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High throughput genome sequencing technologies such as RNA-Seq and Microarray have the potential to transform clinical decision making and biomedical research by enabling high-throughput measurements of the genome at a granular level.…

Notch signaling is an evolutionary conserved cell-cell communication pathway. Besides regulating cell-fate decisions at an individual cell level, Notch signaling coordinates the emergent spatiotemporal patterning in a tissue through…

Directed protein networks with only a few thousand of nodes are rather complex and do not allow to extract easily the effective influence of one protein to another taking into account all indirect pathways via the global network.…

Signal processing traditionally relies on classical statistical modeling techniques. Such model-based methods utilize mathematical formulations that represent the underlying physics, prior information and additional domain knowledge. Simple…

Accurately modeling and designing protein complex structures is a central problem in computational structural biology, with broad implications for understanding cellular function and developing therapeutics. This thesis investigates two…

Biomedical signals carry signature rhythms of complex physiological processes that control our daily bodily activity. The properties of these rhythms indicate the nature of interaction dynamics among physiological processes that maintain a…

Molecular communication (MC) engineering is inspired by the use of chemical signals as information carriers in cell biology. The biological nature of chemical signaling makes MC a promising methodology for interdisciplinary applications…

Identification and characterization of large protein complexes is a mainstay of biochemical toolboxes. Utilization of cross-linking chemicals can facilitate the capture and identification of transient or weak interactions of a transient…

Mechanics and biochemical signaling are both often deregulated in cancer, leading to cancer cell phenotypes that exhibit increased invasiveness, proliferation, and survival. The dynamics and interactions of cytoskeletal components control…

The evolution, regulation and sustenance of biological complexity is determined by protein-protein interaction network that is filled with dynamic events. Recent experimental evidences point out that clustering of proteins has a vital role…

Identifying concentrations of components from an observed mixture is a fundamental problem in signal processing. It has diverse applications in fields ranging from hyperspectral imaging to denoising biomedical sensors. This paper focuses on…

The analysis of correlations of amino acid occurrences in globular proteins has led to the development of statistical tools that can identify native contacts -- portions of the chains that come to close distance in folded structural…

Biological systems are often modeled as a system of ordinary differential equations (ODEs) with time-invariant parameters. However, cell signaling events or pharmacological interventions may alter the cellular state and induce multi-mode…

Advances in single-cell omics allow for unprecedented insights into the transcription profiles of individual cells. When combined with large-scale perturbation screens, through which specific biological mechanisms can be targeted, these…

Biological cells encode information about their environment through biochemical signaling networks that control their internal state and response. This information is often encoded in the dynamical patterns of the signaling molecules,…

Biological signaling pathways based upon proteins binding to one another to relay a signal for genetic expression, such as the Bone Morphogenetic Protein (BMP) signaling pathway, can be modeled by mass action kinetics and conservation laws…

Cellulases hold great promise for the production of biofuels and biochemicals. However, they are modular enzymes acting on a complex heterogeneous substrate. Because of this complexity, the computational prediction of their catalytic…

The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…

Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…

Intracellular transport processes are essential to the healthy development of many organisms as well as more generally to healthy cellular function. The complex dynamics and interactions between protein molecules and filaments on different…