel SR, Kadin JA, Kaufman TC, Kishore R, Laulederkind SJF, Lewis SE, Moxon SAT, Richardson JE, Smith C (). clinical phenomics and pharmaco-proteomics, emerging clinical proteomics In vivo life-cell microscopy, in vivo preclinical imaging, in situ molecular mapping Biopharma: label-free uHTS, biologics R&D, drug & metabolite imaging, pharmaco-proteomics, PAT Applied: food analysis, authenticity and brand protection, forensics Microbiology & Infectious.

    Genomics is an interdisciplinary field of biology focusing on the structure, function, evolution, mapping, and editing of genomes.A genome is an organism's complete set of DNA, including all of its contrast to genetics, which refers to the study of individual genes and their roles in inheritance, genomics aims at the collective characterization and quantification of all of an organism. A complete overview of the subject would be beyond the scope of this article, as virtually all current bioinformatics efforts contain some kind of data integration [for in-depth reviews see (2–5.


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Integration, analysis and presentation of yeast phenomics data by Luciano Fernandez-Ricaud Download PDF EPUB FB2

Connecting genotype to phenotype is fundamental in biomedical research and in our understanding of disease. Phenomics—the large-scale quantitative phenotypic analysis of genotypes on a genome-wide scale—connects automated data generation with the development of novel tools for phenotype data integration, mining and by: Integration, analysis and presentation of yeast phenomics data.

By Luciano Fernandez-Ricaud. Topics: data integration, data visualization, data base Author: Luciano Fernandez-Ricaud. Phenomics is the systematic measurement and analysis of qualitative and quantitative traits, including clinical, biochemical, and imaging methodologies, for the refinement and characterization of a phenotype.

Phenomics requires both “deep phenotyping,” referring to a thorough collection of a wide breadth of accurate and precise phenotypes, and “phenomic analysis,” referring to.

The power and resolution to analyze gene interaction networks is a function of the precision, accuracy, and quantitative resolution of phenotypic data. To advance quantitative analysis of yeast mutant libraries, we have developed an automated workflow with cell-array printing, time-lapse imaging, image analysis, growth-curve fitting, and Cited by:   Phenomics—the large-scale quantitative phenotypic analysis of genotypes on a genome-wide scale—connects automated data generation with the development of novel tools for phenotype data integration, mining and visualization.

Our yeast phenomics database PROPHECY is available at Author Webpage. Via phenotyping of heterozygous diploids for Cited by:   Phenotyping complex traits demands the integration of data on different morphological, physiological and environmental variables [7,72].

Integration Further, there is a need for data with higher temporal and spatial resolution for the characterization of the dynamic responses of plant function to the fluctuations of the environment.

Yeasts have simple nutritional needs and require reduced carbon sources such as glucose, sucrose, fructose and maltose for energy production. The composition of the yeast cell is identical to the. More often, however, yeast is used in a much more narrow sense, analysis and presentation of yeast phenomics data book the species Saccharomyces cerevisiae, or budding yeast.

cerevisiae constitutes one of our oldest and economically most important domesticated organisms, with use in wine, beer, bread and drug production (Fay and Benavides ).

Integration of data from other genome-wide analyses, such as transcriptome analysis and predicted PPI, into the constructed phenome, as well as investigation of the distribution pattern of TFs across the fungal kingdom revealed that deletion of single TFs that are widely-distributed in fungal species exhibited a greater chance of causing.

Luciano Fernandez-Ricaud “Analysis, integration and presentation of yeast phenomics data” Jonathan Esguerra “High-resolution phenotypic profiling of a eukaryotic ribosome” Lars-Göran Ottosson “Cellular Resilience Towards Environmental and Gene Expression Perturbations”.

A popular but inadequate way of coping with LPSN data sets is dimension reduction — that is, decreasing the number of predictor variables before analysis — but in phenomics.

Sources of metabolomicsSources of metabolomics Toxicity assessment Nutrigenomics Forensic analysis Petrochemical analysis Phenotype analysis- (phenomics) PhenomicsPhenomics Phenomics, the study of the phenome, where phenotypes are characterized in a rigorous and formal way, and link these traits to the associated genes and gene variants.

Before omics scale data integration, data normalization is imperative given that data come from different technologies. Figure 1 summarizes a generalized integrated omics workflow. Data integration often requires statistical and even machine-learning tools (Min et al.

) for a multi-omics view (Libbrecht & Noble ). Keywords: Phenomics, Yeast, growth, Data pre-processing, Fitness components, Automation, Data presentation Background Thanks to recent technological innovations we can now detect and assess traits on virtually all phenotypic levels, from molecular to population level phenotypes, with unprecedented speed.

Integrated analysis of SGA results and simulations may eventually be able to delineate a set of likely biochemical pathways responsible for observed genetic interactions.

Snitkin et al. 33 asked whether combining simulations with yeast phenomics data could be used to assess two alternative pathways for raffinose consumption. In the first. Yeasts in food begins by describing the enormous range of yeasts together with methods for detection, identification and analysis.

It then discusses spoilage yeasts, methods of control and stress responses to food preservation techniques. Against this background, the bulk of the book looks at the role of yeasts in particular types of food. The Synthetic Yeast Genome Project (Sc) is the world’s first synthetic eukaryotic genome project that aims to create a novel, rationalized version of the genome of the yeast species Saccharomyces a truly global collaborative effort, research teams across the world have embarked on the challenging but exciting task of building 16 designer synthetic chromosomes encompassing.

Data query. The phenotypic data in the database can be queried through the web interface in two ways: (i) Quick Search visualizes data for one gene at a time, where the user enters either the open reading frame (ORF) name or the gene name to be investigated or (ii) Advanced Query allows analysis of many gene deletions at the same time and provides options for filtering, which.

Trait ontology (TO) analysis is a powerful system for functional annotation and enrichment analysis of genes. However, given the complexity of the molecular mechanisms underlying phenomes, only a few hundred gene-to-TO relationships in plants have been elucidated to date, limiting the pace of research in this “big data” era.

Here, we curated all the available trait associated sites. It combines two processes: a tool that converts the huge NGS mapping or coverage files into light specific coverage files containing information on genetic elements; and a visualization interface allowing a real-time analysis of data with optional integration of statistical results.

(Reference: Monot M. et al. OMICS 18(3): ). About SGD. The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relationships between sequence and gene products in fungi and higher organisms.Cellular phenomics of leaf growth.

(a) Analysis of digitalized epidermal cell drawings using automated image analysis scripts that extract the surface of the drawn area, cell area, stomatal count and pavement cell area (Andriankaja et al., ).

(b) Non-destructive imaging of dividing and expanding cells over different timepoints using dental.Growth of yeast 2 years, genomewide large-scale phenotypic characterization of yeast deletion mu-tants has received a lot of attention.

Some quantitative phenotypic analyses have been performed to a large set of yeast strains (Warringer et al., ). But to provide consistent and more easily interpreted quantitative phenotypic analysis.