gcplyr: an R package for microbial growth curve data analysis

M Blazanin - BMC bioinformatics, 2024 - Springer
Background Characterization of microbial growth is of both fundamental and applied
interest. Modern platforms can automate collection of high-throughput microbial growth …

Dietary prophage inducers and antimicrobials: toward landscaping the human gut microbiome

L Boling, DA Cuevas, JA Grasis, HS Kang… - Gut …, 2020 - Taylor & Francis
The approximately 1011 viruses and microbial cells per gram of fecal matter (dry weight) in
the large intestine are important to human health. The responses of three common gut …

AMiGA: software for automated analysis of microbial growth assays

FS Midani, J Collins, RA Britton - Msystems, 2021 - Am Soc Microbiol
The analysis of microbial growth is one of the central methods in the field of microbiology.
Microbial growth dynamics can be characterized by meaningful parameters, including …

De novo design of symmetric ferredoxins that shuttle electrons in vivo

AC Mutter, AM Tyryshkin, IJ Campbell… - Proceedings of the …, 2019 - National Acad Sciences
A symmetric origin for bacterial ferredoxins was first proposed over 50 y ago, yet, to date, no
functional symmetric molecule has been constructed. It is hypothesized that extant proteins …

Online monitoring of bacterial growth with an electrical sensor

X Zhang, X Jiang, Q Yang, X Wang, Y Zhang… - Analytical …, 2018 - ACS Publications
Herein, we developed an automatic electrical bacterial growth sensor (EBGS) based on a
multichannel capacitively coupled contactless conductivity detector (C4D). With the use of …

[HTML][HTML] BactEXTRACT: an R Shiny app to quickly extract, plot and analyse bacterial growth and gene expression data

J Dénéréaz, JW Veening - Access Microbiology, 2024 - microbiologyresearch.org
To streamline the analysis and visualization of bacterial growth and gene expression data
obtained by microtitre plate readers, we developed BactEXTRACT, an intuitive, easy-to-use …

Inferring fungal growth rates from optical density data

T Hameed, N Motsi, E Bignell… - PLOS Computational …, 2024 - journals.plos.org
Quantifying fungal growth underpins our ability to effectively treat severe fungal infections.
Current methods quantify fungal growth rates from time-course morphology-specific data …

Dashing Growth Curves: a web application for rapid and interactive analysis of microbial growth curves

MA Reiter, JA Vorholt - BMC bioinformatics, 2024 - Springer
Background Recording and analyzing microbial growth is a routine task in the life sciences.
Microplate readers that record dozens to hundreds of growth curves simultaneously are …

When beneficial biofilm on materials is needed: electrostatic attachment of living bacterial cells induces biofilm formation

D Deev, I Rybkin, T Rijavec, A Lapanje - Frontiers in Materials, 2021 - frontiersin.org
Bacterial attachment is crucial in many biotechnological applications, but many important
bacterial strains cannot form biofilms. Biofilms can damage materials, and current strategies …

Sparse-growth-curve: a computational pipeline for parsing cellular growth curves with low temporal resolution

C Cheng, JC Thrash - Microbiology Resource Announcements, 2021 - Am Soc Microbiol
Here, we introduce a Python-based repository, sparse-growth-curve, a software package
designed for parsing cellular growth curves with low temporal resolution. The repository …