Damm, Carsten

[["dc.bibliographiccitation.artnumber","142"],["dc.bibliographiccitation.journal","BMC Bioinformatics"],["dc.bibliographiccitation.volume","7"],["dc.contributor.author","Waack, Stephan"],["dc.contributor.author","Keller, Oliver"],["dc.contributor.author","Asper, Roman"],["dc.contributor.author","Brodag, Thomas"],["dc.contributor.author","Damm, Carsten"],["dc.contributor.author","Fricke, Wolfgang Florian"],["dc.contributor.author","Surovcik, Katharina"],["dc.contributor.author","Meinicke, Peter"],["dc.contributor.author","Merkl, Rainer"],["dc.date.accessioned","2018-11-07T10:05:47Z"],["dc.date.available","2018-11-07T10:05:47Z"],["dc.date.issued","2006"],["dc.description.abstract","Background: Horizontal gene transfer (HGT) is considered a strong evolutionary force shaping the content of microbial genomes in a substantial manner. It is the difference in speed enabling the rapid adaptation to changing environmental demands that distinguishes HGT from gene genesis, duplications or mutations. For a precise characterization, algorithms are needed that identify transfer events with high reliability. Frequently, the transferred pieces of DNA have a considerable length, comprise several genes and are called genomic islands (GIs) or more specifically pathogenicity or symbiotic islands. Results: We have implemented the program SIGI-HMM that predicts GIs and the putative donor of each individual alien gene. It is based on the analysis of codon usage (CU) of each individual gene of a genome under study. CU of each gene is compared against a carefully selected set of CU tables representing microbial donors or highly expressed genes. Multiple tests are used to identify putatively alien genes, to predict putative donors and to mask putatively highly expressed genes. Thus, we determine the states and emission probabilities of an inhomogeneous hidden Markov model working on gene level. For the transition probabilities, we draw upon classical test theory with the intention of integrating a sensitivity controller in a consistent manner. SIGI-HMM was written in JAVA and is publicly available. It accepts as input any file created according to the EMBL-format. It generates output in the common GFF format readable for genome browsers. Benchmark tests showed that the output of SIGI-HMM is in agreement with known findings. Its predictions were both consistent with annotated GIs and with predictions generated by different methods. Conclusion: SIGI-HMM is a sensitive tool for the identification of GIs in microbial genomes. It allows to interactively analyze genomes in detail and to generate or to test hypotheses about the origin of acquired genes."],["dc.identifier.doi","10.1186/1471-2105-7-142"],["dc.identifier.isi","000238903700001"],["dc.identifier.pmid","16542435"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/12509"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/38969"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.notes.status","final"],["dc.notes.submitter","Najko"],["dc.relation.issn","1471-2105"],["dc.rights","CC BY 2.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/2.0/"],["dc.title","Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","17"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Information Processing Letters"],["dc.bibliographiccitation.lastpage","21"],["dc.bibliographiccitation.volume","102"],["dc.contributor.author","Brosenne, Henrik"],["dc.contributor.author","Damm, Carsten"],["dc.contributor.author","Homeister, Matthias"],["dc.contributor.author","Waack, Stephan"],["dc.date.accessioned","2018-11-07T11:03:11Z"],["dc.date.available","2018-11-07T11:03:11Z"],["dc.date.issued","2007"],["dc.description.abstract","We show that for every V-OBDD of quasipolynomial size there is a circle plus-OBDD of quasipolynornial size computing the same function up to a small fraction of the inputs. We also prove that the final step in the approximation cannot be improved and discuss possibilities of proving non-approximability results and connections to lower bounds on matrix rigidity. (c) 2006 Elsevier B.V. All rights reserved."],["dc.identifier.doi","10.1016/j.ipl.2006.10.011"],["dc.identifier.isi","000244631900003"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/51558"],["dc.language.iso","en"],["dc.notes.status","final"],["dc.notes.submitter","Najko"],["dc.relation.issn","0020-0190"],["dc.title","On approximation by circle plus-OBDDs"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","259"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","Journal of Computer and System Sciences"],["dc.bibliographiccitation.lastpage","280"],["dc.bibliographiccitation.volume","69"],["dc.contributor.author","Damm, Carsten"],["dc.contributor.author","Krause, M."],["dc.contributor.author","Meinel, C."],["dc.contributor.author","Waack, S."],["dc.date.accessioned","2018-11-07T10:46:00Z"],["dc.date.available","2018-11-07T10:46:00Z"],["dc.date.issued","2004"],["dc.description.abstract","We develop upper and lower bound arguments for counting acceptance modes of communication protocols. A number of separation results for counting communication complexity classes is established. This extends the investigation of the complexity of communication between two processors in terms of complexity classes initiated by Babai et al. (Proceedings of the 27th IEEE FOCS, 1986, pp. 337-347) and continued in several papers (e.g., J. Comput. System Sci. 41 (1990) 402; 49 (1994) 247; Proceedings of the 36th IEEE FOCS, 1995, pp. 6-15). In particular, it will be shown that for all pairs of distinct primes p and q the communication complexity classes MODpPcc and MODqPcc are incomparable with regard to inclusion. The same is true for PPcc and MODmPcc, for any number m greater than or equal to 2. Moreover, non-determinism and modularity are incomparable to a large extend. On the other hand, if m = p(1)(l1.)...(.)p(r)(lr) is the prime decomposition of m greater than or equal to 2, then the complexity classes MODmPcc and MODrho(m)Pcc coincide, where rho(m) = p(1) (.)...(.) p(r). The results are obtained by characterizing the modular and probabilistic communication complexity in terms of the minimum rank of matrices ranging over certain equivalence classes. Methods from algebra and analytic geometry are used. This paper is the completely revised and strongly extended version of the conference paper Damm et al. (Proc. 9th Ann. STACS, pp. 281-291) where a subset of the results was presented. (C) 2004 Elsevier Inc. All rights reserved."],["dc.identifier.doi","10.1016/j.jcss.2004.03.002"],["dc.identifier.isi","000223292400007"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/47640"],["dc.language.iso","en"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","1090-2724"],["dc.relation.issn","0022-0000"],["dc.title","On relations between counting communication complexity classes"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dspace.entity.type","Publication"]]