ArticleNature communications2016
Inferring time derivatives including cell growth rates using Gaussian processes.
Article in Nature communications, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 51 papers, 1 of them a synthesis that pooled it.
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Who cites it
51 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Analysing and meta-analysing time-series data of microbial growth and gene expression from plate readers.PLoS computational biology · 2022Pooled it
- Overcoming the limits of traditional rate calculations from sparse concentration data: a probabilistic framework for bioprocess modeling.Bioprocess and biosystems engineering · 2026Article
- Mind the Porins: Differential Effects of Porin Knockouts and Overexpression on Glucose and Xylose Uptake and Utilization in Pseudomonas putida.Microbial biotechnology · 2026Article
- Revealing global stoichiometry conservation architecture in cells from Raman spectral patterns.eLife · 2026Article
- Stochasticity in mammalian cell growth rates drives cell-to-cell variability independently of cell size and divisions.Proceedings of the National Academy of Sciences of the United States of America · 2026Article
- Inferring bacterial cell size dynamics across media conditions.Scientific reports · 2026Article
- Consequences of benzalkonium chloride tolerance for selection dynamics and de novo resistance evolution driven by antibiotics.npj antimicrobials and resistance · 2026Article
- A stable and antibiotic-free plasmid expression system foriScience · 2025Article
- Evaluation of Matrix Effects in SIMS Using Gaussian Process Regression: The Case of Olivine Mg Isotope Microanalysis.Rapid communications in mass spectrometry : RCM · 2025Article
- The type of carbon source not the growth rate it supports can determine diauxie in Saccharomyces cerevisiae.Communications biology · 2025Article
- Antibiotics change the population growth rate heterogeneity and morphology of bacteria.PLoS pathogens · 2025Article
- Mathematical modeling reveals cell differentiation processes and progenitor kinetics necessary for proper nephrogenesis.Frontiers in cell and developmental biology · 2025Article
- Differential Selection for Survival and for Growth in Adaptive Laboratory Evolution Experiments With Benzalkonium Chloride.Evolutionary applications · 2024Article
- Bacterial cell size modulation along the growth curve across nutrient conditions.bioRxiv : the preprint server for biology · 2024Article
- gcplyr: an R package for microbial growth curve data analysis.BMC bioinformatics · 2024Article
- Inferring fungal growth rates from optical density data.PLoS computational biology · 2024Article
- Enhancing Escherichia coli abiotic stress resistance through ornithine lipid formation.Applied microbiology and biotechnology · 2024Article
- Synthetically-primed adaptation of Pseudomonas putida to a non-native substrate D-xylose.Nature communications · 2024Article
- Multipad agarose plate: a rapid and high-throughput approach for antibiotic susceptibility testing.Journal of the Royal Society, Interface · 2024Article
- Determining growth rates from bright-field images of budding cells through identifying overlaps.eLife · 2023Article
Corrections and comments
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Authors and funding
7 authors.
Funding
Abstract
Often the time derivative of a measured variable is of as much interest as the variable itself. For a growing population of biological cells, for example, the population's growth rate is typically more important than its size. Here we introduce a non-parametric method to infer first and second time derivatives as a function of time from time-series data. Our approach is based on Gaussian processes and applies to a wide range of data. In tests, the method is at least as accurate as others, but has several advantages: it estimates errors both in the inference and in any summary statistics, such as lag times, and allows interpolation with the corresponding error estimation. As illustrations, we infer growth rates of microbial cells, the rate of assembly of an amyloid fibril and both the speed and acceleration of two separating spindle pole bodies. Our algorithm should thus be broadly applicable.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.