Published in Cell systems
The primary problem with the explosion of biomedical datasets is not the data, not computational resources, and not the required storage space, but the general lack of trained and skilled researchers to manipulate and analyze these data. Eliminating this problem requires development of comprehensive educational resources. Here we present a communit...
Published in Cell systems
Gene expression is thought to be affected not only by the concentration of transcription factors (TFs) but also the dynamics of their nuclear translocation. Testing this hypothesis requires direct control of TF dynamics. Here, we engineer CLASP, an optogenetic tool for rapid and tunable translocation of a TF of interest. Using CLASP fused to Crz1, ...
Published in Cell systems
Accurately profiling systemic immune responses to cancer initiation and progression is necessary for understanding tumor surveillance and, ultimately, improving therapy. Here, we describe the SYLARAS software tool (systemic lymphoid architecture response assessment) and a dataset collected with SYLARAS that describes the frequencies of immune cells...
Published in Cell systems
Complex, time-varying responses have been observed widely in cell signaling, but how specific dynamics are generated or regulated is largely unknown. One major obstacle has been that high-throughput screens are typically incompatible with the live-cell assays used to monitor dynamics. Here, we address this challenge by screening a library of 429 ki...
Published in Cell systems
The assay for transposase-accessible chromatin using sequencing (ATAC-seq) has become the preferred method for mapping chromatin accessibility due to its time and input material efficiency. However, it can be difficult to evaluate data quality and identify sources of technical bias across samples. Here, we present ataqv, a computational toolkit for...
Published in Cell systems
Half of the bacteria in the human gut microbiome are lysogens containing integrated prophages, which may activate in stressful immune environments. Although lysogens are likely to be phagocytosed by macrophages, whether prophage activation occurs or influences the outcome of bacterial infection remains unexplored. To study the dynamics of bacteria-...
Published in Cell systems
Genetic mosaicism can manifest as spatially variable phenotypes that vary from site to site within an organism. Here, we use imaging-based phenomics to quantitate phenotypes at many sites within the axial skeleton of CRISPR-edited G0 zebrafish. Through characterization of loss-of-function cell clusters in the developing skeleton, we identify a dist...
Published in Cell systems
Here, we present Scribe (https://github.com/aristoteleo/Scribe-py), a toolkit for detecting and visualizing causal regulatory interactions between genes and explore the potential for single-cell experiments to power network reconstruction. Scribe employs restricted directed information to determine causality by estimating the strength of informatio...
Published in Cell systems
The simplest configuration of mitochondria in a cell is as small separate organellar units. Instead, mitochondria often form a dynamic, intricately connected network. A basic understanding of the topological properties of mitochondrial networks, and their influence on cell function is lacking. We performed an extensive quantitative analysis of mito...
Published in Cell systems
We compare the "patterns of mutation" in biological and technological networks. Negative selection at central nodes in biological networks has been widely reported; however, we show technological networks have an opposite trend. This suggests a potential contrast: biological evolution involves random tinkering, whereas man-made systems change accor...
