Morgenstern, Burkhard

[["dc.bibliographiccitation.firstpage","e0228070"],["dc.bibliographiccitation.issue","2"],["dc.bibliographiccitation.journal","PLoS One"],["dc.bibliographiccitation.volume","15"],["dc.contributor.author","Röhling, Sophie"],["dc.contributor.author","Linne, Alexander"],["dc.contributor.author","Schellhorn, Jendrik"],["dc.contributor.author","Hosseini, Morteza"],["dc.contributor.author","Dencker, Thomas"],["dc.contributor.author","Morgenstern, Burkhard"],["dc.contributor.editor","Darling, Aaron E."],["dc.date.accessioned","2021-04-14T08:27:24Z"],["dc.date.available","2021-04-14T08:27:24Z"],["dc.date.issued","2020"],["dc.identifier.doi","10.1371/journal.pone.0228070"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/17339"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/82279"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-399"],["dc.notes.intern","Merged from goescholar"],["dc.notes.intern","In goescholar not merged with http://resolver.sub.uni-goettingen.de/purl?gs-1/17161 but duplicate"],["dc.relation.eissn","1932-6203"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.title","The number of k-mer matches between two DNA sequences as a function of k and applications to estimate phylogenetic distances"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","e1010303"],["dc.bibliographiccitation.issue","8"],["dc.bibliographiccitation.journal","PLOS Computational Biology"],["dc.bibliographiccitation.volume","18"],["dc.contributor.author","Birth, Niklas"],["dc.contributor.author","Dencker, Thomas"],["dc.contributor.author","Morgenstern, Burkhard"],["dc.date.accessioned","2022-09-01T09:50:59Z"],["dc.date.available","2022-09-01T09:50:59Z"],["dc.date.issued","2022"],["dc.description.abstract","Most methods for phylogenetic tree reconstruction are based on sequence alignments; they infer phylogenies from substitutions that may have occurred at the aligned sequence positions. Gaps in alignments are usually not employed as phylogenetic signal. In this paper, we explore an alignment-free approach that uses insertions and deletions (indels) as an additional source of information for phylogeny inference. For a set of four or more input sequences, we generate so-called\r\n quartet blocks\r\n of four putative homologous segments each. For\r\n pairs\r\n of such quartet blocks involving the same four sequences, we compare the distances between the two blocks in these sequences, to obtain hints about indels that may have happened between the blocks since the respective four sequences have evolved from their last common ancestor. A prototype implementation that we call\r\n Gap-SpaM\r\n is presented to infer phylogenetic trees from these data, using a\r\n quartet-tree\r\n approach or, alternatively, under the\r\n maximum-parsimony\r\n paradigm. This approach should not be regarded as an alternative to established methods, but rather as a complementary source of phylogenetic information. Interestingly, however, our software is able to produce phylogenetic trees from putative indels alone that are comparable to trees obtained with existing alignment-free methods."],["dc.description.sponsorship","Open-Access-Publikationsfonds 2022"],["dc.identifier.doi","10.1371/journal.pcbi.1010303"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/113851"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-597"],["dc.relation.eissn","1553-7358"],["dc.rights","CC BY 4.0"],["dc.rights.uri","http://creativecommons.org/licenses/by/4.0/"],["dc.title","Insertions and deletions as phylogenetic signal in an alignment-free context"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","unpublished"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","Genome Biology"],["dc.bibliographiccitation.volume","20"],["dc.contributor.author","Zielezinski, Andrzej"],["dc.contributor.author","Girgis, Hani Z."],["dc.contributor.author","Bernard, Guillaume"],["dc.contributor.author","Leimeister, Chris-Andre"],["dc.contributor.author","Tang, Kujin"],["dc.contributor.author","Dencker, Thomas"],["dc.contributor.author","Lau, Anna Katharina"],["dc.contributor.author","Röhling, Sophie"],["dc.contributor.author","Choi, Jae Jin"],["dc.contributor.author","Waterman, Michael S."],["dc.contributor.author","Comin, Matteo"],["dc.contributor.author","Kim, Sung-Hou"],["dc.contributor.author","Vinga, Susana"],["dc.contributor.author","Almeida, Jonas S."],["dc.contributor.author","Chan, Cheong Xin"],["dc.contributor.author","James, Benjamin T."],["dc.contributor.author","Sun, Fengzhu"],["dc.contributor.author","Morgenstern, Burkhard"],["dc.contributor.author","Karlowski, Wojciech M."],["dc.date.accessioned","2020-12-10T18:39:04Z"],["dc.date.available","2020-12-10T18:39:04Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1186/s13059-019-1755-7"],["dc.identifier.eissn","1474-760X"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/16308"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/77534"],["dc.language.iso","en"],["dc.notes.intern","DOI Import GROB-354"],["dc.notes.intern","Merged from goescholar"],["dc.rights","CC BY 4.0"],["dc.rights.uri","https://creativecommons.org/licenses/by/4.0"],["dc.title","Benchmarking of alignment-free sequence comparison methods"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]