@article{ShityakovBencurovaFoersteretal.2020,
  author    = {Shityakov, Sergey and Bencurova, Elena and F{\"o}rster, Carola and Dandekar, Thomas},
  title     = {Modeling of shotgun sequencing of DNA plasmids using experimental and theoretical approaches},
  series = {BMC Bioinformatics},
  volume    = {2020},
  journal   = {BMC Bioinformatics},
  doi       = {10.1186/s12859-020-3461-6},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-229169},
  year      = {2020},
  abstract  = {Background Processing and analysis of DNA sequences obtained from next-generation sequencing (NGS) face some difficulties in terms of the correct prediction of DNA sequencing outcomes without the implementation of bioinformatics approaches. However, algorithms based on NGS perform inefficiently due to the generation of long DNA fragments, the difficulty of assembling them and the complexity of the used genomes. On the other hand, the Sanger DNA sequencing method is still considered to be the most reliable; it is a reliable choice for virtual modeling to build all possible consensus sequences from smaller DNA fragments. Results In silico and in vitro experiments were conducted: (1) to implement and test our novel sequencing algorithm, using the standard cloning vectors of different length and (2) to validate experimentally virtual shotgun sequencing using the PCR technique with the number of cycles from 1 to 9 for each reaction. Conclusions We applied a novel algorithm based on Sanger methodology to correctly predict and emphasize the performance of DNA sequencing techniques as well as in de novo DNA sequencing and its further application in synthetic biology. We demonstrate the statistical significance of our results.},
  language  = {en}
}
@article{KellerGrimmerSteffanDewenter2013,
  author    = {Keller, Alexander and Grimmer, Gudrun and Steffan-Dewenter, Ingolf},
  title     = {Diverse Microbiota Identified in Whole Intact Nest Chambers of the Red Mason Bee Osmia bicornis (Linnaeus 1758)},
  series = {PLoS One},
  journal   = {PLoS One},
  doi       = {10.1371/journal.pone.0078296},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-97305},
  year      = {2013},
  abstract  = {Microbial activity is known to have profound impact on bee ecology and physiology, both by beneficial and pathogenic effects. Most information about such associations is available for colony-building organisms, and especially the honey bee. There, active manipulations through worker bees result in a restricted diversity of microbes present within the colony environment. Microbial diversity in solitary bee nests remains unstudied, although their larvae face a very different situation compared with social bees by growing up in isolated compartments. Here, we assessed the microbiota present in nests and pre-adults of Osmia bicornis, the red mason bee, by culture-independent pyrosequencing. We found high bacterial diversity not comparable with honey bee colonies. We identified a variety of bacteria potentially with positive or negative interactions for bee larvae. However, most of the other diverse bacteria present in the nests seem to originate from environmental sources through incorporated nest building material and stored pollen. This diversity of microorganisms may cause severe larval mortality and require specific physiological or symbiotic adaptations against microbial threats. They may however also profit from such a diverse environment through gain of mutualistic partners. We conclude that further studies of microbiota interaction in solitary bees will improve the understanding of fitness components and populations dynamics.},
  language  = {en}
}