Related papers: Designer Gene Networks: Towards Fundamental Cellul…
The whole complex process to obtain a protein encoded by a gene is difficult to include in a mathematical model. There are many models for describing different aspects of a genetic network. Finding a better model is one of the most…
Cardiac development is complex, multiscale process encompassing cell fate adoption, differentiation and morphogenesis. To elucidate pathways underlying this process, a recently developed algorithm to reverse engineer gene regulatory…
The question of controllability of natural and man-made network systems has recently received considerable attention. In the context of the human brain, the study of controllability may not only shed light into the organization and function…
In recent years, several studies have provided insight on the functioning of the brain which consists of neurons and form networks via interconnection among them by synapses. Neural networks are formed by interconnected systems of neurons,…
The emergence of generative AI models has dramatically expanded the availability and use of synthetic data across scientific, industrial, and policy domains. While these developments open new possibilities for data analysis, they also raise…
Inferring functional relationships within complex networks from static snapshots of a subset of variables is a ubiquitous problem in science. For example, a key challenge of systems biology is to translate cellular heterogeneity data…
A common metaphor for describing development is a rugged "epigenetic landscape" where cell fates are represented as attracting valleys resulting from a complex regulatory network. Here, we introduce a framework for explicitly constructing…
Graph Theoretic Process Network Synthesis is described as an introduction to biological networks. Genetic, protein and metabolic systems are considered. The theoretical work of Kauffman is discussed and amplified by critical property…
Complex networks describe a wide range of systems in nature and society, much quoted examples including the cell, a network of chemicals linked by chemical reactions, or the Internet, a network of routers and computers connected by physical…
Our ability to control network dynamical systems is often hindered by constraints on the number and nature of the available control actions, which make controlling the whole network unfeasible. In this manuscript, we focus on the case where…
Artificial and natural neural network models are a new toolkit which could be potentially have been used for clarifying of complex brain functions. To attend this goal, such models need to be neurobiologically realistic. However, although…
Recent deep generative models are able to provide photo-realistic images as well as visual or textual content embeddings useful to address various tasks of computer vision and natural language processing. Their usefulness is nevertheless…
Gene regulation is an important fundamental biological process. The regulation of gene expression is managed through a variety of methods including epigenetic processes (e.g., DNA methylation). Understanding the role of epigenetic changes…
Cellular automata represent physical systems where both space and time are discrete, and the associated physical quantities assume a limited set of values. While previous research has applied cellular automata in modeling chemical,…
Control of complex processes is a major goal of network analyses. Most approaches to control nonlinearly coupled systems require the network topology and/or network dynamics. Unfortunately, neither the full set of participating nodes nor…
Collaborative Filtering (CF) is widely used in recommender systems to model user-item interactions. With the great success of Deep Neural Networks (DNNs) in various fields, advanced works recently have proposed several DNN-based models for…
Inspired by empirical studies of networked systems such as the Internet, social networks, and biological networks, researchers have in recent years developed a variety of techniques and models to help us understand or predict the behavior…
Living organisms must respond to environmental changes. Generally, accurate and rapid responses are provided by simple, unidirectional networks that connect inputs with outputs. Besides accuracy and speed, biological responses should also…
This paper presents our computational methodology using Genetic Algorithms (GA) for exploring the nature of RNA editing. These models are constructed using several genetic editing characteristics that are gleaned from the RNA editing system…
Diseases involve complex processes and modifications to the cellular machinery. The gene expression profile of the affected cells contains characteristic patterns linked to a disease. Hence, biological knowledge pertaining to a disease can…