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Popular online enrichment analysis tools from the field of molecular systems biology provide users with the ability to submit their experimental results as gene sets for individual analysis. Such queries are kept private, and have never…
Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…
Evolutionary deep intelligence has recently shown great promise for producing small, powerful deep neural network models via the synthesis of increasingly efficient architectures over successive generations. Despite recent research showing…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
A system level view of cellular processes for human and several organisms can be cap- tured by analyzing molecular interaction networks. A molecular interaction network formed of differentially expressed genes and their interactions helps…
Network inference is a rapidly advancing field, with new methods being proposed on a regular basis. Understanding the advantages and limitations of different network inference methods is key to their effective application in different…
The practice of marriage is an understudied phenomenon in behavioural sciences despite being ubiquitous across human cultures. This modelling paper shows that replacing distant direct kin with in-laws increases the interconnectedness of the…
Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput…
Network representations of systems from various scientific and societal domains are neither completely random nor fully regular, but instead appear to contain recurring structural building blocks. These features tend to be shared by…
The advent of accessible ancient DNA technology now allows the direct ascertainment of allele frequencies in ancestral populations, thereby enabling the use of allele frequency time series to detect and estimate natural selection. Such…
Genetic algorithms are considered as one of the most efficient search techniques. Although they do not offer an optimal solution, their ability to reach a suitable solution in considerably short time gives them their respectable role in…
Social networks are organized into communities with dense internal connections, giving rise to high values of the clustering coefficient. In addition, these networks have been observed to be assortative, i.e. highly connected vertices tend…
Among the evolutionary methods, one that is quite prominent is Genetic Programming, and, in recent years, a variant called Geometric Semantic Genetic Programming (GSGP) has shown to be successfully applicable to many real-world problems.…
In many indigenous societies, people are categorised into several cultural groups, or clans, within which they believe to share ancestors. Clan attributions provide certain rules for marriage and descent. Such rules between clans constitute…
In recent years, with the advent of highly scalable artificial-neural-network-based text representation methods the field of natural language processing has seen unprecedented growth and sophistication. It has become possible to distill…
Most genes are part of larger families of evolutionary related genes. The history of gene families typically involves duplications and losses of genes as well as horizontal transfers into other organisms. The reconstruction of detailed gene…
The spanning tree heuristic is a commonly adopted procedure in network inference and estimation. It allows one to generalize an inference method developed for trees, which is usually based on a statistically rigorous approach, to a…
Community detection is an important research topic in complex networks. We present the employment of a genetic algorithm to detect communities in complex networks which is based on optimizing network modularity. It does not need any prior…
We introduce a new algorithm called {\sc Rec-Gen} for reconstructing the genealogy or \textit{pedigree} of an extant population purely from its genetic data. We justify our approach by giving a mathematical proof of the effectiveness of…
We develop a principled methodology to infer assortative communities in networks based on a nonparametric Bayesian formulation of the planted partition model. We show that this approach succeeds in finding statistically significant…