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Bibliographie nach Jahren

2024
1. 61.
  Voß, Björn: Classified Dynamic Programming in RNA Structure Analysis. In: Lorenz, R. (Hrsg.) Methods in Molecular Biology, Methods in Molecular Biology., Springer US (2024), S. 125–141 — ISBN 9781071635193
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  @article{VO:2024, author = {Voß, Björn}, booktitle = {RNA Folding: Methods and Protocols}, doi = {10.1007/978-1-0716-3519-3_6}, editor = {Lorenz, Ronny}, isbn = {9781071635193}, issn = {1940-6029}, journal = {Methods in Molecular Biology}, month = {02}, pages = {125–141}, publisher = {Springer US}, title = {Classified Dynamic Programming in RNA Structure Analysis}, url = {http://dx.doi.org/10.1007/978-1-0716-3519-3_6}, year = 2024 }
  Link
  http://dx.doi.org/10.1007/978-1-0716-3519-3_6
2. 60.
  Hartmann, Laura ; Kristofori, Panajot ; Li, Congxin ; Becker, Kolja ; Hexemer, Lorenz ; Bohn, Stefan ; Lenhardt, Sonja ; Weiss, Sylvia ; u. a.: Transcriptional Regulators Ensuring Specific Gene Expression and Decision-Making at High TGF$\beta$ Doses Bd. 8, Life Science Alliance (2024), Nr. 1
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  @article{Hartmann:2025, abstract = {TGF{$\beta$}-signaling regulates cancer progression by controlling cell division, migration, and death. These outcomes are mediated by gene expression changes, but the mechanisms of decision-making toward specific fates remain unclear. Here, we combine SMAD transcription factor imaging, genome-wide RNA sequencing, and morphological assays to quantitatively link signaling, gene expression, and fate decisions in mammary epithelial cells. Fitting genome-wide kinetic models to our time-resolved data, we find that most of the TGF{$\beta$} target genes can be explained as direct targets of SMAD transcription factors, whereas the remainder show signs of complex regulation, involving delayed regulation and strong amplification at high TGF{$\beta$} doses. Knockdown experiments followed by global RNA sequencing revealed transcription factors interacting with SMADs in feedforward loops to control delayed and dose-discriminating target genes, thereby reinforcing the specific epithelial-to-mesenchymal transition at high TGF{$\beta$} doses. We identified early repressors, preventing premature activation, and a late activator, boosting gene expression responses for a sufficiently strong TGF{$\beta$} stimulus. Taken together, we present a global view of TGF{$\beta$}-dependent gene regulation and describe specificity mechanisms reinforcing cellular decision-making.}, author = {Hartmann, Laura and Kristofori, Panajot and Li, Congxin and Becker, Kolja and Hexemer, Lorenz and Bohn, Stefan and Lenhardt, Sonja and Weiss, Sylvia and Voss, Bj\"orn and Loewer, Alexander and Legewie, Stefan}, doi = {10.26508/lsa.202402859}, eprint = {39542693}, eprinttype = {pmid}, issn = {2575-1077}, journaltitle = {Life Science Alliance}, number = 1, publisher = {Life Science Alliance}, shortjournal = {Life Sci. Alliance}, title = {Transcriptional Regulators Ensuring Specific Gene Expression and Decision-Making at High {{TGF$\beta$}} Doses}, volume = 8, year = 2024 }
2023
1. 59.
  Schäfer, Richard A ; Rabsch, Dominik ; Scholz, Guillaume E ; Stadler, Peter F ; Hess, Wolfgang R ; Backofen, Rolf ; Fallmann, Jörg ; Voß, Björn: RNA Interaction Format---a General Data Format for RNA Interactions (2023), S. btad665
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  @article{Schafer:2023, abstract = {RNA molecules play crucial roles in various biological processes. They mediate their function mainly by interacting with other RNAs or proteins. At present, information about these interactions is distributed over different resources, often providing the data in simple tab-delimited formats that differ between the databases. There is no standardised data format that can capture the nature of all these different interactions in detail.Here, we propose the RNA interaction format (RIF) for the detailed representation of RNA-RNA and RNA-Protein interactions and provide reference implementations in C/C\,++, Python and JavaScript. RIF is released under license GNU General Public License version 3 (GNU GPLv3) and is available on https://github.com/RNABioInfo/rna-interaction-format}, author = {Sch\"afer, Richard A and Rabsch, Dominik and Scholz, Guillaume E and Stadler, Peter F and Hess, Wolfgang R and Backofen, Rolf and Fallmann, J\"org and Vo\ss, Bj\"orn}, doi = {10.1093/bioinformatics/btad665}, issn = {1367-4811}, journaltitle = {Bioinformatics}, pages = {btad665}, shortjournal = {Bioinformatics}, title = {{{RNA Interaction Format}}---a General Data Format for {{RNA}} Interactions}, year = 2023 }
2021
1. 58.
  Schäfer, Richard A ; Voß, Björn: RNAnue: efficient data analysis for RNA–RNA interactomics. In: Nucleic Acids Research, Nucleic Acids Research. (2021), Nr. gkab340
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  @article{Schafer:2021, abstract = {RNA–RNA inter- and intramolecular interactions are fundamental for numerous biological processes. While there are reasonable approaches to map RNA secondary structures genome-wide, understanding how different RNAs interact to carry out their regulatory functions requires mapping of intermolecular base pairs. Recently, different strategies to detect RNA–RNA duplexes in living cells, so called direct duplex detection (DDD) methods, have been developed. Common to all is the Psoralen-mediated in vivo RNA crosslinking followed by RNA Proximity Ligation to join the two interacting RNA strands. Sequencing of the RNA via classical RNA-seq and subsequent specialised bioinformatic analyses the result in the prediction of inter- and intramolecular RNA–RNA interactions. Existing approaches adapt standard RNA-seq analysis pipelines, but often neglect inherent features of RNA–RNA interactions that are useful for filtering and statistical assessment. Here we present RNAnue, a general pipeline for the inference of RNA–RNA interactions from DDD experiments that takes into account hybridisation potential and statistical significance to improve prediction accuracy. We applied RNAnue to data from different DDD studies and compared our results to those of the original methods. This showed that RNAnue performs better in terms of quantity and quality of predictions.}, author = {Schäfer, Richard A and Voß, Björn}, doi = {10.1093/nar/gkab340}, file = {Schäfer_Voß_2021_RNAnue.pdf:/Users/bvoss/Zotero/storage/Q6ZCN5H8/Schäfer_Voß_2021_RNAnue.pdf:application/pdf;Snapshot:/Users/bvoss/Zotero/storage/GJPTLI96/6279844.html:text/html}, issn = {0305-1048}, journal = {Nucleic Acids Research}, month = {05}, number = {gkab340}, shorttitle = {{RNAnue}}, title = {RNAnue: efficient data analysis for RNA–RNA interactomics}, url = {https://doi.org/10.1093/nar/gkab340}, urldate = {2021-06-08}, year = 2021 }
  Link
  https://doi.org/10.1093/nar/gkab340
2. 57.
  Huang, Jiabin ; Voß, Björn: Simulation of Folding Kinetics for Aligned RNAs. In: Genes, Genes. Bd. 12, MDPI AG (2021), Nr. 3, S. 347
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  @article{Huang_2021, author = {Huang, Jiabin and Voß, Björn}, doi = {10.3390/genes12030347}, journal = {Genes}, month = {02}, number = 3, pages = 347, publisher = {{MDPI} {AG}}, title = {Simulation of Folding Kinetics for Aligned {RNAs}}, url = {https://doi.org/10.3390%2Fgenes12030347}, volume = 12, year = 2021 }
  Link
  https://doi.org/10.3390%2Fgenes12030347
3. 56.
  Märkle, Pascal ; Maier, Lisa-Katharina ; Maaß, Sandra ; Hirschfeld, Claudia ; Bartel, Jürgen ; Becher, Dörte ; Voß, Björn ; Marchfelder, Anita: A small RNA is linking CRISPR-Cas and zinc transport. In: Frontiers in Molecular Biosciences, Frontiers in Molecular Biosciences. Bd. 8, Frontiers (2021)
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  @article{marchfelder2021small, abstract = {The function and mode of action of small regulatory RNAs is currently still understudied in archaea. In the halophilic archaeon H. volcanii a plethora of sRNAs have been identified, however, in-depth functional analysis is missing for most of them. We selected a small RNA (s479) from H. volcanii for detailed characterization. The sRNA gene is encoded between a CRISPR RNA locus and the Cas protein gene cluster, the s479 deletion strain is viable and was characterized in detail. Transcriptome studies of wild type Haloferax cells and the deletion mutant revealed up-regulation of six genes in the deletion strain, showing that the sRNA has a clearly defined function. Three of the six up-regulated genes encode potential zinc transporter proteins (ZnuA1, ZnuB1, ZnuC1) suggesting involvement of s479 in regulation of zinc transport. Upregulation of these genes in the deletion strain was confirmed by northern blot and proteome analyses. Furthermore, electrophoretic mobility shift assays demonstrate a direct interaction of s479 with the target znuC1 mRNA. Proteome comparison of wild type and deletion strains further expanded the regulon of s479 deeply rooting this sRNA within the metabolism of H. volcanii especially the regulation of transporter abundance. Interestingly, s479 is not only encoded next to CRISPR-cas genes but the mature s479 contains a crRNA-like 5´ handle and experiments with Cas protein deletion strains indicate maturation by Cas6 and interaction with Cas proteins. Together this might suggest that the CRISPR-Cas system is involved in s479 function. }, author = {Märkle, Pascal and Maier, Lisa-Katharina and Maaß, Sandra and Hirschfeld, Claudia and Bartel, Jürgen and Becher, Dörte and Voß, Björn and Marchfelder, Anita}, doi = {10.3389/fmolb.2021.640440}, issn = {2296-889X}, journal = {Frontiers in Molecular Biosciences}, publisher = {Frontiers}, title = {A small RNA is linking CRISPR-Cas and zinc transport}, type = {article}, url = {https://www.frontiersin.org/articles/10.3389/fmolb.2021.640440/abstract}, volume = 8, year = 2021 }
  Link
  https://www.frontiersin.org/articles/10.3389/fmolb.2021.640440/abstract
2020
1. 55.
  Schäfer, Richard A ; Lott, Steffen C ; Georg, Jens ; Grüning, Björn A ; Hess, Wolfgang R ; Voß, Björn: GLASSGo in Galaxy: High-Throughput, Reproducible and Easy-to-Integrate Prediction of sRNA Homologs. In: Press, O. U. (Hrsg.) Bioinformatics, Bioinformatics. (2020), Nr. btaa556
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  @article{Schafer:2020, abstract = {The correct prediction of bacterial sRNA homologs is a prerequisite for many downstream analyses based on comparative genomics, but it is frequently challenging due to the short length and distinct heterogeneity of such homologs. GLASSGo is an efficient tool for the prediction of sRNA homologs from a single input query. To make the algorithm available to a broader community, we offer a Docker container along with a free-access web service. For non-computer scientists, the web service provides a user-friendly interface. However, capabilities were lacking so far for batch processing, version control, and direct interaction with compatible software applications as a workflow management system can provide.Here we present GLASSGo 1.5.2, an updated version that is fully incorporated into the workflow management system Galaxy. The improved version contains a new feature for extracting the upstream regions, allowing the search for conserved promoter elements. Additionally, it supports the use of accession numbers instead of the outdated GI numbers, which widens the applicability of the tool.GLASSGo is available at https://github.com/lotts/GLASSgo/ under the MIT license and is accompanied by instruction and application data. Furthermore, it can be installed into any Galaxy instance using the Galaxy ToolShed.}, author = {Sch{\"a}fer, Richard A and Lott, Steffen C and Georg, Jens and Gr{\"u}ning, Bj{\"o}rn A and Hess, Wolfgang R and Vo{\ss}, Bj{\"o}rn}, doi = {10.1093/bioinformatics/btaa556}, editor = {Press, Oxford University}, issn = {1367-4803}, journal = {Bioinformatics}, month = {06}, number = {btaa556}, title = {{{GLASSGo}} in {{Galaxy}}: High-Throughput, Reproducible and Easy-to-Integrate Prediction of {{sRNA}} Homologs}, year = 2020 }
2. 54.
  Ankenbauer, Andreas ; Schäfer, Richard A. ; Viegas, Sandra C. ; Pobre, Vânia ; Voß, Björn ; Arraiano, Cecília M. ; Takors, Ralf: Pseudomonas Putida KT2440 Is Naturally Endowed to Withstand Industrial-Scale Stress Conditions. In: Wiley (Hrsg.) Microbial Biotechnology, Microbial Biotechnology. Bd. n/a (2020), Nr. n/a
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  @article{Ankenbauer:, abstract = {Pseudomonas putida is recognized as a very promising strain for industrial application due to its high redox capacity and frequently observed tolerance towards organic solvents. In this research, we studied the metabolic and transcriptional response of P. putida KT2440 exposed to large-scale heterogeneous mixing conditions in the form of repeated glucose shortage. Cellular responses were mimicked in an experimental setup comprising a stirred tank reactor and a connected plug flow reactor. We deciphered that a stringent response-like transcriptional regulation programme is frequently induced, which seems to be linked to the intracellular pool of 3-hydroxyalkanoates (3-HA) that are known to serve as precursors for polyhydroxyalkanoates (PHA). To be precise, P. putida is endowed with a survival strategy likely to access cellular PHA, amino acids and glycogen in few seconds under glucose starvation to obtain ATP from respiration, thereby replenishing the reduced ATP levels and the adenylate energy charge. Notably, cells only need 0.4\% of glucose uptake to build those 3-HA-based energy buffers. Concomitantly, genes that are related to amino acid catabolism and {$\beta$}-oxidation are upregulated during the transient absence of glucose. Furthermore, we provide a detailed list of transcriptional short- and long-term responses that increase the cellular maintenance by about 17\% under the industrial-like conditions tested.}, author = {Ankenbauer, Andreas and Schäfer, Richard A. and Viegas, Sandra C. and Pobre, Vânia and Voß, Björn and Arraiano, Cecília M. and Takors, Ralf}, doi = {10.1111/1751-7915.13571}, editor = {Wiley}, issn = {1751-7915}, journal = {Microbial Biotechnology}, journaltitle = {Microb. Biotechnol.}, number = {n/a}, title = {Pseudomonas Putida KT2440 Is Naturally Endowed to Withstand Industrial-Scale Stress Conditions}, volume = {n/a}, year = 2020 }
3. 53.
  Alkhnbashi, Omer S. ; Meier, Tobias ; Mitrofanov, Alexander ; Backofen, Rolf ; Voß, Björn: CRISPR-Cas Bioinformatics. In: Methods, Methods. Bd. 172 (2020), S. 3–11
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  @article{ALKHNBASHI2019, abstract = {Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated proteins (Cas) are essential genetic elements in many archaeal and bacterial genomes, playing a key role in a prokaryote adaptive immune system against invasive foreign elements. In recent years, the CRISPR-Cas system has also been engineered to facilitate target gene editing in eukaryotic genomes. Bioinformatics played an essential role in the detection and analysis of CRISPR systems and here we review the bioinformatics-based efforts that pushed the field of CRISPR-Cas research further. We discuss the bioinformatics tools that have been published over the last few years and, finally, present the most popular tools for the design of CRISPR-Cas9 guides.}, author = {Alkhnbashi, Omer S. and Meier, Tobias and Mitrofanov, Alexander and Backofen, Rolf and Voß, Björn}, doi = {https://doi.org/10.1016/j.ymeth.2019.07.013}, issn = {1046-2023}, journal = {Methods}, month = {02}, pages = {3-11}, title = {CRISPR-Cas Bioinformatics}, url = {http://www.sciencedirect.com/science/article/pii/S1046202318304717}, volume = 172, year = 2020 }
  Link
  http://www.sciencedirect.com/science/article/pii/S1046202318304717
2018
1. 52.
  Schönberger, Brigitte ; Schaal, Christoph ; Schäfer, Richard ; Voß, Björn: RNA interactomics: recent advances and remaining challenges. In: F1000Research, F1000Research. Bd. 7, F1000 Research, Ltd. (2018), S. 1824
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  @article{Sch_nberger_2018, author = {Schönberger, Brigitte and Schaal, Christoph and Schäfer, Richard and Vo{\ss}, Björn}, doi = {10.12688/f1000research.16146.1}, journal = {F1000Research}, month = {11}, pages = 1824, publisher = {F1000 Research, Ltd.}, title = {{RNA} interactomics: recent advances and remaining challenges}, url = {https://doi.org/10.12688%2Ff1000research.16146.1}, volume = 7, year = 2018 }
  Link
  https://doi.org/10.12688%2Ff1000research.16146.1
2. 51.
  Lott, Steffen Christian ; Schäfer, Richard A. ; Mann, Martin ; Backofen, Rolf ; Hess, Wolfgang R. ; Voß, Björn ; Georg, Jens: GLASSgo - Automated and reliable detection of sRNA homologs from a single input sequence. In: Frontiers in Genetics, Frontiers in Genetics. Bd. 9, Frontiers (2018)
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  @article{hess2018glassgo, abstract = {Bacterial small RNAs (sRNAs) are important post-transcriptional regulators of gene expression. The functional and evolutionary characterization of sRNAs requires the identification of homologs, which is frequently challenging due to their heterogeneity, short length and partly, little sequence conservation. We developed the GLobal Automatic Small RNA Search go (GLASSgo) algorithm to identify sRNA homologs in complex genomic databases starting from a single sequence. GLASSgo combines an iterative BLAST strategy with pairwise identity filtering and a graph-based clustering method that utilizes RNA secondary structure information. We tested the specificity, sensitivity and runtime of GLASSgo, BLAST and the combination RNAlien/cmsearch in a typical use case scenario on 40 bacterial sRNA families. The sensitivity of the tested methods was similar, while the specificity of GLASSgo and RNAlien/cmsearch was significantly higher than that of BLAST. GLASSgo was on average ~87 times faster than RNAlien/cmsearch, and only ~7.5 times slower than BLAST, which shows that GLASSgo optimizes the trade-off between speed and accuracy in the task of finding sRNA homologs. GLASSgo is fully automated, whereas BLAST often recovers only parts of homologs and RNAlien/cmsearch requires extensive additional bioinformatic work to get a comprehensive set of homologs. GLASSgo is available as an easy-to-use web server to find homologous sRNAs in large databases.}, author = {Lott, Steffen Christian and Schäfer, Richard A. and Mann, Martin and Backofen, Rolf and Hess, Wolfgang R. and Voß, Björn and Georg, Jens}, doi = {10.3389/fgene.2018.00124}, issn = {1664-8021}, journal = {Frontiers in Genetics}, publisher = {Frontiers}, title = {GLASSgo - Automated and reliable detection of sRNA homologs from a single input sequence}, type = {article}, url = {https://www.frontiersin.org/articles/10.3389/fgene.2018.00124/abstract}, volume = 9, year = 2018 }
  Link
  https://www.frontiersin.org/articles/10.3389/fgene.2018.00124/abstract
2017
1. 50.
  Pfreundt, Ulrike ; Spungin, Dina ; Hou, Shengwei ; Voß, Björn ; Berman-Frank, Ilana ; Hess, Wolfgang R.: Genome of a giant bacteriophage from a decaying Trichodesmium bloom. In: Marine Genomics, Marine Genomics. Bd. 33 (2017), S. 21–25
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  @article{PFREUNDT201721, abstract = {De-novo assembly of a metagenomic dataset obtained from a decaying cyanobacterial Trichodesmium bloom from the New Caledonian lagoon resulted in a complete giant phage genome of 257,908bp, obtained independently with multiple assembly tools. Noteworthy, gammaproteobacteria were an abundant fraction in the sequenced samples. Mapping of the raw reads with 99% accuracy to the giant phage genome resulted in an average coverage of 262X. The closest sequenced relatives, albeit still distant, are the Pseudomonas phages PaBG from Lake Baikal and Lu11 isolated from a soil sample from the Philippines. The phage reported here might belong to the same family within the Myoviridae as PaBG and Lu11 and would thus be its first marine member, indicating a more widespread occurrence of this group. We named this phage NCTB (New Caledonia Trichodesmium Bloom) after its origin.}, author = {Pfreundt, Ulrike and Spungin, Dina and Hou, Shengwei and Voß, Björn and Berman-Frank, Ilana and Hess, Wolfgang R.}, doi = {https://doi.org/10.1016/j.margen.2017.02.001}, issn = {1874-7787}, journal = {Marine Genomics}, pages = {21 - 25}, title = {Genome of a giant bacteriophage from a decaying Trichodesmium bloom}, url = {http://www.sciencedirect.com/science/article/pii/S1874778717300338}, volume = 33, year = 2017 }
  Link
  http://www.sciencedirect.com/science/article/pii/S1874778717300338
2016
1. 49.
  Stazic, D. ; Voß, B.: The complexity of bacterial transcriptomes. In: Journal of Biotechnology, Journal of Biotechnology. Bd. 232 (2016), S. 69--78. — 00000
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  @article{stazic_complexity_2016, abstract = {For eukaryotes there seems to be no doubt that differences on the trancriptomic level substantially contribute to the process of species diversification, whereas for bacteria this is thought to be less important. Recent years saw a significant increase in full transcriptome studies for bacteria, which provided deep insight into the architecture of bacterial transcriptomes. Most notably, it became evident that, in contrast to previous scientific consensus, bacterial transcriptomes are quite complex. There exist a large number of cis-antisense RNAs, non-coding RNAs, overlapping transcripts and RNA elements that regulate transcription, such as riboswitches. Furthermore, processing and degradation of RNA has gained interest, because it has a significant impact on the composition of the transcriptome. In this review, we summarize recent findings and put them into a broader context with respect to the complexity of bacterial transcriptomes and its putative biological meanings.}, author = {Stazic, D. and Voß, B.}, doi = {10.1016/j.jbiotec.2015.09.041}, file = {ScienceDirect Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/25WS5QUR/S0168165615301474.html:text/html;Stazic_Voß_2016_The complexity of bacterial transcriptomes.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/XBQJF6ER/Stazic_Voß_2016_The complexity of bacterial transcriptomes.pdf:application/pdf}, issn = {0168-1656}, journal = {Journal of Biotechnology}, month = {08}, note = 00000, pages = {69--78}, series = {Bioinformatics for {Biotechnology} and {Biomedicine}}, title = {The complexity of bacterial transcriptomes}, url = {http://www.sciencedirect.com/science/article/pii/S0168165615301474}, urldate = {2016-08-01}, volume = 232, year = 2016 }
  Link
  http://www.sciencedirect.com/science/article/pii/S0168165615301474
2. 48.
  Álvarez, Daniel ; Voß, Björn ; Maass, Dirk ; Wüst, Florian ; Schaub, Patrick ; Beyer, Peter ; Welsch, Ralf: 5’UTR-Mediated Translational Control of Splice Variants of Phytoene Synthase. In: Plant Physiol., Plant Physiol. (2016), S. pp.01262.2016
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  @article{Alvarez:2016, author = {Álvarez, Daniel and Voß, Björn and Maass, Dirk and Wüst, Florian and Schaub, Patrick and Beyer, Peter and Welsch, Ralf}, journal = {Plant Physiol.}, pages = {pp.01262.2016}, title = {5'{{UTR}}-Mediated Translational Control of Splice Variants of Phytoene Synthase}, year = 2016 }
3. 47.
  Schäfer, Richard A. ; Voß, Björn: VisualGraphX: interactive graph visualization within Galaxy. In: Bioinformatics, Bioinformatics. (2016), S. btw414. — 00000 PMID: 27412091
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  @article{schafer_visualgraphx:_2016, abstract = {Motivation: We developed VisualGraphX, a web-based, interactive visualization tool for large-scale graphs. Current graph visualization tools that follow the rich-internet paradigm lack an interactive and scalable visualization of graph-based data. VisualGraphX aims to provide a universal graph visualization tool that empowers the users to efficiently explore the data for themselves at a large scale. It is available as a visualization plugin for the Galaxy platform, such that VisualGraphX can be integrated into custom analysis pipelines. Availability and Implementation: VisualGraphX has been released as a visualization plugin for the Galaxy platform under AFL 3.0 and is available with instructions and application data at http://gitlab.com/comptrans/VisualGraphX/. Contact: bjoern.voss@ibvt.uni-stuttgart.de}, author = {Schäfer, Richard A. and Voß, Björn}, doi = {10.1093/bioinformatics/btw414}, file = {Schäfer_Voß_2016_VisualGraphX.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/S5FNV2W4/Schäfer_Voß_2016_VisualGraphX.pdf:application/pdf;Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/R6ZEX2QH/bioinformatics.html:text/html}, issn = {1367-4803, 1460-2059}, journal = {Bioinformatics}, language = {en}, month = {07}, note = {00000 PMID: 27412091}, pages = {btw414}, shorttitle = {{VisualGraphX}}, title = {{VisualGraphX}: interactive graph visualization within {Galaxy}}, url = {http://bioinformatics.oxfordjournals.org/content/early/2016/07/24/bioinformatics.btw414}, urldate = {2016-08-01}, year = 2016 }
  Link
  http://bioinformatics.oxfordjournals.org/content/early/2016/07/24/bioinformatics.btw414
2015
1. 46.
  Kopf, Matthias ; Klähn, Stephan ; Scholz, Ingeborg ; Hess, Wolfgang R. ; Voß, Björn: Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria. In: Scientific Reports, Scientific Reports. Bd. 5 (2015), Nr. 9560. — 00000
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  @article{kopf_variations_2015, author = {Kopf, Matthias and Klähn, Stephan and Scholz, Ingeborg and Hess, Wolfgang R. and Voß, Björn}, file = {Kopf et al. - 2015 - Variations in the non-coding transcriptome as a dr.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/Z8WVS3X5/Kopf et al. - 2015 - Variations in the non-coding transcriptome as a dr.pdf:application/pdf}, journal = {Scientific Reports}, note = 00000, number = 9560, title = {Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria}, volume = 5, year = 2015 }
2. 45.
  Lott, Steffen C. ; Voß, Björn ; Hess, Wolfgang R. ; Steglich, Claudia: CoVennTree: a new method for the comparative analysis of large datasets. In: Bioinformatics and Computational Biology, Bioinformatics and Computational Biology. Bd. 6 (2015), S. 43. — 00000
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  @article{lott_covenntree:_2015, abstract = {The visualization of massive datasets, such as those resulting from comparative metatranscriptome analyses or the analysis of microbial population structures using ribosomal RNA sequences, is a challenging task. We developed a new method called CoVennTree (Comparative weighted Venn Tree) that simultaneously compares up to three multifarious datasets by aggregating and propagating information from the bottom to the top level and produces a graphical output in Cytoscape. With the introduction of weighted Venn structures, the contents and relationships of various datasets can be correlated and simultaneously aggregated without losing information. We demonstrate the suitability of this approach using a dataset of 16S rDNA sequences obtained from microbial populations at three different depths of the Gulf of Aqaba in the Red Sea. CoVennTree has been integrated into the Galaxy ToolShed and can be directly downloaded and integrated into the user instance.}, author = {Lott, Steffen C. and Voß, Björn and Hess, Wolfgang R. and Steglich, Claudia}, doi = {10.3389/fgene.2015.00043}, file = {Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/GPNQZUNC/Lott et al. - 2015 - CoVennTree a new method for the comparative analy.pdf:application/pdf}, journal = {Bioinformatics and Computational Biology}, note = 00000, pages = 43, shorttitle = {{CoVennTree}}, title = {{CoVennTree}: a new method for the comparative analysis of large datasets}, url = {http://journal.frontiersin.org/article/10.3389/fgene.2015.00043/abstract}, urldate = {2015-03-12}, volume = 6, year = 2015 }
  Link
  http://journal.frontiersin.org/article/10.3389/fgene.2015.00043/abstract
2014
1. 44.
  Kopf, Matthias ; Klähn, Stephan ; Pade, Nadin ; Weingärtner, Christian ; Hagemann, Martin ; Voß, Björn ; Hess, Wolfgang R.: Comparative Genome Analysis of the Closely Related Synechocystis Strains PCC 6714 and PCC 6803. In: DNA Research, DNA Research. Bd. 21 (2014), Nr. 3, S. 255--266. — 00005
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  @article{kopf_comparative_2014-1, abstract = {Synechocystis sp. PCC 6803 is the most popular cyanobacterial model for prokaryotic photosynthesis and for metabolic engineering to produce biofuels. Genomic and transcriptomic comparisons between closely related bacteria are powerful approaches to infer insights into their metabolic potentials and regulatory networks. To enable a comparative approach, we generated the draft genome sequence of Synechocystis sp. PCC 6714, a closely related strain of 6803 (16S rDNA identity 99.4\%) that also is amenable to genetic manipulation. Both strains share 2838 protein-coding genes, leaving 845 unique genes in Synechocystis sp. PCC 6803 and 895 genes in Synechocystis sp. PCC 6714. The genetic differences include a prophage in the genome of strain 6714, a different composition of the pool of transposable elements, and a ∼40 kb genomic island encoding several glycosyltransferases and transport proteins. We verified several physiological differences that were predicted on the basis of the respective genome sequence. Strain 6714 exhibited a lower tolerance to Zn2+ ions, associated with the lack of a corresponding export system and a lowered potential of salt acclimation due to the absence of a transport system for the re-uptake of the compatible solute glucosylglycerol. These new data will support the detailed comparative analyses of this important cyanobacterial group than has been possible thus far. Genome information for Synechocystis sp. PCC 6714 has been deposited in Genbank (accession no AMZV01000000).}, author = {Kopf, Matthias and Klähn, Stephan and Pade, Nadin and Weingärtner, Christian and Hagemann, Martin and Voß, Björn and Hess, Wolfgang R.}, doi = {10.1093/dnares/dst055}, file = {Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/AAE8MTUB/Kopf et al. - 2014 - Comparative Genome Analysis of the Closely Related.pdf:application/pdf;Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/ANEGT6S9/255.html:text/html}, issn = {1340-2838, 1756-1663}, journal = {DNA Research}, language = {en}, month = {06}, note = 00005, number = 3, pages = {255--266}, title = {Comparative {Genome} {Analysis} of the {Closely} {Related} {Synechocystis} {Strains} {PCC} 6714 and {PCC} 6803}, url = {http://dnaresearch.oxfordjournals.org/content/21/3/255}, urldate = {2015-01-13}, volume = 21, year = 2014 }
  Link
  http://dnaresearch.oxfordjournals.org/content/21/3/255
2. 43.
  Kopf, Matthias ; Klähn, Stephan ; Voß, Björn ; Stüber, Kurt ; Huettel, Bruno ; Reinhardt, Richard ; Hess, Wolfgang R.: Finished Genome Sequence of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC 6714. In: Genome Announcements, Genome Announcements. Bd. 2 (2014), Nr. 4, S. e00757--14. — 00005
  - BibTeX
  - Link
  BibTeX
  @article{kopf_finished_2014, abstract = {Synechocystis sp. strain PCC 6714 is a unicellular cyanobacterium closely related to the popular model organism Synechocystis sp. strain PCC 6803. A combination of PacBio SMRT and Illumina GAIIx data results in a highly accurate finished genome sequence that provides a reliable resource for further comparative analyses.}, author = {Kopf, Matthias and Klähn, Stephan and Voß, Björn and Stüber, Kurt and Huettel, Bruno and Reinhardt, Richard and Hess, Wolfgang R.}, doi = {10.1128/genomeA.00757-14}, file = {Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/KDQTGRGT/Kopf et al. - 2014 - Finished Genome Sequence of the Unicellular Cyanob.pdf:application/pdf;Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/5MW2HKU4/e00757-14.html:text/html}, issn = {, 2169-8287}, journal = {Genome Announcements}, language = {en}, month = {08}, note = 00005, number = 4, pages = {e00757--14}, title = {Finished {Genome} {Sequence} of the {Unicellular} {Cyanobacterium} {Synechocystis} sp. {Strain} {PCC} 6714}, url = {http://genomea.asm.org/content/2/4/e00757-14}, urldate = {2014-09-26}, volume = 2, year = 2014 }
  Link
  http://genomea.asm.org/content/2/4/e00757-14
3. 42.
  Voß, Björn ; Hess, Wolfgang R.: The identification of bacterial non-coding RNAs through complementary approaches. In: Handbook of RNA Biochemistry, Handbook of RNA Biochemistry. Bd. 2. 2. Aufl. : WILEY-VCH, Weinheim, Germany, 2014. — 00000, S. 787--800
  - BibTeX
  BibTeX
  @incollection{vos_identification_2014, author = {Voß, Björn and Hess, Wolfgang R.}, booktitle = {Handbook of {RNA} {Biochemistry}}, collaborator = {Hartmann, Roland K. and Bindereif, Albrecht and Schön, Astrid and Westhof, Eric}, edition = 2, note = 00000, pages = {787--800}, publisher = {WILEY-VCH, Weinheim, Germany}, title = {The identification of bacterial non-coding {RNAs} through complementary approaches}, volume = 2, year = 2014 }
4. 41.
  Bischler, Thorsten ; Kopf, Matthias ; Voß, Björn: Transcript mapping based on dRNA-seq data. In: BMC Bioinformatics, BMC Bioinformatics. Bd. 15 (2014), Nr. 1, S. 122. — 00002
  - BibTeX
  - Link
  BibTeX
  @article{bischler_transcript_2014, abstract = {RNA-seq and its variant differential RNA-seq (dRNA-seq) are today routine methods for transcriptome analysis in bacteria. While expression profiling and transcriptional start site prediction are standard tasks today, the problem of identifying transcriptional units in a genome-wide fashion is still not solved for prokaryotic systems. PMID: 24780064}, author = {Bischler, Thorsten and Kopf, Matthias and Voß, Björn}, copyright = {http://creativecommons.org/licenses/by/2.0/}, doi = {10.1186/1471-2105-15-122}, file = {Bischler et al. - 2014 - Transcript mapping based on dRNA-seq data.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/3W4MQWMV/Bischler et al. - 2014 - Transcript mapping based on dRNA-seq data.pdf:application/pdf;Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/JJIH269B/abstract.html:text/html}, issn = {1471-2105}, journal = {BMC Bioinformatics}, language = {en}, month = {04}, note = 00002, number = 1, pages = 122, title = {Transcript mapping based on {dRNA}-seq data}, url = {http://www.biomedcentral.com/1471-2105/15/122/abstract}, urldate = {2014-05-05}, volume = 15, year = 2014 }
  Link
  http://www.biomedcentral.com/1471-2105/15/122/abstract
5. 40.
  Kopf, Matthias ; Klähn, Stephan ; Scholz, Ingeborg ; Matthiessen, Jasper K. F. ; Hess, Wolfgang R. ; Voß, Björn: Comparative Analysis of the Primary Transcriptome of Synechocystis sp. PCC 6803. In: DNA Research, DNA Research. Bd. 21 (2014), Nr. 5, S. 527--539. — 00005
  - BibTeX
  - Link
  BibTeX
  @article{kopf_comparative_2014, abstract = {RNA-seq and especially differential RNA-seq-type transcriptomic analyses (dRNA-seq) are powerful analytical tools, as they not only provide insights into gene expression changes but also provide detailed information about all promoters active at a given moment, effectively giving a deep insight into the transcriptional landscape. Synechocystis sp. PCC 6803 (Synechocystis 6803) is a unicellular model cyanobacterium that is widely used in research fields from ecology, photophysiology to systems biology, modelling and biotechnology. Here, we analysed the response of the Synechocystis 6803 primary transcriptome to different, environmentally relevant stimuli. We established genome-wide maps of the transcriptional start sites active under 10 different conditions relevant for photosynthetic growth and identified 4091 transcriptional units, which provide information about operons, 5′ and 3′ untranslated regions (UTRs). Based on a unique expression factor, we describe regulons and relevant promoter sequences at single-nucleotide resolution. Finally, we report several sRNAs with an intriguing expression pattern and therefore likely function, specific for carbon depletion (CsiR1), nitrogen depletion (NsiR4), phosphate depletion (PsiR1), iron stress (IsaR1) or photosynthesis (PsrR1). This dataset is accompanied by comprehensive information providing extensive visualization and data access to allow an easy-to-use approach for the design of experiments, the incorporation into modelling studies of the regulatory system and for comparative analyses.}, author = {Kopf, Matthias and Klähn, Stephan and Scholz, Ingeborg and Matthiessen, Jasper K. F. and Hess, Wolfgang R. and Voß, Björn}, doi = {10.1093/dnares/dsu018}, file = {Kopf et al. - 2014 - Comparative Analysis of the Primary Transcriptome .pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/7UA65KGH/Kopf et al. - 2014 - Comparative Analysis of the Primary Transcriptome .pdf:application/pdf;Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/P3GNTAWC/dnares.dsu018.html:text/html}, issn = {1340-2838, 1756-1663}, journal = {DNA Research}, language = {en}, month = {06}, note = 00005, number = 5, pages = {527--539}, title = {Comparative {Analysis} of the {Primary} {Transcriptome} of {Synechocystis} sp. {PCC} 6803}, url = {http://dnaresearch.oxfordjournals.org/content/21/5/527}, urldate = {2014-06-17}, volume = 21, year = 2014 }
  Link
  http://dnaresearch.oxfordjournals.org/content/21/5/527
6. 39.
  Huang, Jiabin ; Voß, Björn: Analysing RNA-kinetics based on folding space abstraction. In: BMC Bioinformatics, BMC Bioinformatics. Bd. 15 (2014), Nr. 1, S. 60. — 00001
  - BibTeX
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  BibTeX
  @article{huang_analysing_2014, abstract = {RNA molecules, especially non-coding RNAs, play vital roles in the cell and their biological functions are mostly determined by structural properties. Often, these properties are related to dynamic changes in the structure, as in the case of riboswitches, and thus the analysis of RNA folding kinetics is crucial for their study. Exact approaches to kinetic folding are computationally expensive and, thus, limited to short sequences. In a previous study, we introduced a position-specific abstraction based on helices which we termed helix index shapes (hishapes) and a hishape-based algorithm for near-optimal folding pathway computation, called HiPath. The combination of these approaches provides an abstract view of the folding space that offers information about the global features. PMID: 24575751}, author = {Huang, Jiabin and Voß, Björn}, copyright = {2014 Huang and Voß; licensee BioMed Central Ltd.}, doi = {10.1186/1471-2105-15-60}, file = {Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/XZTRD2WX/Huang und Voß - 2014 - Analysing RNA-kinetics based on folding space abst.pdf:application/pdf;Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/A3ZZHFQN/60.html:text/html}, issn = {1471-2105}, journal = {BMC Bioinformatics}, language = {en}, month = {02}, note = 00001, number = 1, pages = 60, title = {Analysing {RNA}-kinetics based on folding space abstraction}, url = {http://www.biomedcentral.com/1471-2105/15/60/abstract}, urldate = {2014-03-17}, volume = 15, year = 2014 }
  Link
  http://www.biomedcentral.com/1471-2105/15/60/abstract
7. 38.
  Voigt, Karsten ; Sharma, Cynthia M. ; Mitschke, Jan ; Joke Lambrecht, S. ; Voß, Björn ; Hess, Wolfgang R. ; Steglich, Claudia: Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity. In: The ISME Journal, The ISME Journal. (2014). — 00007
  - BibTeX
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  BibTeX
  @article{voigt_comparative_2014, abstract = {Prochlorococcus is a genus of abundant and ecologically important marine cyanobacteria. Here, we present a comprehensive comparison of the structure and composition of the transcriptomes of two Prochlorococcus strains, which, despite their similarities, have adapted their gene pool to specific environmental constraints. We present genome-wide maps of transcriptional start sites (TSS) for both organisms, which are representatives of the two most diverse clades within the two major ecotypes adapted to high- and low-light conditions, respectively. Our data suggest antisense transcription for three-quarters of all genes, which is substantially more than that observed in other bacteria. We discovered hundreds of TSS within genes, most notably within 16 of the 29 prochlorosin genes, in strain MIT9313. A direct comparison revealed very little conservation in the location of TSS and the nature of non-coding transcripts between both strains. We detected extremely short 5′ untranslated regions with a median length of only 27 and 29 nt for MED4 and MIT9313, respectively, and for 8\% of all protein-coding genes the median distance to the start codon is only 10 nt or even shorter. These findings and the absence of an obvious Shine–Dalgarno motif suggest that leaderless translation and ribosomal protein S1-dependent translation constitute alternative mechanisms for translation initiation in Prochlorococcus. We conclude that genome-wide antisense transcription is a major component of the transcriptional output from these relatively small genomes and that a hitherto unrecognized high degree of complexity and variability of gene expression exists in their transcriptional architecture.}, author = {Voigt, Karsten and Sharma, Cynthia M. and Mitschke, Jan and Joke Lambrecht, S. and Voß, Björn and Hess, Wolfgang R. and Steglich, Claudia}, copyright = {© 2014 Nature Publishing Group}, doi = {10.1038/ismej.2014.57}, file = {Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/DVKZWIMX/ismej201457a.html:text/html;Voigt et al. - 2014 - Comparative transcriptomics of two environmentally.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/6P46BW9M/Voigt et al. - 2014 - Comparative transcriptomics of two environmentally.pdf:application/pdf}, issn = {1751-7370}, journal = {The ISME Journal}, language = {en}, month = {04}, note = 00007, title = {Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity}, url = {http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201457a.html}, urldate = {2014-04-25}, year = 2014 }
  Link
  http://www.nature.com/ismej/journal/vaop/ncurrent/full/ismej201457a.html
8. 37.
  Rogato, Alessandra ; Richard, Hugues ; Sarazin, Alexis ; Voß, Björn ; Navarro, Soizic Cheminant ; Champeimont, Raphaël ; Navarro, Lionel ; Carbone, Alessandra ; u. a.: The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum. In: BMC Genomics, BMC Genomics. Bd. 15 (2014), Nr. 1, S. 698. — 00000
  - BibTeX
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  BibTeX
  @article{rogato_diversity_2014, abstract = {Marine diatoms constitute a major component of eukaryotic phytoplankton and stand at the crossroads of several evolutionary lineages. These microalgae possess peculiar genomic features and novel combinations of genes acquired from bacterial, animal and plant ancestors. Furthermore, they display both DNA methylation and gene silencing activities. Yet, the biogenesis and regulatory function of small RNAs (sRNAs) remain ill defined in diatoms. PMID: 25142710}, author = {Rogato, Alessandra and Richard, Hugues and Sarazin, Alexis and Voß, Björn and Navarro, Soizic Cheminant and Champeimont, Raphaël and Navarro, Lionel and Carbone, Alessandra and Hess, Wolfgang R. and Falciatore, Angela}, copyright = {http://creativecommons.org/licenses/by/2.0/}, doi = {10.1186/1471-2164-15-698}, file = {Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/2CAB3K4N/Rogato et al. - 2014 - The diversity of small non-coding RNAs in the diat.pdf:application/pdf;Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/7ZZ8DQHR/abstract.html:text/html}, issn = {1471-2164}, journal = {BMC Genomics}, language = {en}, month = {08}, note = 00000, number = 1, pages = 698, title = {The diversity of small non-coding {RNAs} in the diatom {Phaeodactylum} tricornutum}, url = {http://www.biomedcentral.com/1471-2164/15/698/abstract}, urldate = {2014-08-26}, volume = 15, year = 2014 }
  Link
  http://www.biomedcentral.com/1471-2164/15/698/abstract
9. 36.
  Giegerich, Robert ; Voß, Björn: RNA Secondary Structure Analysis Using Abstract Shapes. In: Handbook of RNA Biochemistry, Handbook of RNA Biochemistry. Bd. 2. 2. Aufl. : WILEY-VCH, Weinheim, Germany, 2014. — 00000, S. 579--594
  - BibTeX
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  @incollection{giegerich_rna_2014, author = {Giegerich, Robert and Voß, Björn}, booktitle = {Handbook of {RNA} {Biochemistry}}, collaborator = {Hartmann, Roland K. and Bindereif, Albrecht and Schön, Astrid and Westhof, Eric}, edition = 2, note = 00000, pages = {579--594}, publisher = {WILEY-VCH, Weinheim, Germany}, title = {{RNA} {Secondary} {Structure} {Analysis} {Using} {Abstract} {Shapes}}, volume = 2, year = 2014 }
2013
1. 35.
  Hein, Stephanie ; Scholz, Ingeborg ; Voß, Björn ; Hess, Wolfgang R.: Adaptation and modification of three CRISPR loci in two closely related cyanobacteria. In: RNA Biology, RNA Biology. Bd. 10 (2013), Nr. 5, S. 93--92. — 00027
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  @article{hein_adaptation_2013, author = {Hein, Stephanie and Scholz, Ingeborg and Voß, Björn and Hess, Wolfgang R.}, journal = {RNA Biology}, note = 00027, number = 5, pages = {93--92}, title = {Adaptation and modification of three {CRISPR} loci in two closely related cyanobacteria}, url = {http://www.landesbioscience.com/journals/rnabiology/article/24160/}, volume = 10, year = 2013 }
  Link
  http://www.landesbioscience.com/journals/rnabiology/article/24160/
2. 34.
  Voß, Björn ; Bolhuis, Henk ; Fewer, David P. ; Kopf, Matthias ; Möke, Fred ; Haas, Fabian ; El-Shehawy, Rehab ; Hayes, Paul ; u. a.: Insights into the Physiology and Ecology of the Brackish-Water-Adapted Cyanobacterium Nodularia spumigena CCY9414 Based on a Genome-Transcriptome Analysis. In: PLoS ONE, PLoS ONE. Bd. 8 (2013), Nr. 3, S. e60224. — 00013
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  @article{vos_insights_2013, abstract = {Nodularia spumigena is a filamentous diazotrophic cyanobacterium that dominates the annual late summer cyanobacterial blooms in the Baltic Sea. But N. spumigena also is common in brackish water bodies worldwide, suggesting special adaptation allowing it to thrive at moderate salinities. A draft genome analysis of N. spumigena sp. CCY9414 yielded a single scaffold of 5,462,271 nucleotides in length on which genes for 5,294 proteins were annotated. A subsequent strand-specific transcriptome analysis identified more than 6,000 putative transcriptional start sites (TSS). Orphan TSSs located in intergenic regions led us to predict 764 non-coding RNAs, among them 70 copies of a possible retrotransposon and several potential RNA regulators, some of which are also present in other N2-fixing cyanobacteria. Approximately 4\% of the total coding capacity is devoted to the production of secondary metabolites, among them the potent hepatotoxin nodularin, the linear spumigin and the cyclic nodulapeptin. The transcriptional complexity associated with genes involved in nitrogen fixation and heterocyst differentiation is considerably smaller compared to other Nostocales. In contrast, sophisticated systems exist for the uptake and assimilation of iron and phosphorus compounds, for the synthesis of compatible solutes, and for the formation of gas vesicles, required for the active control of buoyancy. Hence, the annotation and interpretation of this sequence provides a vast array of clues into the genomic underpinnings of the physiology of this cyanobacterium and indicates in particular a competitive edge of N. spumigena in nutrient-limited brackish water ecosystems.}, author = {Voß, Björn and Bolhuis, Henk and Fewer, David P. and Kopf, Matthias and Möke, Fred and Haas, Fabian and El-Shehawy, Rehab and Hayes, Paul and Bergman, Birgitta and Sivonen, Kaarina and Dittmann, Elke and Scanlan, Dave J. and Hagemann, Martin and Stal, Lucas J. and Hess, Wolfgang R.}, doi = {10.1371/journal.pone.0060224}, file = {PLoS Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/Z57Q5QQM/Voß et al. - 2013 - Insights into the Physiology and Ecology of the Br.pdf:application/pdf}, journal = {PLoS ONE}, note = 00013, number = 3, pages = {e60224}, title = {Insights into the {Physiology} and {Ecology} of the {Brackish}-{Water}-{Adapted} {Cyanobacterium} {Nodularia} spumigena {CCY}9414 {Based} on a {Genome}-{Transcriptome} {Analysis}}, url = {http://dx.doi.org/10.1371/journal.pone.0060224}, urldate = {2013-04-05}, volume = 8, year = 2013 }
  Link
  http://dx.doi.org/10.1371/journal.pone.0060224
2012
1. 33.
  Gierga, Gregor ; Voß, Björn ; Hess, Wolfgang R.: Non-coding RNAs in marine Synechococcus and their regulation under environmentally relevant stress conditions. In: The ISME Journal, The ISME Journal. Bd. 6 (2012), Nr. 8, S. 1544--1557. — 00008
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  @article{gierga_non-coding_2012, abstract = {Regulatory small RNAs (sRNAs) have crucial roles in the adaptive responses of bacteria to changes in the environment. Thus far, potential regulatory RNAs have been studied mainly in marine picocyanobacteria in genetically intractable Prochlorococcus, rendering their molecular analysis difficult. Synechococcus sp. WH7803 is a model cyanobacterium, representative of the picocyanobacteria from the mesotrophic areas of the ocean. Similar to the closely related Prochlorococcus it possesses a relatively streamlined genome and a small number of genes, but is genetically tractable. Here, a comparative genome analysis was performed for this and four additional marine Synechococcus to identify the suite of possible sRNAs and other RNA elements. Based on the prediction and on complementary microarray profiling, we have identified several known as well as 32 novel sRNAs. Some sRNAs overlap adjacent coding regions, for instance for the central photosynthetic gene psbA. Several of these novel sRNAs responded specifically to environmentally relevant stress conditions. Among them are six sRNAs changing their accumulation level under cold stress, six responding to high light and two to iron limitation. Target predictions suggested genes encoding components of the light-harvesting apparatus as targets of sRNAs originating from genomic islands and that one of the iron-regulated sRNAs might be a functional homolog of RyhB. These data suggest that marine Synechococcus mount adaptive responses to these different stresses involving regulatory sRNAs.}, author = {Gierga, Gregor and Voß, Björn and Hess, Wolfgang R.}, copyright = {© 2012 Nature Publishing Group}, doi = {10.1038/ismej.2011.215}, issn = {1751-7362}, journal = {The ISME Journal}, language = {en}, month = {08}, note = 00008, number = 8, pages = {1544--1557}, title = {Non-coding {RNAs} in marine {Synechococcus} and their regulation under environmentally relevant stress conditions}, url = {http://www.nature.com/ismej/journal/v6/n8/full/ismej2011215a.html}, urldate = {2012-10-17}, volume = 6, year = 2012 }
  Link
  http://www.nature.com/ismej/journal/v6/n8/full/ismej2011215a.html
2. 32.
  Trautmann, Danika ; Voß, Björn ; Wilde, Annegret ; Al-Babili, Salim ; Hess, Wolfgang R.: Microevolution in Cyanobacteria: Re-sequencing a Motile Substrain of Synechocystis sp. PCC 6803. In: DNA Research, DNA Research. (2012). — 00025
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  @article{trautmann_microevolution_2012, abstract = {Synechocystis sp. PCC 6803 is a widely used model cyanobacterium for studying photosynthesis, phototaxis, the production of biofuels and many other aspects. Here we present a re-sequencing study of the genome and seven plasmids of one of the most widely used Synechocystis sp. PCC 6803 substrains, the glucose tolerant and motile Moscow or ‘PCC-M’ strain, revealing considerable evidence for recent microevolution. Seven single nucleotide polymorphisms (SNPs) specifically shared between ‘PCC-M’ and the ‘PCC-N and PCC-P’ substrains indicate that ‘PCC-M’ belongs to the ‘PCC’ group of motile strains. The identified indels and SNPs in ‘PCC-M’ are likely to affect glucose tolerance, motility, phage resistance, certain stress responses as well as functions in the primary metabolism, potentially relevant for the synthesis of alkanes. Three SNPs in intergenic regions could affect the promoter activities of two protein-coding genes and one cis-antisense RNA. Two deletions in ‘PCC-M’ affect parts of clustered regularly interspaced short palindrome repeats-associated spacer-repeat regions on plasmid pSYSA, in one case by an unusual recombination between spacer sequences.}, author = {Trautmann, Danika and Voß, Björn and Wilde, Annegret and Al-Babili, Salim and Hess, Wolfgang R.}, doi = {10.1093/dnares/dss024}, file = {Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/BFD3TC8Z/Trautmann et al. - 2012 - Microevolution in Cyanobacteria Re-sequencing a M.pdf:application/pdf;Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/UTP3PZDD/dnares.dss024.html:text/html}, issn = {1340-2838, 1756-1663}, journal = {DNA Research}, language = {en}, month = {10}, note = 00025, shorttitle = {Microevolution in {Cyanobacteria}}, title = {Microevolution in {Cyanobacteria}: {Re}-sequencing a {Motile} {Substrain} of {Synechocystis} sp. {PCC} 6803}, url = {http://dnaresearch.oxfordjournals.org/content/early/2012/10/13/dnares.dss024}, urldate = {2012-10-16}, year = 2012 }
  Link
  http://dnaresearch.oxfordjournals.org/content/early/2012/10/13/dnares.dss024
3. 31.
  Madhugiri, Ramakanth ; Pessi, Gabriella ; Voß, Björn ; Hahn, Julia ; Sharma, Cynthia M. ; Reinhardt, Richard ; Vogel, Jörg ; Hess, Wolfgang R. ; u. a.: Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis. In: RNA Biology, RNA Biology. Bd. 9 (2012), Nr. 1, S. 45--56. — 00011
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  @article{madhugiri_small_2012, author = {Madhugiri, Ramakanth and Pessi, Gabriella and Voß, Björn and Hahn, Julia and Sharma, Cynthia M. and Reinhardt, Richard and Vogel, Jörg and Hess, Wolfgang R. and Fischer, Hans-Martin and Evguenieva-Hackenberg, Elena}, doi = {10.4161/rna.9.1.18008}, file = {2011RNABIOL0040R1.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/QSAZJS4X/2011RNABIOL0040R1.pdf:application/pdf;2011RNABIOL0040R1-Sup.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/XXCVJS8P/2011RNABIOL0040R1-Sup.pdf:application/pdf;Landes Bioscience Journals\: RNA Biology:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/MWDEB3KI/18008.html:text/html}, issn = {1547-6286}, journal = {RNA Biology}, month = {01}, note = 00011, number = 1, pages = {45--56}, title = {Small {RNAs} of the {Bradyrhizobium}/{Rhodopseudomonas} lineage and their analysis}, url = {https://www.tandfonline.com/doi/full/10.4161/rna.9.1.18008}, urldate = {2012-03-14}, volume = 9, year = 2012 }
  Link
  https://www.tandfonline.com/doi/full/10.4161/rna.9.1.18008
4. 30.
  Huang, Jiabin ; Backofen, Rolf ; Voß, Björn: Abstract folding space analysis based on helices. In: RNA, RNA. Bd. 18 (2012), Nr. 12, S. 2135--2147. — 00005
  - BibTeX
  - Link
  BibTeX
  @article{huang_abstract_2012, abstract = {RNA has many pivotal functions especially in the regulation of gene expression by ncRNAs. Identification of their structure is an important requirement for understanding their function. Structure prediction alone is often insufficient for this task, due to algorithmic problems, parameter inaccuracies, and biological peculiarities. Among the latter, there are base modifications, cotranscriptional folding leading to folding traps, and conformational switching as in the case of riboswitches. All these require more in-depth analysis of the folding space. The major drawback, which all methods have to cope with, is the exponential growth of the folding space. Therefore, methods are often limited in the sequence length they can analyze, or they make use of heuristics, sampling, or abstraction. Our approach adopts the abstraction strategy and remedies some problems of existing methods. We introduce a position-specific abstraction based on helices that we term helix index shapes, or hishapes for short. Utilizing a dynamic programming framework, we have implemented this abstraction in the program RNAHeliCes. Furthermore, we developed two hishape-based methods, one for energy barrier estimation, called HiPath, and one for abstract structure comparison, termed HiTed. We demonstrate the superior performance of HiPath compared to other existing methods and the competitive accuracy of HiTed. RNAHeliCes, together with HiPath and HiTed, are available for download at http://www.cyanolab.de/software/RNAHeliCes.htm.}, author = {Huang, Jiabin and Backofen, Rolf and Voß, Björn}, doi = {10.1261/rna.033548.112}, file = {Huang et al. - 2012 - Abstract folding space analysis based on helices.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/R6VTXCK2/Huang et al. - 2012 - Abstract folding space analysis based on helices.pdf:application/pdf;Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/IEET4I5T/2135.html:text/html}, issn = {1355-8382, 1469-9001}, journal = {RNA}, language = {en}, month = {12}, note = 00005, number = 12, pages = {2135--2147}, title = {Abstract folding space analysis based on helices}, url = {http://rnajournal.cshlp.org/content/18/12/2135}, urldate = {2012-11-19}, volume = 18, year = 2012 }
  Link
  http://rnajournal.cshlp.org/content/18/12/2135
5. 29.
  Pfreundt, Ulrike ; Stal, Lucas J ; Voß, Bjorn ; Hess, Wolfgang R: Dinitrogen fixation in a unicellular chlorophyll d-containing cyanobacterium. In: ISME J, ISME J. (2012). — 00011
  - BibTeX
  - Link
  BibTeX
  @article{pfreundt_dinitrogen_2012, author = {Pfreundt, Ulrike and Stal, Lucas J and Voß, Bjorn and Hess, Wolfgang R}, file = {Nature Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/682MWSAU/Pfreundt et al. - 2012 - Dinitrogen fixation in a unicellular chlorophyll d.html:}, issn = {1751-7370}, journal = {ISME J}, month = {01}, note = 00011, title = {Dinitrogen fixation in a unicellular chlorophyll d-containing cyanobacterium}, url = {http://dx.doi.org/10.1038/ismej.2011.199}, urldate = {2012-01-16}, year = 2012 }
  Link
  http://dx.doi.org/10.1038/ismej.2011.199
2011
1. 28.
  Mitschke, Jan ; Georg, Jens ; Scholz, Ingeborg ; Sharma, Cynthia M. ; Dienst, Dennis ; Bantscheff, Jens ; Voß, Björn ; Steglich, Claudia ; u. a.: An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences. Bd. 108 (2011), Nr. 5, S. 2124--2129. — 00150
  - BibTeX
  - Link
  BibTeX
  @article{mitschke_experimentally_2011, abstract = {There has been an increasing interest in cyanobacteria because these photosynthetic organisms convert solar energy into biomass and because of their potential for the production of biofuels. However, the exploitation of cyanobacteria for bioengineering requires knowledge of their transcriptional organization. Using differential RNA sequencing, we have established a genome-wide map of 3,527 transcriptional start sites (TSS) of the model organism Synechocystis sp. PCC6803. One-third of all TSS were located upstream of an annotated gene; another third were on the reverse complementary strand of 866 genes, suggesting massive antisense transcription. Orphan TSS located in intergenic regions led us to predict 314 noncoding RNAs (ncRNAs). Complementary microarray-based RNA profiling verified a high number of noncoding transcripts and identified strong ncRNA regulations. Thus, ∼64\% of all TSS give rise to antisense or ncRNAs in a genome that is to 87\% protein coding. Our data enhance the information on promoters by a factor of 40, suggest the existence of additional small peptide-encoding mRNAs, and provide corrected 5′ annotations for many genes of this cyanobacterium. The global TSS map will facilitate the use of Synechocystis sp. PCC6803 as a model organism for further research on photosynthesis and energy research.}, author = {Mitschke, Jan and Georg, Jens and Scholz, Ingeborg and Sharma, Cynthia M. and Dienst, Dennis and Bantscheff, Jens and Voß, Björn and Steglich, Claudia and Wilde, Annegret and Vogel, Jörg and Hess, Wolfgang R.}, doi = {10.1073/pnas.1015154108}, file = {Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/H6XF29F9/Mitschke et al. - 2011 - An experimentally anchored map of transcriptional .pdf:application/pdf;Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/NT4S5FJN/2124.html:text/html}, journal = {Proceedings of the National Academy of Sciences}, month = {02}, note = 00150, number = 5, pages = {2124 --2129}, title = {An experimentally anchored map of transcriptional start sites in the model cyanobacterium {Synechocystis} sp. {PCC}6803}, url = {http://www.pnas.org/content/108/5/2124.abstract}, urldate = {2011-02-09}, volume = 108, year = 2011 }
  Link
  http://www.pnas.org/content/108/5/2124.abstract
2. 27.
  Babski, Julia ; Tjaden, Brian ; Voß, Björn ; Jellen-Ritter, Angelika ; Marchfelder, Anita ; Hess, Wolfgang R. ; Soppa, Jörg: Bioinformatic prediction and experimental verification of sRNAs in the haloarchaeon Haloferax volcanii. In: RNA Biology, RNA Biology. Bd. 8 (2011), Nr. 5, S. 806--816. — 00010
  - BibTeX
  - Link
  BibTeX
  @article{babski_bioinformatic_2011, author = {Babski, Julia and Tjaden, Brian and Voß, Björn and Jellen-Ritter, Angelika and Marchfelder, Anita and Hess, Wolfgang R. and Soppa, Jörg}, doi = {10.4161/rna.8.5.16039}, file = {BabskiRNA8-5.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/G98XSVP4/BabskiRNA8-5.pdf:application/pdf;BabskiRNA-Supp.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/G3EHUJFT/BabskiRNA-Supp.pdf:application/pdf;Landes Bioscience Journals\: RNA Biology:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/7TM35BV2/16039.html:text/html}, issn = {1547-6286}, journal = {RNA Biology}, month = {09}, note = 00010, number = 5, pages = {806--816}, title = {Bioinformatic prediction and experimental verification of {sRNAs} in the haloarchaeon {Haloferax} volcanii}, url = {https://www.tandfonline.com/doi/abs/10.4161/rna.8.5.16039}, urldate = {2012-03-14}, volume = 8, year = 2011 }
  Link
  https://www.tandfonline.com/doi/abs/10.4161/rna.8.5.16039
3. 26.
  Huang, Jiabin ; Voß, Björn: RNAHeliCes – Folding space analysis based on position aware structure abstraction. In: Proceedings of the German Conference on Bioinformatics 2011 (GCB 2011), Proceedings of the German Conference on Bioinformatics 2011 (GCB 2011), 2011. — 00000, S. RT--31
  - BibTeX
  BibTeX
  @inproceedings{huang_rnahelices_2011, abstract = {RNA has many pivotal functions especially in the regulation of gene expression by ncRNAs. Identification of their structure is an important requirement for understanding their function. Structure prediction alone is often insufficient for this task, due to algorithmic problems, parameter inaccuracies and also due to biological peculiarities. Among the latter we have base modifications, co-transcriptional folding leading to folding traps and conformational switching as in the case of riboswitches. All these require more in-depth analysis of the folding space. The major drawback, which all methods have to cope with, is the exponential growth of the folding space. Therefore, methods are often limited in the sequence length they can analyze or make use of heuristics, sampling or abstraction. Our approach adopts the abstraction strategy and remedies some problems of existing methods. We introduce a position-specific abstraction based on helices which we term helix index shapes or hishapes for short. Utilizing a dynamic programming framework, we have implemented this abstraction in the program RNAHeliCes. Furthermore, we present results of empirical studies on the size of the search space, showing that it is a reasonable extension to existing methods. We further show the application of RNAHeliCes to some well-studied classes of RNAs and discuss possible use cases of our method. RNAHeliCes is available for download at http://www.cyanolab.de/software/RNAHeliCes.htm.}, author = {Huang, Jiabin and Voß, Björn}, booktitle = {Proceedings of the {German} {Conference} on {Bioinformatics} 2011 ({GCB} 2011)}, file = {RT-31.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/5JXQM92T/RT-31.pdf:application/pdf}, month = {07}, note = 00000, pages = {RT--31}, title = {{RNAHeliCes} – {Folding} space analysis based on position aware structure abstraction}, year = 2011 }
2010
1. 25.
  Bogomolov, Sergiy ; Mann, Martin ; Voß, Björn ; Podelski, Andreas ; Backofen, Rolf: Shape-based barrier estimation for RNAs. In: In Proceedings of German Conference on Bioinformatics GCB’10, In Proceedings of German Conference on Bioinformatics GCB’10. Bd. 173 : GI, 2010. — 00004, S. 42--51
  - BibTeX
  BibTeX
  @inproceedings{bogomolov_shape-based_2010, abstract = {The ability of some RNA molecules to switch between different metastable conformations plays an important role in cellular processes. In order to identify such molecules and to predict their conformational changes one has to investigate the refolding pathways. As a qualitative measure of these transitions, the barrier height marks the energy peak along such refolding paths. We introduce a meta-heuristic to estimate such barriers, which is an NP-complete problem. To guide an arbitrary path heuristic, the method uses RNA shape representative structures as intermediate checkpoints for detours. This enables a broad but estimationcient search for refolding pathways. The resulting Shape Triples meta-heuristic enables a close to optimal estimation of the barrier height that outperforms the precision of the employed path heuristic.}, author = {Bogomolov, Sergiy and Mann, Martin and Voß, Björn and Podelski, Andreas and Backofen, Rolf}, booktitle = {In {Proceedings} of {German} {Conference} on {Bioinformatics} {GCB}'10}, file = {Bogomolov et al. - 2010 - Shape-based barrier estimation for RNAs.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/H6HT3MR2/Bogomolov et al. - 2010 - Shape-based barrier estimation for RNAs.pdf:application/pdf}, note = 00004, pages = {42--51}, publisher = {GI}, series = {{LNI}}, title = {Shape-based barrier estimation for {RNAs}}, volume = 173, year = 2010 }
2. 24.
  Ionescu, Danny ; Voß, Björn ; Oren, Aharon ; Hess, Wolfgang R. ; Muro-Pastor, Alicia M.: Heterocyst-Specific Transcription of NsiR1, a Non-Coding RNA Encoded in a Tandem Array of Direct Repeats in Cyanobacteria. In: Journal of Molecular Biology, Journal of Molecular Biology. Bd. 398 (2010), Nr. 2, S. 177--188. — 00016
  - BibTeX
  - Link
  BibTeX
  @article{ionescu_heterocyst-specific_2010, abstract = {In response to nitrogen deficiency, some cyanobacteria develop heterocysts, a terminally differentiated cell type, specialized for the fixation of atmospheric nitrogen. In Nostocales, this differentiation process is controlled by two major regulators, NtcA and HetR, but additional unknown factors are likely to be involved as well. In the context of a genome-wide search for potential non-coding RNAs, we identified an array of 12 tandem repeats that is transcribed in large amounts when cells enter conditions that trigger cell differentiation and switch to nitrogen fixation. The main accumulating transcript, which we suggest designating nitrogen stress-induced RNA 1 (NsiR1), has properties similar to regulatory non-coding RNAs. In Anabaena sp. PCC 7120, it is about 60 nt in length, has a very distinct predicted secondary structure, and is expressed very early and transiently after nitrogen step-down. Moreover, its expression requires HetR and NtcA and is restricted to cells that are differentiating into heterocysts, clearly placing NsiR1 within the regulon that controls the switch to nitrogen fixation and heterocyst formation. The genomic arrangement of NsiR1, located upstream of hetF, a gene whose product is involved in heterocyst formation, is conserved in all five Nostocales whose genomes are completely sequenced. Additionally, we detected NsiR1 expression in 19 different heterocyst-forming cyanobacteria. Our data suggest that every repeat is a complete transcriptional unit furnished with a cell-type-specific promoter and a Rho-independent terminator, which gives rise to a very high NsiR1 transcript level. NsiR1 is the first known bacterial non-coding RNA that is specifically upregulated in response to nitrogen step-down.}, author = {Ionescu, Danny and Voß, Björn and Oren, Aharon and Hess, Wolfgang R. and Muro-Pastor, Alicia M.}, doi = {10.1016/j.jmb.2010.03.010}, file = {ScienceDirect Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/CSQ9WRR6/Ionescu et al. - 2010 - Heterocyst-Specific Transcription of NsiR1, a Non-.pdf:application/pdf;ScienceDirect Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/N3IM83UT/science.html:text/html}, issn = {0022-2836}, journal = {Journal of Molecular Biology}, month = {04}, note = 00016, number = 2, pages = {177--188}, title = {Heterocyst-{Specific} {Transcription} of {NsiR}1, a {Non}-{Coding} {RNA} {Encoded} in a {Tandem} {Array} of {Direct} {Repeats} in {Cyanobacteria}}, url = {http://www.sciencedirect.com/science/article/B6WK7-4YKGJD5-2/2/75655bf41bd704ca1103eec520dab974}, urldate = {2010-11-16}, volume = 398, year = 2010 }
  Link
  http://www.sciencedirect.com/science/article/B6WK7-4YKGJD5-2/2/75655bf41bd704ca1103eec520dab974
3. 23.
  Voß, Bjoern ; Meinecke, Linda ; Kurz, Thorsten ; Al-Babili, Salim ; Beck, Christoph F. ; Hess, Wolfgang R.: Hemin and Mg-Protoporphyrin IX Induce Global Changes in Gene Expression in Chlamydomonas reinhardtii. In: Plant Physiol., Plant Physiol. (2010), S. pp.110.158683. — 00025
  - BibTeX
  - Link
  BibTeX
  @article{vos_hemin_2010, abstract = {Retrograde signaling is a pathway of communication from mitochondria and plastids to the nucleus in the context of cell differentiation, development and stress response. In Chlamydomonas reinhardtii, the tetrapyrroles Mg-protoporphyrin IX (MgProto) and heme are only synthesized within the chloroplast, and they have been implicated in the retrograde control of nuclear gene expression in this unicellular green alga. Feeding the two tetrapyrroles to Chlamydomonas cultures was previously shown to transiently induce five nuclear genes, three of which encode the heat shock proteins HSP70A, B, and E. In contrast, controversial results exist on the possible role of MgProto in the repression of genes for light harvesting proteins in higher plants, raising the question of how important this mode of regulation is. Here we used genome-wide transcriptional profiling to measure the global impact of these tetrapyrroles on gene regulation and the scope of the response. We identified almost 1000 genes whose expression level changed transiently but significantly. Among them were only a few genes for photosynthetic proteins but several encoding enzymes of the TCA cycle, heme-binding proteins, stress-response proteins, as well as proteins involved in protein folding and degradation. More than {\textgreater}50\% of the latter class of genes were also regulated by heat shock. The observed drastic fold changes at RNA level did not correlate with similar changes of protein concentrations under the tested experimental conditions. Phylogenetic profiling revealed that genes of putative endosymbiontic origin are not overrepresented among the responding genes. This and the transient nature of changes in gene expression suggest a signaling role of both tetrapyrroles as secondary messengers for adaptive responses affecting the entire cell and not only organellar proteins.}, author = {Voß, Bjoern and Meinecke, Linda and Kurz, Thorsten and Al-Babili, Salim and Beck, Christoph F. and Hess, Wolfgang R.}, doi = {10.1104/pp.110.158683}, file = {HighWire Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/SJFFH63G/Voss et al. - 2010 - Hemin and Mg-Protoporphyrin IX Induce Global Chang.pdf:application/pdf;HighWire Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/FIVH9TET/pp.110.html:text/html}, journal = {Plant Physiol.}, note = 00025, pages = {pp.110.158683}, title = {Hemin and {Mg}-{Protoporphyrin} {IX} {Induce} {Global} {Changes} in {Gene} {Expression} in {Chlamydomonas} reinhardtii}, url = {http://www.plantphysiol.org/cgi/content/abstract/pp.110.158683v1}, urldate = {2010-12-09}, year = 2010 }
  Link
  http://www.plantphysiol.org/cgi/content/abstract/pp.110.158683v1
4. 22.
  Mohr, Remus ; Voß, Bjorn ; Schliep, Martin ; Kurz, Thorsten ; Maldener, Iris ; Adams, David G ; Larkum, Anthony D W ; Chen, Min ; u. a.: A new chlorophyll d-containing cyanobacterium: evidence for niche adaptation in the genus Acaryochloris. In: ISME J, ISME J. Bd. 4 (2010), Nr. 11, S. 1456--1469. — 00022
  - BibTeX
  - Link
  BibTeX
  @article{mohr_new_2010, author = {Mohr, Remus and Voß, Bjorn and Schliep, Martin and Kurz, Thorsten and Maldener, Iris and Adams, David G and Larkum, Anthony D W and Chen, Min and Hess, Wolfgang R}, file = {Mohr et al. - 2010 - A new chlorophyll d-containing cyanobacterium evi.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/RAJHE8CB/Mohr et al. - 2010 - A new chlorophyll d-containing cyanobacterium evi.pdf:application/pdf;Nature Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/XJ5BIG7E/ismej201067a.html:text/html}, issn = {1751-7362}, journal = {ISME J}, month = {11}, note = 00022, number = 11, pages = {1456--1469}, shorttitle = {A new chlorophyll d-containing cyanobacterium}, title = {A new chlorophyll d-containing cyanobacterium: evidence for niche adaptation in the genus {Acaryochloris}}, url = {http://dx.doi.org/10.1038/ismej.2010.67}, urldate = {2010-11-05}, volume = 4, year = 2010 }
  Link
  http://dx.doi.org/10.1038/ismej.2010.67
5. 21.
  Georg, J. ; Honsel, A. ; Voß, B. ; Rennenberg, H. ; Hess, W. R.: A long antisense RNA in plant chloroplasts. In: New Phytologist, New Phytologist. Bd. 186 (2010), Nr. 3, S. 615--622. — 00023
  - BibTeX
  - Link
  BibTeX
  @article{georg_long_2010, abstract = {Based on computational prediction of RNA secondary structures, a long antisense RNA (asRNA) was found in chloroplasts of Arabidopsis, Nicotiana tabacum and poplar, which occurs in two to three major transcripts. Mapping of primary 5' ends, northern hybridizations and quantitative real-time reverse transcription polymerase chain reaction (qPCR) experiments demonstrated that these transcripts originate from a promoter that is typical for the plastid-encoded RNA polymerase and are over their full length in antisense orientation to the gene ndhB and therefore were designated asRNA\_ndhB. The asRNA\_ndhB transcripts predominantly accumulate in young leaves and at physiological growth temperatures. Two nucleotide positions in the mRNA that are subject to C-to-U RNA editing and which were previously found to be sensitive to elevated temperatures are covered by asRNA\_ndhB. Nevertheless, the correlation between the accumulation of asRNA\_ndhB and RNA editing appeared weak in a temperature shift experiment. With asRNA\_ndhB, we describe the first asRNA of plant chloroplasts that covers RNA editing sites, as well as a group II intron splice acceptor site, and that is under developmental control, raising the possibility that long asRNAs could be involved in RNA maturation or the control of RNA stability.}, author = {Georg, J. and Honsel, A. and Voß, B. and Rennenberg, H. and Hess, W. R.}, doi = {10.1111/j.1469-8137.2010.03203.x}, file = {Wiley Interscience PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/MEBIFJU3/Georg et al. - 2010 - A long antisense RNA in plant chloroplasts.pdf:application/pdf}, journal = {New Phytologist}, note = 00023, number = 3, pages = {615--622}, title = {A long antisense {RNA} in plant chloroplasts}, url = {http://dx.doi.org/10.1111/j.1469-8137.2010.03203.x}, urldate = {2010-05-04}, volume = 186, year = 2010 }
  Link
  http://dx.doi.org/10.1111/j.1469-8137.2010.03203.x
2009
1. 20.
  Voß, Björn ; Hölscher, Marion ; Baumgarth, Birgit ; Kalbfleisch, Andreas ; Kaya, Ceren ; Hess, Wolfgang R. ; Becker, Anke ; Elena Evguenieva-Hackenberg: Expression of small RNAs in Rhizobiales and protection of a small RNA and its degradation products by Hfq in Sinorhizobium meliloti. In: Biochemical and Biophysical Research Communications, Biochemical and Biophysical Research Communications. Bd. 390 (2009), Nr. 2, S. 331--336. — 00000
  - BibTeX
  - Link
  BibTeX
  @article{vos_expression_2009, abstract = {Regulatory RNA plays a pivotal role in the regulation of bacterial gene expression. Here, five small RNAs were studied in Sinorhizobium meliloti - SmrC15, SmrC16, Sra33, 6S and the signal recognition particle (SRP) RNA, which are conserved among at least seven different Rhizobium and Sinorhizobium species. The amount of SmrC16 decreased in stationary phase, while the other RNAs were up-regulated. The smallest changes, maximally 2-fold, were observed for 6S RNA. In the distantly related Bradyrhizobium japonicum, the amount of 6S RNA was not increased in stationary phase, suggesting some functional divergence in the roles of this molecule in Rhizobiales in comparison to Escherichia coli. Different decay rates were observed for SmrC15 and SmrC16 of S. meliloti upon rifampicin treatment, revealing posttranscriptional regulation during growth. The use of a [Delta]hfq mutant showed that Hfq protects full-length SmrC16 from degradation and stabilises its specific degradation products.}, author = {Voß, Björn and Hölscher, Marion and Baumgarth, Birgit and Kalbfleisch, Andreas and Kaya, Ceren and Hess, Wolfgang R. and Becker, Anke and {Elena Evguenieva-Hackenberg}}, doi = {10.1016/j.bbrc.2009.09.125}, file = {ScienceDirect Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/ZH2WHJ8A/science.html:text/html;Voss et al. - 2009 - Expression of small RNAs in Rhizobiales and protec.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/FTDWG524/Voss et al. - 2009 - Expression of small RNAs in Rhizobiales and protec.pdf:application/pdf}, issn = {0006-291X}, journal = {Biochemical and Biophysical Research Communications}, note = 00000, number = 2, pages = {331--336}, title = {Expression of small {RNAs} in {Rhizobiales} and protection of a small {RNA} and its degradation products by {Hfq} in {Sinorhizobium} meliloti}, url = {http://www.sciencedirect.com/science/article/B6WBK-4XC57DX-2/2/32de0bcdf98272e9a9b196b95327e646}, urldate = {2010-02-24}, volume = 390, year = 2009 }
  Link
  http://www.sciencedirect.com/science/article/B6WBK-4XC57DX-2/2/32de0bcdf98272e9a9b196b95327e646
2. 19.
  Gierga, Gregor ; Voß, Björn ; Hess, Wolfgang R.: The Yfr2 ncRNA family, a group of abundant RNA molecules widely conserved in cyanobacteria. In: RNA Biology, RNA Biology. Bd. 6 (2009), Nr. 3, S. 222--227. — 00011
  - BibTeX
  - Link
  BibTeX
  @article{gierga_yfr2_2009, author = {Gierga, Gregor and Voß, Björn and Hess, Wolfgang R.}, doi = {10.4161/rna.6.3.8921}, file = {GiergaRNA6-3.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/TDKVZ62X/GiergaRNA6-3.pdf:application/pdf;Landes Bioscience Journals\: RNA Biology:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/CTA4464T/8921.html:text/html}, issn = {1547-6286}, journal = {RNA Biology}, month = {07}, note = 00011, number = 3, pages = {222--227}, title = {The {Yfr}2 {ncRNA} family, a group of abundant {RNA} molecules widely conserved in cyanobacteria}, url = {http://www.landesbioscience.com/journals/11/article/8921/}, urldate = {2010-07-06}, volume = 6, year = 2009 }
  Link
  http://www.landesbioscience.com/journals/11/article/8921/
3. 18.
  Voß, Bjoern ; Georg, Jens ; Schon, Verena ; Ude, Susanne ; Hess, Wolfgang: Biocomputational prediction of non-coding RNAs in model cyanobacteria. In: BMC Genomics, BMC Genomics. Bd. 10 (2009), Nr. 1, S. 123. — 00054
  - BibTeX
  - Link
  BibTeX
  @article{vos_biocomputational_2009, abstract = {BACKGROUND:In bacteria, non-coding RNAs (ncRNA) are crucial regulators of gene expression, controlling various stress responses, virulence, and motility. Previous work revealed a relatively high number of ncRNAs in some marine cyanobacteria. However, for efficient genetic and biochemical analysis it would be desirable to identify a set of ncRNA candidate genes in model cyanobacteria that are easy to manipulate and for which extended mutant, transcriptomic and proteomic data sets are available.RESULTS:Here we have used comparative genome analysis for the biocomputational prediction of ncRNA genes and other sequence/structure-conserved elements in intergenic regions of the three unicellular model cyanobacteria Synechocystis PCC6803, Synechococcus elongatus PCC6301 and Thermosynechococcus elongatus BP1 plus the toxic Microcystis aeruginosa NIES843. The unfiltered numbers of predicted elements in these strains is 383, 168, 168, and 809, respectively, combined into 443 sequence clusters, whereas the numbers of individual elements with high support are 94, 56, 64, and 406, respectively. Removing also transposon-associated repeats, finally 78, 53, 42 and 168 sequences, respectively, are left belonging to 109 different clusters in the data set. Experimental analysis of selected ncRNA candidates in Synechocystis PCC6803 validated new ncRNAs originating from the fabF-hoxH and apcC-prmA intergenic spacers and three highly expressed ncRNAs belonging to the Yfr2 family of ncRNAs. Yfr2a promoter-luxAB fusions confirmed a very strong activity of this promoter and indicated a stimulation of expression if the cultures were exposed to elevated light intensities.CONCLUSION:Comparison to entries in Rfam and experimental testing of selected ncRNA candidates in Synechocystis PCC6803 indicate a high reliability of the current prediction, despite some contamination by the high number of repetitive sequences in some of these species. In particular, we identified in the four species altogether 8 new ncRNA homologs belonging to the Yfr2 family of ncRNAs. Modelling of RNA secondary structures indicated two conserved single-stranded sequence motifs that might be involved in RNA-protein interactions or in the recognition of target RNAs. Since our analysis has been restricted to find ncRNA candidates with a reasonable high degree of conservation among these four cyanobacteria, there might be many more, requiring direct experimental approaches for their identification.}, author = {Voß, Bjoern and Georg, Jens and Schon, Verena and Ude, Susanne and Hess, Wolfgang}, doi = {10.1186/1471-2164-10-123}, file = {biomedcentral Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/SRWMT3GQ/123.html:text/html;Voß et al. - 2009 - Biocomputational prediction of non-coding RNAs in .pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/XJIEK2AT/Voß et al. - 2009 - Biocomputational prediction of non-coding RNAs in .pdf:application/pdf}, issn = {1471-2164}, journal = {BMC Genomics}, note = 00054, number = 1, pages = 123, title = {Biocomputational prediction of non-coding {RNAs} in model cyanobacteria}, url = {http://www.biomedcentral.com/1471-2164/10/123}, urldate = {2009-03-30}, volume = 10, year = 2009 }
  Link
  http://www.biomedcentral.com/1471-2164/10/123
4. 17.
  Georg, Jens ; Voß, Bjorn ; Scholz, Ingeborg ; Mitschke, Jan ; Wilde, Annegret ; Hess, Wolfgang R: Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. In: Mol Syst Biol, Mol Syst Biol. Bd. 5 (2009). — 00112
  - BibTeX
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  BibTeX
  @article{georg_evidence_2009, author = {Georg, Jens and Voß, Bjorn and Scholz, Ingeborg and Mitschke, Jan and Wilde, Annegret and Hess, Wolfgang R}, doi = {10.1038/msb.2009.63}, file = {Georg et al. - 2009 - Evidence for a major role of antisense RNAs in cya.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/X7TGIEBP/Georg et al. - 2009 - Evidence for a major role of antisense RNAs in cya.pdf:application/pdf;Nature Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/RKK7ETHW/msb200963.html:text/html}, journal = {Mol Syst Biol}, note = 00112, title = {Evidence for a major role of antisense {RNAs} in cyanobacterial gene regulation}, url = {http://dx.doi.org/10.1038/msb.2009.63}, urldate = {2009-09-18}, volume = 5, year = 2009 }
  Link
  http://dx.doi.org/10.1038/msb.2009.63
5. 16.
  Soppa, Jörg ; Straub, Julia ; Brenneis, Mariam ; Jellen-Ritter, Angelika ; Heyer, Ruth ; Fischer, Susan ; Granzow, Michaela ; Voß, Björn ; u. a.: Small RNAs of the halophilic archaeon Haloferax volcanii. In: Biochemical Society Transactions, Biochemical Society Transactions. Bd. 37 (2009), Nr. Pt 1, S. 133--136. — 00017
  - BibTeX
  - Link
  BibTeX
  @article{soppa_small_2009, abstract = {In recent years, sRNAs (small non-coding RNAs) have been found to be abundant in eukaryotes and bacteria and have been recognized as a novel class of gene expression regulators. In contrast, much less is known about sRNAs in archaea, except for snoRNAs (small nucleolar RNAs) that are involved in the modification of bases in stable RNAs. Therefore bioinformatic and experimental RNomics approaches were undertaken to search for the presence of sRNAs in the model archaeon Haloferax volcanii, resulting in more than 150 putative sRNA genes being identified. Northern blot analyses were used to study (differential) expression of sRNA genes. Several chromosomal deletion mutants of sRNA genes were generated and compared with the wild-type. It turned out that two sRNAs are essential for growth at low salt concentrations and high temperatures respectively, and one is involved in the regulation of carbon metabolism. Taken together, it could be shown that sRNAs are as abundant in H. volcanii as they are in well-studied bacterial species and that they fulfil important biological roles under specific conditions.}, author = {Soppa, Jörg and Straub, Julia and Brenneis, Mariam and Jellen-Ritter, Angelika and Heyer, Ruth and Fischer, Susan and Granzow, Michaela and Voß, Björn and Hess, Wolfgang R and Tjaden, Brian and Marchfelder, Anita}, doi = {10.1042/BST0370133}, file = {PubMed Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/2PAT955S/19143617.html:text/html;Soppa_2009_Minireview_sRNAs.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/WHVZ4KNJ/Soppa_2009_Minireview_sRNAs.pdf:application/pdf}, issn = {1470-8752}, journal = {Biochemical Society Transactions}, month = {02}, note = 00017, number = {Pt 1}, pages = {133--136}, title = {Small {RNAs} of the halophilic archaeon {Haloferax} volcanii}, url = {http://www.ncbi.nlm.nih.gov/pubmed/19143617}, urldate = {2009-05-04}, volume = 37, year = 2009 }
  Link
  http://www.ncbi.nlm.nih.gov/pubmed/19143617
2008
1. 15.
  Steglich, Claudia ; Futschik, Matthias E. ; Lindell, Debbie ; Voß, Bjoern ; Chisholm, Sallie W. ; Hess, Wolfgang R.: The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus. In: PLoS Genet, PLoS Genet. Bd. 4 (2008), Nr. 8, S. e1000173. — 00069
  - BibTeX
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  BibTeX
  @article{steglich_challenge_2008, abstract = {Prochlorococcus is the most abundant phototroph in the vast, nutrient-poor areas of the ocean. It plays an important role in the ocean carbon cycle, and is a key component of the base of the food web. All cells share a core set of about 1,200 genes, augmented with a variable number of “flexible” genes. Many of the latter are located in genomic islands—hypervariable regions of the genome that encode functions important in differentiating the niches of “ecotypes.” Of major interest is how cells with such a small genome regulate cellular processes, as they lack many of the regulatory proteins commonly found in bacteria. We show here that contrary to the regulatory proteins, ncRNAs are present at levels typical of bacteria, revealing that they might have a disproportional regulatory role in Prochlorococcus—likely an adaptation to the extremely low-nutrient conditions of the open oceans, combined with the constraints of a small genome. Some of the ncRNAs were differentially expressed under stress conditions, and a high number of them were found to be associated with genomic islands, suggesting functional links between these RNAs and the response of Prochlorococcus to particular environmental challenges.}, author = {Steglich, Claudia and Futschik, Matthias E. and Lindell, Debbie and Voß, Bjoern and Chisholm, Sallie W. and Hess, Wolfgang R.}, doi = {10.1371%2Fjournal.pgen.1000173}, file = {PLoS Genetics\: The Challenge of Regulation in a Minimal Photoautotroph\: Non-Coding RNAs in Prochlorococcus:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/EQCDT4UC/info3Adoi2F10.13712Fjournal.pgen.html:text/html;PLoS One Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/5EV4XNI6/Steglich et al - 2008 - The Challenge of Regulation in a Minimal Photoauto.pdf:application/pdf}, journal = {PLoS Genet}, note = 00069, number = 8, pages = {e1000173}, shorttitle = {The {Challenge} of {Regulation} in a {Minimal} {Photoautotroph}}, title = {The {Challenge} of {Regulation} in a {Minimal} {Photoautotroph}: {Non}-{Coding} {RNAs} in {Prochlorococcus}}, url = {http://dx.doi.org/10.1371%2Fjournal.pgen.1000173}, urldate = {2009-03-10}, volume = 4, year = 2008 }
  Link
  http://dx.doi.org/10.1371%2Fjournal.pgen.1000173
2007
1. 14.
  Fattash, Isam ; Voß, Bjoern ; Reski, Ralf ; Hess, Wolfgang ; Frank, Wolfgang: Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. In: BMC Plant Biology, BMC Plant Biology. Bd. 7 (2007), Nr. 1, S. 13. — 00085
  - BibTeX
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  BibTeX
  @article{fattash_evidence_2007, abstract = {BACKGROUND:MicroRNAs (miRNAs) are regulatory RNA molecules that are specified by their mode of action, the structure of primary transcripts, and their typical size of 20-24 nucleotides. Frequently, not only single miRNAs but whole families of closely related miRNAs have been found in animals and plants. Some families are widely conserved among different plant taxa. Hence, it is evident that these conserved miRNAs are of ancient origin and indicate essential functions that have been preserved over long evolutionary time scales. In contrast, other miRNAs seem to be species-specific and consequently must possess very distinct functions. Thus, the analysis of an early-branching species provides a window into the early evolution of fundamental regulatory processes in plants.RESULTS:Based on a combined experimental-computational approach, we report on the identification of 48 novel miRNAs and their putative targets in the moss Physcomitrella patens. From these, 18 miRNAs and two targets were verified in independent experiments. As a result of our study, the number of known miRNAs in Physcomitrella has been raised to 78. Functional assignments to mRNAs targeted by these miRNAs revealed a bias towards genes that are involved in regulation, cell wall biosynthesis and defense. Eight miRNAs were detected with different expression in protonema and gametophore tissue. The miRNAs 1-50 and 2-51 are located on a shared precursor that are separated by only one nucleotide and become processed in a tissue-specific way.CONCLUSION:Our data provide evidence for a surprisingly diverse and complex miRNA population in Physcomitrella. Thus, the number and function of miRNAs must have significantly expanded during the evolution of early land plants. As we have described here within, the coupled maturation of two miRNAs from a shared precursor has not been previously identified in plants.}, author = {Fattash, Isam and Voß, Bjoern and Reski, Ralf and Hess, Wolfgang and Frank, Wolfgang}, doi = {10.1186/1471-2229-7-13}, file = {biomedcentral PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/REX33DIV/Fattash et al - 2007 - Evidence for the rapid expansion of microRNA-media.pdf:application/pdf;biomedcentral Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/5T7HUXAA/13.html:text/html}, issn = {1471-2229}, journal = {BMC Plant Biology}, note = 00085, number = 1, pages = 13, title = {Evidence for the rapid expansion of {microRNA}-mediated regulation in early land plant evolution}, url = {http://www.biomedcentral.com/1471-2229/7/13}, urldate = {2009-03-10}, volume = 7, year = 2007 }
  Link
  http://www.biomedcentral.com/1471-2229/7/13
2. 13.
  Axmann, Ilka M. ; Holtzendorff, Julia ; Voß, Bjoern ; Kensche, Philip ; Hess, Wolfgang R.: Two distinct types of 6S RNA in Prochlorococcus. In: Gene, Gene. Bd. 406 (2007), Nr. 1–2, S. 69--78. — 00025
  - BibTeX
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  BibTeX
  @article{axmann_two_2007, abstract = {Different forms of the 6S non-coding RNA (ncRNA) exist in enterobacteria and in B. subtilis but there is only limited information about this RNA from other groups of bacteria. Prochlorococcus is an oceanic, ecologically important, cyanobacterium. It possesses the most streamlined genome within the cyanobacterial phylum, lacking many regulatory proteins and mechanisms well-known from other bacteria. Here we show the accumulation of two distinct types of 6S RNA in Prochlorococcus MED4. One of these RNAs is transcribed from a specific promoter located 23 nucleotides downstream the terminal codon of the purK gene, whereas the longer transcript is produced by processing from a purK-6S RNA precursor. The expression of both 6S transcripts is under diel control, reaching maxima during the day and minima coinciding with the S- and G2-like phases which are typical for synchronized cultures of this prokaryote. Based on data from four closely related Prochlorococcus strains and 11 environmental sequences from the Sargasso Sea, a previously unknown structural element is predicted within the 6S RNA 5' domain by comparative computational analysis. The divergent expression in synchronized cultures and unusual structural domains that were detected based on metagenomic data sets indicate that 6S RNA is an extremely important global regulator in these marine cyanobacteria.}, author = {Axmann, Ilka M. and Holtzendorff, Julia and Voß, Bjoern and Kensche, Philip and Hess, Wolfgang R.}, doi = {10.1016/j.gene.2007.06.011}, file = {ScienceDirect Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/32SI24MV/Axmann et al - 2007 - Two distinct types of 6S RNA in Prochlorococcus.pdf:application/pdf;ScienceDirect Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/VR72AJ8I/science.html:text/html}, issn = {0378-1119}, journal = {Gene}, note = 00025, number = {1-2}, pages = {69--78}, title = {Two distinct types of 6S {RNA} in {Prochlorococcus}}, url = {http://www.sciencedirect.com/science/article/B6T39-4P1G9M5-1/2/ce8afc109c209d358201e708c73d3ae5}, urldate = {2009-03-30}, volume = 406, year = 2007 }
  Link
  http://www.sciencedirect.com/science/article/B6T39-4P1G9M5-1/2/ce8afc109c209d358201e708c73d3ae5
3. 12.
  Chen, Xiao Hua ; Koumoutsi, Alexandra ; Scholz, Romy ; Eisenreich, Andreas ; Schneider, Kathrin ; Heinemeyer, Isabelle ; Morgenstern, Burkhard ; Voß, Bjoern ; u. a.: Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. In: Nat Biotech, Nat Biotech. Bd. 25 (2007), Nr. 9, S. 1007--1014. — 00244
  - BibTeX
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  BibTeX
  @article{chen_comparative_2007, author = {Chen, Xiao Hua and Koumoutsi, Alexandra and Scholz, Romy and Eisenreich, Andreas and Schneider, Kathrin and Heinemeyer, Isabelle and Morgenstern, Burkhard and Voß, Bjoern and Hess, Wolfgang R and Reva, Oleg and Junge, Helmut and Voigt, Birgit and Jungblut, Peter R and Vater, Joachim and Sussmuth, Roderich and Liesegang, Heiko and Strittmatter, Axel and Gottschalk, Gerhard and Borriss, Rainer}, doi = {10.1038/nbt1325}, file = {Nature Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/FANZPQRQ/Chen et al - 2007 - Comparative analysis of the complete genome sequen.pdf:application/pdf;Nature Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/ZGKZKTZU/nbt1325.html:text/html}, issn = {1087-0156}, journal = {Nat Biotech}, note = 00244, number = 9, pages = {1007--1014}, title = {Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium {Bacillus} amyloliquefaciens {FZB}42}, url = {http://dx.doi.org/10.1038/nbt1325}, urldate = {2009-03-10}, volume = 25, year = 2007 }
  Link
  http://dx.doi.org/10.1038/nbt1325
4. 11.
  Voß, Björn ; Gierga, Gregor ; Axmann, Ilka ; Hess, Wolfgang: A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria. In: BMC Genomics, BMC Genomics. Bd. 8 (2007), Nr. 1, S. 375. — 00025
  - BibTeX
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  BibTeX
  @article{vos_motif-based_2007, abstract = {BACKGROUND:Non-coding RNAs (ncRNA) are regulators of gene expression in all domains of life. They control growth and differentiation, virulence, motility and various stress responses. The identification of ncRNAs can be a tedious process due to the heterogeneous nature of this molecule class and the missing sequence similarity of orthologs, even among closely related species. The small ncRNA Yfr1 has previously been found in the Prochlorococcus/Synechococcus group of marine cyanobacteria.RESULTS:Here we show that screening available genome sequences based on an RNA motif and followed by experimental analysis works successfully in detecting this RNA in all lineages of cyanobacteria. Yfr1 is an abundant ncRNA between 54 and 69 nt in size that is ubiquitous for cyanobacteria except for two low light-adapted strains of Prochlorococcus, MIT 9211 and SS120, in which it must have been lost secondarily. Yfr1 consists of two predicted stem-loop elements separated by an unpaired sequence of 16-20 nucleotides containing the ultraconserved undecanucleotide 5'-ACUCCUCACAC-3'.CONCLUSION:Starting with an ncRNA previously found in a narrow group of cyanobacteria only, we show here the highly specific and sensitive identification of its homologs within all lineages of cyanobacteria, whereas it was not detected within the genome sequences of E. coli and of 7 other eubacteria belonging to the alpha-proteobacteria, chlorobiaceae and spirochaete. The integration of RNA motif prediction into computational pipelines for the detection of ncRNAs in bacteria appears as a promising step to improve the quality of such predictions.}, author = {Voß, Björn and Gierga, Gregor and Axmann, Ilka and Hess, Wolfgang}, doi = {10.1186/1471-2164-8-375}, file = {biomedcentral PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/PANIU6G5/VoSZ et al. - 2007 - A motif-based search in bacterial genomes identifi.pdf:application/pdf;biomedcentral Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/5FU5MN9S/375.html:text/html}, issn = {1471-2164}, journal = {BMC Genomics}, note = 00025, number = 1, pages = 375, title = {A motif-based search in bacterial genomes identifies the ortholog of the small {RNA} {Yfr}1 in all lineages of cyanobacteria}, url = {http://www.biomedcentral.com/1471-2164/8/375}, urldate = {2010-07-06}, volume = 8, year = 2007 }
  Link
  http://www.biomedcentral.com/1471-2164/8/375
2006
1. 10.
  Talmor-Neiman, Mali ; Stav, Ran ; Frank, Wolfgang ; Voß, Bjoern ; Arazi, Tzahi: Novel micro-RNAs and intermediates of micro-RNA biogenesis from moss. In: The Plant Journal, The Plant Journal. Bd. 47 (2006), Nr. 1, S. 25--37. — 00075
  - BibTeX
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  BibTeX
  @article{talmor-neiman_novel_2006, abstract = {Micro-RNAs (miRNAs) are one class of small non-coding RNAs that have important regulatory roles in higher plants. Much less is known about their prevalence and function in lower land plants. Previously we cloned 100 non-structural small RNAs from the moss Physcomitrella patens but could annotate only 11 as miRNAs. To identify additional moss miRNAs among cloned small RNAs we have analyzed their genomic sequences for a characteristic miRNA precursor-like structure. This analysis revealed 19 new moss miRNAs that are predicted to be encoded by 22 putative foldbacks. Northern blot analysis confirmed the expression of 14 new miRNA representatives. Half of these were gametophore specific, the rest were detected at low levels in the protonema. We predicted 12 genes as targets of nine new miRNAs. Three of these show homology to transcription factors and the others appear to play roles in diverse physiological processes including light and cytokine signaling, which have not to date been shown to be regulated by a miRNA in flowering plants. Four target genes, which show homology to ATN1-like protein kinase, NAC transcription factors and a cytokinin receptor, have been validated by miRNA-mediated mRNA cleavage. In addition, our analysis revealed that seven small RNAs represent miRNA* and three represent intermediates of pre-miRNA processing, providing evidence for specific DICER-like cleavage steps during miRNA biogenesis in moss. Our findings suggest that miRNAs are common in mosses and set the stage for the elucidation of their varied biological functions.}, author = {Talmor-Neiman, Mali and Stav, Ran and Frank, Wolfgang and Voß, Bjoern and Arazi, Tzahi}, doi = {10.1111/j.1365-313X.2006.02768.x}, file = {Wiley Interscience PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/G69MDV5T/Talmor-Neiman et al - 2006 - Novel micro-RNAs and intermediates of micro-RNA bi.pdf:application/pdf}, journal = {The Plant Journal}, note = 00075, number = 1, pages = {25--37}, title = {Novel micro-{RNAs} and intermediates of micro-{RNA} biogenesis from moss}, url = {http://dx.doi.org/10.1111/j.1365-313X.2006.02768.x}, urldate = {2009-03-10}, volume = 47, year = 2006 }
  Link
  http://dx.doi.org/10.1111/j.1365-313X.2006.02768.x
2. 9.
  Voß, Bjoern ; Giegerich, Robert ; Rehmsmeier, Marc: Complete probabilistic analysis of RNA shapes. In: BMC Biology, BMC Biology. Bd. 4 (2006), Nr. 1, S. 5. — 00071
  - BibTeX
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  BibTeX
  @article{vos_complete_2006, abstract = {BACKGROUND:Soon after the first algorithms for RNA folding became available, it was recognised that the prediction of only one energetically optimal structure is insufficient to achieve reliable results. An in-depth analysis of the folding space as a whole appeared necessary to deduce the structural properties of a given RNA molecule reliably. Folding space analysis comprises various methods such as suboptimal folding, computation of base pair probabilities, sampling procedures and abstract shape analysis. Common to many approaches is the idea of partitioning the folding space into classes of structures, for which certain properties can be derived.RESULTS:In this paper we extend the approach of abstract shape analysis. We show how to compute the accumulated probabilities of all structures that share the same shape. While this implies a complete (non-heuristic) analysis of the folding space, the computational effort depends only on the size of the shape space, which is much smaller. This approach has been integrated into the tool RNAshapes, and we apply it to various RNAs.CONCLUSION:Analyses of conformational switches show the existence of two shapes with probabilities approximately 23 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaadaWcaaqaaiabikdaYaqaaiabiodaZaaaaaa@2EA2@ vs. 13 MathType@MTEF@5@5@+=feaafiart1ev1aaatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacH8akY=wiFfYdH8Gipec8Eeeu0xXdbba9frFj0=OqFfea0dXdd9vqai=hGuQ8kuc9pgc9s8qqaq=dirpe0xb9q8qiLsFr0=vr0=vr0dc8meaabaqaciaacaGaaeqabaqabeGadaaakeaadaWcaaqaaiabigdaXaqaaiabiodaZaaaaaa@2EA0@, whereas the analysis of a microRNA precursor reveals one shape with a probability near to 1.0. Furthermore, it is shown that a shape can outperform an energetically more favourable one by achieving a higher probability. From these results, and the fact that we use a complete and exact analysis of the folding space, we conclude that this approach opens up new and promising routes for investigating and understanding RNA secondary structure.}, author = {Voß, Bjoern and Giegerich, Robert and Rehmsmeier, Marc}, doi = {10.1186/1741-7007-4-5}, file = {biomedcentral PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/CCSVEKCS/VoSZ et al - 2006 - Complete probabilistic analysis of RNA shapes.pdf:application/pdf;biomedcentral Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/WTTSNNRU/5.html:text/html}, issn = {1741-7007}, journal = {BMC Biology}, note = {00071 bibtex: Voss:2006}, number = 1, pages = 5, title = {Complete probabilistic analysis of {RNA} shapes}, url = {http://www.biomedcentral.com/1741-7007/4/5}, urldate = {2009-03-10}, volume = 4, year = 2006 }
  Link
  http://www.biomedcentral.com/1741-7007/4/5
3. 8.
  Reeder, Jens ; Höchsmann, Matthias ; Rehmsmeier, Marc ; Voß, Bjoern ; Giegerich, Robert: Beyond Mfold: Recent advances in RNA bioinformatics. In: Journal of Biotechnology, Journal of Biotechnology. Bd. 124 (2006), Nr. 1, S. 41--55. — 00057
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  @article{reeder_beyond_2006, abstract = {Computational analysis of RNA secondary structure is a classical field of biosequence analysis, which has recently gained momentum due to the manyfold regulatory functions of RNA that have become apparent. We present five recent computational approaches that address the problems of synoptic folding space analysis, pseudoknot prediction, structure alignment, comparative structure prediction, and miRNA target prediction. All these programs are in current use and are available via the Bielefeld Bioinformatics Server at http://bibiserv.techfak.uni-bielefeld.de.}, author = {Reeder, Jens and Höchsmann, Matthias and Rehmsmeier, Marc and Voß, Bjoern and Giegerich, Robert}, doi = {10.1016/j.jbiotec.2006.01.034}, file = {Reeder et al. - 2006 - Beyond Mfold Recent advances in RNA bioinformatic.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/9KECB5QB/Reeder et al. - 2006 - Beyond Mfold Recent advances in RNA bioinformatic.pdf:application/pdf;ScienceDirect Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/ZCKWDGCP/science.html:text/html}, issn = {0168-1656}, journal = {Journal of Biotechnology}, month = {06}, note = 00057, number = 1, pages = {41--55}, shorttitle = {Beyond {Mfold}}, title = {Beyond {Mfold}: {Recent} advances in {RNA} bioinformatics}, url = {http://www.sciencedirect.com/science/article/B6T3C-4JFHDS5-1/2/cdc38facf439d671b17c4f84d1729468}, urldate = {2009-03-10}, volume = 124, year = 2006 }
  Link
  http://www.sciencedirect.com/science/article/B6T3C-4JFHDS5-1/2/cdc38facf439d671b17c4f84d1729468
4. 7.
  Steffen, Peter ; Voß, Bjoern ; Rehmsmeier, Marc ; Reeder, Jens ; Giegerich, Robert: RNAshapes: an integrated RNA analysis package based on abstract shapes. In: Bioinformatics, Bioinformatics. Bd. 22 (2006), Nr. 4, S. 500--503. — 00193
  - BibTeX
  - Link
  BibTeX
  @article{steffen_rnashapes:_2006, abstract = {Summary: We introduce RNAshapes, a new software package that integrates three RNA analysis tools based on the abstract shapes approach: the analysis of shape representatives, the calculation of shape probabilities and the consensus shapes approach. This new package is completely reimplemented in C and outruns the original implementations significantly in runtime and memory requirements. Additionally, we added a number of useful features like suboptimal folding with correct dangling energies, structure graph output, shape matching and a sliding window approach. Availability: RNAshapes is freely available at http://bibiserv.techfak.uni-bielefeld.de/rnashapes/ as C source code, and as compiled binaries for the most common computer architectures. For Microsoft Windows, we also offer a graphical user interface with convenient access to the complete functionality of the package. Contact: psteffen@techfak.uni-bielefeld.de}, author = {Steffen, Peter and Voß, Bjoern and Rehmsmeier, Marc and Reeder, Jens and Giegerich, Robert}, doi = {10.1093/bioinformatics/btk010}, file = {HighWire Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/PDQ4ZP99/500.html:text/html;Steffen et al. - 2006 - RNAshapes an integrated RNA analysis package base.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/95RB83UZ/Steffen et al. - 2006 - RNAshapes an integrated RNA analysis package base.pdf:application/pdf}, journal = {Bioinformatics}, month = {02}, note = 00193, number = 4, pages = {500--503}, shorttitle = {{RNAshapes}}, title = {{RNAshapes}: an integrated {RNA} analysis package based on abstract shapes}, url = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/4/500}, urldate = {2009-03-10}, volume = 22, year = 2006 }
  Link
  http://bioinformatics.oxfordjournals.org/cgi/content/abstract/22/4/500
5. 6.
  Backofen, R. ; Borrmann, H.-G. ; Deck, W. ; Dedner, A. ; Raedt, L. De ; Desch, K. ; Diesmann, M. ; Geier, M. ; u. a.: A Bottom-up approach to Grid-Computing at a University: the Black-Forest-Grid Initiative. In: Praxis der Informationsverarbeitung und Kommunikation, Praxis der Informationsverarbeitung und Kommunikation. Bd. 29 (2006), Nr. 2, S. 81--87. — 00004
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  @article{backofen_bottom-up_2006, abstract = {Recent years have seen a rapid increase in the need for highperformance computing. These demands come from disciplines such as particle physics traditionally relying on High Performance Computing (HPC) but lately also from the various branches of life science that have matured into quantitative disciplines. The classical infrastructure of university computer centres results to be unsuited to cope with the new requirements for a multitude of reasons. Here we discuss the causes of this failure and present a solution developed at the University of Freiburg in a collaborative effort of several faculties. We demonstrate that using state of the art grid computing technology the problem can now be addressed in a bottom-up approach. The organizational, technical, and financial components of our framework, the Black Forest Grid Initiative (BFG) are described and results of its implementation are presented. In the process, a number of new questions have emerged which the next phase of our project needs to address.}, author = {Backofen, R. and Borrmann, H.-G. and Deck, W. and Dedner, A. and Raedt, L. De and Desch, K. and Diesmann, M. and Geier, M. and Greiner, A. and Hess, W. R. and Honerkamp, J. and Jankowski, St and Krossing, I. and Liehr, A. W. and Karwath, A. and Klöfkorn, R. and Pesché, R. and Potjans, T. and Röttger, M. C. and Schmidt-Thieme, L. and Schneider, G. and Voß, B. and Wiebelt, B. and Wienemann, P. and Winterer, V.-H.}, file = {Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/ZWTX858W/Backofen et al. - 2006 - A Bottom-up approach to Grid-Computing at a Univer.pdf:application/pdf;Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/FSHH3ZMZ/piko.2006.81.html:text/html}, journal = {Praxis der Informationsverarbeitung und Kommunikation}, note = 00004, number = 2, pages = {81--87}, shorttitle = {A {Bottom}-up approach to {Grid}-{Computing} at a {University}}, title = {A {Bottom}-up approach to {Grid}-{Computing} at a {University}: the {Black}-{Forest}-{Grid} {Initiative}}, url = {http://www.degruyter.com/view/j/piko.2006.29.issue-2/piko.2006.81/piko.2006.81.xml}, urldate = {2015-06-23}, volume = 29, year = 2006 }
  Link
  http://www.degruyter.com/view/j/piko.2006.29.issue-2/piko.2006.81/piko.2006.81.xml
6. 5.
  Voß, Bjoern: Structural analysis of aligned RNAs. In: Nucl. Acids Res., Nucl. Acids Res. Bd. 34 (2006), Nr. 19, S. 5471--5481. — 00020 bibtex: Voss:2006a
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  @article{vos_structural_2006, abstract = {The knowledge about classes of non-coding RNAs (ncRNAs) is growing very fast and it is mainly the structure which is the common characteristic property shared by members of the same class. For correct characterization of such classes it is therefore of great importance to analyse the structural features in great detail. In this manuscript I present RNAlishapes which combines various secondary structure analysis methods, such as suboptimal folding and shape abstraction, with a comparative approach known as RNA alignment folding. RNAlishapes makes use of an extended thermodynamic model and covariance scoring, which allows to reward covariation of paired bases. Applying the algorithm to a set of bacterial trp-operon leaders using shape abstraction it was able to identify the two alternating conformations of this attenuator. Besides providing in-depth analysis methods for aligned RNAs, the tool also shows a fairly well prediction accuracy. Therefore, RNAlishapes provides the community with a powerful tool for structural analysis of classes of RNAs and is also a reasonable method for consensus structure prediction based on sequence alignments. RNAlishapes is available for online use and download at http://rna.cyanolab.de.}, author = {Voß, Bjoern}, doi = {10.1093/nar/gkl692}, file = {HighWire Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/743MGGZG/Voss - 2006 - Structural analysis of aligned RNAs.pdf:application/pdf;HighWire Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/6ADNU3G3/5471.html:text/html}, journal = {Nucl. Acids Res.}, month = {11}, note = {00020 bibtex: Voss:2006a}, number = 19, pages = {5471--5481}, title = {Structural analysis of aligned {RNAs}}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/34/19/5471}, urldate = {2009-03-10}, volume = 34, year = 2006 }
  Link
  http://nar.oxfordjournals.org/cgi/content/abstract/34/19/5471
2005
1. 4.
  Voß, Bjoern: Advanced tools for RNA secondary structure analysis, Universitätsbibliothek Bielefeld, 2005. — 00000
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  @phdthesis{vos_advanced_2005, abstract = {The analysis of RNA secondary structure has become more and more important throughout the last decades after it was recognised that RNA does not only serve as a passive messenger (mRNA), but also as a functional compound of the cell. Furthermore, it was elucidated that mainly the structure rather than the sequence determines the function of such non-protein-coding RNA. This means that two RNA molecules which have low sequence similarity but high structure similarity are likely to have a similar function. The prediction of RNA secondary structure is based on parameters that have been measured in vitro. This results in rather static parameters, that do not incorporate the dynamic change of environment occurring in living organisms. Nevertheless, the use of these parameters, that are summarised in the energy model, gave valuable results, especially for short sequences. Several refinements throughout the years improved the predictions, but still the calculated optimal structure is not guaranteed to correspond to the native one. In this case, and due to the fact that the native structure is feasible under the energy model, it is common practice to additionally calculate suboptimal structures and incorporate these in the study. The set of all suboptimal structures is referred to as the structure space, which actually holds the information needed to answer questions such as: Is the optimal structure also the native one? Are there more than one structure an RNA molecule can adopt? How well-defined is the optimal structure? Major problems in the analysis of the structure space are its size and its shape. The number of suboptimal structures is exponential in the sequence length, which means that for sequences of moderate length the size quickly exceeds several billion. Besides the size, the appearance of the structure space complicates its study. The structure space can be imagined as a rough landscape with valleys, holding local optimal structures, separated by mountains and saddles. This landscape is not smooth but cliffy and complex, which prevents the development of a practical and still intuitive visualisation. In general, the intention of structure space analysis is not its visualisation, but its complexity also hampers approaches to derive specific features hidden in the structure space. Despite these problems, several tools exist that analyse the complete structure space or at least a part of it to answer the aforementioned questions. Among these are MFOLD which produces a subset of all possible structures according to a threshold of structural similarity, SFOLD which samples the structures in a probabilistic fashion and provides a method to identify alternating structures, RNAsubopt to produce all suboptimal structures within a given energy threshold, barriers to identify valleys, mountains and saddles of the structure landscape, and others. My contribution to this area of research is twofold: First, I present paRNAss (prediction of alternating RNA secondary structures) which focuses on the detection of conformational switches and analyses the structure space based on pairwise comparisons. paRNAss has been available since 1997 and I could improve its predictive power as well as its speed which made possible a systematic evaluation. During this evaluation it turned out that paRNAss can even be used to identify more than two competing structures and hence get a deeper insight into the structure space. The second tool I introduce is RNAshapes which facilitates different kinds of analyses. The algorithm makes use of abstract representations of the secondary structure to compute only those that are morphologically dissimilar, i.e. are composed of different structural elements. Structures being morphologically similar are pooled in a class of structures and each class is represented by its best member. The list of these representatives gives a general overview of what is there in the structure space. In addition to this, I introduce an algorithm to compute probabilities of the aforementioned classes of structures. This gives hints to properties such as alternating secondary structures (two classes with similar probabilities) and structural well-definedness (one class with very high probability).}, author = {Voß, Bjoern}, file = {Diss.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/4D9KU5F2/Diss.pdf:application/pdf;Zugang zum Volltext der Veröffentlichung:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/FI8M9HHZ/frontdoor.html:text/html}, language = {Englisch}, month = {04}, note = 00000, school = {Universitätsbibliothek Bielefeld}, title = {Advanced tools for {RNA} secondary structure analysis}, url = {http://bieson.ub.uni-bielefeld.de/volltexte/2005/664/}, urldate = {2009-04-02}, year = 2005 }
  Link
  http://bieson.ub.uni-bielefeld.de/volltexte/2005/664/
2004
1. 3.
  Höchsmann, Matthias ; Voß, Bjoern ; Giegerich, Robert: Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach. In: IEEE/ACM Transactions on Computational Biology and Bioinformatics, IEEE/ACM Transactions on Computational Biology and Bioinformatics. Bd. 1 (2004), Nr. 1, S. 53--62. — 00117
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  BibTeX
  @article{hochsmann_pure_2004, author = {Höchsmann, Matthias and Voß, Bjoern and Giegerich, Robert}, doi = {http://doi.ieeecomputersociety.org/10.1109/TCBB.2004.11}, file = {Hoechsmann et al - 2004 - Pure Multiple RNA Secondary Structure Alignments - A Progressive Profile Approach.pdf:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/87X7RQDC/Hoechsmann et al - 2004 - Pure Multiple RNA Secondary Structure Alignments - A Progressive Profile Approach.pdf:application/pdf}, issn = {1545-5963}, journal = {IEEE/ACM Transactions on Computational Biology and Bioinformatics}, note = 00117, number = 1, pages = {53--62}, title = {Pure {Multiple} {RNA} {Secondary} {Structure} {Alignments}: {A} {Progressive} {Profile} {Approach}}, volume = 1, year = 2004 }
2. 2.
  Giegerich, Robert ; Voß, Bjoern ; Rehmsmeier, Marc: Abstract shapes of RNA. In: Nucl. Acids Res., Nucl. Acids Res. Bd. 32 (2004), Nr. 16, S. 4843--4851. — 00166
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  @article{giegerich_abstract_2004, abstract = {The function of a non-protein-coding RNA is often determined by its structure. Since experimental determination of RNA structure is time-consuming and expensive, its computational prediction is of great interest, and efficient solutions based on thermodynamic parameters are known. Frequently, however, the predicted minimum free energy structures are not the native ones, leading to the necessity of generating suboptimal solutions. While this can be accomplished by a number of programs, the user is often confronted with large outputs of similar structures, although he or she is interested in structures with more fundamental differences, or, in other words, with different abstract shapes. Here, we formalize the concept of abstract shapes and introduce their efficient computation. Each shape of an RNA molecule comprises a class of similar structures and has a representative structure of minimal free energy within the class. Shape analysis is implemented in the program RNAshapes. We applied RNAshapes to the prediction of optimal and suboptimal abstract shapes of several RNAs. For a given energy range, the number of shapes is considerably smaller than the number of structures, and in all cases, the native structures were among the top shape representatives. This demonstrates that the researcher can quickly focus on the structures of interest, without processing up to thousands of near-optimal solutions. We complement this study with a large-scale analysis of the growth behaviour of structure and shape spaces. RNAshapes is available for download and as an online version on the Bielefeld Bioinformatics Server.}, author = {Giegerich, Robert and Voß, Bjoern and Rehmsmeier, Marc}, doi = {10.1093/nar/gkh779}, file = {HighWire Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/T4TW9ICR/Giegerich et al - 2004 - Abstract shapes of RNA.pdf:application/pdf;HighWire Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/MDPTS2HX/4843.html:text/html}, journal = {Nucl. Acids Res.}, month = {09}, note = 00166, number = 16, pages = {4843--4851}, title = {Abstract shapes of {RNA}}, url = {http://nar.oxfordjournals.org/cgi/content/abstract/32/16/4843}, urldate = {2009-03-10}, volume = 32, year = 2004 }
  Link
  http://nar.oxfordjournals.org/cgi/content/abstract/32/16/4843
3. 1.
  Voß, Björn ; Meyer, Carsten ; Giegerich, Robert: Evaluating the predictability of conformational switching in RNA. In: Bioinformatics, Bioinformatics. Bd. 20 (2004), Nr. 10, S. 1573--1582. — 00000
  - BibTeX
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  @article{vos_evaluating_2004, abstract = {Motivation: There are various cases where the biological function of an RNA molecule involves a reversible change of conformation. paRNAss is a software approach to the prediction of such structural switching in RNA. It is based on three hypotheses about the secondary structure space of a switching RNA molecule that can be evaluated by RNA folding and structure comparison. In the positive case, the predicted structural switching must be verified experimentally. Results: After reviewing the strategy used in paRNAss, we present recent improvements on the algorithmic level of the approach, and the results of an evaluation procedure, comprising 1500 RNA sequences. It could be shown that the paRNAss approach performs well on known examples for conformational switching in RNA. The overall number of positive predictions was small, whereas for human 3′ UTRs, representing regulatory important regions, it was substantially higher than for arbitrary natural and random sequences. Availability: paRNAss is available as a Web service at http://bibiserv.techfak.uni-bielefeld.de/parnass Supplementary information: Detailed information on the analyses summarized in Table 1 can be found at http://bibiserv.techfak.uni-bielefeld.de/parnass/examples.html}, author = {Voß, Björn and Meyer, Carsten and Giegerich, Robert}, doi = {10.1093/bioinformatics/bth129}, file = {Full Text PDF:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/RCPHRSZA/Voss et al. - 2004 - Evaluating the predictability of conformational sw.pdf:application/pdf;Snapshot:/Users/bvoss/Library/Application Support/Firefox/Profiles/a6kceokb.default/zotero/storage/NFFN6IWG/1573.html:text/html}, issn = {1367-4803, 1460-2059}, journal = {Bioinformatics}, language = {en}, month = {07}, note = 00000, number = 10, pages = {1573--1582}, title = {Evaluating the predictability of conformational switching in {RNA}}, url = {http://bioinformatics.oxfordjournals.org/content/20/10/1573}, urldate = {2014-12-05}, volume = 20, year = 2004 }
  Link
  http://bioinformatics.oxfordjournals.org/content/20/10/1573

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