scholarly journals Functional Genomics of the Chicken—A Model Organism

2007 ◽  
Vol 86 (10) ◽  
pp. 2059-2094 ◽  
Author(s):  
L.A. Cogburn ◽  
T.E. Porter ◽  
M.J. Duclos ◽  
J. Simon ◽  
S.C. Burgess ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Model Organism

scholarly journals Meeting Highlights: Genome Sequencing and Biology 2001

2001 ◽  
Vol 2 (4) ◽  
pp. 243-251
Author(s):  
Jo Wixon
Keyword(s):  
Comparative Genomics ◽  
Functional Genomics ◽  
Genome Sequencing ◽  
Large Scale ◽  
Model Organism

We bring you a report from the CSHL Genome Sequencing and Biology Meeting, which has a long and prestigious history. This year there were sessions on large-scale sequencing and analysis, polymorphisms (covering discovery and technologies and mapping and analysis), comparative genomics of mammalian and model organism genomes, functional genomics and bioinformatics.

New Data and New Features of the FunRiceGenes (Functionally Characterized Rice Genes) Database: 2021 Update

2021 ◽  
Author(s):  
Fangfang Huang ◽  
Yingru Jiang ◽  
Tiantian Chen ◽  
Haoran Li ◽  
Mengjia Fu ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Rice Genome ◽  
Model Organism ◽  
Gene Families ◽  
Food Crop ◽  
Protein Coding ◽  
Protein Coding Genes ◽  
Major Food

Abstract As a major food crop and model organism, rice has been mostly studied with the largest number of functionally characterized genes among all crops. We previously built the funRiceGenes database including ∼2800 functionally characterized rice genes and ∼5000 members of different gene families. Since being published, the funRiceGenes database has been accessed by more than 49,000 users with over 490,000 page views. The funRiceGenes database has been continuously updated with newly cloned rice genes and newly published literature, based on the progress of rice functional genomics studies. Up to Nov 2021, ≥4100 functionally characterized rice genes and ∼6000 members of different gene families were collected in funRiceGenes, accounting for 22.3% of the 39,045 annotated protein-coding genes in the rice genome. Here, we summarized the update of the funRiceGenes database with new data and new features in the last five years.

scholarly journals Colony size measurement of the yeast gene deletion strains for functional genomics

2021 ◽  
Author(s):  
Negar Memarian ◽  
Matthew Jessulat ◽  
Javad Alirezaie ◽  
Nadereh Mir-Rashed ◽  
Jianhua Xu ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Colony Size ◽  
Large Scale ◽  
Model Organism ◽  
Antifungal Compound ◽  
Image Analysis System ◽  
Yeast Saccharomyces Cerevisiae ◽  
Inspection Method ◽  
Manual Inspection ◽  
Growth Differences

Background Numerous functional genomics approaches have been developed to study the model organism yeast, Saccharomyces cerevisiae, with the aim of systematically understanding the biology of the cell. Some of these techniques are based on yeast growth differences under different conditions, such as those generated by gene mutations, chemicals or both. Manual inspection of the yeast colonies that are grown under different conditions is often used as a method to detect such growth differences. Results Here, we developed a computerized image analysis system called Growth Detector (GD), to automatically acquire quantitative and comparative information for yeast colony growth. GD offers great convenience and accuracy over the currently used manual growth measurement method. It distinguishes true yeast colonies in a digital image and provides an accurate coordinate oriented map of the colony areas. Some post-processing calculations are also conducted. Using GD, we successfully detected a genetic linkage between the molecular activity of the plant-derived antifungal compound berberine and gene expression components, among other cellular processes. A novel association for the yeast mek1 gene with DNA damage repair was also identified by GD and confirmed by a plasmid repair assay. The results demonstrate the usefulness of GD for yeast functional genomics research. Conclusion GD offers significant improvement over the manual inspection method to detect relative yeast colony size differences. The speed and accuracy associated with GD makes it an ideal choice for large-scale functional genomics investigations.

scholarly journals Website Review: How to Get the Best From Fission Yeast Genome Data

2002 ◽  
Vol 3 (3) ◽  
pp. 282-288 ◽  
Author(s):  
Valerie Wood ◽  
Jürg Bähler
Keyword(s):  
Functional Genomics ◽  
Schizosaccharomyces Pombe ◽  
Fission Yeast ◽  
Model Organism ◽  
Research Community ◽  
Yeast Genome ◽  
Biological Databases ◽  
Genome Data ◽  
Internet Resources ◽  
Continuous Feedback

Researchers are increasingly depending on various centralized resources to access the vast amount of information reported in the literature and generated by systematic sequencing and functional genomics projects. Biological databases have become everyday working tools for many researchers. This dependency goes both ways in that the databases require continuous feedback from the research community to maintain accurate, reliable, and upto- date information. The fission yeastSchizosaccharomyces pombehas recently been sequenced, setting the stage for the post-genome era of this popular model organism. Here, we provide an overview of relevant databases available, or being developed, together with a compilation of Internet resources containing useful information and tools for fission yeast.

scholarly journals Integration of heterogeneous functional genomics data in gerontology research identifies genes and pathway underlying aging across species

2018 ◽  
Author(s):  
Jason A Bubier ◽  
George L Sutphin ◽  
Timothy J Reynolds ◽  
Ron Korstanje ◽  
Axis Fuksman-Kumpa ◽  
...  
Keyword(s):  
Functional Genomics ◽  
Model Organism ◽  
Heterogeneous Data ◽  
Related Genome ◽  
C Elegans ◽  
Gene Sets ◽  
Genome Wide ◽  
Analysis System ◽  
The Cost

Understanding the biological mechanisms behind aging, lifespan and healthspan is becoming increasingly important as the proportion of the world's population over the age of 65 grows, along with the cost and complexity of their care. BigData oriented approaches and analysis methods for integrative functional genomics enable current and future bio-gerontologists to synthesize, distill and interpret vast, heterogeneous data. GeneWeaver is an analysis system for integration of data that allows investigators to store, search, and analyze immense amounts of data including user-submitted experimental data, data from primary publications, and data in other databases. Aging related genome-wide gene sets from primary publications were curated into this system in concert with data from other model-organism and aging-specific databases, and used in several application using GeneWeavers analysis tools. For example, we identified Cd63 as a frequently represented gene among aging-related genome-wide results. To evaluate the role of Cd63 in aging, we performed RNAi knockdown of the C. elegans ortholog, tsp-7, demonstrating that this manipulation is capable of extending lifespan. The tools in GeneWeaver enable aging researchers to make new discoveries into the associations between the genes, normal biological processes, and diseases that affect aging, healthspan, and lifespan.

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