Related papers: scellop: A Scalable Redesign of Cell Population Pl…
We present a modelling framework for the dynamics of cells structured by the concentration of a micromolecule they contain. We derive general equations for the evolution of the cell population and of the extra-cellular concentration of the…
Solving population balance equations, we derive analytical steady-state cell size distributions for single-lineage experiments, such as the mother machine. These experiments are fundamentally different from batch cultures where populations…
For various species of biological cells, experimental observations indicate the existence of universal distributions of the cellular size, scaling relations between the cell-size moments and simple rules for the cell-size control. We…
Parallel coordinate plots (PCPs) are among the most useful techniques for the visualization and exploration of high-dimensional data spaces. They are especially useful for the representation of correlations among the dimensions, which…
Detecting variation in the evolutionary process along chromosomes is increasingly important as whole-genome data becomes more widely available. For example, factors such as incomplete lineage sorting, horizontal gene transfer, and…
The axes ordering in PCP presents a particular story from the data based on the user perception of PCP polylines. Existing works focus on directly optimizing for PCP axes ordering based on some common analysis tasks like clustering,…
Tracking individual cells in live-cell imaging provides fundamental insights, inevitable for studying causes and consequences of phenotypic heterogeneity, responses to changing environmental conditions or stressors. Microbial cell tracking,…
Processing time-dependent information requires cells to quantify the duration of past regulatory events and program the time span of future signals. At the single-cell level, timer mechanisms can be implemented with genetic circuits: sets…
Cell-based, mathematical modeling of collective cell behavior has become a prominent tool in developmental biology. Cell-based models represent individual cells as single particles or as sets of interconnected particles, and predict the…
Human physiology and pathology arise from the coordinated interactions of diverse single cells. However, analyzing single cells has been limited by the low sensitivity and throughput of analytical methods. DNA sequencing has recently made…
We study the effect of correlations in generation times on the dynamics of population growth of microorganisms. We show that any non-zero correlation that is due to cell-size regulation, no matter how small, induces long-term oscillations…
As a living information and communications system, the genome encodes patterns in single nucleotide polymorphisms (SNPs) reflecting human adaption that optimizes population survival in differing environments. This paper mathematically…
Mass spectrometry (MS) based single-cell proteomics (SCP) explores cellular heterogeneity by focusing on the functional effectors of the cells - proteins. However, extracting meaningful biological information from MS data is far from…
This paper studies an application of a recurrent neural network to clustering method for the S-P chart: a binary data set used widely in education. As the number of students increases, the S-P chart becomes hard to handle. In order to…
In most biological studies and processes, cell proliferation and population dynamics play an essential role. Due to this ubiquity, a multitude of mathematical models has been developed to describe these processes. While the simplest models…
Rapidly growing data sizes of scientific simulations pose significant challenges for interactive visualization and analysis techniques. In this work, we propose a compact probabilistic representation to interactively visualize large…
The simplest model of a smart spatial redistribution of individuals is proposed. A single-species population is considered, to be composed of two discrete subpopulations inhabiting two stations; migration is a transfer between them. The…
For clustering of an undirected graph, this paper presents an exact algorithm for the maximization of modularity density, a more complicated criterion to overcome drawbacks of the well-known modularity. The problem can be interpreted as the…
Metagenomics is the study of environments through genetic sampling of their microbiota. Metagenomic studies produce large datasets that are estimated to grow at a faster rate than the available computational capacity. A key step in the…
This article introduces Unsub Extender, a free tool to help libraries analyze their Unsub data export files. Unsub is a collection development dashboard that gathers and forecasts journal-level usage metrics to provide academic libraries…