% IMPORTANT: The following is UTF-8 encoded.  This means that in the presence
% of non-ASCII characters, it will not work with BibTeX 0.99 or older.
% Instead, you should use an up-to-date BibTeX implementation like “bibtex8” or
% “biber”.

@ARTICLE{Weichenberger:127764,
      author       = {C. X. Weichenberger and H. Blankenburg and A. Palermo and
                      Y. D'Elia and E. König and E. Bernstein$^*$ and F. S.
                      Domingues},
      title        = {{D}intor: functional annotation of genomic and proteomic
                      data.},
      journal      = {BMC genomics},
      volume       = {16},
      number       = {1},
      issn         = {1471-2164},
      address      = {London},
      publisher    = {BioMed Central},
      reportid     = {DKFZ-2017-03786},
      pages        = {1081},
      year         = {2015},
      abstract     = {During the last decade, a great number of extremely
                      valuable large-scale genomics and proteomics datasets have
                      become available to the research community. In addition,
                      dropping costs for conducting high-throughput sequencing
                      experiments and the option to outsource them considerably
                      contribute to an increasing number of researchers becoming
                      active in this field. Even though various computational
                      approaches have been developed to analyze these data, it is
                      still a laborious task involving prudent integration of many
                      heterogeneous and frequently updated data sources, creating
                      a barrier for interested scientists to accomplish their own
                      analysis.We have implemented Dintor, a data integration
                      framework that provides a set of over 30 tools to assist
                      researchers in the exploration of genomics and proteomics
                      datasets. Each of the tools solves a particular task and
                      several tools can be combined into data processing
                      pipelines. Dintor covers a wide range of frequently required
                      functionalities, from gene identifier conversions and
                      orthology mappings to functional annotation of proteins and
                      genetic variants up to candidate gene prioritization and
                      Gene Ontology-based gene set enrichment analysis. Since the
                      tools operate on constantly changing datasets, we provide a
                      mechanism to unambiguously link tools with different
                      versions of archived datasets, which guarantees reproducible
                      results for future tool invocations. We demonstrate a
                      selection of Dintor's capabilities by analyzing datasets
                      from four representative publications. The open source
                      software can be downloaded and installed on a local Unix
                      machine. For reasons of data privacy it can be configured to
                      retrieve local data only. In addition, the Dintor tools are
                      available on our public Galaxy web service at
                      http://dintor.eurac.edu .Dintor is a computational
                      annotation framework for the analysis of genomic and
                      proteomic datasets, providing a rich set of tools that cover
                      the most frequently encountered tasks. A major advantage is
                      its capability to consistently handle multiple versions of
                      tool-associated datasets, supporting the researcher in
                      delivering reproducible results.},
      cin          = {W310},
      ddc          = {570},
      cid          = {I:(DE-He78)W310-20160331},
      pnm          = {312 - Functional and structural genomics (POF3-312)},
      pid          = {G:(DE-HGF)POF3-312},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:26691694},
      pmc          = {pmc:PMC4687148},
      doi          = {10.1186/s12864-015-2279-5},
      url          = {https://inrepo02.dkfz.de/record/127764},
}