scholarly journals Choosing a genome browser for a Model Organism Database: surveying the Maize community

Database ◽  
2010 ◽  
Vol 2010 ◽  
Author(s):  
Taner Z. Sen ◽  
Lisa C. Harper ◽  
Mary L. Schaeffer ◽  
Carson M. Andorf ◽  
Trent E. Seigfried ◽  
...  
Keyword(s):  
Model Organism ◽  
Genome Browser ◽  
Model Organism Database ◽  
A Genome

scholarly journals riboCIRC: a comprehensive database of translatable circRNAs

2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Huihui Li ◽  
Mingzhe Xie ◽  
Yan Wang ◽  
Ludong Yang ◽  
Zhi Xie ◽  
...  
Keyword(s):  
De Novo ◽  
Species Conservation ◽  
Structure And Function ◽  
Research Community ◽  
Genome Browser ◽  
Valuable Resource ◽  
Sequence Structure ◽  
A Genome ◽  
Context Specific ◽  
And Function

AbstractriboCIRC is a translatome data-oriented circRNA database specifically designed for hosting, exploring, analyzing, and visualizing translatable circRNAs from multi-species. The database provides a comprehensive repository of computationally predicted ribosome-associated circRNAs; a manually curated collection of experimentally verified translated circRNAs; an evaluation of cross-species conservation of translatable circRNAs; a systematic de novo annotation of putative circRNA-encoded peptides, including sequence, structure, and function; and a genome browser to visualize the context-specific occupant footprints of circRNAs. It represents a valuable resource for the circRNA research community and is publicly available at http://www.ribocirc.com.

Quantitative Trait Loci for the Monoamine-Related Traits Heart Rate and Headless Behavior inDrosophila melanogaster

Genetics ◽  
2001 ◽  
Vol 157 (1) ◽  
pp. 283-294 ◽  
Author(s):  
Kristie Ashton ◽  
Ana Patricia Wagoner ◽  
Roland Carrillo ◽  
Greg Gibson
Keyword(s):  
Heart Rate ◽  
Genetic Variation ◽  
Recombinant Inbred Lines ◽  
Model Organism ◽  
Interval Mapping ◽  
Activity Levels ◽  
Environmental Variance ◽  
Genome Wide ◽  
A Genome ◽  
Monoamine Receptors

AbstractDrosophila melanogaster appears to be well suited as a model organism for quantitative pharmacogenetic analysis. A genome-wide deficiency screen for haploinsufficient effects on prepupal heart rate identified nine regions of the genome that significantly reduce (five deficiencies) or increase (four deficiencies) heart rate across a range of genetic backgrounds. Candidate genes include several neurotransmitter receptor loci, particularly monoamine receptors, consistent with results of prior pharmacological manipulations of heart rate, as well as genes associated with paralytic phenotypes. Significant genetic variation is also shown to exist for a suite of four autonomic behaviors that are exhibited spontaneously upon decapitation, namely, grooming, grasping, righting, and quivering. Overall activity levels are increased by application of particular concentrations of the drugs octopamine and nicotine, but due to high environmental variance both within and among replicate vials, the significance of genetic variation among wild-type lines for response to the drugs is difficult to establish. An interval mapping design was also used to map two or three QTL for each behavioral trait in a set of recombinant inbred lines derived from the laboratory stocks Oregon-R and 2b.

scholarly journals MaizeGDB update: new tools, data and interface for the maize model organism database

2015 ◽  
Vol 44 (D1) ◽  
pp. D1195-D1201 ◽  
Author(s):  
Carson M. Andorf ◽  
Ethalinda K. Cannon ◽  
John L. Portwood ◽  
Jack M. Gardiner ◽  
Lisa C. Harper ◽  
...  
Keyword(s):  
Model Organism ◽  
Model Organism Database

scholarly journals Identification of potential drug targets in Salmonella enterica sv. Typhimurium using metabolic modelling and experimental validation

Microbiology ◽  
2014 ◽  
Vol 160 (6) ◽  
pp. 1252-1266 ◽  
Author(s):  
Hassan B. Hartman ◽  
David A. Fell ◽  
Sergio Rossell ◽  
Peter Ruhdal Jensen ◽  
Martin J. Woodward ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Energy Demand ◽  
Drug Targets ◽  
Minimal Medium ◽  
Model Organism ◽  
Metabolic Model ◽  
Scale Model ◽  
Glucose Minimal Medium ◽  
A Genome ◽  
Genome Scale

Salmonella enterica sv. Typhimurium is an established model organism for Gram-negative, intracellular pathogens. Owing to the rapid spread of resistance to antibiotics among this group of pathogens, new approaches to identify suitable target proteins are required. Based on the genome sequence of S. Typhimurium and associated databases, a genome-scale metabolic model was constructed. Output was based on an experimental determination of the biomass of Salmonella when growing in glucose minimal medium. Linear programming was used to simulate variations in the energy demand while growing in glucose minimal medium. By grouping reactions with similar flux responses, a subnetwork of 34 reactions responding to this variation was identified (the catabolic core). This network was used to identify sets of one and two reactions that when removed from the genome-scale model interfered with energy and biomass generation. Eleven such sets were found to be essential for the production of biomass precursors. Experimental investigation of seven of these showed that knockouts of the associated genes resulted in attenuated growth for four pairs of reactions, whilst three single reactions were shown to be essential for growth.

scholarly journals ZFIN, The zebrafish model organism database: Updates and new directions

genesis ◽  
2015 ◽  
Vol 53 (8) ◽  
pp. 498-509 ◽  
Author(s):  
Leyla Ruzicka ◽  
Yvonne M. Bradford ◽  
Ken Frazer ◽  
Douglas G. Howe ◽  
Holly Paddock ◽  
...  
Keyword(s):  
Model Organism ◽  
Model Organism Database ◽  
Zebrafish Model ◽  
Database Updates ◽  
New Directions

scholarly journals MaizeGDB: The Maize Model Organism Database for Basic, Translational, and Applied Research

2008 ◽  
Vol 2008 ◽  
pp. 1-10 ◽  
Author(s):  
Carolyn J. Lawrence ◽  
Lisa C. Harper ◽  
Mary L. Schaeffer ◽  
Taner Z. Sen ◽  
Trent E. Seigfried ◽  
...  
Keyword(s):  
Model Organism ◽  
Basic Research ◽  
Model Organism Database ◽  
High Productivity ◽  
Group Activities ◽  
Food And Agriculture ◽  
Food And Agriculture Organization ◽  
Genetics And Genomics ◽  
Excellent Source ◽  
By Products

In 2001 maize became the number one production crop in the world with the Food and Agriculture Organization of the United Nations reporting over 614 million tonnes produced. Its success is due to the high productivity per acre in tandem with a wide variety of commercial uses. Not only is maize an excellent source of food, feed, and fuel, but also its by-products are used in the production of various commercial products. Maize's unparalleled success in agriculture stems from basic research, the outcomes of which drive breeding and product development. In order for basic, translational, and applied researchers to benefit from others' investigations, newly generated data must be made freely and easily accessible. MaizeGDB is the maize research community's central repository for genetics and genomics information. The overall goals of MaizeGDB are to facilitate access to the outcomes of maize research by integrating new maize data into the database and to support the maize research community by coordinating group activities.

scholarly journals ZFIN, the Zebrafish Model Organism Database: increased support for mutants and transgenics

2012 ◽  
Vol 41 (D1) ◽  
pp. D854-D860 ◽  
Author(s):  
Douglas G. Howe ◽  
Yvonne M. Bradford ◽  
Tom Conlin ◽  
Anne E. Eagle ◽  
David Fashena ◽  
...  
Keyword(s):  
Model Organism ◽  
Model Organism Database ◽  
Zebrafish Model

scholarly journals 1000 Genomes Selection Browser 1.0: a genome browser dedicated to signatures of natural selection in modern humans

2013 ◽  
Vol 42 (D1) ◽  
pp. D903-D909 ◽  
Author(s):  
Marc Pybus ◽  
Giovanni M. Dall’Olio ◽  
Pierre Luisi ◽  
Manu Uzkudun ◽  
Angel Carreño-Torres ◽  
...  
Keyword(s):  
Natural Selection ◽  
Genome Browser ◽  
Modern Humans ◽  
1000 Genomes ◽  
A Genome

scholarly journals BeetleBase: the model organism database for Tribolium castaneum

2007 ◽  
Vol 35 (Database) ◽  
pp. D476-D479 ◽  
Author(s):  
L. Wang ◽  
S. Wang ◽  
Y. Li ◽  
M. S. R. Paradesi ◽  
S. J. Brown
Keyword(s):  
Tribolium Castaneum ◽  
Model Organism ◽  
Model Organism Database
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