Related papers: scellop: A Scalable Redesign of Cell Population Pl…
Scaling in complex supply networks is a population-level optimization phenomenon thought to arise from the evolutions of the underlying individual networks, but the evolution-scaling connection has not been empirically demonstrated. Here,…
A rigorous understanding of how multicellular behaviors arise from the actions of single cells requires quantitative frameworks that bridge the gap between genetic circuits, the arrangement of cells in space, and population-level behaviors.…
Counting circular objects such as cell colonies is an important source of information for biologists. Although this task is often time-consuming and subjective, it is still predominantly performed manually. The aim of the present work is to…
Human embryonic stem cells (hESCs) and induced pluripotent stem cells (iPSCs) have promising clinical applications which often rely on clonally-homogeneous cell populations. To achieve this, cross-contamination and merger of colonies should…
Data visualization is essential for developing an understanding of a complex system. The power grid is one of the most complex systems in the world and effective power grid research visualization software must 1) be easy to use, 2) support…
Background: To understand individual genomes it is necessary to look at the variations that lead to changes in phenotype and possibly to disease. However, genotype information alone is often not sufficient and additional knowledge regarding…
Single-cell proteomics (SCP) is transforming our understanding of biological complexity by shifting from bulk proteomics, where signals are averaged over thousands of cells, to the proteome analysis of individual cells. This granular…
Population-wise matching of the cortical fold is necessary to identify biomarkers of neurological or psychiatric disorders. The difficulty comes from the massive interindividual variations in the morphology and spatial organization of the…
Spatial transcriptomics methods capture cellular measurements such as gene expression and cell types at specific locations in a cell, helping provide a localized picture of tissue health. Traditional visualization techniques superimpose the…
We study the mathematical properties of a general model of cell division structured with several internal variables. We begin with a simpler and specific model with two variables, we solve the eigenvalue problem with strong or weak…
Scatterplots are a common tool for exploring multidimensional datasets, especially in the form of scatterplot matrices (SPLOMs). However, scatterplots suffer from overplotting when categorical variables are mapped to one or two axes, or the…
A fundamental question in biology is how cell populations evolve into different subtypes based on homogeneous processes at the single cell level. Here we show that population bimodality can emerge even when biological processes are…
Scatterplots are one of the simplest and most commonly-used visualizations for understanding quantitative, multidimensional data. However, since scatterplots only depict two attributes at a time, analysts often need to manually generate and…
We present EzGal, a flexible python program designed to easily generate observable parameters (magnitudes, colors, mass-to-light ratios) for any stellar population synthesis (SPS) model. As has been demonstrated by various authors, the…
In the last years many powerful techniques have emerged to measure protein interactions as well as gene expression. Many progresses have been done since the introduction of these techniques but not toward quantitative analysis of data. In…
We define BioScapeL, a stochastic pi-calculus in 3D-space. A novel aspect of BioScapeL is that entities have programmable locations. The programmer can specify a particular location where to place an entity, or a location relative to the…
Single-cell experiments revealed substantial variability in generation times, growth rates but also in birth and division sizes between genetically identical cells. Understanding how these fluctuations determine the fitness of the…
This paper takes a new look at Cell-free Massive MIMO (multiple-input multiple-output) through the lens of the dynamic cooperation cluster framework from the Network MIMO literature. The purpose is to identify and address scalability issues…
Images of the natural world, collected by a variety of cameras, from drones to individual phones, are increasingly abundant sources of biological information. There is an explosion of computational methods and tools, particularly computer…
Constructing cell developmental trajectories is a critical task in single-cell RNA sequencing (scRNA-seq) analysis, enabling the inference of potential cellular progression paths. However, current automated methods are limited to…