Towards a genome-wide transcriptogram: the Saccharomyces cerevisiae case

A genome modular classification that associates cellular processes to modules could lead to a method to quantify the differences in gene expression levels in different cellular stages or conditions: the transcriptogram, a powerful tool for assessing cell performance, would be at hand. Here we present a computational method to order genes on a line that clusters strongly interacting genes, defining functional modules associated with gene ontology terms. The starting point is a list of genes and a matrix specifying their interactions, available at large gene interaction databases. Considering the Saccharomyces cerevisiae genome we produced a succession of plots of gene transcription levels for a fermentation process. These plots discriminate the fermentation stage the cell is going through and may be regarded as the first versions of a transcriptogram. This method is useful for extracting information from cell stimuli/responses experiments, and may be applied with diagnostic purposes to different organisms

Clustering and Community Detection in Directed Networks: A Survey

Networks (or graphs) appear as dominant structures in diverse domains, including sociology, biology, neuroscience and computer science. In most of the aforementioned cases graphs are directed - in the sense that there is directionality on the edges, making the semantics of the edges non symmetric. An interesting feature that real networks present is the clustering or community structure property, under which the graph topology is organized into modules commonly called communities or clusters. The essence here is that nodes of the same community are highly similar while on the contrary, nodes across communities present low similarity. Revealing the underlying community structure of directed complex networks has become a crucial and interdisciplinary topic with a plethora of applications. Therefore, naturally there is a recent wealth of research production in the area of mining directed graphs - with clustering being the primary method and tool for community detection and evaluation. The goal of this paper is to offer an in-depth review of the methods presented so far for clustering directed networks along with the relevant necessary methodological background and also related applications. The survey commences by offering a concise review of the fundamental concepts and methodological base on which graph clustering algorithms capitalize on. Then we present the relevant work along two orthogonal classifications. The first one is mostly concerned with the methodological principles of the clustering algorithms, while the second one approaches the methods from the viewpoint regarding the properties of a good cluster in a directed network. Further, we present methods and metrics for evaluating graph clustering results, demonstrate interesting application domains and provide promising future research directions.Comment: 86 pages, 17 figures. Physics Reports Journal (To Appear

A citation-based map of concepts in invasion biology

Invasion biology has been quickly expanding in the last decades so that it is now metaphorically flooded with publications, concepts, and hypotheses. Among experts, there is no clear consensus about the relationships between invasion concepts, and almost no one seems to have a good overview of the literature anymore. Similar observations can be made for other research fields. Science needs new navigation tools so that researchers within and outside of a research field as well as science journalists, students, teachers, practitioners, policy-makers, and others interested in the field can more easily understand its key ideas. Such navigation tools could, for example, be maps of the major concepts and hypotheses of a research field. Applying a bibliometric method, we created such maps for invasion biology. We analysed research papers of the last two decades citing at least two of 35 common invasion hypotheses. Co-citation analysis yields four distinct clusters of hypotheses. These clusters can describe the main directions in invasion biology and explain basic driving forces behind biological invasions. The method we outline here for invasion biology can be easily applied for other research fields

Fast Detection of Community Structures using Graph Traversal in Social Networks

Finding community structures in social networks is considered to be a challenging task as many of the proposed algorithms are computationally expensive and does not scale well for large graphs. Most of the community detection algorithms proposed till date are unsuitable for applications that would require detection of communities in real-time, especially for massive networks. The Louvain method, which uses modularity maximization to detect clusters, is usually considered to be one of the fastest community detection algorithms even without any provable bound on its running time. We propose a novel graph traversal-based community detection framework, which not only runs faster than the Louvain method but also generates clusters of better quality for most of the benchmark datasets. We show that our algorithms run in O(|V | + |E|) time to create an initial cover before using modularity maximization to get the final cover. Keywords - community detection; Influenced Neighbor Score; brokers; community nodes; communitiesComment: 29 pages, 9 tables, and 13 figures. Accepted in "Knowledge and Information Systems", 201

Identifying the community structure of the international food-trade multi network

Achieving international food security requires improved understanding of how international trade networks connect countries around the world through the import-export flows of food commodities. The properties of food trade networks are still poorly documented, especially from a multi-network perspective. In particular, nothing is known about the community structure of food networks, which is key to understanding how major disruptions or 'shocks' would impact the global food system. Here we find that the individual layers of this network have densely connected trading groups, a consistent characteristic over the period 2001 to 2011. We also fit econometric models to identify social, economic and geographic factors explaining the probability that any two countries are co-present in the same community. Our estimates indicate that the probability of country pairs belonging to the same food trade community depends more on geopolitical and economic factors -- such as geographical proximity and trade agreements co-membership -- than on country economic size and/or income. This is in sharp contrast with what we know about bilateral-trade determinants and suggests that food country communities behave in ways that can be very different from their non-food counterparts.Comment: 47 pages, 19 figure