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@ARTICLE{Rahman:139797,
      author       = {Rahman, Raza-Ur and Gautam, Abhivyakti and Bethune, Jörn
                      and Sattar, Abdul and Fiosins, Maksims and Magruder, Daniel
                      Sumner and Capece, Vincenzo and Shomroni, Orr and Bonn,
                      Stefan},
      title        = {{O}asis 2: improved online analysis of small {RNA}-seq
                      data.},
      journal      = {BMC bioinformatics},
      volume       = {19},
      number       = {1},
      issn         = {1471-2105},
      address      = {Heidelberg},
      publisher    = {Springer},
      reportid     = {DZNE-2020-06119},
      pages        = {54},
      year         = {2018},
      abstract     = {Small RNA molecules play important roles in many biological
                      processes and their dysregulation or dysfunction can cause
                      disease. The current method of choice for genome-wide sRNA
                      expression profiling is deep sequencing.Here we present
                      Oasis 2, which is a new main release of the Oasis web
                      application for the detection, differential expression, and
                      classification of small RNAs in deep sequencing data.
                      Compared to its predecessor Oasis, Oasis 2 features a novel
                      and speed-optimized sRNA detection module that supports the
                      identification of small RNAs in any organism with higher
                      accuracy. Next to the improved detection of small RNAs in a
                      target organism, the software now also recognizes potential
                      cross-species miRNAs and viral and bacterial sRNAs in
                      infected samples. In addition, novel miRNAs can now be
                      queried and visualized interactively, providing essential
                      information for over 700 high-quality miRNA predictions
                      across 14 organisms. Robust biomarker signatures can now be
                      obtained using the novel enhanced classification
                      module.Oasis 2 enables biologists and medical researchers to
                      rapidly analyze and query small RNA deep sequencing data
                      with improved precision, recall, and speed, in an
                      interactive and user-friendly environment.Oasis 2 is
                      implemented in Java, J2EE, mysql, Python, R, PHP and
                      JavaScript. It is freely available at
                      https://oasis.dzne.de.},
      keywords     = {Base Sequence / Gene Expression Profiling / High-Throughput
                      Nucleotide Sequencing / MicroRNAs: genetics / RNA, Small
                      Untranslated: genetics / Sequence Analysis, RNA: methods /
                      Software / Statistics as Topic: methods / MicroRNAs (NLM
                      Chemicals) / RNA, Small Untranslated (NLM Chemicals)},
      cin          = {AG Bonn 1 / AG Bonn 2 / AG Fischer},
      ddc          = {610},
      cid          = {I:(DE-2719)1410003 / I:(DE-2719)1440012 /
                      I:(DE-2719)1410002},
      pnm          = {342 - Disease Mechanisms and Model Systems (POF3-342)},
      pid          = {G:(DE-HGF)POF3-342},
      typ          = {PUB:(DE-HGF)16},
      pubmed       = {pmid:29444641},
      pmc          = {pmc:PMC5813365},
      doi          = {10.1186/s12859-018-2047-z},
      url          = {https://pub.dzne.de/record/139797},
}