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1.  Bioinformatic approaches for functional annotation and pathway inference in metagenomics data 
Briefings in Bioinformatics  2012;13(6):696-710.
Metagenomic approaches are increasingly recognized as a baseline for understanding the ecology and evolution of microbial ecosystems. The development of methods for pathway inference from metagenomics data is of paramount importance to link a phenotype to a cascade of events stemming from a series of connected sets of genes or proteins. Biochemical and regulatory pathways have until recently been thought and modelled within one cell type, one organism, one species. This vision is being dramatically changed by the advent of whole microbiome sequencing studies, revealing the role of symbiotic microbial populations in fundamental biochemical functions. The new landscape we face requires a clear picture of the potentialities of existing tools and development of new tools to characterize, reconstruct and model biochemical and regulatory pathways as the result of integration of function in complex symbiotic interactions of ontologically and evolutionary distinct cell types.
doi:10.1093/bib/bbs070
PMCID: PMC3505041  PMID: 23175748
metagenomics; next-generation sequencing; microbiome; pathway analysis; gene annotation
2.  Knowledge sharing and collaboration in translational research, and the DC-THERA Directory 
Briefings in Bioinformatics  2011;12(6):562-575.
Biomedical research relies increasingly on large collections of data sets and knowledge whose generation, representation and analysis often require large collaborative and interdisciplinary efforts. This dimension of ‘big data’ research calls for the development of computational tools to manage such a vast amount of data, as well as tools that can improve communication and access to information from collaborating researchers and from the wider community. Whenever research projects have a defined temporal scope, an additional issue of data management arises, namely how the knowledge generated within the project can be made available beyond its boundaries and life-time. DC-THERA is a European ‘Network of Excellence’ (NoE) that spawned a very large collaborative and interdisciplinary research community, focusing on the development of novel immunotherapies derived from fundamental research in dendritic cell immunobiology. In this article we introduce the DC-THERA Directory, which is an information system designed to support knowledge management for this research community and beyond. We present how the use of metadata and Semantic Web technologies can effectively help to organize the knowledge generated by modern collaborative research, how these technologies can enable effective data management solutions during and beyond the project lifecycle, and how resources such as the DC-THERA Directory fit into the larger context of e-science.
doi:10.1093/bib/bbr051
PMCID: PMC3220873  PMID: 21969471
semantic web; ontology; immunology; eScience; data integration

Results 1-2 (2)