Dmitrij Frishman

Summary

Country: Germany

Publications

  1. pmc Assignment of isochores for all completely sequenced vertebrate genomes using a consensus
    Thorsten Schmidt
    Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universitat Munchen, D 85350 Freising, Germany
    Genome Biol 9:R104. 2008
  2. pmc Protein abundance profiling of the Escherichia coli cytosol
    Yasushi Ishihama
    Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
    BMC Genomics 9:102. 2008
  3. pmc Testis-specific glyceraldehyde-3-phosphate dehydrogenase: origin and evolution
    Mikhail L Kuravsky
    Faculty of Bioengineering and Bioinformatics, MV Lomonosov Moscow State University, Moscow, Russian Federation
    BMC Evol Biol 11:160. 2011
  4. pmc Alternative splicing and protein function
    A D Neverov
    State Scientific Center GosNIIGenetika, 1st Dorozhny Proezd 1, Moscow, 117545, Russia
    BMC Bioinformatics 6:266. 2005
  5. pmc TargetSpy: a supervised machine learning approach for microRNA target prediction
    Martin Sturm
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
    BMC Bioinformatics 11:292. 2010
  6. pmc No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions
    Marc N Offman
    Department of Genome Oriented Bioinformatics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
    BMC Bioinformatics 5:41. 2004
  7. pmc Applying negative rule mining to improve genome annotation
    Irena I Artamonova
    Institute for Bioinformatics, GSF National Research Center for Environment and Health, Neuherberg, Germany
    BMC Bioinformatics 8:261. 2007
  8. pmc An evolutionary and structural characterization of mammalian protein complex organization
    Philip Wong
    Helmholtz Center Munich German Research Center for Environmental Health GmbH, Institute of Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, Neuherberg, Germany
    BMC Genomics 9:629. 2008
  9. doi request reprint Ionic interactions promote transmembrane helix-helix association depending on sequence context
    Jana R Herrmann
    Lehrstuhl für Chemie der Biopolymere, Department für biowissenschaftliche Grundlagen, Technische Universitat Munchen, Freising, Germany
    J Mol Biol 396:452-61. 2010
  10. pmc DIMA 2.0--predicted and known domain interactions
    Philipp Pagel
    Lehrstuhl für Genomorientierte Bioinformatik, Wissenschaftszentrum Weihenstephan, Technische Universitat Munchen, Am Forum 1, D 85350 Freising, Germany
    Nucleic Acids Res 36:D651-5. 2008

Collaborators

Detail Information

Publications32

  1. pmc Assignment of isochores for all completely sequenced vertebrate genomes using a consensus
    Thorsten Schmidt
    Department of Genome Oriented Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universitat Munchen, D 85350 Freising, Germany
    Genome Biol 9:R104. 2008
    ..We present a new consensus isochore assignment method based on majority voting and provide IsoBase, a comprehensive on-line database of isochore maps for all completely sequenced vertebrate genomes...
  2. pmc Protein abundance profiling of the Escherichia coli cytosol
    Yasushi Ishihama
    Institute for Advanced Biosciences, Keio University, Tsuruoka, Yamagata 997 0017, Japan
    BMC Genomics 9:102. 2008
    ..Thus far, protein concentrations have been difficult to measure on a large scale, but proteomic technologies have now advanced to a stage where this information becomes readily accessible...
  3. pmc Testis-specific glyceraldehyde-3-phosphate dehydrogenase: origin and evolution
    Mikhail L Kuravsky
    Faculty of Bioengineering and Bioinformatics, MV Lomonosov Moscow State University, Moscow, Russian Federation
    BMC Evol Biol 11:160. 2011
    ..In this study we investigate the evolutionary history of GAPD and gain some insights into specialization of GAPD-2 as a testis-specific protein...
  4. pmc Alternative splicing and protein function
    A D Neverov
    State Scientific Center GosNIIGenetika, 1st Dorozhny Proezd 1, Moscow, 117545, Russia
    BMC Bioinformatics 6:266. 2005
    ..The problem is obscured by uneven coverage of genes by ESTs and a large number of artifacts in the EST data...
  5. pmc TargetSpy: a supervised machine learning approach for microRNA target prediction
    Martin Sturm
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, Neuherberg, Germany
    BMC Bioinformatics 11:292. 2010
    ..Recently however, it has been shown that this requirement might be too stringent, leading to a substantial number of missed target sites...
  6. pmc No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions
    Marc N Offman
    Department of Genome Oriented Bioinformatics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
    BMC Bioinformatics 5:41. 2004
    ..The objective of this work was to test the hypothesis that alternative splicing is correlated with contact regions of protein-protein interactions...
  7. pmc Applying negative rule mining to improve genome annotation
    Irena I Artamonova
    Institute for Bioinformatics, GSF National Research Center for Environment and Health, Neuherberg, Germany
    BMC Bioinformatics 8:261. 2007
    ..Here we investigate the applicability of negative association rule mining to revealing erroneously assigned annotation items...
  8. pmc An evolutionary and structural characterization of mammalian protein complex organization
    Philip Wong
    Helmholtz Center Munich German Research Center for Environmental Health GmbH, Institute of Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, Neuherberg, Germany
    BMC Genomics 9:629. 2008
    ..Combining CORUM with other resources, we assembled a dataset of over 2700 mammalian complexes. The availability of a rich information resource allows us to search for organizational properties concerning these complexes...
  9. doi request reprint Ionic interactions promote transmembrane helix-helix association depending on sequence context
    Jana R Herrmann
    Lehrstuhl für Chemie der Biopolymere, Department für biowissenschaftliche Grundlagen, Technische Universitat Munchen, Freising, Germany
    J Mol Biol 396:452-61. 2010
    ..We conclude that intramembrane charge-charge interactions depend on sequence context. Moreover, they appear important for homotypic and heterotypic interactions of numerous natural TMDs...
  10. pmc DIMA 2.0--predicted and known domain interactions
    Philipp Pagel
    Lehrstuhl für Genomorientierte Bioinformatik, Wissenschaftszentrum Weihenstephan, Technische Universitat Munchen, Am Forum 1, D 85350 Freising, Germany
    Nucleic Acids Res 36:D651-5. 2008
    ..Taken together, these two resources yielded 3653 distinct interacting domain pairs. DIMA is available at http://mips.gsf.de/genre/proj/dima...
  11. doi request reprint Complex patterns of histidine, hydroxylated amino acids and the GxxxG motif mediate high-affinity transmembrane domain interactions
    Jana R Herrmann
    Lehrstuhl für Chemie der Biopolymere, Department für biowissenschaftliche Grundlagen, Technische Universitat Munchen, Weihenstephaner Berg 3, 85354 Freising, Germany
    J Mol Biol 385:912-23. 2009
    ..Notably, a similar motif contributes to self-interaction of the BNIP3 transmembrane domain...
  12. ncbi request reprint Co-evolving residues in membrane proteins
    Angelika Fuchs
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
    Bioinformatics 23:3312-9. 2007
    ..Membrane proteins, which constitute between one-fourth and one-third of all proteins in an organism, were only considered in few individual case studies...
  13. pmc PROMPT: a protein mapping and comparison tool
    Thorsten Schmidt
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
    BMC Bioinformatics 7:331. 2006
    ....
  14. doi request reprint Current status of membrane protein structure classification
    Sindy Neumann
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, D 85354 Freising, Germany
    Proteins 78:1760-73. 2010
    ....
  15. ncbi request reprint Protein solubility: sequence based prediction and experimental verification
    Pawel Smialowski
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
    Bioinformatics 23:2536-42. 2007
    ..Accurate theoretical prediction of solubility from sequence is instrumental for setting priorities on targets in large-scale proteomics projects...
  16. doi request reprint Structural comparison and classification of alpha-helical transmembrane domains based on helix interaction patterns
    Angelika Fuchs
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, Freising 85354, Germany
    Proteins 78:2587-99. 2010
    ....
  17. ncbi request reprint The DIMA web resource--exploring the protein domain network
    Philipp Pagel
    Department of Genome Oriented Bioinformatics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
    Bioinformatics 22:997-8. 2006
    ..A powerful yet simple user interface enables the user to compute, visualize, navigate and download domain networks based on specific search criteria. Availability: http://mips.gsf.de/genre/proj/dima..
  18. doi request reprint Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks
    Angelika Fuchs
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, 85354 Freising, Germany
    Proteins 74:857-71. 2009
    ..Because the reliable prediction of helix interaction patterns is an important step in the classification and prediction of membrane protein folds, our method will be a helpful tool in compiling a structural census of membrane proteins...
  19. doi request reprint Prediction of beta-turns and beta-turn types by a novel bidirectional Elman-type recurrent neural network with multiple output layers (MOLEBRNN)
    Andreas Kirschner
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Weihenstephan, Germany
    Gene 422:22-9. 2008
    ..The MOLEBRNN presented here is a generic method applicable in a variety of research fields where multiple mutually depending target classes need to be predicted. Availability: http://webclu.bio.wzw.tum.de/predator-web/...
  20. doi request reprint Designability and disease
    Philip Wong
    Institute for Bioinformatics, GSF National Research Center for Environment and Health, Neuherberg, Germany
    Methods Mol Biol 484:491-504. 2008
    ..Here, we describe definitions and principles underlying the concept of designability and discuss its relation to disease...
  21. ncbi request reprint Predicting experimental properties of proteins from sequence by machine learning techniques
    Pawel Smialowski
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
    Curr Protein Pept Sci 8:121-33. 2007
    ..We also describe experimental data repositories and machine learning techniques used for classification and feature selection...
  22. ncbi request reprint Predicting experimental properties of integral membrane proteins by a naive Bayes approach
    Antonio J Martin-Galiano
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenchaftszentrum Weihenstephan, 85350 Freising, Germany
    Proteins 70:1243-56. 2008
    ..In most cases, sets of 10-20 protein features were found actually relevant, most notably, the content of isoleucine, valine, and positively-charged residues...
  23. pmc PEDANT covers all complete RefSeq genomes
    Mathias C Walter
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Munchen, German Research Center for Environmental Health GmbH, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    Nucleic Acids Res 37:D408-11. 2009
    ..PEDANT is freely accessible to academic users at http://pedant.gsf.de. For programmatic access Web Services are available at http://pedant.gsf.de/webservices.jsp...
  24. ncbi request reprint Defining the fold space of membrane proteins: the CAMPS database
    Antonio J Martin-Galiano
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Freising, Germany
    Proteins 64:906-22. 2006
    ....
  25. ncbi request reprint Mining sequence annotation databanks for association patterns
    Irena I Artamonova
    Institute for Bioinformatics, GSF National Research Center for Environment and Health, Neuherberg, Germany
    Bioinformatics 21:iii49-57. 2005
    ..A possible approach to this problem is to detect anomalies in annotation items based on association rule mining...
  26. ncbi request reprint Protein annotation at genomic scale: the current status
    Dmitrij Frishman
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenchaftszentrum Weihenstephan, 85350 Freising, Germany
    Chem Rev 107:3448-66. 2007
  27. ncbi request reprint Will my protein crystallize? A sequence-based predictor
    Pawel Smialowski
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, Freising, Germany
    Proteins 62:343-55. 2006
    ..A Web server for protein crystallizability prediction called SECRET is available at http://webclu.bio.wzw.tum.de:8080/secret...
  28. ncbi request reprint Phenylalanine promotes interaction of transmembrane domains via GxxxG motifs
    Stephanie Unterreitmeier
    Technische Universitat Munchen, Lehrstuhl für Chemie der Biopolymere, Weihenstephaner Berg 3, D 85354 Freising Weihenstephan, and Munich Center For Integrated Protein Science CIPS M, Germany
    J Mol Biol 374:705-18. 2007
    ..We conclude that Phe stabilises membrane-spanning GxxxG motifs. This is one example of how the role of certain side-chains in helix-helix interfaces is modulated by sequence context...
  29. pmc DIMA 3.0: Domain Interaction Map
    Qibin Luo
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
    Nucleic Acids Res 39:D724-9. 2011
    ..The DIMA Web site allows to calculate domain interaction networks either for a domain of interest or for entire organisms, and to explore them interactively using the Flash-based Cytoscape Web software...
  30. pmc STRIDE: a web server for secondary structure assignment from known atomic coordinates of proteins
    Matthias Heinig
    Department of Genome Oriented Bioinformatics, Technical University of Munich, Wissenschaftszentrum Weihenstephan, 85354 Freising, Germany
    Nucleic Acids Res 32:W500-2. 2004
    ..A searchable database of STRIDE assignments for the latest PDB release is also provided. The STRIDE server is accessible from http://webclu.bio.wzw.tum.de/stride/...
  31. doi request reprint Complex principal component and correlation structure of 16 yeast genomic variables
    Fabian J Theis
    Helmholtz Center Munich German Research Center for Environmental Health, Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, Neuherberg, Germany
    Mol Biol Evol 28:2501-12. 2011
    ..cerevisiae, and Homo sapiens (http://webclu.bio.wzw.tum.de:18080/quagmire)...
  32. pmc Fold designability, distribution, and disease
    Philip Wong
    Institute for Bioinformatics, GSF National Research Center for Environment and Health, Neuherberg, Germany
    PLoS Comput Biol 2:e40. 2006
    ..These results suggest that family counts reflect how certain structures are distributed in nature and is an important characteristic associated with many human diseases...