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Large-scale perturbations in the microbiome constitution are strongly correlated, whether as a driver or a consequence, with the health and functioning of human physiology. However, understanding the difference in the microbiome profiles of…
Understanding kinetics and thermodynamics profile of biomolecules is necessary to understand their functional roles which has a major impact in mechanism driven drug discovery. Molecular dynamics simulation has been routinely used to…
We introduce an approach to partitioning networks into communities that not only determines the best community structure, but also provides a range of characterization techniques to assess how significant that structure is. We study the…
Mathematical models are increasingly used in both academia and the pharmaceutical industry to understand how phenotypes emerge from systems of molecular interactions. However, their current construction as monolithic sets of equations…
Molecular motors do not work in isolation {\it in-vivo}. We highlight some of the coordinations, cooperations and competitions that determine the collective properties of molecular motors in eukaryotic cells. In the context of traffic-like…
This is the first report, to our knowledge, on a systematic method for constructing a large scale kinetic metabolic model with incomplete information on kinetic parametersr, and its initial application to the modeling of central metabolism…
Representation of cities as organisms with metabolic processes is a useful analogy for urban design, development and sustainability. Urban metabolism can be modeled by representing urban systems as networks. The various networks included in…
Many complex systems in nature and society can be described in terms of networks capturing the intricate web of connections among the units they are made of. A key question is how to interpret the global organization of such networks as the…
Organisms from microbes to humans engage in a variety of social behaviors, which affect fitness in complex, often nonlinear ways. The question of how these behaviors evolve has consequences ranging from antibiotic resistance to human…
Living systems are made of active materials with microscopic components that work together to perform macroscopic biological tasks. The breakdown of these collective functionalities leads to diseases, which, conversely, could be treated by…
Networks coming from protein-protein interactions, transcriptional regulation, signaling, or metabolism may appear to have "unusual" properties. To quantify this, it is appropriate to randomize the network and test the hypothesis that the…
In many social mammals, early life social adversity and social integration largely predict individual health, lifespan and reproductive success. Efforts in identifying the physiological mechanisms mediating the relationship between the…
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…
Cooperative behavior is widespread in nature, even though cooperating individuals always run the risk to be exploited by free-riders. Population structure effectively promotes cooperation given that a threshold in the level of cooperation…
In a complex system, the individual components are neither so tightly coupled or correlated that they can all be treated as a single unit, nor so uncorrelated that they can be approximated as independent entities. Instead, patterns of…
Community structure is one of the most relevant features encountered in numerous real-world applications of networked systems. Despite the tremendous effort of scientists working on this subject over the past few decades to characterize,…
Understanding the system level adaptive changes taking place in an organism in response to variations in the environment is a key issue of contemporary biology. Current modeling approaches such as the constraint-based flux balance analyses…
Microbial networks, representing microbes as nodes and their interactions as edges, are crucial for understanding community dynamics in various environments. Analyzing microbiome networks is crucial for identifying keystone taxa that play…
Lately, experimental research on microbial symbioses based on nutrient exchange and interdependence has yielded a number of interesting findings, however an in-depth mathematical description of the exact underlying dynamics of such…
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…