@article{GhylinGarciaMoyaetal.2014,
  author    = {Ghylin, Trevor W. and Garcia, Sarahi L. and Moya, Francisco and Oyserman, Ben O. and Schwientek, Patrick and Forest, Katrina T. and Mutschler, James and Dwulit-Smith, Jeffrey and Chan, Leong-Keat and Martinez-Garcia, Manuel and Sczyrba, Alexander and Stepanauskas, Ramunas and Grossart, Hans-Peter and Woyke, Tanja and Warnecke, Falk and Malmstrom, Rex and Bertilsson, Stefan and McMahon, Katherine D.},
  title     = {Comparative single-cell genomics reveals potential ecological niches for the freshwater acl Actinobacteria lineage},
  series = {The ISME journal : multidisciplinary journal of microbial ecology},
  volume    = {8},
  journal   = {The ISME journal : multidisciplinary journal of microbial ecology},
  number    = {12},
  publisher = {Nature Publ. Group},
  address   = {London},
  issn      = {1751-7362},
  doi       = {10.1038/ismej.2014.135},
  pages     = {2503 -- 2516},
  year      = {2014},
  abstract  = {Members of the acI lineage of Actinobacteria are the most abundant microorganisms in most freshwater lakes; however, our understanding of the keys to their success and their role in carbon and nutrient cycling in freshwater systems has been hampered by the lack of pure cultures and genomes. We obtained draft genome assemblies from 11 single cells representing three acI tribes (acI-A1, acI-A7, acI-B1) from four temperate lakes in the United States and Europe. Comparative analysis of acI SAGs and other available freshwater bacterial genomes showed that acI has more gene content directed toward carbohydrate acquisition as compared to Polynucleobacter and LD12 Alphaproteobacteria, which seem to specialize more on carboxylic acids. The acI genomes contain actinorhodopsin as well as some genes involved in anaplerotic carbon fixation indicating the capacity to supplement their known heterotrophic lifestyle. Genome-level differences between the acI-A and acI-B clades suggest specialization at the clade level for carbon substrate acquisition. Overall, the acI genomes appear to be highly streamlined versions of Actinobacteria that include some genes allowing it to take advantage of sunlight and N-rich organic compounds such as polyamines, di-and oligopeptides, branched-chain amino acids and cyanophycin. This work significantly expands the known metabolic potential of the cosmopolitan freshwater acI lineage and its ecological and genetic traits.},
  language  = {en}
}
@misc{LamprechtMargariaSteffenetal.2008,
  author    = {Lamprecht, Anna-Lena and Margaria, Tiziana and Steffen, Bernhard and Sczyrba, Alexander and Hartmeier, Sven and Giegerich, Robert},
  title     = {GeneFisher-P},
  series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  journal   = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe},
  number    = {868},
  issn      = {1866-8372},
  doi       = {10.25932/publishup-43424},
  url       = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-434241},
  pages     = {17},
  year      = {2008},
  abstract  = {Background: PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using workflow techniques. We apply a service-oriented approach to model and implement GeneFisher-P, a process-based version of the GeneFisher web application, as a part of the Bio-jETI platform for service modeling and execution. We show how to introduce a flexible process layer to meet the growing demand for improved user-friendliness and flexibility. Results: Within Bio-jETI, we model the process using the jABC framework, a mature model-driven, service-oriented process definition platform. We encapsulate remote legacy tools and integrate web services using jETI, an extension of the jABC for seamless integration of remote resources as basic services, ready to be used in the process. Some of the basic services used by GeneFisher are in fact already provided as individual web services at BiBiServ and can be directly accessed. Others are legacy programs, and are made available to Bio-jETI via the jETI technology. The full power of service-based process orientation is required when more bioinformatics tools, available as web services or via jETI, lead to easy extensions or variations of the basic process. This concerns for instance variations of data retrieval or alignment tools as provided by the European Bioinformatics Institute (EBI). Conclusions: The resulting service-and process-oriented GeneFisher-P demonstrates how basic services from heterogeneous sources can be easily orchestrated in the Bio-jETI platform and lead to a flexible family of specialized processes tailored to specific tasks.},
  language  = {en}
}
@book{LamprechtMagariaSteffenetal.2007,
  author    = {Lamprecht, Anna-Lena and Magaria, Tiziana and Steffen, Bernhard and Sczyrba, Alexander and Hartmeier, Sven and Giegerich, Robert},
  title     = {GeneFisher-P},
  series = {Preprint / Universit{\"a}t Potsdam, Institut f{\"u}r Informatik},
  volume    = {2007, 3},
  journal   = {Preprint / Universit{\"a}t Potsdam, Institut f{\"u}r Informatik},
  publisher = {Univ.},
  address   = {Potsdam},
  issn      = {0946-7580},
  pages     = {17 S.},
  year      = {2007},
  language  = {en}
}