@article{YuVogelFoerstner2018,
  author    = {Yu, Sung-Huan and Vogel, J{\"o}rg and F{\"o}rstner, Konrad U.},
  title     = {ANNOgesic: a Swiss army knife for the RNA-seq based annotation of bacterial/archaeal genomes},
  series = {GigaScience},
  volume    = {7},
  journal   = {GigaScience},
  doi       = {10.1093/gigascience/giy096},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-178942},
  year      = {2018},
  abstract  = {To understand the gene regulation of an organism of interest, a comprehensive genome annotation is essential. While some features, such as coding sequences, can be computationally predicted with high accuracy based purely on the genomic sequence, others, such as promoter elements or noncoding RNAs, are harder to detect. RNA sequencing (RNA-seq) has proven to be an efficient method to identify these genomic features and to improve genome annotations. However, processing and integrating RNA-seq data in order to generate high-resolution annotations is challenging, time consuming, and requires numerous steps. We have constructed a powerful and modular tool called ANNOgesic that provides the required analyses and simplifies RNA-seq-based bacterial and archaeal genome annotation. It can integrate data from conventional RNA-seq and differential RNA-seq and predicts and annotates numerous features, including small noncoding RNAs, with high precision. The software is available under an open source license (ISCL) at https://pypi.org/project/ANNOgesic/.},
  language  = {en}
}
@article{FoerstnerReuscherHaberzettletal.2018,
  author    = {F{\"o}rstner, Konrad U and Reuscher, Carina M and Haberzettl, Kerstin and Weber, Lennart and Klug, Gabriele},
  title     = {RNase E cleavage shapes the transcriptome of Rhodobacter sphaeroides and strongly impacts phototrophic growth},
  series = {Life Science Alliance},
  volume    = {1},
  journal   = {Life Science Alliance},
  number    = {4},
  doi       = {10.26508/lsa.201800080},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-177139},
  pages     = {e201800080},
  year      = {2018},
  abstract  = {Bacteria adapt to changing environmental conditions by rapid changes in their transcriptome. This is achieved not only by adjusting rates of transcription but also by processing and degradation of RNAs. We applied TIER-Seq (transiently inactivating an endoribonuclease followed by RNA-Seq) for the transcriptome-wide identification of RNase E cleavage sites and of 5′ RNA ends, which are enriched when RNase E activity is reduced in Rhodobacter sphaeroides. These results reveal the importance of RNase E for the maturation and turnover of mRNAs, rRNAs, and sRNAs in this guanine-cytosine-rich α-proteobacterium, some of the latter have well-described functions in the oxidative stress response. In agreement with this, a role of RNase E in the oxidative stress response is demonstrated. A remarkably strong phenotype of a mutant with reduced RNase E activity was observed regarding the formation of photosynthetic complexes and phototrophic growth, whereas there was no effect on chemotrophic growth.},
  language  = {en}
}