Searching for Communities in Bipartite Networks

Bipartite networks are a useful tool for representing and investigating interaction networks. We consider methods for identifying communities in bipartite networks. Intuitive notions of network community groups are made explicit using Newman's modularity measure. A specialized version of the modularity, adapted to be appropriate for bipartite networks, is presented; a corresponding algorithm is described for identifying community groups through maximizing this measure. The algorithm is applied to networks derived from the EU Framework Programs on Research and Technological Development. Community groups identified are compared using information-theoretic methods.Comment: 12 pages, 4 figures, to appear in "Proceedings of the 5th Jagna International Workshop: Stochastic and Quantum Dynamics of Biomolecular Systems," C. C. Bernido and M. V. Carpio-Bernido, editors. A version with full-quality figures and larger file size is available at http://ccm.uma.pt/publications/Barber-Faria-Streit-Strogan-2008.pd

Exploring and challenging the network of angiogenesis

Angiogenesis is one of the hallmarks of cancer and, as such, one of the alternative general targets for anticancer therapy. Since angiogenesis is a complex process involving a high number of interconnected components, a network approach would be a convenient systemic way to analyse responses to directed drug attacks. Herein we show that, although the angiogenic network is easily broken by short combinations of directed attacks, it still remains essentially functional by keeping the global patterns and local efficiency essentially unaltered after these attacks. This is a clear sign of its high robustness and resilience and stresses the need of directed, combined attacks for an effective blockade of the process. The results of this theoretical study could be relevant for the design of new antiangiogenic therapies and the selection of their targets

Реакція наукової спільноти на Чорнобильську аварію: аналіз розвитку тематики публікацій

Науку як різновид людської діяльності, що має на меті отримання нового знання, також можна розглядати як об’єкт вивчення. На цьому твердженні ґрунтується так звана «наука про науку» — наукометрія. У пропонованій роботі представлено результати наукометричного дослідження, метою якого було проаналізувати, як наукова спільнота реагує на певну подію, тобто як виглядає еволюція певної наукової тематики. На основі інформації з реферативних баз даних «Scopus» та «Україніка наукова» проаналізовано дані про наукові публікації, що висвітлюють проблему Чорнобильської аварії та її наслідків. Вивчено активність публікування робіт на чорнобильську тематику від 1986 і до 2011 рр., внесок науковців із різних країн, тематичний спектр досліджень.Наука как разновидность человеческой деятельности, имеющая своей целью получение нового знания, сама по себе тоже может быть рассмотрена как объект изучения. Такое утверждение лежит в основе так называемой «науки о науке» — наукометрии. В данной работе представлены результаты наукометрического исследования, целью которого было проанализировать, как научное сообщество реагирует на определенное событие, то есть как выглядит эволюция определенной научной тематики. На основе информации из реферативных баз данных «Scopus» и «Україніка наукова» были проанализированы данные о научных публикациях, освещающих проблему Чернобыльской аварии и ее последствий. Была изучена активность публикаций работ на чернобыльскую тематику в период от 1986 и до 2011 гг., вклад ученых из разных стран, тематический спектр исследований.In our study we analyze how does an academic community react on a particular urgent task which abruptly arises and poses also scientific problems. To this end, we have chosen to examine a body of research strictly concerning Chornobyl disaster that occurred on 26 April 1986. We analyzed data about the papers that appeared in scientific journals since 1986 using the Scopus database and the Ukrainian bibliographic database Ukrainika Naukova. In order to quantify our analysis, we measured distribution of papers between different scientific fields, constructed coauthorship network and defined its main characteristics, calculated growth rates of research in different fields. In particular, our analysis allows to compare contribution of the international community to the Chornobyl-related research as well as integration of Ukraine in the international research on this subject

An approach for the identification of targets specific to bone metastasis using cancer genes interactome and gene ontology analysis

Metastasis is one of the most enigmatic aspects of cancer pathogenesis and is a major cause of cancer-associated mortality. Secondary bone cancer (SBC) is a complex disease caused by metastasis of tumor cells from their primary site and is characterized by intricate interplay of molecular interactions. Identification of targets for multifactorial diseases such as SBC, the most frequent complication of breast and prostate cancers, is a challenge. Towards achieving our aim of identification of targets specific to SBC, we constructed a 'Cancer Genes Network', a representative protein interactome of cancer genes. Using graph theoretical methods, we obtained a set of key genes that are relevant for generic mechanisms of cancers and have a role in biological essentiality. We also compiled a curated dataset of 391 SBC genes from published literature which serves as a basis of ontological correlates of secondary bone cancer. Building on these results, we implement a strategy based on generic cancer genes, SBC genes and gene ontology enrichment method, to obtain a set of targets that are specific to bone metastasis. Through this study, we present an approach for probing one of the major complications in cancers, namely, metastasis. The results on genes that play generic roles in cancer phenotype, obtained by network analysis of 'Cancer Genes Network', have broader implications in understanding the role of molecular regulators in mechanisms of cancers. Specifically, our study provides a set of potential targets that are of ontological and regulatory relevance to secondary bone cancer.Comment: 54 pages (19 pages main text; 11 Figures; 26 pages of supplementary information). Revised after critical reviews. Accepted for Publication in PLoS ON

The structure of R&D collaboration networks in the European Framework Programmes

Using a large and novel data source, we study the structure of R&D collaboration net-works in the first five EU Framework Programmes (FPs). The networks display proper-ties typical for complex networks, including scale-free degree distributions and the small-world property. Structural features are common across FPs, indicating similar network formation mechanisms despite changes in governance rules. Several findings point towards the existence of a stable core of interlinked actors since the early FPs with integration increasing over time. This core consists mainly of universities and research organisations. We observe assortative mixing by degree of projects, but not by degree of organisations. Unexpectedly, we find only weak association between central projects and project size, suggesting that different types of projects attract different groups of actors. In particular, large projects appear to have included few of the pivotal actors in the networks studied. Central projects only partially mirror funding priorities, indicating field-specific differences in network structures. The paper concludes with an agenda for future research.R&D collaboration, EU Framework Programmes, Complex Networks, Small World Effect, Centrality Measures, European Research Area