Morgenstern, Burkhard

[["dc.bibliographiccitation.firstpage","1654"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Molecular Biology and Evolution"],["dc.bibliographiccitation.lastpage","1663"],["dc.bibliographiccitation.volume","16"],["dc.contributor.author","Morgenstern, B."],["dc.contributor.author","Atchley, W. R."],["dc.date.accessioned","2022-06-08T07:59:11Z"],["dc.date.available","2022-06-08T07:59:11Z"],["dc.date.issued","1999"],["dc.identifier.doi","10.1093/oxfordjournals.molbev.a026079"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/110661"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-575"],["dc.relation.eissn","1537-1719"],["dc.relation.issn","0737-4038"],["dc.title","Evolution of bHLH transcription factors: modular evolution by domain shuffling?"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","W647"],["dc.bibliographiccitation.journal","Nucleic Acids Research"],["dc.bibliographiccitation.lastpage","W651"],["dc.bibliographiccitation.volume","37"],["dc.contributor.author","Schultz, Anne-Kathrin"],["dc.contributor.author","Zhang, M."],["dc.contributor.author","Bulla, Ingo"],["dc.contributor.author","Leitner, Thomas"],["dc.contributor.author","Korber, Bette"],["dc.contributor.author","Morgenstern, Burkhard"],["dc.contributor.author","Stanke, Mario"],["dc.date.accessioned","2018-11-07T08:28:27Z"],["dc.date.available","2018-11-07T08:28:27Z"],["dc.date.issued","2009"],["dc.description.abstract","Previously, we developed jumping profile hidden Markov model (jpHMM), a new method to detect recombinations in HIV-1 genomes. The jpHMM predicts recombination breakpoints in a query sequence and assigns to each position of the sequence one of the major HIV-1 subtypes. Since incorrect subtype assignment or recombination prediction may lead to wrong conclusions in epidemiological or vaccine research, information about the reliability of the predicted parental subtypes and breakpoint positions is valuable. For this reason, we extended the output of jpHMM to include such information in terms of 'uncertainty' regions in the recombination prediction and an interval estimate of the breakpoint. Both types of information are computed based on the posterior probabilities of the subtypes at each query sequence position. Our results show that this extension strongly improves the reliability of the jpHMM recombination prediction. The jpHMM is available online at http://jphmm.gobics.de/."],["dc.identifier.doi","10.1093/nar/gkp371"],["dc.identifier.isi","000267889100111"],["dc.identifier.pmid","19443440"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/16423"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","0305-1048"],["dc.title","jpHMM: Improving the reliability of recombination prediction in HIV-1"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","89"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","CLADISTICS-THE INTERNATIONAL JOURNAL OF THE WILLI HENNIG SOCIETY"],["dc.bibliographiccitation.lastpage","90"],["dc.bibliographiccitation.volume","20"],["dc.contributor.author","Morgenstern, Burkhard"],["dc.date.accessioned","2018-11-07T10:51:17Z"],["dc.date.available","2018-11-07T10:51:17Z"],["dc.date.issued","2004"],["dc.identifier.isi","000220447100056"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/48858"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Academic Press Ltd Elsevier Science Ltd"],["dc.publisher.place","London"],["dc.relation.conference","22nd Annual Meeting of the Willi-Hennig-Society"],["dc.relation.eventlocation","New York Botan Garden, Bronx, NY"],["dc.relation.issn","0748-3007"],["dc.title","The DIALIGN multiple alignment program: Recent developments and applications"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","203"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.bibliographiccitation.lastpage","210"],["dc.bibliographiccitation.volume","15"],["dc.contributor.author","Lenhof, H."],["dc.contributor.author","Morgenstern, B."],["dc.contributor.author","Reinert, K"],["dc.date.accessioned","2022-06-08T07:59:04Z"],["dc.date.available","2022-06-08T07:59:04Z"],["dc.date.issued","1999"],["dc.identifier.doi","10.1093/bioinformatics/15.3.203"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/110621"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-575"],["dc.relation.eissn","1460-2059"],["dc.relation.issn","1367-4803"],["dc.title","An exact solution for the segment-to-segment multiple sequence alignment problem"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1271"],["dc.bibliographiccitation.issue","7"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.bibliographiccitation.lastpage","1273"],["dc.bibliographiccitation.volume","21"],["dc.contributor.author","Morgenstern, Burkhard"],["dc.contributor.author","Werner, N."],["dc.contributor.author","Prohaska, Sonja J."],["dc.contributor.author","Steinkamp, R."],["dc.contributor.author","Schneider, I."],["dc.contributor.author","Subramanian, A. R."],["dc.contributor.author","Stadler, Peter F."],["dc.contributor.author","Weyer-Menkhoff, J."],["dc.date.accessioned","2018-11-07T11:09:37Z"],["dc.date.available","2018-11-07T11:09:37Z"],["dc.date.issued","2005"],["dc.description.abstract","Summary: Most multi-alignment methods are fully automated, i.e. they are based on a fixed set of mathematical rules. For various reasons, such methods may fail to produce biologically meaningful alignments. Herein, we describe a semi-automatic approach to multiple sequence alignment where biological expert knowledge can be used to influence the alignment procedure. The user can specify parts of the sequences that are biologically related to each other; our software program uses these sites as anchor points and creates a multiple alignment respecting these user-defined constraints. By using known functionally, structurally or evolutionarily related positions of the input sequences as anchor points, our method can produce alignments that reflect the true biological relationships among the input sequences more accurately than fully automated procedures can do."],["dc.identifier.doi","10.1093/bioinformatics/bti142"],["dc.identifier.isi","000227977800058"],["dc.identifier.pmid","15546937"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/53048"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","1367-4803"],["dc.title","Multiple sequence alignment with user-defined constraints at GOBICS"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.journal","Geburtshilfe und Frauenheilkunde"],["dc.bibliographiccitation.volume","82"],["dc.contributor.author","Götze, TO"],["dc.contributor.author","Al-Batran, S-E"],["dc.contributor.author","Bankstahl, US"],["dc.contributor.author","Fleckenstein, A-S"],["dc.contributor.author","Engel, JB"],["dc.contributor.author","Aktas, B"],["dc.contributor.author","Martin, M"],["dc.contributor.author","Weisgerber, C"],["dc.contributor.author","Hunold, P"],["dc.contributor.author","Gallwas, J"],["dc.contributor.author","Kulenkampff, D"],["dc.contributor.author","Maintz, D"],["dc.contributor.author","Morgenstern, B"],["dc.contributor.author","Püsken, M"],["dc.contributor.author","Keim, S"],["dc.contributor.author","Matzko, M"],["dc.contributor.author","Düx, M"],["dc.date.accessioned","2022-11-01T10:16:51Z"],["dc.date.available","2022-11-01T10:16:51Z"],["dc.date.issued","2022"],["dc.identifier.doi","10.1055/s-0042-1756822"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/116670"],["dc.notes.intern","DOI-Import GROB-605"],["dc.publisher","Georg Thieme Verlag"],["dc.relation.conference","64. Kongress der Deutschen Gesellschaft für Gynäkologie und Geburtshilfe e. V."],["dc.relation.eventend","2022-10-15"],["dc.relation.eventlocation","München"],["dc.relation.eventstart","2022-10-12"],["dc.title","Multizentrische, randomisierte Phase III-Studie zur Magnetresonanztomographie-gesteuerten hochfokussierten Ultraschalltherapie zur Behandlung des Uterusmyoms (MRgFUS-TUF) im Vergleich zur Myomektomie bei symptomatischen und medikamentös nicht ausreichend therapierbaren Uterusmyomen (MARGI-T)"],["dc.type","conference_abstract"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3568"],["dc.bibliographiccitation.issue","17"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.bibliographiccitation.lastpage","3569"],["dc.bibliographiccitation.volume","21"],["dc.contributor.author","Tech, Maike"],["dc.contributor.author","Pfeifer, N."],["dc.contributor.author","Morgenstern, Burkhard"],["dc.contributor.author","Meinicke, Peter"],["dc.date.accessioned","2018-11-07T10:55:56Z"],["dc.date.available","2018-11-07T10:55:56Z"],["dc.date.issued","2005"],["dc.description.abstract","We provide the tool 'TICO' (Translation Initiation site COrrection) for improving the results of conventional gene finders for prokaryotic genomes with regard to exact localization of the translation initiation site (TIS). At the current state TICO provides an interface for direct post processing of the predictions obtained from the widely used program GLIMMER. Our program is based on a clustering algorithm for completely unsupervised scoring of potential TIS locations."],["dc.identifier.doi","10.1093/bioinformatics/bti563"],["dc.identifier.isi","000231472500017"],["dc.identifier.pmid","15994191"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/49897"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","1367-4803"],["dc.title","TICO: a tool for improving predictions of prokaryotic translation initiation sites"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1983"],["dc.bibliographiccitation.issue","9"],["dc.bibliographiccitation.journal","Molecular Biology and Evolution"],["dc.bibliographiccitation.lastpage","1987"],["dc.bibliographiccitation.volume","27"],["dc.contributor.author","Pick, Kerstin"],["dc.contributor.author","Philippe, Herve"],["dc.contributor.author","Schreiber, F."],["dc.contributor.author","Erpenbeck, D."],["dc.contributor.author","Jackson, Daniel John"],["dc.contributor.author","Wrede, P."],["dc.contributor.author","Wiens, M."],["dc.contributor.author","Alie, A."],["dc.contributor.author","Morgenstern, Burkhard"],["dc.contributor.author","Manuel, Michael"],["dc.contributor.author","Woerheide, Gert"],["dc.date.accessioned","2018-11-07T08:39:58Z"],["dc.date.available","2018-11-07T08:39:58Z"],["dc.date.issued","2010"],["dc.description.abstract","Despite expanding data sets and advances in phylogenomic methods, deep-level metazoan relationships remain highly controversial. Recent phylogenomic analyses depart from classical concepts in recovering ctenophores as the earliest branching metazoan taxon and propose a sister-group relationship between sponges and cnidarians (e.g., Dunn CW, Hejnol A, Matus DQ, et al. (18 co-authors). 2008. Broad phylogenomic sampling improves resolution of the animal tree of life. Nature 452:745-749). Here, we argue that these results are artifacts stemming from insufficient taxon sampling and long-branch attraction (LBA). By increasing taxon sampling from previously unsampled nonbilaterians and using an identical gene set to that reported by Dunn et al., we recover monophyletic Porifera as the sister group to all other Metazoa. This suggests that the basal position of the fast-evolving Ctenophora proposed by Dunn et al. was due to LBA and that broad taxon sampling is of fundamental importance to metazoan phylogenomic analyses. Additionally, saturation in the Dunn et al. character set is comparatively high, possibly contributing to the poor support for some nonbilaterian nodes."],["dc.identifier.doi","10.1093/molbev/msq089"],["dc.identifier.isi","000281184100002"],["dc.identifier.pmid","20378579"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/19123"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","1537-1719"],["dc.relation.issn","0737-4038"],["dc.title","Improved Phylogenomic Taxon Sampling Noticeably Affects Nonbilaterian Relationships"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","337"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","Future Generation Computer Systems"],["dc.bibliographiccitation.lastpage","345"],["dc.bibliographiccitation.volume","25"],["dc.contributor.author","Sommerfeld, Dietmar"],["dc.contributor.author","Lingner, Thomas"],["dc.contributor.author","Stanke, Mario"],["dc.contributor.author","Morgenstern, Burkhard"],["dc.contributor.author","Richter, Harald"],["dc.date.accessioned","2018-11-07T08:32:06Z"],["dc.date.available","2018-11-07T08:32:06Z"],["dc.date.issued","2009"],["dc.description.abstract","In past years, researchers from many domains have discovered Grid technology which opens up new possibilities in solving problems that are difficult to handle with traditional cluster computing. With the rapidly increasing number of partially or completely sequenced genomes, computational genome annotation is a particularly challenging task in computational biology. In this paper, we describe how we adapted the gene-finding tool AUGUSTUS to Grid computing in the context of the German MediGRID project. The gridification process starts with providing security requirements and running the application manually using Grid middleware. Afterwards, the application is described as a workflow of successive program executions, which are automatically distributed to appropriate Grid resources by a workflow engine. Finally, we show how a convenient graphical user interface for end users is created by means of a portal framework. (C) 2008 Elsevier B.V. All rights reserved."],["dc.description.sponsorship","German Federal Ministry of Education and Research (BMBF) [01AK803A-H]"],["dc.identifier.doi","10.1016/j.future.2008.05.010"],["dc.identifier.isi","000262278200015"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/17266"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.relation.issn","1872-7115"],["dc.relation.issn","0167-739X"],["dc.relation.orgunit","Gesellschaft für wissenschaftliche Datenverarbeitung"],["dc.title","AUGUSTUS at MediGRID: Adaption of a bioinformatics application to grid computing for efficient genome analysis"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original_ja"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1409"],["dc.bibliographiccitation.issue","11"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.bibliographiccitation.lastpage","1415"],["dc.bibliographiccitation.volume","26"],["dc.contributor.author","Bulla, Ingo"],["dc.contributor.author","Schultz, Anne-Kathrin"],["dc.contributor.author","Schreiber, Fabian"],["dc.contributor.author","Zhang, M."],["dc.contributor.author","Leitner, Thomas"],["dc.contributor.author","Korber, Bette"],["dc.contributor.author","Morgenstern, Burkhard"],["dc.contributor.author","Stanke, Mario"],["dc.date.accessioned","2018-11-07T08:42:27Z"],["dc.date.available","2018-11-07T08:42:27Z"],["dc.date.issued","2010"],["dc.description.abstract","Motivation: Existing coalescent models and phylogenetic tools based on them are not designed for studying the genealogy of sequences like those of HIV, since in HIV recombinants with multiple cross-over points between the parental strains frequently arise. Hence, ambiguous cases in the classification of HIV sequences into subtypes and circulating recombinant forms (CRFs) have been treated with ad hoc methods in lack of tools based on a comprehensive coalescent model accounting for complex recombination patterns. Results: We developed the program ARGUS that scores classifications of sequences into subtypes and recombinant forms. It reconstructs ancestral recombination graphs (ARGs) that reflect the genealogy of the input sequences given a classification hypothesis. An ARG with maximal probability is approximated using a Markov chain Monte Carlo approach. ARGUS was able to distinguish the correct classification with a low error rate from plausible alternative classifications in simulation studies with realistic parameters. We applied our algorithm to decide between two recently debated alternatives in the classification of CRF02 of HIV-1 and find that CRF02 is indeed a recombinant of Subtypes A and G."],["dc.identifier.doi","10.1093/bioinformatics/btq159"],["dc.identifier.isi","000277985500004"],["dc.identifier.pmid","20400454"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/19707"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","1367-4803"],["dc.title","HIV classification using the coalescent theory"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]