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Molecular gastronomy is a distinct sub-discipline of food science that takes an active role in examining chemical and physical properties of ingredients and as such lends itself to more scientific approaches to finding novel ingredient…
Proteomics will celebrate its 20th year in 2014. In this relatively short period of time, it has invaded most areas of biology and its use will probably continue to spread in the future. These two decades have seen a considerable increase…
A detailed understanding of biochemical networks at the molecular level is essential for studying complex cellular processes. In this paper, we provide a comprehensive description of biochemical networks by considering individual atoms and…
Network science has become an essential interdisciplinary tool for understanding complex biological systems. However, because these systems undergo continuous, often stimulus-driven changes in both structure and function, traditional static…
Understanding the origins of complexity is a fundamental challenge with implications for biological and technological systems. Network theory emerges as a powerful tool to model complex systems. Networks are an intuitive framework to…
Biomedical networks (or graphs) are universal descriptors for systems of interacting elements, from molecular interactions and disease co-morbidity to healthcare systems and scientific knowledge. Advances in artificial intelligence,…
Pathway enrichment analysis has become a key tool for biomedical researchers to gain insight into the underlying biology of differentially expressed genes, proteins and metabolites. It reduces complexity and provides a system-level view of…
Interactive visualization tools are highly desirable to biologist and cancer researchers to explore the complex structures, detect patterns and find out the relationships among bio-molecules responsible for a cancer type. A pathway contains…
Motivation: Molecular interaction networks summarize complex biological processes as graphs, whose structure is informative of biological function at multiple scales. Simultaneously, omics technologies measure the variation or activity of…
A major issue in biology is the understanding of the interactions between proteins. These interactions can be described by a network, where the proteins are modeled by nodes and the interactions by edges. The origin of these protein…
This dissertation contributes to mathematical and algorithmic problems that arise in the analysis of network and biological data.
High-throughput protein interaction detection methods are strongly affected by false positive and false negative results. Focused experiments are needed to complement the large-scale methods by validating previously detected interactions…
Reliability on complex biological networks reconstructions remains a concern. Although observations are getting more and more precise, the data collection process is yet error prone and the proofs display uneven certitude. In the case of…
Empirical studies of graphs have contributed enormously to our understanding of complex systems. Known today as network science, what was originally a theoretical study of graphs has grown into a more scientific exploration of communities…
The vast amount of biological knowledge accumulated over the years has allowed researchers to identify various biochemical interactions and define different families of pathways. There is an increased interest in identifying pathways and…
Increasing evidence has shown that gene-gene interactions have important effects on biological processes of human diseases. Due to the high dimensionality of genetic measurements, existing interaction analysis methods usually suffer from a…
Many biological networks have been labelled scale-free as their degree distribution can be approximately described by a powerlaw distribution. While the degree distribution does not summarize all aspects of a network it has often been…
One approach to studying the system-wide organization of biochemistry is to use statistical graph theory. Even in such a heavily simplified method, which disregards most of the dynamic aspects of biochemistry, one is faced with fundamental…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
System and synthetic biology are rapidly evolving systems, but both lack tools such as those used in engineering environments to shift the their focus from the design of parts (details) to the design of systems (behaviors); to aggravate,…