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BioNumbers specifications

Information


Unique identifier OMICS_20923
Name BioNumbers
Alternative name B10NUMB3R5
Restrictions to use None
Database management system MSSQL Server
Community driven No
Data access Browse
User data submission Allowed
Maintained No
Wikipedia https://en.wikipedia.org/wiki/Bionumbers

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Publication for BioNumbers

BioNumbers citations

 (3)
library_books

A chiral selectivity relaxed paralog of DTD for proofreading tRNA mischarging in Animalia

2018
Nat Commun
PMCID: 5802732
PMID: 29410408
DOI: 10.1038/s41467-017-02204-w

[…] sms whose genomes have been completely sequenced was obtained from KEGG GENOME database (http://www.genome.jp/kegg/genome.html). Information about genome size was taken from the web server http://www.bionumbers.hms.harvard.edu/default.aspx. Multiple sequence alignment of tRNAThr and tRNAThr(G4•U69) was prepared using T-Coffee server in M-Coffee mode (http://tcoffee.crg.cat/apps/tcoffee/do:mcoffee) […]

library_books

Predictive biophysical modeling and understanding of the dynamics of mRNA translation and its evolution

2016
Nucleic Acids Res
PMCID: 5100582
PMID: 27591251
DOI: 10.1093/nar/gkw764

[…] y parameters related to translation (e.g. ribosomes’ size, initiation rates, codon decoding rates, diffusion coefficients, etc) based on measurements or estimations is the biological numbers database BioNumbers (). Parameters from this database can be used in future development of translation models.It is important to emphasize that some of the translation parameters (e.g. ribosome footprint size) […]

library_books

Stochastic Cellular Fate Decision Making by Multiple Infecting Lambda Phage

2014
PLoS One
PMCID: 4126663
PMID: 25105971
DOI: 10.1371/journal.pone.0103636

[…] proach used the Gibson-Bruck implementation of the Gillespie algorithm. Spatial modelling was carried using a Monte Carlo particle-based tool, Smoldyn . The diffusion constants used were found using Bionumbers and are shown in . For both spatial and non-spatial simulations, data points were output at every minutes. The analysis of the generated data was carried out in Matlab (version R2012a). T […]

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BioNumbers institution(s)
Department of Plant Sciences, Weizmann Institute of Science, Rehovot, Israel; Department of Systems Biology, Harvard Medical School, Boston, MA, USA; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON, Canada; Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA

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