Research Topics
Genomes and Genes | Mario AlbrechtSummaryCountry: Germany Publications
| Collaborators
|
Detail Information
Publications
Novel Sm-like proteins with long C-terminal tails and associated methyltransferasesMario Albrecht
Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
FEBS Lett 569:18-26. 2004..Further computational analyses revealed that some methyltransferases contain putative RNA-binding helix-turn-helix domains and zinc fingers...
FunSimMat update: new features for exploring functional similarityAndreas Schlicker
Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrucken, Germany
Nucleic Acids Res 38:D244-8. 2010..Additional changes include a revised user front-end and a new RESTlike interface for improving the user-friendliness and online accessibility of FunSimMat...- DASMI: exchanging, annotating and assessing molecular interaction dataHagen Blankenburg
Max Planck Institute for Informatics, Campus E 1 4, 66123 Saarbrucken, Germany
Bioinformatics 25:1321-8. 2009..New techniques are required for retrieving, sharing and presenting data spread over the Internet... 
An integrative approach for predicting interactions of protein regionsSven Eric Schelhorn
Max Planck Institute for Informatics, Saarbrucken, Germany
Bioinformatics 24:i35-41. 2008..Computational identification of interacting protein regions aids in the detailed understanding of protein networks and supports the prediction of novel protein interactions and the reconstruction of protein complexes...- Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequenceMario Albrecht
Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
Bioinformatics 19:2171-5. 2003..Our findings suggest that evolutionary gene duplication can give rise to disease families because variants affect conserved sequence in a similar fashion... - Functional evaluation of domain-domain interactions and human protein interaction networksAndreas Schlicker
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
Bioinformatics 23:859-65. 2007..The applied measure particularly addresses the frequent annotation of proteins or domains with multiple GO terms... - Computational analysis of human protein interaction networksFidel Ramirez
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
Proteomics 7:2541-52. 2007..We could further demonstrate that protein interactions predicted by more than one method achieve an elevated reliability... - Improving disease gene prioritization using the semantic similarity of Gene Ontology termsAndreas Schlicker
Max Planck Institute for Informatics, Department of Computational Biology and Applied Algorithmics, Saarbrucken, Germany
Bioinformatics 26:i561-7. 2010..Recent studies discovered that genes involved in phenotypically similar diseases are often functionally related on the molecular level... - Computing topological parameters of biological networksYassen Assenov
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
Bioinformatics 24:282-4. 2008..It is an interactive and highly customizable application that requires no expert knowledge in graph theory from the user. AVAILABILITY: NetworkAnalyzer can be downloaded via the Cytoscape web site: http://www.cytoscape.org.. - Decomposing protein networks into domain-domain interactionsMario Albrecht
Max Planck Institute for Informatics, Saarbrucken, Germany
Bioinformatics 21:ii220-1. 2005..An additional plugin provides supplementary web links to Internet resources on domain function and structure. AVAILABILITY: Both Cytoscape plugins can be downloaded from http://www.cytoscape.org.. - Structural and functional analysis of ataxin-2 and ataxin-3Mario Albrecht
Max Planck Institute for Informatics, Saarbrucken, Germany
Eur J Biochem 271:3155-70. 2004..We also speculate about distant evolutionary relationships of ubiquitin-binding UIM, GAT, UBA and CUE domains and helical ANTH and UBX domain extensions... - Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2Mario Albrecht
Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
FEBS Lett 554:520-8. 2003..The implications on the domain functions such as NTP-hydrolysis or oligomerization are discussed... - Novel search method for the discovery of functional relationshipsFidel Ramirez
Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrucken, Germany
Bioinformatics 28:269-76. 2012..We observed that the search performance improved substantially for almost all methods when multiple annotation sources were included. In particular, our method outperformed the other methods in terms of recall and average precision... - Topological analysis and interactive visualization of biological networks and protein structuresNadezhda T Doncheva
Max Planck Institute for Informatics, Saarbrucken, Germany
Nat Protoc 7:670-85. 2012..The third workflow combines NetworkAnalyzer and RINalyzer to compare residue networks. The full protocol can be completed in ∼2 h... - FunSimMat: a comprehensive functional similarity databaseAndreas Schlicker
Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
Nucleic Acids Res 36:D434-9. 2008..All results can be downloaded in tab-delimited files for use with other tools. An additional XML-RPC interface gives automatic online access to FunSimMat for programs and remote services... - AltAnalyze and DomainGraph: analyzing and visualizing exon expression dataDorothea Emig
Max Planck Institute for Informatics, 66123 Saarbrucken, Germany
Nucleic Acids Res 38:W755-62. 2010..Our programs are available at http://www.altanalyze.org and http://www.domaingraph.de. These websites also include extensive documentation, tutorials and sample data... - DASMIweb: online integration, analysis and assessment of distributed protein interaction dataHagen Blankenburg
Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrucken, Germany
Nucleic Acids Res 37:W122-8. 2009..The retrieved results can be exported in different file formats like MITAB or SIF. DASMIweb is freely available at http://www.dasmiweb.de... - Pyranose oxidase identified as a member of the GMC oxidoreductase familyMario Albrecht
Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
Bioinformatics 19:1216-20. 2003..The identified homology also suggests a three-dimensional protein structure similar to the functionally related glucose oxidase... - Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virusChristoph Welsch
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, 66123 Saarbrucken, Germany
Genome Biol 9:R16. 2008..These mutations are located in the protein interior and far away from the ligand binding pocket... - Integrating expression data with domain interaction networksDorothea Emig
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrucken, Germany
Bioinformatics 24:2546-8. 2008..AVAILABILITY: The plugin DomainGraph and the online documentation are available at http://domaingraph.bioinf.mpi-inf.mpg.de... - Structure collisions between interacting proteinsDorothea Emig
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
PLoS ONE 6:e19581. 2011..However, we discovered a number of collisions that originate from alternative protein conformations or quaternary structures due to different experimental conditions... - Survey on the PABC recognition motif PAM2Mario Albrecht
Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, Saarbrucken 66123, Germany
Biochem Biophys Res Commun 316:129-38. 2004..It is also striking that the PAM2 motif appears to occur solely outside globular protein domains... - Tissue-specific proteins and functional implicationsDorothea Emig
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrücken, Germany
J Proteome Res 10:1893-903. 2011..Interestingly, the number of alternative transcripts is increased for widely expressed genes. This suggests that alternative splicing plays a prominent role in generating specific functional characteristics of tissues... - The HIN domain of IFI-200 proteins consists of two OB foldsMario Albrecht
Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
Biochem Biophys Res Commun 327:679-87. 2005..Our results also raise the possibility of as yet unexplored functional roles of IFI-200 proteins as transcriptional regulators and as interaction partners of proteins involved in immunomodulatory and apoptotic processes... - Inferring physical protein contacts from large-scale purification data of protein complexesSven Eric Schelhorn
Max Planck Institute for Informatics, Saarbrucken, Germany
Mol Cell Proteomics 10:M110.004929. 2011.... - Functional characterization of human genes from exon expression and RNA interference resultsDorothea Emig
Max Planck Institute for Informatics, Saarbrucken, Germany
Methods Mol Biol 910:33-53. 2012..In particular, our exemplary application studies show how to analyze the function of human genes that play a major role in human stem cells or viral infections... - GOTax: investigating biological processes and biochemical activities along the taxonomic treeAndreas Schlicker
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
Genome Biol 8:R33. 2007..In particular, a measure of functional similarity is available for comparing proteins and protein families, establishing functional relationships independent of evolution... - Simple consensus procedures are effective and sufficient in secondary structure predictionMario Albrecht
Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
Protein Eng 16:459-62. 2003..Our analysis also provides valuable insight into the similarity of the results of the prediction methods that we combine as well as the higher confidence in consistently predicted secondary structure... - Recent approaches to the prioritization of candidate disease genesNadezhda T Doncheva
Max Planck Institute for Informatics, Saarbrucken, Germany
Wiley Interdiscip Rev Syst Biol Med 4:429-42. 2012..We focus on approaches that use network information and integrate heterogeneous data sources. Furthermore, we discuss current benchmarking procedures for evaluating and comparing different prioritization methods... - Analyzing and visualizing residue networks of protein structuresNadezhda T Doncheva
Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrucken, Germany
Trends Biochem Sci 36:179-82. 2011..Here, we present the new software tools RINerator and RINalyzer for the automatized generation, 2D visualization, and interactive analysis of residue interaction networks, and highlight their use in different application scenarios... - Update on the domain architectures of NLRs and R proteinsMario Albrecht
Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, , Germany
Biochem Biophys Res Commun 339:459-62. 2006 - Identification of mammalian orthologs associates PYPAF5 with distinct functional rolesMario Albrecht
Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
FEBS Lett 538:173-7. 2003..In particular, based on a comprehensive sequence analysis, we propose a structural model for this hormone receptor that is different from the model suggested previously... - Measuring and analyzing tissue specificity of human genes and protein complexesDorothea Emig
Max Planck Institute for Informatics, Campus E1, 4, 66123 Saarbrucken, Germany
EURASIP J Bioinform Syst Biol 2011:5. 2011..Functional analyses based on microarray data are thus biased towards high expressed genes. This also means that previous biological findings based on microarrays might have to be re-examined using high-throughput sequencing results... - Structural modeling of ataxin-3 reveals distant homology to adaptinsMario Albrecht
Fraunhofer Institute for Algorithms and Scientific Computing SCAI, Schloss Birlinghoven, Sankt Augustin, Germany
Proteins 50:355-70. 2003..Our database searches also identified an as yet uncharacterized family of proteins, which we named josephins because of their pronounced homology to the Josephin domain of ataxin-3... - Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiencyJorg Bojunga
Internal Medicine II, Saarland University Hospital, Kirrberger Strasse, 66421 Homburg Saar, Germany
Hum Genet 117:558-64. 2005..In addition, the results support previous findings in which heterozygous CYP21 mutations are associated with symptoms of hyperandrogenism in susceptible individuals... - Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivationWladimir I L Tameling
Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, 1090 GB Amsterdam, The Netherlands
Plant Physiol 140:1233-45. 2006..Based on these data, we propose that the NB-ARC domain of I-2, and likely of related R proteins, functions as a molecular switch whose state (on/off) depends on the nucleotide bound (ATP/ADP)... - An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesisAnnett Boeddrich
Department of Neuroproteomics, Max Delbrueck Center for Molecular Medicine MDC, Berlin, Germany
EMBO J 25:1547-58. 2006..Together, these results define the VCP-Atx-3 association as a potential target for therapeutic intervention and suggest that it might influence the progression of spinocerebellar ataxia type 3... - Structure-function analysis of the NB-ARC domain of plant disease resistance proteinsGerben van Ooijen
Plant Pathology, Swammerdam Institute for Life Sciences, University of Amsterdam, PO Box 94062, 1090 GB Amsterdam, The Netherlands
J Exp Bot 59:1383-97. 2008..The presented 3D model provides a framework for the formulation of hypotheses on how mutations in the NB-ARC exert their effects...