Mapping the Structure and Dynamics of Genomics-Related MeSH Terms Complex Networks

It has been proposed that the history and evolution of scientific ideas may reflect certain aspects of the underlying socio-cognitive frameworks in which science itself is developing. Systematic analyses of the development of scientific knowledge may help us to construct models of the collective dynamics of science. Aiming at scientific rigor, these models should be built upon solid empirical evidence, analyzed with formal tools leading to ever-improving results that support the related conclusions. Along these lines we studied the dynamics and structure of the development of research in genomics as represented by the entire collection of genomics-related scientific papers contained in the PubMed database. The analyzed corpus consisted in more than 49,000 articles published in the years 1987 (first appeareance of the term Genomics) to 2011, categorized by means of the Medical Subheadings (MeSH) content-descriptors. Complex networks were built where two MeSH terms were connected if they are descriptors of the same article(s). The analysis of such networks revealed a complex structure and dynamics that to certain extent resembled small-world networks. The evolution of such networks in time reflected interesting phenomena in the historical development of genomic research, including what seems to be a phase-transition in a period marked by the completion of the first draft of the Human Genome Project. We also found that different disciplinary areas have different dynamic evolution patterns in their MeSH connectivity networks. In the case of areas related to science, changes in topology were somewhat fast while retaining a certain core-stucture, whereas in the humanities, the evolution was pretty slow and the structure resulted highly redundant and in the case of technology related issues, the evolution was very fast and the structure remained tree-like with almost no overlapping terms.

PLoS ONE: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0092639

Information theoretical methods for complex network structure reconstruction

Complex networks seem to be ubiquitous objects in contemporary research, both in the natural and social sciences. An important area of research regarding the applicability and modeling of graph- theoretical-oriented approaches to complex systems, is the probabilistic inference of such networks. There exist different methods and algorithms designed for this purpose, most of them are inspired in statistical mechanics and rely on information theoretical grounds. An important shortcoming for most of these methods, when it comes to disentangle the actual structure of complex networks, is that they fail to distinguish between direct and indirect interactions. Here, we suggest a method to discover and assess for such indirect interactions within the framework of information theory.

CASM: http://www.casmodeling.com/content/1/1/8