Related papers: Answering open questions in biology using spatial …
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…
Recent advances in human mobility research have revealed consistent pairwise characteristics in movement behavior, yet existing mobility models often overlook the spatial and topological structure of mobility networks. By analyzing millions…
Spatial networks are ubiquitous in social, geographical, physical, and biological applications. To understand the large-scale structure of networks, it is important to develop methods that allow one to directly probe the effects of space on…
Different cell types aggregate and sort into hierarchical architectures during the formation of animal tissues. The resulting spatial organization depends (in part) on the strength of adhesion of one cell type to itself relative to other…
In systems biology, it is becoming increasingly common to measure biochemical entities at different levels of the same biological system. Hence, data fusion problems are abundant in the life sciences. With the availability of a multitude of…
Both the current trends in technology such as smartphones, general mobile devices, stationary sensors, and satellites as well as a new user mentality of using this technology to voluntarily share enriched location information produces a…
Most models of biological pattern formation are simulated on continuous domains even though cells are discrete objects that provide internal boundaries to the diffusion of regulatory components. In our previous papers on simulating…
The relationship between microscopic observations and macroscopic behavior is a fundamental open question in biophysical systems. Here, we develop a unified approach that---in contrast with existing methods---predicts cell type from…
Much of the genome is expressed in the vertebrate brain, with individual genes exhibiting different spatially-varying patterns of expression. These variations are not independent, with pairs of genes exhibiting complex patterns of…
This paper investigates the problem of adjusting for spatial effects in genomic prediction. Despite being seldomly considered in genomic prediction, spatial effects often affect phenotypic measurements of plants. We consider a Gaussian…
Rapid advances in high-throughput technologies have led to considerable interest in analyzing genome-scale data in the context of biological pathways, with the goal of identifying functional systems that are involved in a given phenotype.…
Systems biology models are useful models of complex biological systems that may require a large amount of experimental data to fit each model's parameters or to approximate a likelihood function. These models range from a few to thousands…
Spatially resolved transcriptomics is a fast-developing set of technologies that enables the measurement of localized gene expression across spatial locations in a sample. Detecting spatially varying genes is critical for analyzing such…
Cells can often choose among several stably heritable phenotypes. Examples are the expression of genes in eukaryotic cells where long chromosomal regions can adopt persistent and heritable silenced or active states, that may be associated…
Bone remodeling is a complex process involving cell-cell interactions, biochemical signaling and mechanical stimuli. Early models of the biological aspects of remodeling were non-spatial and focused on the local dynamics at a fixed location…
The molecular biology revolution of the last seventy five years has transformed our view of living systems. Scientific explanations of biological phenomena are now synonymous with the identification of the genes, proteins, and signaling…
Evolution has fascinated quantitative and physical scientists for decades: how can the random process of mutation, recombination, and duplication of genetic information generate the diversity of life? What determines the rate of evolution?…
Despite the ubiquity of large language models (LLMs) in AI research, the question of embodiment in LLMs remains underexplored, distinguishing them from embodied systems in robotics where sensory perception directly informs physical action.…
Biological functions stem from coordinated interactions among proteins, nucleic acids and small molecules. Mass spectrometry technologies for reliable, high throughput single-cell proteomics will add a new modality to genomics and enable…
Spatial transcriptomics has revolutionized tissue analysis by simultaneously mapping gene expression, spatial topography, and histological context across consecutive tissue sections, enabling systematic investigation of spatial…