Curriculum Vitae

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name cobi
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scientific interests

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my publications

VisualGraphX: interactive graph visualization within Galaxy. In Bioinformatics, btw414, Year 2016.
Bioinformatic prediction and experimental verification of sRNAs in the haloarchaeon Haloferax volcanii. In RNA Biology, (8) 5: 806--816, Year 2011.
RNA Secondary Structure Analysis Using Abstract Shapes. Handbook of RNA Biochemistry. (2) 579--594, WILEY-VCH, Weinheim, Germany, Year 2014.
Small RNAs of the Bradyrhizobium/Rhodopseudomonas lineage and their analysis. In RNA Biology, (9) 1: 45--56, Year 2012.
Comparative Genome Analysis of the Closely Related Synechocystis Strains PCC 6714 and PCC 6803. In DNA Research, (21) 3: 255--266, Year 2014.
Finished Genome Sequence of the Unicellular Cyanobacterium Synechocystis sp. Strain PCC 6714. In Genome Announcements, (2) 4: e00757--14, Year 2014.
An experimentally anchored map of transcriptional start sites in the model cyanobacterium Synechocystis sp. PCC6803. In Proceedings of the National Academy of Sciences, (108) 5: 2124 --2129, Year 2011.
A long antisense RNA in plant chloroplasts. In New Phytologist, (186) 3: 615--622, Year 2010.
Abstract folding space analysis based on helices. In RNA, (18) 12: 2135--2147, Year 2012.
Non-coding RNAs in marine Synechococcus and their regulation under environmentally relevant stress conditions. In The ISME Journal, (6) 8: 1544--1557, Year 2012.
Complete probabilistic analysis of RNA shapes. In BMC Biology, (4) 1: 5, Year 2006.
Microevolution in Cyanobacteria: Re-sequencing a Motile Substrain of Synechocystis sp. PCC 6803. In DNA Research, Year 2012.
Beyond Mfold: Recent advances in RNA bioinformatics. In Journal of Biotechnology, (124) 1: 41--55, Year 2006.
A Bottom-up approach to Grid-Computing at a University: the Black-Forest-Grid Initiative. In Praxis der Informationsverarbeitung und Kommunikation, (29) 2: 81--87, Year 2006.
Genome of a giant bacteriophage from a decaying Trichodesmium bloom. In Marine Genomics, (33) 21 - 25, Year 2017.
A new chlorophyll d-containing cyanobacterium: evidence for niche adaptation in the genus Acaryochloris. In ISME J, (4) 11: 1456--1469, Year 2010.
Comparative transcriptomics of two environmentally relevant cyanobacteria reveals unexpected transcriptome diversity. In The ISME Journal, Year 2014.
Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. In Nat Biotech, (25) 9: 1007--1014, Year 2007.
Insights into the Physiology and Ecology of the Brackish-Water-Adapted Cyanobacterium Nodularia spumigena CCY9414 Based on a Genome-Transcriptome Analysis. In PLoS ONE, (8) 3: e60224, Year 2013.
5'UTR-Mediated Translational Control of Splice Variants of Phytoene Synthase. In Plant Physiol., pp.01262.2016, Year 2016.
Dinitrogen fixation in a unicellular chlorophyll d-containing cyanobacterium. In ISME J, Year 2012.
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, (390) 2: 331--336, Year 2009.
Evaluating the predictability of conformational switching in RNA. In Bioinformatics, (20) 10: 1573--1582, Year 2004.
Evidence for a major role of antisense RNAs in cyanobacterial gene regulation. In Mol Syst Biol, (5) Year 2009.
The complexity of bacterial transcriptomes. In Journal of Biotechnology, Bioinformatics for Biotechnology and Biomedicine, (232) 69--78, Year 2016.
Hemin and Mg-Protoporphyrin IX Induce Global Changes in Gene Expression in Chlamydomonas reinhardtii. In Plant Physiol., pp.110.158683, Year 2010.
Biocomputational prediction of non-coding RNAs in model cyanobacteria. In BMC Genomics, (10) 1: 123, Year 2009.
Structural analysis of aligned RNAs. In Nucl. Acids Res., (34) 19: 5471--5481, Year 2006.
The Yfr2 ncRNA family, a group of abundant RNA molecules widely conserved in cyanobacteria. In RNA Biology, (6) 3: 222--227, Year 2009.
Abstract shapes of RNA. In Nucl. Acids Res., (32) 16: 4843--4851, Year 2004.
GLASSgo - Automated and reliable detection of sRNA homologs from a single input sequence. In Frontiers in Genetics, (9) Frontiers, Year 2018.
Pure Multiple RNA Secondary Structure Alignments: A Progressive Profile Approach. In IEEE/ACM Transactions on Computational Biology and Bioinformatics, (1) 1: 53--62, Year 2004.
The diversity of small non-coding RNAs in the diatom Phaeodactylum tricornutum. In BMC Genomics, (15) 1: 698, Year 2014.
Two distinct types of 6S RNA in Prochlorococcus. In Gene, (406) 1-2: 69--78, Year 2007.
Small RNAs of the halophilic archaeon Haloferax volcanii. In Biochemical Society Transactions, (37) Pt 1: 133--136, Year 2009.
Shape-based barrier estimation for RNAs. In Proceedings of German Conference on Bioinformatics GCB'10. LNI, (173) 42--51, GI, Year 2010.
Heterocyst-Specific Transcription of NsiR1, a Non-Coding RNA Encoded in a Tandem Array of Direct Repeats in Cyanobacteria. In Journal of Molecular Biology, (398) 2: 177--188, Year 2010.
Transcript mapping based on dRNA-seq data. In BMC Bioinformatics, (15) 1: 122, Year 2014.
The Challenge of Regulation in a Minimal Photoautotroph: Non-Coding RNAs in Prochlorococcus. In PLoS Genet, (4) 8: e1000173, Year 2008.
Analysing RNA-kinetics based on folding space abstraction. In BMC Bioinformatics, (15) 1: 60, Year 2014.
Evidence for the rapid expansion of microRNA-mediated regulation in early land plant evolution. In BMC Plant Biology, (7) 1: 13, Year 2007.
Novel micro-RNAs and intermediates of micro-RNA biogenesis from moss. In The Plant Journal, (47) 1: 25--37, Year 2006.
Comparative Analysis of the Primary Transcriptome of Synechocystis sp. PCC 6803. In DNA Research, (21) 5: 527--539, Year 2014.
A motif-based search in bacterial genomes identifies the ortholog of the small RNA Yfr1 in all lineages of cyanobacteria. In BMC Genomics, (8) 1: 375, Year 2007.
Variations in the non-coding transcriptome as a driver of inter-strain divergence and physiological adaptation in bacteria. In Scientific Reports, (5) 9560: Year 2015.
The identification of bacterial non-coding RNAs through complementary approaches. Handbook of RNA Biochemistry. (2) 787--800, WILEY-VCH, Weinheim, Germany, Year 2014.
CoVennTree: a new method for the comparative analysis of large datasets. In Bioinformatics and Computational Biology, (6) 43, Year 2015.
RNAshapes: an integrated RNA analysis package based on abstract shapes. In Bioinformatics, (22) 4: 500--503, Year 2006.
RNAHeliCes – Folding space analysis based on position aware structure abstraction. Proceedings of the German Conference on Bioinformatics 2011 (GCB 2011). RT--31, Year 2011.
Adaptation and modification of three CRISPR loci in two closely related cyanobacteria. In RNA Biology, (10) 5: 93--92, Year 2013.

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