Related papers: Computer algebra in systems biology
Programming languages are engineered languages that allow to instruct a machine and share algorithmic information; they have a great influence on the society since they underlie almost every information technology artefact, and they are at…
In multicellular organisms, cells coordinate their activities through cell-cell communication (CCC), which is crucial for development, tissue homeostasis, and disease progression. Recent advances in single-cell and spatial omics…
Computational problems can be classified according to their algorithmic complexity, which is defined based on how the resources needed to solve the problem, e.g. the execution time, scale with the problem size. Many problems in…
The aim of this paper is to discuss some applications of general topology in computer algorithms including modeling and simulation, and also in computer graphics and image processing. While the progress in these areas heavily depends on…
The complexity of human biology and its intricate systems holds immense potential for advancing human health, disease treatment, and scientific discovery. However, traditional manual methods for studying biological interactions are often…
One of the major challenges in biology concerns the integration of data across length and time scales into a consistent framework: how do macroscopic properties and functionalities arise from the molecular regulatory networks - and how can…
Motivation: Many problems in biomedicine and other areas of the life sciences can be characterized as control problems, with the goal of finding strategies to change a disease or otherwise undesirable state of a biological system into…
This paper discusses the meaning and scope of biological hypercomputation (BH). The framework here is computational, and from the outset it should be clear that life is not a standard Turing Machine. Living systems hypercompute, but the…
A primary motivation for our research in Digital Ecosystems is the desire to exploit the self-organising properties of biological ecosystems. Ecosystems are thought to be robust, scalable architectures that can automatically solve complex,…
In this master thesis, I discuss how the theory of operator algebras, also called operator theory, can be applied in quantum computer science.
Recent attacks of various viruses with having deep and extensive impact at a global scale has warranted that microbiome be studied extensively and in a robust analytic framework. Microbiome typically refers to the collective genomes of such…
Cells receive a wide variety of cellular and environmental signals, which must be processed combinatorially to generate specific and timely genetic responses. We present here a theoretical study on the combinatorial control and integration…
Computational intelligence is broadly defined as biologically-inspired computing. Usually, inspiration is drawn from neural systems. This article shows how to analyze neural systems using information theory to obtain constraints that help…
This work exposes which mechanisms and procesess in the Nature of evolution compute a function not computable by Turing machine. The computer with intelligence that is not higher than one bacteria population could have, but with efficency…
This review was written for the Encyclopedia of Complexity and System Science (Springer-Verlag, Berlin, 2008), and is intended as a guide to the growing literature which approaches the phenomena of cell biology from a more theoretical point…
Bacteria are easily characterizable model organisms with an impressively complicated set of capabilities. Among their capabilities is quorum sensing, a detailed cell-cell signaling system that may have a common origin with eukaryotic…
The high energy consumption of electronic data processors, together with physical challenges limiting their further improvement, has triggered intensive interest in alternative computation paradigms. Here we focus on network-based…
Studies of issues related to computability and computational complexity involve the use of a model of computation. Pivotal to such a model are the computational processes considered. Processes of this kind can be described using an…
Gene and protein networks are very important to model complex large-scale systems in molecular biology. Inferring or reverseengineering such networks can be defined as the process of identifying gene/protein interactions from experimental…
The dynamics of systems biological processes are usually modeled by a system of ordinary differential equations (ODEs) with many unknown parameters that need to be inferred from noisy and sparse measurements. Here, we introduce…