相关论文: scellop: A Scalable Redesign of Cell Population Pl…
Cellular populations are typically heterogenous collections of cells at different points in their respective cell cycles, each with a cell cycle time that varies from individual to individual. As a result, true single-cell behavior,…
Single-cell analysis is currently one of the most high-resolution techniques to study biology. The large complex datasets that have been generated have spurred numerous developments in computational biology, in particular the use of…
The processes taking place inside the living cell are now understood to the point where predictive computational models can be used to gain detailed understanding of important biological phenomena. A key challenge is to extrapolate this…
How are granular details of stochastic growth and division of individual cells reflected in smooth deterministic growth of population numbers? We provide an integrated, multiscale perspective of microbial growth dynamics by formulating a…
Establishing a quantitative connection between the population growth rate and the generation times of single cells is a prerequisite for understanding evolutionary dynamics of microbes. However, existing theories fail to account for the…
Important tasks in the study of genomic data include the identification of groups of similar cells (for example by clustering), and visualisation of data summaries (for example by dimensional reduction). In this paper, we develop a novel…
Challenges of assessing complexity and clonality in populations of mixed species arise in diverse areas of modern biology, including estimating diversity and clonality in microbiome populations, measuring patterns of T and B cell clonality,…
We present Artificial Stellar Populations (ArtPop), an open-source Python package for synthesizing stellar populations and generating artificial images of fully populated stellar systems. The code is designed to be intuitive to use and as…
This article introduces SCALPEL3, a scalable open-source framework for studies involving Large Observational Databases (LODs). Its design eases medical observational studies thanks to abstractions allowing concept extraction, high-level…
Microscopy imaging plays a vital role in understanding many biological processes in development and disease. The recent advances in automation of microscopes and development of methods and markers for live cell imaging has led to rapid…
The paper advocates the use of a statistical tool dedicated to the exploration of data samples populated by several sources of events. This new technique, called sPlot, is able to unfold the contributions of the different sources to the…
This paper presents Living Globe, an application for visualization of demo- graphic data supporting the temporal comparison of data from several countries represented on a 3D globe. Living Globe allows the visual exploration of the…
We evaluate several augmentations to the choropleth map to convey additional information, including glyphs, 3D, cartograms, juxtaposed maps, and shading methods. While choropleth maps are a common method used to represent societal data,…
We introduce a graphical method originating from the computer graphics domain that is used for the arbitrary and intuitive placement of cells over a two-dimensional manifold. Using a bitmap image as input, where the color indicates the…
Clustered cell-free networking, which dynamically partitions the whole network into nonoverlapping subnetworks, has been recently proposed to mitigate the cell-edge problem in cellular networks. However, prior works only focused on…
The rate at which individual bacterial cells grow depends on the concentrations of cellular components such as ribosomes and proteins. These concentrations continuously fluctuate over time and are inherited from mother to daughter cells,…
High-dimensional single-cell data poses significant challenges in identifying underlying biological patterns due to the complexity and heterogeneity of cellular states. We propose a comprehensive gene-cell dependency visualization via…
Modern high-throughput single-cell immune profiling technologies, such as flow and mass cytometry and single-cell RNA sequencing can readily measure the expression of a large number of protein or gene features across the millions of cells…
Population stratification is a problem encountered in several areas of biology and public health. We tackle this problem by mapping a population and its elements attributes into a hypergraph, a natural extension of the concept of graph or…
This paper deals with the derivation of a collective model of cell populations out of an individual-based description of the underlying physical particle system. By looking at the spatial distribution of cells in terms of time-evolving…