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Understanding design principles of complex cellular organization is one of the major challenges in biology. Recent analysis of the large-scale cellular organization has revealed the scale-free nature and robustness of metabolic and protein…
The origin and early evolution of eukaryotes are one of the major transitions in the evolution of life on earth. One of its most interesting aspects is the emergence of cellular organelles, their dynamics, their functions, and their…
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…
The metabolism is the motor behind the biological complexity of an organism. One problem of characterizing its large-scale structure is that it is hard to know what to compare it to. All chemical reaction systems are shaped by the same…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Even closely related prokaryotes show an astounding diversity in their ability to grow in different nutritional environments. Mechanistically, this diversity arises predominantly through horizontal gene transfer, the exchange of DNA between…
It has been reported that the number of transcription factors encoded in prokaryotic genomes scales approximately quadratically with their total number of genes. We propose a conceptual explanation of this finding and illustrate it using a…
Ecological systems are emergent features of ecological and adaptive dynamics of a community of interacting species. By natural selection through the abiotic environment and by co-adaptation within the community, species evolve, thereby…
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…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
The possibility that evolutionary forces -- together with a few fundamental factors such as thermodynamic constraints, specific computational features enabling information processing, and ecological processes -- might constrain the logic of…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
In a cell or microorganism the processes that generate mass, energy, information transfer, and cell fate specification are seamlessly integrated through a complex network of various cellular constituents and reactions. However, despite the…
In biology, the evolution of increasingly cooperative groups has shaped the history of life. Genes collaborate in the control of cells; cells efficiently divide tasks to produce cohesive multicellular individuals; individual members of…
Biological and social systems are structured at multiple scales, and the incentives of individuals who interact in a group may diverge from the collective incentive of the group as a whole. Mechanisms to resolve this tension are responsible…
Cellular metabolism, the integrated interconversion of thousands of metabolic substrates through enzyme-catalyzed biochemical reactions, is the most investigated complex intercellular web of molecular interactions. While the topological…
The path toward the emergence of life in our biosphere involved several key events allowing for the persistence, reproduction and evolution of molecular systems. All these processes took place in a given environmental context and required…
Evolutionary dynamics is often viewed as a subtle process of change accumulation that causes a divergence among organisms and their genomes. However, this interpretation is an inheritance of a gradualistic view that has been challenged at…
Metabolism displays striking and robust regularities in the forms of modularity and hierarchy, whose composition may be compactly described. This renders metabolic architecture comprehensible as a system, and suggests the order in which…
The structure of molecular networks derives from dynamical processes on evolutionary time scales. For protein interaction networks, global statistical features of their structure can now be inferred consistently from several…