Related papers: Molecular Diversity and Network Complexity in Grow…
Metabolic networks are complex systems that comprise hundreds of chemical reactions which synthesize biomass molecules from chemicals in an organism's environment. The metabolic network of any one organism is encoded by a metabolic…
Deep generative models have been shown powerful in generating novel molecules with desired chemical properties via their representations such as strings, trees or graphs. However, these models are limited in recommending synthetic routes…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
In a molecular communication network, transmitters may encode information in concentration or frequency of signalling molecules. When the signalling molecules reach the receivers, they react, via a set of chemical reactions or a molecular…
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…
In multiplex networks with a large number of layers, the nodes can have different activities, indicating the total number of layers in which the nodes are present. Here we model multiplex networks with heterogeneous activity of the nodes…
Cellular life requires the presence of a set of biochemical mechanisms in order to maintain a predictable process of growth and division. Several attempts have been made towards the building of minimal protocells from a top-down approach,…
It has been proposed that cultural evolution was made possible by a cognitive transition brought about by onset of the capacity for self-triggered recall and rehearsal. Here we develop a novel idea that models of collectively autocatalytic…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
The capacity of cells and organisms to respond to challenging conditions in a repeatable manner is limited by a finite repertoire of pre-evolved adaptive responses. Beyond this capacity, cells can use exploratory dynamics to cope with a…
We explore the emergence of complex structures within reaction networks, focusing on nuclear reaction networks relevant to stellar nucleosynthesis. The work presents a theoretical framework rooted in Chemical Organization Theory (COT) to…
In this Master's thesis, the graph properties of a multi-level drug-protein network are studied, as well as how the network's shape has informed discoveries over the years, identifying primarily crawling discoveries and a smaller number of…
Living matter moves, deforms, and organizes itself. In cells this is made possible by networks of polymer filaments and crosslinking molecules that connect filaments to each other and that act as motors to do mechanical work on the network.…
Metabolism plays a central role in cell physiology because it provides the molecular machinery for growth. At the genome-scale, metabolism is made up of thousands of reactions interacting with one another. Untangling this complexity is key…
Designing a neural network architecture for molecular representation is crucial for AI-driven drug discovery and molecule design. In this work, we propose a new framework for molecular representation learning. Our contribution is threefold:…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
Complex networks serve as abstract models for understanding real-world complex systems and provide frameworks for studying structured dynamical systems. This article addresses limitations in current studies on the exploration of individual…
Although species longevity is subject to a diverse range of selective forces, the mortality curves of a wide variety of organisms are rather similar. We argue that aging and its universal characteristics may have evolved by means of a…
High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major…