QurvE: user-friendly software for the analysis of biological growth and fluorescence data

NT Wirth, J Funk, S Donati, PI Nikel - Nature Protocols, 2023 - nature.com
The study of growth (of cells, organ-isms or populations) is inherent to all biological
disciplines. The fundamental properties of a biological system or the physiological effects of …

Software tools for single-cell tracking and quantification of cellular and molecular properties

O Hilsenbeck, M Schwarzfischer, S Skylaki… - Nature …, 2016 - nature.com
Figure 1 Continuous single-cell quantification with tTt and qTfy.(a) Iterative image analysis
workflow of tTt: graphical overview of raw data for inspection and loading only of relevant …

Measuring calcium signaling using genetically targetable fluorescent indicators

AE Palmer, RY Tsien - Nature protocols, 2006 - nature.com
Genetically encoded Ca2+ indicators allow researchers to quantitatively measure Ca2+
dynamics in a variety of experimental systems. This protocol summarizes the indicators that …

An unbiased metric of antiproliferative drug effect in vitro

LA Harris, PL Frick, SP Garbett, KN Hardeman… - Nature …, 2016 - nature.com
In vitro cell proliferation assays are widely used in pharmacology, molecular biology, and
drug discovery. Using theoretical modeling and experimentation, we show that current …

Robust research needs many lines of evidence

MR Munafò, G Davey Smith - 2018 - nature.com
Several studies across many fields estimate that only around 40% of published findings can
be replicated reliably. Various funders and communities are promoting ways for …

Metabolic profiling on the right path

N Glassbrook, C Beecher, J Ryals - Nature Biotechnology, 2000 - nature.com
In the post-genomics era, high-throughput techniques for monitoring RNA1 and protein2
levels are well on their way to becoming mainstream tools for monitoring global cell …

Microarrays--guilt by association

J Quackenbush - Science, 2003 - science.org
Single-molecule methods (8) overcome the latter difficulty. Like an orchestra, a molecular
ensemble needs to be synchronized for the outcome to be comprehensible. In contrast, a …

FPbase: a community-editable fluorescent protein database

TJ Lambert - Nature methods, 2019 - nature.com
To the Editor—The cloning and subsequent engineering of fluorescent proteins (FPs) has
revolutionized methods in biological research1, 2. There are now thousands of FPs …

Nextflow enables reproducible computational workflows

P Di Tommaso, M Chatzou, EW Floden, PP Barja… - Nature …, 2017 - nature.com
The increasing complexity of readouts for omics analyses goes hand-in-hand with concerns
about the reproducibility of experiments that analyze'big data'1, 2, 3. When analyzing very …

An “Electronic Fluorescent Pictograph” browser for exploring and analyzing large-scale biological data sets

D Winter, B Vinegar, H Nahal, R Ammar, GV Wilson… - PloS one, 2007 - journals.plos.org
Background The exploration of microarray data and data from other high-throughput projects
for hypothesis generation has become a vital aspect of post-genomic research. For the non …