Dmitrij Frishman

Summary

Country: Germany

Publications

  1. 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
  2. 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
  3. pmc Classification of α-helical membrane proteins using predicted helix architectures
    Sindy Neumann
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, Freising, Germany
    PLoS ONE 8:e77491. 2013
  4. pmc The PEDANT genome database in 2005
    M Louise Riley
    Institute for Bioinformatics, GSF National Research Center for Health and Environment, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    Nucleic Acids Res 33:D308-10. 2005
  5. pmc The Negatome database: a reference set of non-interacting protein pairs
    Pawel Smialowski
    Institute for Bioinformatics and Systems Biology MIPS, HMGU German Research Center for Environmental Health Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
    Nucleic Acids Res 38:D540-4. 2010
  6. pmc Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus
    Andrey Chursov
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftzentrum Weihenstephan, Freising, Germany
    RNA Biol 9:1266-74. 2012
  7. pmc Sequence-structure relationships in yeast mRNAs
    Andrey Chursov
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftzentrum Weihenstephan, Maximus von Imhof Forum 3, D 85354, Freising, Germany
    Nucleic Acids Res 40:956-62. 2012
  8. pmc Phosphorylation variation during the cell cycle scales with structural propensities of proteins
    Stefka Tyanova
    Genome Oriented Bioinformatics Department, Technische Universitat Munchen, Freising, Germany
    PLoS Comput Biol 9:e1002842. 2013
  9. pmc QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis
    Dmitry N Ivankov
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, Maximus von Imhof Forum 3, 85354 Freising, Germany
    Nucleic Acids Res 41:W459-64. 2013
  10. pmc Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution
    Andrey Chursov
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftzentrum Weihenstephan, Maximus von Imhof Forum 3, D 85354, Freising, Germany, Helmholtz Center Munich German Research Center for Environmental Health GmbH, Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, D 85764 Neuherberg, Germany and Cure Lab, Inc, 43 Rybury Hillway, Needham, MA 02492, USA
    Nucleic Acids Res 41:7854-60. 2013

Collaborators

Detail Information

Publications58

  1. 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...
  2. 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...
  3. pmc Classification of α-helical membrane proteins using predicted helix architectures
    Sindy Neumann
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, Freising, Germany
    PLoS ONE 8:e77491. 2013
    ....
  4. pmc The PEDANT genome database in 2005
    M Louise Riley
    Institute for Bioinformatics, GSF National Research Center for Health and Environment, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    Nucleic Acids Res 33:D308-10. 2005
    ..At present, the PEDANT database contains exhaustive annotation of over 1,240,000 proteins from 270 eubacterial, 23 archeal and 41 eukaryotic genomes...
  5. pmc The Negatome database: a reference set of non-interacting protein pairs
    Pawel Smialowski
    Institute for Bioinformatics and Systems Biology MIPS, HMGU German Research Center for Environmental Health Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany
    Nucleic Acids Res 38:D540-4. 2010
    ..It can be used to evaluate protein and domain interactions from new experiments and improve the training of interaction prediction algorithms. The Negatome database is available at http://mips.helmholtz-muenchen.de/proj/ppi/negatome...
  6. pmc Specific temperature-induced perturbations of secondary mRNA structures are associated with the cold-adapted temperature-sensitive phenotype of influenza A virus
    Andrey Chursov
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftzentrum Weihenstephan, Freising, Germany
    RNA Biol 9:1266-74. 2012
    ..Differences in temperature-induced structural changes of wt and ca/ts mRNA structures may constitute a yet unappreciated molecular mechanism of the cold adaptation/temperature sensitivity phenomena...
  7. pmc Sequence-structure relationships in yeast mRNAs
    Andrey Chursov
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftzentrum Weihenstephan, Maximus von Imhof Forum 3, D 85354, Freising, Germany
    Nucleic Acids Res 40:956-62. 2012
    ..Apparently, the need to maintain stable three-dimensional structures of encoded proteins places a much higher evolutionary pressure on mRNA sequences than on their RNA structures...
  8. pmc Phosphorylation variation during the cell cycle scales with structural propensities of proteins
    Stefka Tyanova
    Genome Oriented Bioinformatics Department, Technische Universitat Munchen, Freising, Germany
    PLoS Comput Biol 9:e1002842. 2013
    ..They also imply that phosphorylation sites are associated with different time scales that serve different functional needs...
  9. pmc QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis
    Dmitry N Ivankov
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, Maximus von Imhof Forum 3, 85354 Freising, Germany
    Nucleic Acids Res 41:W459-64. 2013
    ..The web server is available at http://webclu.bio.wzw.tum.de/qarip/. This website is free and open to all users and there is no login requirement. ..
  10. pmc Conservation of mRNA secondary structures may filter out mutations in Escherichia coli evolution
    Andrey Chursov
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftzentrum Weihenstephan, Maximus von Imhof Forum 3, D 85354, Freising, Germany, Helmholtz Center Munich German Research Center for Environmental Health GmbH, Institute of Bioinformatics and Systems Biology, Ingolstädter Landstraße 1, D 85764 Neuherberg, Germany and Cure Lab, Inc, 43 Rybury Hillway, Needham, MA 02492, USA
    Nucleic Acids Res 41:7854-60. 2013
    ..These results demonstrate that the need to maintain intact mRNA structures imposes additional evolutionary constraints on bacterial genomes, which go beyond preservation of structure and function of the encoded proteins. ..
  11. pmc PEDANT genome database: 10 years online
    M Louise Riley
    Institute for Bioinformatics, GSF National Research Center for Health and Environment, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    Nucleic Acids Res 35:D354-7. 2007
    ..Finally, we report on the application of association rule mining for automatic detection of potential annotation errors. PEDANT is freely accessible to academic users at http://pedant.gsf.de...
  12. 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...
  13. 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...
  14. 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...
  15. 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...
  16. 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..
  17. 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...
  18. 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...
  19. ncbi request reprint The MIPS mammalian protein-protein interaction database
    Philipp Pagel
    Institute for Bioinformatics MIPS, GSF National Research Center for Environment and Health, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    Bioinformatics 21:832-4. 2005
    ..The content is based on published experimental evidence that has been processed by human expert curators. We provide the full dataset for download and a flexible and powerful web interface for users with various requirements...
  20. pmc The PEDANT genome database
    Dmitrij Frishman
    Institute for Bioinformatics, GSF National Research Center for Environment and Health, Ingolstadter Landstrasse 1, 85764 Neueherberg, Germany
    Nucleic Acids Res 31:207-11. 2003
    ..The availability of functional and structural predictions for 650 000 genomic proteins in well organized form makes PEDANT a useful resource for both functional and structural genomics...
  21. pmc The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context
    Andreas Ruepp
    Institute for Bioinformatics MIPS, GSF National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 34:D568-71. 2006
    ..MfunGD is implemented in GenRE, a J2EE-based component-oriented multi-tier architecture following the separation of concern principle...
  22. 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...
  23. doi request reprint Camps 2.0: exploring the sequence and structure space of prokaryotic, eukaryotic, and viral membrane proteins
    Sindy Neumann
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftszentrum Weihenstephan, 85354 Freising, Germany
    Proteins 80:839-57. 2012
    ..We therefore estimate that ∼1300 structures would need to be determined to provide a sufficient structural coverage of polytopic membrane proteins. CAMPS 2.0 is available at http://webclu.bio.wzw.tum.de/CAMPS2.0/...
  24. ncbi request reprint A domain interaction map based on phylogenetic profiling
    Philipp Pagel
    Institute for Bioinformatics, GSF National Research Center for Environment and Health, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    J Mol Biol 344:1331-46. 2004
    ..We provide a list of novel domain associations predicted by our method...
  25. 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
    ....
  26. 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...
  27. 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...
  28. ncbi request reprint Designability, aggregation propensity and duplication of disease-associated proteins
    Philip Wong
    Institute for Bioinformatics, GSF, National Research Center for Environment and Health, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Protein Eng Des Sel 18:503-8. 2005
    ..Another finding in this work is that many disease proteins are highly sequence similar to other disease proteins, suggesting that gene duplication has contributed to the expansion of disease-prone protein families...
  29. 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...
  30. ncbi request reprint SNAPper: gene order predicts gene function
    Grigory Kolesov
    Institute for Bioinformatics, GSF National Research Center for Environment and Heath, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    Bioinformatics 18:1017-9. 2002
    ..SNAPper is a network service for predicting gene function based on the conservation of gene order...
  31. 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
    ....
  32. 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...
  33. 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
    ....
  34. 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)...
  35. ncbi request reprint Conservation of protein-protein interactions - lessons from ascomycota
    Philipp Pagel
    Institute for Bioinformatics, GSF National Research Center for Environment and Health, Ingolstadter Landstrasse 1, Neuherberg 85764, Germany
    Trends Genet 20:72-6. 2004
    ..The conservation of interacting protein pairs between different organisms does not exhibit any bias with respect to protein functional roles...
  36. 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...
  37. pmc RNAtips: Analysis of temperature-induced changes of RNA secondary structure
    Andrey Chursov
    Department of Genome Oriented Bioinformatics, Technische Universitat Munchen, Wissenschaftzentrum Weihenstephan, Maximus von Imhof Forum 3, D 85354 Freising, Germany
    Nucleic Acids Res 41:W486-91. 2013
    ..The RNAtips web server is freely accessible without any login requirement at http://rnatips.org...
  38. pmc Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation and protein structure analysis
    Philipp Blohm
    Institute for Bioinformatics and Systems Biology MIPS, HMGU German Research Center for Environmental Health, Ingolstaedter Landstrasse 1, 85764 Neuherberg, Germany, Clueda AG, Elsenheimerstraße 59, 80687 Munich, Germany and Department of Genome Oriented Bioinformatics, Technische Universitaet Muenchen Wissenschaftszentrum Weihenstephan, 85350 Freising, Germany
    Nucleic Acids Res 42:D396-400. 2014
    ..Manual verification shows that nearly a half of the text mining results with the highest confidence values correspond to NIP pairs. Compared to the first version the contents of the database have grown by over 300%. ..
  39. pmc MIPS: curated databases and comprehensive secondary data resources in 2010
    H Werner Mewes
    Institute for Bioinformatics and Systems Biology, MIPS, Helmholtz Center F Health and Environment, Ingolstadter Landstr 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 39:D220-4. 2011
    ..All databases described here, as well as the detailed descriptions of our projects can be accessed through the MIPS WWW server (http://mips.helmholtz-muenchen.de)...
  40. pmc How many signal peptides are there in bacteria?
    Dmitry N Ivankov
    Technische Universitat Munchen, Department of Genome Oriented Bioinformatics, 85354, Freising, Germany
    Environ Microbiol 15:983-90. 2013
    ..coli genome with the latest version of SignalP program, show that the fraction of proteins containing signal peptides is only about 10%, or half of previous estimates...
  41. ncbi 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
    ....
  42. 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...
  43. 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...
  44. 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...
  45. ncbi 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/...
  46. 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...
  47. 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/...
  48. 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...
  49. doi request reprint PROSO II--a new method for protein solubility prediction
    Pawel Smialowski
    Department of Genome Oriented Bioinformatics, Technische Universitat Muenchen, Freising, Germany
    FEBS J 279:2192-200. 2012
    ..PROSO II is available at http://mips.helmholtz-muenchen.de/prosoII...
  50. 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
  51. ncbi request reprint Online genomics facilities in the new millennium
    Dmitrij Frishman
    Institute for Bioinformatics, GSF National Research Center for Environment and Heatlh, Ingolstadter Landstrasse 1, 85764 Neueherberg, Germany
    Pharmacogenomics 3:265-71. 2002
    ..The role of community efforts in curating and annotating genome data is discussed. The crucial role of data integration and interoperability in developing next-generation genomic facilities is underscored...
  52. 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...
  53. ncbi request reprint What we have learned about prokaryotes from structural genomics
    Dmitrij Frishman
    Department of Genome Oriented Bioinformatics, Technical University of Munich, Freising Weihenstephan, Germany
    OMICS 7:211-24. 2003
    ....
  54. 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...
  55. 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...
  56. ncbi request reprint Knowledge-based selection of targets for structural genomics
    Dmitrij Frishman
    Institute for Bioinformatics, GSF National Research Center for Environment and Health, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    Protein Eng 15:169-83. 2002
    ..The results of a large-scale computation experiment in which exemplary target selection for 32 prokaryotic genomes was conducted are presented...
  57. 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...
  58. doi request reprint Importance of mRNA secondary structural elements for the expression of influenza virus genes
    Petr O Ilyinskii
    Cure Lab, Inc, Needham, Massachusetts 02492, USA
    OMICS 13:421-30. 2009
    ..Finally, introducing mutations into viral genes while preserving their secondary RNA structure, suggests a new method for the generation of efficiently expressed recombinants of viral proteins...