Related papers: Emerging whole-cell modeling principles and method…
Accurate predictions and representations of plant growth patterns in simulated and controlled environments are important for addressing various challenges in plant phenomics research. This review explores various works on state-of-the-art…
In recent times whole-genome gene expression analysis has turned out to be a highly important tool to study the coordinated function of a very large number of genes within their corresponding cellular environment, especially in relation to…
Life science is entering a new era of petabyte-level sequencing data. Converting such big data to biological insights represents a huge challenge for computational analysis. To this end, we developed DeepMetabolism, a biology-guided deep…
Modeling galaxy formation in a cosmological context presents one of the greatest challenges in astrophysics today, due to the vast range of scales and numerous physical processes involved. Here we review the current status of models that…
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…
Declarative modeling uses symbolic expressions to represent models. With such expressions one can formalize high-level mathematical computations on models that would be difficult or impossible to perform directly on a lower-level simulation…
This series presents an approach to mathematical biology which makes precise the function of biological molecules. Because biological systems compute, the theory is a general purpose computer language. I build a language for efficiently…
Machine learning provides a broad framework for addressing high-dimensional prediction problems in classification and regression. While machine learning is often applied for imaging problems in medical physics, there are many efforts to…
Cell growth and gene expression, essential elements of all living systems, have long been the focus of biophysical interrogation. Advances in single-cell methods have invigorated theoretical studies into these processes. However, until…
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…
The grand challenges in biology today are being shaped by powerful high-throughput technologies that have revealed the genomes of many organisms, global expression patterns of genes and detailed information about variation within…
In this paper, we introduce the first diffusion model designed to generate complete synthetic human genotypes, which, by standard protocols, one can straightforwardly expand into full-length, DNA-level genomes. The synthetic genotypes mimic…
This paper introduces a continuous model for Multi-cellular Developmental Design. The cells are fixed on a 2D grid and exchange "chemicals" with their neighbors during the growth process. The quantity of chemicals that a cell produces, as…
Modeling environmental ecosystems is essential for effective resource management, sustainable development, and understanding complex ecological processes. However, traditional methods frequently struggle with the inherent complexity,…
The applicability of computational models to the biological world is an active topic of debate. We argue that a useful path forward results from abandoning hard boundaries between categories and adopting an observer-dependent, pragmatic…
One of the main properties of biological systems is modularity, which manifests itself at all levels of their organization, starting with the level of molecular genetics, ending with the level of whole organisms and their communities. In a…
The speed and the versatility of today's computers open up new opportunities to simulate complex biological systems. Here we review a computational approach recently proposed by us to model large tumor cell populations and spheroids, and we…
Molecular electronics is envisioned as a promising candidate for the nanoelectronics of the future. More than a possible answer to ultimate miniaturization problem in nanoelectronics, molecular electronics is foreseen as a possible way to…
Recent tumor genome sequencing confirmed that one tumor often consists of multiple cell subpopulations (clones) which bear different, but related, genetic profiles such as mutation and copy number variation profiles. Thus far, one tumor has…
Throughout the evolution of biological species on Earth, cells and organs have developed many complex structures and processes to ensure their interactions with individual chemical molecules (small and macromolecular) and nanoscale objects…