Genome-Wide Associations of Signaling Pathways in Glioblastoma Multiforme

Background: eQTL analysis is a powerful method that allows the identification of causal genomic alterations, providing an explanation of expression changes of single genes. However, genes mediate their biological roles in groups rather than in isolation, prompting us to extend the concept of eQTLs to whole gene pathways. Methods: We combined matched genomic alteration and gene expression data of glioblastoma patients and determined associations between the expression of signaling pathways and genomic copy number alterations with a non-linear machine learning approach. Results: Expectedly, over-expressed pathways were largely associated to tag-loci on chromosomes with signature alterations. Surprisingly, tag-loci that were associated to under-expressed pathways were largely placed on other chromosomes, an observation that held for composite effects between chromosomes as well. Indicating their biological relevance, identified genomic regions were highly enriched with genes having a reported driving role in gliomas. Furthermore, we found pathways that were significantly enriched with such driver genes. Conclusions: Driver genes and their associated pathways may represent a functional core that drive the tumor emergence and govern the signaling apparatus in GBMs. In addition, such associations may be indicative of drug combinations for the treatment of brain tumors that follow similar patterns of common and diverging alterations

Untangling the Web of E-Research: Towards a Sociology of Online Knowledge

e-Research is a rapidly growing research area, both in terms of publications and in terms of funding. In this article we argue that it is necessary to reconceptualize the ways in which we seek to measure and understand e-Research by developing a sociology of knowledge based on our understanding of how science has been transformed historically and shifted into online forms. Next, we report data which allows the examination of e-Research through a variety of traces in order to begin to understand how the knowledge in the realm of e-Research has been and is being constructed. These data indicate that e-Research has had a variable impact in different fields of research. We argue that only an overall account of the scale and scope of e-Research within and between different fields makes it possible to identify the organizational coherence and diffuseness of e-Research in terms of its socio-technical networks, and thus to identify the contributions of e-Research to various research fronts in the online production of knowledge

Computational methods in cancer gene networking

In the past few years, many high-throughput techniques have been developed and applied to biological studies. These techniques such as “next generation” genome sequencing, chip-on-chip, microarray and so on can be used to measure gene expression and gene regulatory elements in a genome-wide scale. Moreover, as these technologies become more affordable and accessible, they have become a driving force in modern biology. As a result, huge amount biological data have been produced, with the expectation of increasing number of such datasets to be generated in the future. High-throughput data are more comprehensive and unbiased, but ‘real signals’ or biological insights, molecular mechanisms and biological principles are buried in the flood of data. In current biological studies, the bottleneck is no longer a lack of data, but the lack of ingenuity and computational means to extract biological insights and principles by integrating knowledge and high-throughput data. 

Here I am reviewing the concepts and principles of network biology and the computational methods which can be applied to cancer research. Furthermore, I am providing a practical guide for computational analysis of cancer gene networks

Authorship analysis of specialized vs diversified research output

The present work investigates the relations between amplitude and type of collaboration (intramural, extramural domestic or international) and output of specialized versus diversified research. By specialized or diversified research, we mean within or beyond the author's dominant research topic. The field of observation is the scientific production over five years from about 23,500 academics. The analyses are conducted at the aggregate and disciplinary level. The results lead to the conclusion that in general, the output of diversified research is no more frequently the fruit of collaboration than is specialized research. At the level of the particular collaboration types, international collaborations weakly underlie the specialized kind of research output; on the contrary, extramural domestic and intramural collaborations are weakly associated with diversified research. While the weakness of association remains, exceptions are observed at the level of the individual disciplines