BioNumbers—the database of key numbers in molecular and cell biology

By Ron Milo, Paul Jorgensen, Uri Moran, Griffin M. Weber, Michael Springer. Nucleic Acids Res., 2009

1,041 citations recorded by the source corpus.

BioNumbers (http://www.bionumbers.hms.harvard.edu) is a database of key numbers in molecular and cell biology—the quantitative properties of biological systems of interest to computational, systems and molecular cell biologists. Contents of the database range from cell sizes to metabolite concentrations, from reaction rates to generation times, from genome sizes to the number of mitochondria in a cell. While always of importance to biologists, having numbers in hand is becoming increasingly critical for experimenting, modeling, and analyzing biological systems. BioNumbers was motivated by an appreciation of how long it can take to find even the simplest number in the vast biological literature. All numbers are taken directly from a literature source and that reference is provided with the number. BioNumbers is designed to be highly searchable and queries can be performed by keywords or browsed by menus. BioNumbers is a collaborative community platform where registered users can add content and make comments on existing data. All new entries and commentary are curated to maintain high quality. Here we describe the database characteristics and implementation, demonstrate its use, and discuss future directions for its development.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/462098bcc81f5d8b8a067aa0b8988adba0eef91f

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Citations in the corpus

An evolutionarily conserved mechanism for controlling the efficiency of protein translation. (2010, background): “We thus defined and identified the ‘‘bottleneck’’ region in each individual gene—a sequence window of 15 codons in length (that represents the length of the ribosome footprint region on mRNAs (Alberts et al., 2002; Ingolia et al., 2009; Kaczanowska and Ryden-Aulin, 2007; Menetret et al., 2000; Milo ”
Noise2Self: Blind Denoising by Self-Supervision (2019, background): “In modern, highly parallel experiments, only a few thousand of the hundreds of thousands of mRNA molecules present in a cell are successfully captured and sequenced (Milo et al., 2010).”
An Integrated Mechanistic Model of Pan-Cancer Driver Pathways Predicts Stochastic Proliferation and Death (2017, methodology): “We acquired a value for initial ribosome level from the literature; we found a range of values from ~2 million to ~10 million copies per cell across mammalian cells (Milo et al., 2009), thus we estimated 6 million copies of ribosomes copies per cell as an intermediate value.”
Proteome-wide post-translational modification statistics: frequency analysis and curation of the swiss-prot database (2011, background): “The statistics/probabilities can also be cross-referenced into the BioNumbers database 16 .”
SCoPE-MS: mass spectrometry of single mammalian cells quantifies proteome heterogeneity during cell differentiation (2017, background): “We were motivated by the realization that most proteins are present at over 50,000 copies per cell [19, 20] while modern MS instruments have sensitivity to identify and quantify ions present at hundreds of copies [21, 22].”