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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…
Computing has revolutionized the biological sciences over the past several decades, such that virtually all contemporary research in the biosciences utilizes computer programs. The computational advances have come on many fronts, spurred by…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
In this review, we discuss the applications of the theory of birth-and-death processes to problems in biology, primarily, those of evolutionary genomics. The mathematical principles of the theory of these processes are briefly described.…
The visual pathway involves complex networks of cells and regions which contribute to the encoding and processing of visual information. While some aspects of visual perception are understood, there are still many unanswered questions…
The correlation and interactions among different biological entities comprise the biological system. Although already revealed interactions contribute to the understanding of different existing systems, researchers face many questions…
Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
One of the most compelling problems in science consists in understanding how living systems process information. After all, the way they process information defines their capacities to learning and adaptation. There is an increasing…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
Genomic alterations lead to cancer complexity and form a major hurdle for a comprehensive understanding of the molecular mechanisms underlying oncogenesis. In this review, we describe the recent advances in studying cancer-associated genes…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
This paper deals with temporal enzyme distribution in the activation of biochemical pathways. Pathway activation arises when production of a certain biomolecule is required due to changing environmental conditions. Under the premise that…
Molecular biology is a nanotechnology that works--it has worked for billions of years and in an amazing variety of circumstances. At its core is a system for acquiring, processing and communicating information that is universal, from…
Efficient energy transduction is one driver of evolution; and thus understanding biomolecular energy transduction is crucial to understanding living organisms. As an energy-orientated modelling methodology, bond graphs provide a useful…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…
With the rise of computers, simulation models have emerged beside the more traditional statistical and mathematical models as a third pillar for ecological analysis. Broadly speaking, a simulation model is an algorithm, typically…
This survey paper focuses on modulation aspects of molecular communication, an emerging field focused on building biologically-inspired systems that embed data within chemical signals. The primary challenges in designing these systems are…
Biological and artificial information processing systems form representations of the world that they can use to categorize, reason, plan, navigate, and make decisions. How can we measure the similarity between the representations formed by…
This paper surveys foundation models for AI-enabled biological design, focusing on recent developments in applying large-scale, self-supervised models to tasks such as protein engineering, small molecule design, and genomic sequence design.…