Related papers: SANTA: quantifying the functional content of molec…
In this paper, we present SANTA, a scalable framework to automatically normalize E-commerce attribute values (e.g. "Win 10 Pro") to a fixed set of pre-defined canonical values (e.g. "Windows 10"). Earlier works on attribute normalization…
In this perspective article, we present a multidisciplinary approach for characterizing protein structure networks. We first place our approach in its historical context and describe the manner in which it synthesizes concepts from quantum…
Four chapters of the synthesis represent four major areas of my research interests: 1) data analysis in molecular biology, 2) mathematical modeling of biological networks, 3) genome evolution, and 4) cancer systems biology. The first…
A key challenge in systems biology is the elucidation of the underlying principles, or fundamental laws, which determine the cellular phenotype. Understanding how these fundamental principles are altered in diseases like cancer is important…
Networks describe a variety of interacting complex systems in social science, biology and information technology. Usually the nodes of real networks are identified not only by their connections but also by some other characteristics.…
Networks are useful for describing systems of interacting objects, where the nodes represent the objects and the edges represent the interactions between them. The applications include chemical and metabolic systems, food webs as well as…
The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy cellular state is therefore of critical importance for gaining systems-level…
Network inference approaches are now widely used in biological applications to probe regulatory relationships between molecular components such as genes or proteins. Many methods have been proposed for this setting, but the connections and…
Studies into the statistical properties of biological networks have led to important biological insights, such as the presence of hubs and hierarchical modularity. There is also a growing interest in studying the statistical properties of…
The ability to compare complex systems can provide new insight into the fundamental nature of the processes captured in ways that are otherwise inaccessible to observation. Here, we introduce the $n$-tangle method to directly compare two…
Despite the common misconception of nearly static organisms, plants do interact continuously with the environment and with each other. It is fair to assume that during their evolution they developed particular features to overcome problems…
Biological systems operate under simultaneous energetic and informational constraints, yet direct evidence that such constraints shape real metabolic networks is limited. The Network-Weighted Action Principle predicts that networks under…
While progress has been made in identifying common genetic variants associated with human diseases, for most of common complex diseases, the identified genetic variants only account for a small proportion of heritability. Challenges remain…
Over the past decade, a number of researchers in systems biology have sought to relate the function of biological systems to their network-level descriptions -- lists of the most important players and the pairwise interactions between them.…
Randomized experiments, or "A/B" tests, remain the gold standard for evaluating the causal effect of a policy intervention or product change. However, experimental settings, such as social networks, where users are interacting and…
This paper presents a statistically sound method for measuring the accuracy with which a probabilistic model reflects the growth of a network, and a method for optimising parameters in such a model. The technique is data-driven, and can be…
Protein interaction networks are a promising type of data for studying complex biological systems. However, despite the rich information embedded in these networks, they face important data quality challenges of noise and incompleteness…
The interactions among the constituent members of a microbial community play a major role in determining the overall behavior of the community and the abundance levels of its members. These interactions can be modeled using a network whose…
The identification of predefined groups of genes ("gene-sets") which are differentially expressed between two conditions ("gene-set analysis", or GSA) is a very popular analysis in bioinformatics. GSA incorporates biological knowledge by…
The empirical validation of community detection methods is often based on available annotations on the nodes that serve as putative indicators of the large-scale network structure. Most often, the suitability of the annotations as…