Related papers: Single-cell spatial (scs) omics: Recent developmen…
Analyzing proteins from single cells by tandem mass spectrometry (MS) has become technically feasible. While such analysis has the potential to accurately quantify thousands of proteins across thousands of single cells, the accuracy and…
Environmental and climate processes are often distributed over large space-time domains. Their complexity and the amount of available data make modelling and analysis a challenging task. Statistical modelling of environment and climate data…
Spatial statistics is an area of study devoted to the statistical analysis of data that have a spatial label associated with them. Geographers often refer to the "location information" associated with the "attribute information," whose…
Development and homeostasis in multicellular systems both require exquisite control over spatial molecular pattern formation and maintenance. Advances in spatially-resolved and high-throughput molecular imaging methods such as multiplexed…
Biological processes involve a variety of spatial and temporal scales. A holistic understanding of many biological processes therefore requires multi-scale models which capture the relevant properties on all these scales. In this manuscript…
Since the advent of optogenetics, technology development has focused on new methods to optically interact with single nervous cells. This gave rise to the field of photonic neural interfaces, intended as the set of technologies that can…
Sparse coding aims to model data vectors as sparse linear combinations of basis elements, but a majority of related studies are restricted to continuous data without spatial or temporal structure. A new model-based sparse coding (MSC)…
Massive single-cell profiling efforts have accelerated our discovery of the cellular composition of the human body, while at the same time raising the need to formalise this new knowledge. Here, we review current cell ontology efforts to…
Understanding the dynamic nature of biological systems is fundamental to deciphering cellular behavior, developmental processes, and disease progression. Single-cell RNA sequencing (scRNA-seq) has provided static snapshots of gene…
Over the last decade, the term spatial computing has grown to have two different, though not entirely unrelated, definitions. The first definition of spatial computing stems from industry, where it refers primarily to new kinds of…
Today's astronomical projects need computational systems capable to store and analyze large amounts of scientific data, to effectively share data with other research Institutes and to easily implement information services to present data…
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…
This work presents an omics-driven modeling pipeline that integrates machine-learning tools to facilitate the dynamic modeling of multiscale biological systems. Random forests and permutation feature importance are proposed to mine omics…
Single-cell RNA-sequencing technologies may provide valuable insights to the understanding of the composition of different cell types and their functions within a tissue. Recent technologies such as spatial transcriptomics, enable the…
The definition of complexity through Statistical Complexity Measures (SCM) has recently seen major improvements. Mostly, effort is concentrated in measures on time series. We propose a SCM definition for spatial dynamical systems. Our…
Enrichment of predictive models with new biomolecular markers is an important task in high-dimensional omic applications. Increasingly, clinical studies include several sets of such omics markers available for each patient, measuring…
The computational study of lexical semantic change (LSC) has taken off in the past few years and we are seeing increasing interest in the field, from both computational sciences and linguistics. Most of the research so far has focused on…
This article aims to provide a unified and technical approach to semantic information, communication, and their interplay through the lens of probabilistic logic. To this end, on top of the existing technical communication (TC) layer, we…
Single-cell technologies are revolutionizing the entire field of biology. The large volumes of data generated by single-cell technologies are high-dimensional, sparse, heterogeneous, and have complicated dependency structures, making…
Recent research on formal verification for Collective Adaptive Systems (CAS) pushed advancements in spatial and spatio-temporal model checking, and as a side result provided novel image analysis methodologies, rooted in logical methods for…