Mario Albrecht

Summary

Country: Germany

Publications

  1. ncbi Novel Sm-like proteins with long C-terminal tails and associated methyltransferases
    Mario Albrecht
    Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
    FEBS Lett 569:18-26. 2004
  2. pmc FunSimMat update: new features for exploring functional similarity
    Andreas Schlicker
    Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrucken, Germany
    Nucleic Acids Res 38:D244-8. 2010
  3. pmc DASMI: exchanging, annotating and assessing molecular interaction data
    Hagen Blankenburg
    Max Planck Institute for Informatics, Campus E 1 4, 66123 Saarbrucken, Germany
    Bioinformatics 25:1321-8. 2009
  4. doi An integrative approach for predicting interactions of protein regions
    Sven Eric Schelhorn
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Bioinformatics 24:i35-41. 2008
  5. ncbi Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence
    Mario Albrecht
    Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
    Bioinformatics 19:2171-5. 2003
  6. ncbi Functional evaluation of domain-domain interactions and human protein interaction networks
    Andreas Schlicker
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
    Bioinformatics 23:859-65. 2007
  7. ncbi Computational analysis of human protein interaction networks
    Fidel Ramirez
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Saarbrucken, Germany
    Proteomics 7:2541-52. 2007
  8. doi Functional characterization of human genes from exon expression and RNA interference results
    Dorothea Emig
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Methods Mol Biol 910:33-53. 2012
  9. pmc Improving disease gene prioritization using the semantic similarity of Gene Ontology terms
    Andreas Schlicker
    Max Planck Institute for Informatics, Department of Computational Biology and Applied Algorithmics, Saarbrucken, Germany
    Bioinformatics 26:i561-7. 2010
  10. ncbi Computing topological parameters of biological networks
    Yassen Assenov
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
    Bioinformatics 24:282-4. 2008

Collaborators

Detail Information

Publications39

  1. ncbi Novel Sm-like proteins with long C-terminal tails and associated methyltransferases
    Mario 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...
  2. pmc FunSimMat update: new features for exploring functional similarity
    Andreas 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...
  3. pmc DASMI: exchanging, annotating and assessing molecular interaction data
    Hagen 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...
  4. doi An integrative approach for predicting interactions of protein regions
    Sven 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...
  5. ncbi Disease-associated variants in PYPAF1 and NOD2 result in similar alterations of conserved sequence
    Mario 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...
  6. ncbi Functional evaluation of domain-domain interactions and human protein interaction networks
    Andreas 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...
  7. ncbi Computational analysis of human protein interaction networks
    Fidel 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...
  8. doi Functional characterization of human genes from exon expression and RNA interference results
    Dorothea 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...
  9. pmc Improving disease gene prioritization using the semantic similarity of Gene Ontology terms
    Andreas 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...
  10. ncbi Computing topological parameters of biological networks
    Yassen 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..
  11. ncbi Decomposing protein networks into domain-domain interactions
    Mario 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...
  12. ncbi Structural localization of disease-associated sequence variations in the NACHT and LRR domains of PYPAF1 and NOD2
    Mario 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...
  13. ncbi Structural and functional analysis of ataxin-2 and ataxin-3
    Mario 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...
  14. doi Recent approaches to the prioritization of candidate disease genes
    Nadezhda 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...
  15. pmc Novel search method for the discovery of functional relationships
    Fidel Ramirez
    Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrucken, Germany
    Bioinformatics 28:269-76. 2012
    ..However, most current similarity methods are focused only on annotations from the Gene Ontology (GO) and do not take other annotation sources into account...
  16. doi Topological analysis and interactive visualization of biological networks and protein structures
    Nadezhda 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...
  17. pmc AltAnalyze and DomainGraph: analyzing and visualizing exon expression data
    Dorothea 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...
  18. ncbi Pyranose oxidase identified as a member of the GMC oxidoreductase family
    Mario 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...
  19. pmc DASMIweb: online integration, analysis and assessment of distributed protein interaction data
    Hagen 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...
  20. pmc FunSimMat: a comprehensive functional similarity database
    Andreas 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...
  21. pmc Integrating expression data with domain interaction networks
    Dorothea Emig
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Campus E1 4, 66123 Saarbrucken, Germany
    Bioinformatics 24:2546-8. 2008
    ..Different expression patterns between human tissues or cells can be identified by comparing the generated domain graphs...
  22. pmc Molecular basis of telaprevir resistance due to V36 and T54 mutations in the NS3-4A protease of the hepatitis C virus
    Christoph 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...
  23. ncbi Survey on the PABC recognition motif PAM2
    Mario 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...
  24. pmc Structure collisions between interacting proteins
    Dorothea 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...
  25. doi Tissue-specific proteins and functional implications
    Dorothea 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...
  26. pmc Inferring physical protein contacts from large-scale purification data of protein complexes
    Sven Eric Schelhorn
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Mol Cell Proteomics 10:M110.004929. 2011
    ....
  27. ncbi The HIN domain of IFI-200 proteins consists of two OB folds
    Mario 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...
  28. ncbi Simple consensus procedures are effective and sufficient in secondary structure prediction
    Mario 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...
  29. pmc GOTax: investigating biological processes and biochemical activities along the taxonomic tree
    Andreas 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...
  30. pmc NetworkPrioritizer: a versatile tool for network-based prioritization of candidate disease genes or other molecules
    Tim Kacprowski
    Max Planck Institute for Informatics, Saarbrucken, Germany
    Bioinformatics 29:1471-3. 2013
    ..Our versatile software tool computes a number of important centrality measures to rank nodes based on their relevance for network connectivity and provides different methods to aggregate and compare rankings...
  31. doi Analyzing and visualizing residue networks of protein structures
    Nadezhda 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...
  32. ncbi Identification of mammalian orthologs associates PYPAF5 with distinct functional roles
    Mario 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...
  33. pmc Measuring and analyzing tissue specificity of human genes and protein complexes
    Dorothea 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...
  34. ncbi Update on the domain architectures of NLRs and R proteins
    Mario Albrecht
    Department of Computational Biology and Applied Algorithmics, Max Planck Institute for Informatics, Stuhlsatzenhausweg 85, 66123 Saarbrucken, Germany
    Biochem Biophys Res Commun 339:459-62. 2006
  35. ncbi Structural modeling of ataxin-3 reveals distant homology to adaptins
    Mario 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...
  36. ncbi Structural and functional analysis of a novel mutation of CYP21B in a heterozygote carrier of 21-hydroxylase deficiency
    Jorg 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...
  37. pmc Mutations in the NB-ARC domain of I-2 that impair ATP hydrolysis cause autoactivation
    Wladimir 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)...
  38. pmc An arginine/lysine-rich motif is crucial for VCP/p97-mediated modulation of ataxin-3 fibrillogenesis
    Annett 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...
  39. doi Structure-function analysis of the NB-ARC domain of plant disease resistance proteins
    Gerben 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...