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.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"]]

[["dc.bibliographiccitation.firstpage","293-299"],["dc.bibliographiccitation.issue","3"],["dc.bibliographiccitation.journal","RNA biology"],["dc.bibliographiccitation.lastpage","299"],["dc.bibliographiccitation.volume","14"],["dc.contributor.author","Kollmar, Martin"],["dc.contributor.author","Mühlhausen, Stefanie"],["dc.date.accessioned","2018-11-28T09:12:33Z"],["dc.date.available","2018-11-28T09:12:33Z"],["dc.date.issued","2017"],["dc.description.abstract","mRNA decoding by tRNAs and tRNA charging by aminoacyl-tRNA synthetases are biochemically separated processes that nevertheless in general involve the same nucleotides. The combination of charging and decoding determines the genetic code. Codon reassignment happens when a differently charged tRNA replaces a former cognate tRNA. The recent discovery of the polyphyly of the yeast CUG sense codon reassignment challenged previous mechanistic considerations and led to the proposal of the so-called tRNA loss driven codon reassignment hypothesis. Accordingly, codon capture is caused by loss of a tRNA or by mutations in the translation termination factor, subsequent reduction of the codon frequency through reduced translation fidelity and final appearance of a new cognate tRNA. Critical for codon capture are sequence and structure of the new tRNA, which must be compatible with recognition regions of aminoacyl-tRNA synthetases. The proposed hypothesis applies to all reported nuclear and organellar codon reassignments."],["dc.identifier.doi","10.1080/15476286.2017.1279785"],["dc.identifier.pmid","28095181"],["dc.identifier.uri","https://resolver.sub.uni-goettingen.de/purl?gro-2/56971"],["dc.language.iso","en"],["dc.notes.status","zu prüfen"],["dc.relation.eissn","1555-8584"],["dc.title","How tRNAs dictate nuclear codon reassignments: Only a few can capture non-cognate codons"],["dc.type","journal_article"],["dc.type.internalPublication","unknown"],["dspace.entity.type","Publication"]]