Publications from Prof. Dr. D Frishman

  1. Unterreitmeier S, Fuchs A, Schaeffler T, Heym RG, Frishman D, and Langosch D (2007) Phenylalanine promotes interaction of transmembrane domains via GxxxG motifs. J Mol Biol 374(3):705–18
  2. Pagel P, Strack N, Oesterheld M, Stümpflen V and Frishman D (2007) Computational prediction of domain interactions. Methods Mol Biol 396:3–16
  3. Fuchs A, Martin-Galiano AJ, Kalman M, Fleishman S, Ben-Tal S and Frishman D (2007) Co-Evolving Residues in Membrane Proteins. Bioinformatics 23:3312–9
  4. Artamonova I, Frishman G and Frishman D (2007) Applying negative rule mining to improve genome annotation. BMC Bioinformatics 8:261
  5. Frishman D (2007) Protein annotation at genomic scale: the current status. Chem Rev 107:3448–66
  6. Smialowski P, Martin-Galiano AJ, Mikolajka A, Girschick T, Holak TA and Frishman D (2007) Protein solubility: sequence based prediction and experimental verification. Bioinformatics 23:2536–42
  7. Smialowski P, Martin-Galiano AJ, Cox J and Frishman D (2007) Predicting experimental properties of proteins from sequence by machine learning. Curr Prot Pept Sci 8:121–33
  8. Riley L, Schmidt T, Artamonova II, Wagner C, Volz A, Heumann K, Mewes HW and Frishman D (2007) PEDANT genome database: 10 years online.Nucleic Acids Res 35(Database issue):D354–7
  9. Lehner A, Grimm M, Rattei T, Ruepp A, Frishman D, Manzardo GG and Stephan R (2006) Cloning and characterization of Enterobacter sakazakii pigment genes and in situ spectroscopic analysis of the pigment. FEMS Microbiol Lett 265:244–8
  10. Lehner A, Riedel K, Rattei T, Ruepp A, Frishman D, Breeuwer P, Diep B, Eberl L and Stephan R (2006) Molecular characterization of the alpha-glucosidase activity in Enterobacter sakazakii reveals the presence of a putative gene cluster for palatinose metabolism. Syst Appl Microbiol 29:609–25
  11. Martin-Galiano AJ and Frishman D (2006) Defining the fold space of membrane proteins: the CAMPS database. Proteins 64:906–22
  12. Schmidt T and Frishman D (2006) PROMPT: A protein mapping and comparison tool. BMC Bioinformatics 7(1):331
  13. Strous M, Pelletier E, Mangenot S, Rattei T, Lehner A, Taylor MW, Horn M, Daims H, Bartol-Mavel D, Wincker P, Barbe V, Fonknechten N, Vallenet D, Segurens B, Schenowitz-Truong C, Medigue C, Collingro A, Snel B, Dutilh BE, Op den Camp HJ, van der Drift C, Cirpus I, van de Pas-Schoonen KT, Harhangi HR, van Niftrik L, Schmid M, Keltjens J, van de Vossenberg J, Kartal B, Meier H, Frishman D, Huynen MA, Mewes HW, Weissenbach J, Jetten MS, Wagner M and Le Paslier D (2006) Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature 440:790–794
  14. Frishman D, Heumann K and Mewes H-W (2006) The PEDANT genome database. In Mulder N, ed. In Silico Genomics and Proteomics: Functional Annotation of Genomes and Proteins, Nova Science Publishers, Inc, New York
  15. Martin-Galiano AJ and Frishman D (2006) Defining the fold space of membrane proteins: The CAMPS database. Proteins in press
  16. Wong P and Frishman D (2006) Fold designability, distribution and disease. PLoS Comput Biol 2(5):e40
  17. Lehner A, Riedel K, Rattei T, Ruepp A, Frishman D, Breeuwer P, Diep B, Eberl L and Stephan R (2006) Molecular characterization of the alpha glucosidase activity in Enterobacter sakazakii reveals the presence of a putative gene cluster for palatinose metabolism. Syst Appl Microbiol in press
  18. Pagel P, Oesterheld M, Stuempflen V and Frishman D (2006) The DIMA Web Resource — Exploring the Protein Domain Network. Bioinformatics 22:997–998
  19. Mewes HW, Frishman D, Mayer KF, Münsterkötter M, Nobibou O, Pagel P, Rattei T, Oesterheld M, Ruepp A, Stümpflen V (2006) MIPS: analysis and annotation of proteins from whole genomes in 2005. Nucleic Acids Res 34:D169–72
  20. Ruepp A, Doudieu ON, van den Oever J, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Skornia C, Wanka S, Rattei T, Pagel P, Riley L, Frishman D, Surmeli D, Tetko I, Oesterheld M, Stümpflen V and Mewes HW (2006) The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. Nucleic Acids Res 34:D568–71
  21. Neverov AD, Artamonova II, Nurtdinov RN, Frishman D, Gelfand MS and Mironov AA (2005) Alternative splicing and protein function. BMC Bioinformatics 6:266
  22. Frishman D (2005) Target selection for structural genomics. In Jorde LB, Little PFR, Dunn MJ and Subramaniam S, eds. Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons Ltd, Chichester, pp 2552–64
  23. Borodovsky M, Rzhetsky A and Frishman D (2005) The Fifth Georgia Tech—Oak Ridge National Laboratory International Conference in Bioinformatics: in silico Biology, Computational Genomics and Evolutionary Biology. Bioinformatics 21:Suppl_3:iii1
  24. Artamonova II, Frishman G, Gelfand MS and Frishman D (2005) Mining sequence annotation databanks for association patterns. Bioinformatics 21:Suppl_3:iii49–iii57
  25. Smialowski P, Schmidt T, Cox J, Kirschner A and Frishman D (2005) Will my protein crystallize? A sequence-based predictor. Proteins 62:343–55
  26. Wong P, Fritz A and Frishman D (2005) Designability, aggregation propensity and duplication of disease-associated proteins. Protein Eng Des Sel 18(10):503–8
  27. Kerner MJ, Naylor DJ, Ishihama Y, Maier T, Chang HC, Stines AP, Georgopoulos C, Frishman D, Hayer-Hartl M, Mann M and Hartl FU (2005) Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell 22:209–20
  28. Pagel P, Kovac S, Oesterheld M, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Mark P, Stumpflen V, Mewes HW, Ruepp A and Frishman D (2005) The MIPS mammalian protein-protein interaction database. Bioinformatics 21:832–4
  29. Riley ML, Schmid T, Wagner C, Mewes HW and Frishman D (2005) The PEDANT genome database in 2005. Nucleic Acids Res 33:D308–10
  30. Pagel P, Wong P and Frishman D (2004) A domain interaction network based on phylogenetic profiling. J Mol Biol 344:1331–46
  31. Huang Y, Frishman D and Muchnik I (2004) Predicting Protein-Protein Interactions by a Supervised Learning Classifier. Comput Biol Chem 28:291–301
  32. Meyer TE, Tsapin AI, Vandenberghe I, De Smet L, Frishman D, Nealson KH, Cusanovich MA and Van Beeumen JJ (2004) Identification of 42 Possible Cytochrome C Genes in the Shewanella oneidensis Genome and Characterization of Six Soluble Cytochromes. OMICS 8:57–77
  33. Offman M, Nurtdinov RN, Gelfand MS and Frishman D (2004) No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions. BMC Bioinformatics 19:41
  34. Heinig M and Frishman D (2004) STRIDE: a Web server for secondary structure assignment from known atomic coordinates of proteins. Nucleic Acids Res 32:W500–2
  35. Kolker E, Makarova K, Shabalina S, Picone A, Purvine S, Holzman T, Cherny T, Armbruster D, Munson R, Kolesov G, Frishman D and Galperin M (2004) Identification and Functional Analysis of "Conserved Hypothetical" Genes Expressed in Haemophilus influenzae. Nucleic Acids Res 32:2353–61
  36. Horn M, Collingro A, Schmitz-Esser S, Beier CL, Purkhold U, Fartmann B, Brandt P, Byakatura GJ, Droege M, Frishman D, Rattei T, Mewes HW and Wagner M (2004) Illuminating the evolutionary history of Chlamydiae via genomic analysis of a Chlamydia-related symbiont of amoebae. Science 304:728–30
  37. Frishman D (2005) Target selection for structural genomics. In Dunn MJ, Jorde LB, Little PFR and Subramaniam S, eds. Genetics, Genomics, Proteomics and Bioinformatics, John Wiley & Sons, Hoboken
  38. Pagel P, Mewes HW and Frishman D (2004) Conservation of protein-protein interactions — lessons from ascomycota. Trends Genet 20:72–6
  39. Mewe HW, Amid C, Arnold R, Frishman D, Gueldener U, Mannhaupt G, Muensterkoetter M, Pagel P, Strack N, Stuempflen V, Warfsmann J and Ruepp A (2004) MIPS: analysis and annotation of proteins from whole genomes.Nucleic Acids Res 32:D41–D44
  40. Frishman D (2003) What We Have Learned about Prokaryotes from Structural Genomics. OMICS 7:211–24
  41. Galagan JE, Calvo SE, Borkovich KA, Selker EU, Read DD, FitzHugh W, Ma LJ, Smirnov S, Purcell S, Rehman B, Elkins T, Engels R, Wang S, Nielsen CB, Butler J, Jaffe D, Endrizzi M, Qui D, Ianakie P, Bell-Pedersen D, Nelson MA, Werner-Washburne M, Selitrennikoff CP, Kinsey JA, Braun EL, Zelter A, Schulte U, Kothe GO, Jedd G, Mewes W, Staben C, Marcotte E, Greenberg D, Roy A, Foley K, Naylor J, Stange-Thomann N, Barrett R, Gnerre S, Kamal M, Kamvysselis M, Bielke C, Rudd S, Frishman D, Krystofova S, Rasmussen C, Metzenberg RL, Perkins DD, Kroken S, Catcheside D, Li W, Pratt RJ, Osmani SA, DeSouza CPC, Glass L, Orbach MJ, Berglund JA, Voelker R, Yarden O, Plamann M, Seiler S, Dunlap J, Radford A, Aramayo R, Natvig DO, Alex LA, Mannhaup G, Ebbole DJ, Freitag M, Paulsen I, Sachs MS, Lander ES, Nusbaum C and Birren B (2003) The Genome Sequence of the Filamentous Fungus Neurospora crassa. Nature 422:859–68
  42. Wong P, Kolesov G, Frishman D and Houry WA (2003) Phylogenetic Web Profiler. Bioinformatics 19:782–3
  43. Frishman D, Mokrejs M, Kosykh D, Kastenmueller G, Kolesov G, Zubrzycki I, Gruber C, Geier B, Kaps A, Albermann K, Volz A, Wagner C, Fellenberg M, Heumann K and Mewes HW (2003) The PEDANT genome database. Nucleic Acids Res 31:207–11
  44. Kolesov G, Mewes HW and Frishman D (2002) SNAPper: gene order predicts gene function. Bioinformatics 18:1017–9
  45. Mewes HW, Frishman D, Guldener U, Mannhaupt G, Mayer K, Mokrejs M, Morgenstern B, Munsterkotter M, Rudd S and Weil B (2002) MIPS: a database for genomes and protein sequences. Nucleic Acids Res 30:31–4
  46. Frishman D (2001) Knowledge-based selection of targets for structural genomics. Protein Eng 15:169–83
  47. Kolesov G, Mewes HW, Frishman D (2002) SNAPping functionally related genes based on context information: a collinearity-free approach. In Mewes HW, Weiss B, Seidel H, eds. Ernst Schering Research Foundation Workshop Volume 38: Bioinformatics and Genome Analysis. Springer-Verlag, Berlin Heidelberg, p 29–63
  48. Kolesov G, Mewes HW and Frishman D (2001) SNAPping up functionally related genes based on context information: a colinearity-free approach. J Mol Biol 311:639–56
  49. Frishman D, Albermann K, Hani J, Heumann K, Metanomski A, Zollner A and Mewes HW (2001) Functional and structural genomics using PEDANT Bioinformatics 17:44–57
  50. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815
  51. Ruepp A, Graml W, Santos-Martinez ML, Koretke KK, Volker C, Mewes HW, Frishman D, Stocker S, Lupas AN and Baumeister W (2000) The genome of the thermoacidophilic scavengerThermoplasma acidophilum. Nature 407:508–13
  52. Frishman D, Goldstein RA and Pollock DD (2000) Protein evolution and structural genomics. Pac Symp Biocomput 12:3–5
  53. Mewes HW et al (2000) MIPS: a database for genomes and protein sequences. Nucleic Acids Res 28:37–40
  54. Wambutt R et al (2000) Progress in Arabidopsis genome sequencing and functional genomics. J Biotechnol 78:281–92
  55. Frishman D, Goldstein RA and Pollock DD (2000) Protein Evolution and Structural Genomics. Pac Symp Biocomput p 3
  56. Mayer K et al (1999) Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 402:769–77
  57. Houry WA, Frishman D, Eckerskorn C, Lottspeich F and Hartl FU (1999) Identification of in vivo substrates of the chaperonin GroEL Nature 402:147–54
  58. Frishman D, Mironov A and Gelfand M (1999). Starts of bacterial genes: estimating the reliability of computer predictions.Gene 234:257–265
  59. Frishman D and Mewes HW (1999) Genome-based structural biology. Prog Biophys Mol Biol 72:1–17
  60. Frishman D, Mironov A and Gelfand M (1999) Starts of bacterial genes: estimating the reliability of computer predictions. Gene 234:257–65
  61. Mewes HW, Heumann K, Kaps A, Mayer K, Pfeiffer F, Stocker S and Frishman D (1999) MIPS: a database for genomes and protein sequences. Nucleic Acids Res 27:44–8
  62. Mironov AA, Frishman D and Gelfand MS (1999) Computer analysis of regulatory signals in complete bacterial genomes. Participation of ribosome binding. Mol Biol (Mosk) 33:133–40
  63. Frishman D, Mironov A, Mewes HW and Gelfand M (1998) Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Nucleic Acids Res 26:2941–7
  64. Hartung K, Frishman D, Hinnen A and Wolfl S (1998) Single-read sequence tags of a limited number of genomic DNA fragments provide an inexpensive tool for comparative genome analysis. Yeast 14:1327–32
  65. Frishman D, Heumann K, Lesk A and Mewes HW (1998) Comprehensive, comprehensible, distributed and intelligent databases: current status. Bioinformatics 14:551–61
  66. Muckenthaler M, Gunkel N, Frishman D, Cyrklaff A, Tomancak P and Hentze MW (1998) Iron-regulatory protein-1 (IRP-1) is highly conserved in two invertebrate species—characterization of IRP-1 homologues in Drosophila melanogaster and Caenorhabditis elegans. Eur J Biochem 254:230–7
  67. Kosel S, Grasbon-Frodl EM, Mautsch U, Egensperger R, von Eitzen U, Frishman D, Hofmann S, Gerbitz KD, Mehraein and Graeber MB (1998) Novel mutations of mitochondrial complex I in pathologically proven Parkinson disease. Neurogenetics 1:197–204
  68. Mewes HW, Hani J, Pfeiffer F and Frishman D (1998) MIPS: a database for protein sequences and complete genomes. Nucleic Acids Res 26:33–7
  69. Frishman D and Mewes HW (1998) The German Conference on Bioinformatics 1997. Bioinformatics 14:231
  70. Frishman D (1998) Intelligent and Distributed Databases (Session Introduction). Pac Symp Biocomput p 681–2
  71. Mewes HW, Maierl A and Frishman D (1998) Protein sequences and genome databases. In Kellner R, Lottspeich F and Meyer HE, eds. Microcharacterization of proteins, VCH, Weinheim, p 301–317
  72. Galperin MY and Frishman D (1998) Toward automated prediction of protein function from microbial genomic sequences. Methods in Microbiol 28:245–63
  73. Mewes HW, Frishman D, Zollner A and Heumann K (1998) The bioinformatics of the yeast genome. Meth Microbiol 26:33–51
  74. Frishman D and Mewes HW (1997) Protein structural classes in five complete genomes. Nat Struct Biol 4:626–8
  75. Frishman D and Mewes HW (1997) PEDANTic genome analysis. Trends Genet 13:415–6
  76. Mewes HW, Albermann K, Bahr M, Frishman D, Gleissner A, Hani J, Heumann K, Kleine K, Maierl A, Oliver SG, Pfeiffer F and Zollner A (1997) Overview of the yeast genome. Nature 387:7–65
  77. Bohm S, Frishman D and Mewes HW (1997) Variations of the C2H2 zinc finger motif in the yeast genome and classification of yeast zinc finger proteins. Nucleic Acids Res 25:2464–9
  78. Frishman D and Argos P (1997) The future of the secondary structure prediction accuracy. Fold Des 2:159–62
  79. Frishman D and Argos P (1997) Seventy-five percent accuracy in protein secondary structure prediction. Proteins 27:329–35
  80. Argos P, Mewes HW and Frishman D (1997) Intelligent and Distributed Databases (Session Introduction). Pac Symp Biocomput p 3
  81. Kaps A, Heumann K, Frishman D, Baehr M and Mewes HW (1997) Visuslization and analysis of the complete yeast genome. In Hofestaedt R, Lengauer T, Loeffler M and Schomburg D, eds. German Conference on Bioinformatics, GCB' 96, Leipzig, Germany, September 30 – October 2, 1996. Selected Papers Series: Lecture Notes in Computer Science, Vol. 1278, Springer-Verlag, Berlin Heidelberg, p 178–199
  82. Heringa J, Frishman D and Argos P (1997) Computational methods relating protein sequences and structure. In Allen G, ed. Proteins: a comprehensive treatise Vol 1, Principles of Protein Structure. JAI Press, Greenwich, p 171–277
  83. Frishman D and Argos P (1997) Neural network that recognizes distantly related protein sequences. In Fiesler E and Beale R, eds. Handbook of Neural Computation. Taylor & Francis, London
  84. Frishman D and Argos P (1996) Incorporation of non-local interactions in protein secondary structure prediction from the amino acid sequence. Protein Eng 9:133–42
  85. Frishman D and Hentze MW (1996) Conservation of aconitase residues revealed by multiple sequence analysis. Implications for structure/function relationships. Eur J Biochem 239:197–200
  86. Frishman D (1996) DSBC protein: a new member of the thioredoxin fold-containing family. Biochem Biophys Res Commun 219:686–9
  87. Frishman D and Argos P (1995) Knowledge-based protein secondary structure assignment. Proteins 23:566–79
  88. Abagyan R, Frishman D and Argos P (1994) Recognition of distantly related proteins through energy calculations. Proteins 19:132–40
  89. Vogt G, Frishman D and Argos P (1994) A parallel processor implementation of an algorithm to delineate distantly related protein sequences with conserved motifs and neural networks. In HH Bock, W Lenski and MM Richter, eds. Information systems and data analysis Proc. 17th Annual Conference of the Gesellschaft für Klassification. Springer-Verlag, Berlin Heidelberg, p 397–408
  90. Frishman D and Argos P (1992) Recognition of distantly related protein sequences using conserved motifs and neural networks. J Mol Biol 228:951–62
  91. Frishman DI (1992) The classification of signal receptor proteins based on their amino acid sequences. Zh Evol Biokhim Fiziol 28:73–83
  92. Berman AL, Dityatev AE and Frishman D (1991) Physicochemical properties of signal receptor domains as the basis for sequence comparison. Comp Biochem Physiol B 98:445–9
  93. Frishman D, Berman AL and Kiselev OI (1990) G-proteins have a sequence similar to the ganglioside-binding hemagglutinins from the influenza virus. Mol Biol (Mosk) 24:1241–5
  94. Frishman D and Berman AL (1990) The evolution of signal receptor proteins: conserved regions and the similarity to GTP-binding proteins. Zh Evol Biokhim Fiziol 26:14–29
  95. Frishman D and Berman AL (1989) Similarity between arrestin and octopus rhodopsin. Sensory Systems 3:428–9
  96. Tsendina MB, Frishman DI, Levchenko VF and Berman AL (1988) Primary structure similarity and homology between rhodopsin, b-adrenoreceptor and muscarinic cholinoceptor. Zh Evol Biokhim Fiziol 24:797–807