An ultimate complexity is the machinery of life. From molecules to populations, from biochemistry to ecology, the devil is in the detail. The “reductionist” approaches that have led to resounding success in physical science seem reckless considering the formidable biological details. What can we do? Here is the need for phenomenology based on biological numeracy and quantitative abstraction. A success story comes from the earlier development of thermodynamics, where the notions of atoms and molecules had remained only a metaphysical insight. We try to find, in close collaboration with wet biologists, effective coarse-graining schemes that map “form” onto “function” and vice versa.
Nature, Nurture, and “Chance”
Stochastic fluctuations in a cell: noise propagation in signal transduction, transcription regulation, and cellular metabolism.
Chemical kinetics of a single enzyme and dynamic disorder
Microbial Cell Factory
Constraint-based modeling for synthetic biology and metabolic engineering
Interplay between growth physiology and regulation of gene expression
Inference in Biological Networks
Causation from correlation in neural information processing.
Tumorigenesis reconstructed by genetic heterogeneity and mutational trajectories.
Retroviral forensics based on quasispecies evolution
Dynamics on Structured Populations
Propagation of information in spatially structured media.
Evolutionary graph theory in correlated graphs.