Kollmar, Martin

[["dc.bibliographiccitation.firstpage","1302-4"],["dc.bibliographiccitation.issue","8"],["dc.bibliographiccitation.journal","Bioinformatics (Oxford, England)"],["dc.bibliographiccitation.lastpage","1304"],["dc.bibliographiccitation.volume","31"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.contributor.author","Hellkamp, Marcel"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2018-11-28T09:35:18Z"],["dc.date.available","2018-11-28T09:35:18Z"],["dc.date.issued","2015-04-15"],["dc.description.abstract","Conserved intron positions in eukaryotic genes can be used to reconstruct phylogenetic trees, to resolve ambiguous subfamily relationships in protein families and to infer the history of gene families. This version of GenePainter facilitates working with large datasets through options to select specific subsets for analysis and visualization, and through providing exhaustive statistics. GenePainter's application in phylogenetic analyses is considerably extended by the newly implemented integration of the exon-intron pattern conservation with phylogenetic trees."],["dc.identifier.doi","10.1093/bioinformatics/btu798"],["dc.identifier.pmid","25434742"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/56975"],["dc.language.iso","en"],["dc.notes.status","zu prüfen"],["dc.relation.eissn","1367-4811"],["dc.title","GenePainter v. 2.0 resolves the taxonomic distribution of intron positions"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","193"],["dc.bibliographiccitation.lastpage","206"],["dc.bibliographiccitation.seriesnr","1962"],["dc.contributor.author","Kollmar, Martin"],["dc.contributor.editor","Kollmar, Martin"],["dc.date.accessioned","2021-06-02T10:44:27Z"],["dc.date.available","2021-06-02T10:44:27Z"],["dc.date.issued","2019"],["dc.identifier.doi","10.1007/978-1-4939-9173-0_11"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/87043"],["dc.notes.intern","DOI-Import GROB-425"],["dc.publisher","Springer New York"],["dc.publisher.place","New York, NY"],["dc.relation.crisseries","Methods in Molecular Biology"],["dc.relation.eisbn","978-1-4939-9173-0"],["dc.relation.isbn","978-1-4939-9172-3"],["dc.relation.ispartof","Methods in Molecular Biology"],["dc.relation.ispartof","Gene Prediction : Methods and Protocols"],["dc.relation.ispartofseries","Methods in Molecular Biology; 1962"],["dc.title","Predicting Genes in Closely Related Species with Scipio and WebScipio"],["dc.type","book_chapter"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","103"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC Genomics"],["dc.bibliographiccitation.volume","8"],["dc.contributor.author","Odronitz, Florian"],["dc.contributor.author","Hellkamp, Marcel"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2021-06-01T10:47:58Z"],["dc.date.available","2021-06-01T10:47:58Z"],["dc.date.issued","2007"],["dc.identifier.doi","10.1186/1471-2164-8-103"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/85785"],["dc.notes.intern","DOI-Import GROB-425"],["dc.relation.issn","1471-2164"],["dc.title","diArk – a resource for eukaryotic genome research"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","757"],["dc.bibliographiccitation.issue","6"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.bibliographiccitation.lastpage","763"],["dc.bibliographiccitation.volume","27"],["dc.contributor.author","Keller, Oliver"],["dc.contributor.author","Kollmar, Martin"],["dc.contributor.author","Stanke, Mario"],["dc.contributor.author","Waack, Stephan"],["dc.date.accessioned","2018-11-07T08:58:07Z"],["dc.date.available","2018-11-07T08:58:07Z"],["dc.date.issued","2011"],["dc.description.abstract","Mitovation: As improved DNA sequencing techniques have increased enormously the speed of producing new eukaryotic genome assemblies, the further development of automated gene prediction methods continues to be essential. While the classification of proteins into families is a task heavily relying on correct gene predictions, it can at the same time provide a source of additional information for the prediction, complementary to those presently used. Results: We extended the gene prediction software AUGUSTUS by a method that employs block profiles generated from multiple sequence alignments as a protein signature to improve the accuracy of the prediction. Equipped with profiles modelling human dynein heavy chain (DHC) proteins and other families, AUGUSTUS was run on the genomic sequences known to contain members of these families. Compared with AUGUSTUS' ab initio version, the rate of genes predicted with high accuracy showed a dramatic increase."],["dc.description.sponsorship","Deutsche Forschungsgemeinschaft [KO 2251/3-1, KO 2251/6-1, WA 766/6-1]"],["dc.identifier.doi","10.1093/bioinformatics/btr010"],["dc.identifier.isi","000288277300003"],["dc.identifier.pmid","21216780"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/23566"],["dc.notes.status","zu prüfen"],["dc.notes.submitter","Najko"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","1460-2059"],["dc.relation.issn","1367-4803"],["dc.title","A novel hybrid gene prediction method employing protein multiple sequence alignments"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.status","published"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","959"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Molecular systems biology"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Hatje, Klas"],["dc.contributor.author","Rahman, Raza-Ur"],["dc.contributor.author","Vidal, Ramon O."],["dc.contributor.author","Simm, Dominic"],["dc.contributor.author","Hammesfahr, Björn"],["dc.contributor.author","Bansal, Vikas"],["dc.contributor.author","Rajput, Ashish"],["dc.contributor.author","Mickael, Michel Edwar"],["dc.contributor.author","Sun, Ting"],["dc.contributor.author","Bonn, Stefan"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2019-07-30T10:25:25Z"],["dc.date.available","2019-07-30T10:25:25Z"],["dc.date.issued","2017"],["dc.description.abstract","Mutually exclusive splicing of exons is a mechanism of functional gene and protein diversification with pivotal roles in organismal development and diseases such as Timothy syndrome, cardiomyopathy and cancer in humans. In order to obtain a first genomewide estimate of the extent and biological role of mutually exclusive splicing in humans, we predicted and subsequently validated mutually exclusive exons (MXEs) using 515 publically available RNA-Seq datasets. Here, we provide evidence for the expression of over 855 MXEs, 42% of which represent novel exons, increasing the annotated human mutually exclusive exome more than fivefold. The data provide strong evidence for the existence of large and multi-cluster MXEs in higher vertebrates and offer new insights into MXE evolution. More than 82% of the MXE clusters are conserved in mammals, and five clusters have homologous clusters in Drosophila Finally, MXEs are significantly enriched in pathogenic mutations and their spatio-temporal expression might predict human disease pathology."],["dc.identifier.doi","10.15252/msb.20177728"],["dc.identifier.pmid","29242366"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/62194"],["dc.language.iso","en"],["dc.relation.eissn","1744-4292"],["dc.relation.issn","1744-4292"],["dc.relation.issn","1744-4292"],["dc.relation.issn","1744-4292"],["dc.title","The landscape of human mutually exclusive splicing"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","3249"],["dc.bibliographiccitation.issue","12"],["dc.bibliographiccitation.journal","Molecular Biology and Evolution"],["dc.bibliographiccitation.lastpage","3267"],["dc.bibliographiccitation.volume","33"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2021-06-01T10:51:20Z"],["dc.date.available","2021-06-01T10:51:20Z"],["dc.date.issued","2016"],["dc.identifier.doi","10.1093/molbev/msw213"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/86978"],["dc.language.iso","en"],["dc.notes.intern","DOI-Import GROB-425"],["dc.relation.eissn","1537-1719"],["dc.relation.issn","0737-4038"],["dc.title","Fine-Tuning Motile Cilia and Flagella: Evolution of the Dynein Motor Proteins from Plants to Humans at High Resolution"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.artnumber","173"],["dc.bibliographiccitation.journal","BMC Genomics"],["dc.bibliographiccitation.volume","10"],["dc.contributor.author","Odronitz, Florian"],["dc.contributor.author","Becker, Sebastian"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2019-07-09T11:52:53Z"],["dc.date.available","2019-07-09T11:52:53Z"],["dc.date.issued","2009"],["dc.description.abstract","Background: Motor proteins have extensively been studied in the past and consist of large superfamilies. They are involved in diverse processes like cell division, cellular transport, neuronal transport processes, or muscle contraction, to name a few. Vertebrates contain up to 60 myosins and about the same number of kinesins that are spread over more than a dozen distinct classes. Results: Here, we present the comparative genomic analysis of the motor protein repertoire of 21 completely sequenced arthropod species using the owl limpet Lottia gigantea as outgroup. Arthropods contain up to 17 myosins grouped into 13 classes. The myosins are in almost all cases clear paralogs, and thus the evolution of the arthropod myosin inventory is mainly determined by gene losses. Arthropod species contain up to 29 kinesins spread over 13 classes. In contrast to the myosins, the evolution of the arthropod kinesin inventory is not only determined by gene losses but also by many subtaxon-specific and species-specific gene duplications. All arthropods contain each of the subunits of the cytoplasmic dynein/dynactin complex. Except for the dynein light chains and the p150 dynactin subunit they contain single gene copies of the other subunits. Especially the roadblock light chain repertoire is very species-specific. Conclusion: All 21 completely sequenced arthropods, including the twelve sequenced Drosophila species, contain a species-specific set of motor proteins. The phylogenetic analysis of all genes as well as the protein repertoire placed Daphnia pulex closest to the root of the Arthropoda. The louse Pediculus humanus corporis is the closest relative to Daphnia followed by the group of the honeybee Apis mellifera and the jewel wasp Nasonia vitripennis. After this group the rust-red flour beetle Tribolium castaneum and the silkworm Bombyx mori diverged very closely from the lineage leading to the Drosophila species."],["dc.identifier.doi","10.1186/1471-2164-10-173"],["dc.identifier.purl","https://resolver.sub.uni-goettingen.de/purl?gs-1/6141"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/60300"],["dc.language.iso","en"],["dc.notes.intern","Merged from goescholar"],["dc.rights","Goescholar"],["dc.rights.uri","https://goescholar.uni-goettingen.de/licenses"],["dc.subject.ddc","540"],["dc.title","Reconstructing the phylogeny of 21 completely sequenced arthropod species based on their motor proteins"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.version","published_version"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","202"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC evolutionary biology"],["dc.bibliographiccitation.volume","13"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2018-11-28T09:38:51Z"],["dc.date.available","2018-11-28T09:38:51Z"],["dc.date.issued","2013-09-22"],["dc.description.abstract","The evolution of land plants is characterized by whole genome duplications (WGD), which drove species diversification and evolutionary novelties. Detecting these events is especially difficult if they date back to the origin of the plant kingdom. Established methods for reconstructing WGDs include intra- and inter-genome comparisons, KS age distribution analyses, and phylogenetic tree constructions."],["dc.identifier.doi","10.1186/1471-2148-13-202"],["dc.identifier.pmid","24053117"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/56979"],["dc.language.iso","en"],["dc.notes.status","zu prüfen"],["dc.relation.eissn","1471-2148"],["dc.title","Whole genome duplication events in plant evolution reconstructed and predicted using myosin motor proteins"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","211"],["dc.bibliographiccitation.issue","1"],["dc.bibliographiccitation.journal","BMC evolutionary biology"],["dc.bibliographiccitation.volume","17"],["dc.contributor.author","Kollmar, Martin"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.date.accessioned","2018-11-28T09:11:10Z"],["dc.date.available","2018-11-28T09:11:10Z"],["dc.date.issued","2017"],["dc.description.abstract","The last eukaryotic common ancestor already had an amazingly complex cell possessing genomic and cellular features such as spliceosomal introns, mitochondria, cilia-dependent motility, and a cytoskeleton together with several intracellular transport systems. In contrast to the microtubule-based dyneins and kinesins, the actin-filament associated myosins are considerably divergent in extant eukaryotes and a unifying picture of their evolution has not yet emerged."],["dc.identifier.doi","10.1186/s12862-017-1056-2"],["dc.identifier.pmid","28870165"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/56969"],["dc.language.iso","en"],["dc.notes.status","zu prüfen"],["dc.relation.eissn","1471-2148"],["dc.title","Myosin repertoire expansion coincides with eukaryotic diversification in the Mesoproterozoic era"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]

[["dc.bibliographiccitation.firstpage","1819"],["dc.bibliographiccitation.issue","14"],["dc.bibliographiccitation.journal","Bioinformatics"],["dc.bibliographiccitation.lastpage","1820"],["dc.bibliographiccitation.volume","29"],["dc.contributor.author","Mazur, Adam"],["dc.contributor.author","Hammesfahr, Björn"],["dc.contributor.author","Griesinger, Christian"],["dc.contributor.author","Lee, Donghan"],["dc.contributor.author","Kollmar, Martin"],["dc.date.accessioned","2017-09-07T11:47:39Z"],["dc.date.available","2017-09-07T11:47:39Z"],["dc.date.issued","2013"],["dc.description.abstract","Dynamics governing the function of biomolecule is usually described as exchange processes and can be monitored at atomic resolution with nuclear magnetic resonance (NMR) relaxation dispersion data. Here, we present a new tool for the analysis of CPMG relaxation dispersion profiles (ShereKhan). The web interface to ShereKhan provides a user-friendly environment for the analysis."],["dc.identifier.doi","10.1093/bioinformatics/btt286"],["dc.identifier.gro","3142323"],["dc.identifier.isi","000321747800020"],["dc.identifier.pmid","23698862"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/7009"],["dc.notes.intern","WoS Import 2017-03-10"],["dc.notes.status","final"],["dc.notes.submitter","PUB_WoS_Import"],["dc.publisher","Oxford Univ Press"],["dc.relation.issn","1367-4803"],["dc.title","ShereKhan-calculating exchange parameters in relaxation dispersion data from CPMG experiments"],["dc.type","journal_article"],["dc.type.internalPublication","yes"],["dc.type.peerReviewed","yes"],["dc.type.subtype","original"],["dspace.entity.type","Publication"]]