Related papers: scellop: A Scalable Redesign of Cell Population Pl…
Continuum models for the spatial dynamics of growing cell populations have been widely used to investigate the mechanisms underpinning tissue development and tumour invasion. These models consist of nonlinear partial differential equations…
Induced pluripotent stem cells (iPSCs) provide a great model to study the process of reprogramming and differentiation of stem cells. Single-cell RNA sequencing (scRNA-seq) enables us to investigate the reprogramming process at single-cell…
Stochastic simulation can make the molecular processes of cellular control more vivid than the traditional differential-equation approach by generating typical system histories instead of just statistical measures such as the mean and…
We present SynthPop, a new open source, modular population synthesis Galactic modeling software to simulate catalogs of Milky Way stars along any sightline outward from the Sun. Motivated by a lack flexibility in existing Galactic models,…
As astronomy becomes increasingly invested in large surveys, the ample representation of an individual target becomes a significant challenge. Tabulations of basic properties can convey the message in an absolute sense, but not within the…
Single-particle tracking (SPT) grants unprecedented insight into cellular function at the molecular scale [1]. Throughout the cell, the movement of single-molecules is generally heterogeneous and complex. Hence, there is an imperative to…
As supercomputers continue to grow in scale and capabilities, it is becoming increasingly difficult to isolate processor and system level causes of performance degradation. Over the last several years, a significant number of performance…
Accurate cell type annotation is a crucial step in analyzing single-cell RNA sequencing (scRNA-seq) data, which provides valuable insights into cellular heterogeneity. However, due to the high dimensionality and prevalence of zero elements…
In this paper, a first sample-based formulation of the recently considered population observers, or ensemble observers, which estimate the state distribution of dynamic populations from measurements of the output distribution is…
We present results from a preregistered and crowdsourced user study where we asked members of the general population to determine whether two samples represented using different forms of data visualizations are drawn from the same or…
Cell tracking is an essential tool in live-cell imaging to determine single-cell features, such as division patterns or elongation rates. Unlike in common multiple object tracking, in microbial live-cell experiments cells are growing,…
Large tree structures are ubiquitous and real-world relational datasets often have information associated with nodes (e.g., labels or other attributes) and edges (e.g., weights or distances) that need to be communicated to the viewers. Yet,…
Computational modeling of single-cell gene expression is crucial for understanding cellular processes, but generating realistic expression profiles remains a major challenge. This difficulty arises from the count nature of gene expression…
Comparisons of single-cell RNA sequencing (scRNA-seq) data across species can reveal links between cellular gene expression and the evolution of cell functions, features, and phenotypes. These comparisons invoke evolutionary histories, as…
We present Clusterplot, a multi-class high-dimensional data visualization tool designed to visualize cluster-level information offering an intuitive understanding of the cluster inter-relations. Our unique plots leverage 2D blobs devised to…
Biologists who want to analyse their single-cell transcriptomics dataset must install and use specialist software via the command line. This is often impractical for non-bioinformaticians. Whilst the popular CELLxGENE software provides an…
SLiM is an efficient forward population genetic simulation designed for studying the effects of linkage and selection on a chromosome-wide scale. The program can incorporate complex scenarios of demography and population substructure,…
Population protocols are a model of distributed computation intended for the study of networks of independent computing agents with dynamic communication structure. Each agent has a finite number of states, and communication opportunities…
Recent experimental advances in biology allow researchers to obtain gene expression profiles at single-cell resolution over hundreds, or even thousands of cells at once. These single-cell measurements provide snapshots of the states of the…
Helping end users comprehend the abstract distribution shifts can greatly facilitate AI deployment. Motivated by this, we propose a novel task, dataset explanation. Given two image data sets, dataset explanation aims to automatically point…