Publications

BOOKS

  • Frishman, D. (Ed) Structural bioinformatics of membrane proteins. Springer, Wien 2009. ISBN 978-3709100448
  • Frishman, D. and Valencia, A. (Eds) Modern Genome Annotation. The BioSapiens Network. Springer, Wien 2009. ISBN 978-3-211-75122-0

 


ARTICLES

2017

  • Tarnovskaya S, Kiselev A, Kostareva A, Frishman D. (2017) Structural consequences of mutations associated with idiopathic restrictive cardiomyopathy. Amino Acids, in press.
  • Flisikowska T, Stachowiak M, Xu H, Wagner A, Hernandez-Caceres A, Wurmser C, Perleberg C, Pausch H, Perkowska A, Fischer K, Frishman D, Fries R, Switonski M, Kind A, Saur D, Schnieke A, Flisikowski K. (2017) Porcine familial adenomatous polyposis model enables systematic analysis of early events in adenoma progression. Sci Rep., 7, 6613.
  • Xu H, Pausch H, Venhoranta H, Rutkowska K, Wurmser C, Rieblinger B, Flisikowska T, Frishman D, Zwierzchowski L, Fries R, Andersson M, Kind A, Schnieke A, Flisikowski K. (2017) Maternal placenta modulates a deleterious fetal mutation. Biology Reprod, in press.
  • Marx H, Hahne H, Ulbrich SE, Schnieke A, Rottmann O, Frishman D, Kuster B. (2017) Annotation of the Domestic Pig Genome by Quantitative Proteogenomics. J Proteome Res, 16, 2887-2898.
  • Smida J, Xu H, Zhang Y, Baumhoer D, Ribi S, Kovac M, von Luettichau I, Bielack S, O'Leary VB, Leib-Mösch C, Frishman D, Nathrath M. (2017) Genome-wide analysis of somatic copy number alterations and chromosomal breakages in osteosarcoma. Int J Cancer, 141, 816-828.
  • Qi F, Frishman D. (2017) Melting temperature highlights functionally important RNA structure and sequence elements in yeast mRNA coding regions. Nucl. Acids Res., 45, 6109-6118.
  • Jaravine, V., Raffegerst, S., Schendel, D.J., Frishman D. (2017) Assessment of cancer and virus antigens for cross-reactivity in human tissues. Bioinformatics33, 104-111. 

2016

  • Kostareva, A., Kiselev, A., Gudkova, A., Frishman, G., Ruepp, A., Frishman, D., Smolina, N., Tarnovskaya, S., Nilsson, D., Zlotina, A., Khodyuchenko, T., Vershinina, T., Pervunina, T., Klyushina, A., Kozlenok, A., Sjoberg, G., Golovljova, I., Sejersen, T., Shlyakhto, E. (2016) Genetic Spectrum of Idiopathic Restrictive Cardiomyopathy Uncovered by Next-Generation Sequencing. PLoS One, 23, e0163362.
  • Karabulut, N.P., Frishman D. (2016) Sequence- and Structure-Based Analysis of Tissue-Specific Phosphorylation Sites. PLoS One, 11, e0157896
  • Hönigschmid, P., Frishman, D. (2016) Acurate prediction of helix interactions and residue contacts in membrane proteins. J. Struct. Biol., 194, 112-123.
  • Zhang, Y., Xu, H., Frishman, D. (2016) Genomic determinants of somatic copy number alterations in human cancers. Human Molecular Genetics, 25, 1019-1030.

2015

  • Kristensen D.M., Saeed U., Frishman, D., Koonin EV. (2015) A census of alpha-helical membrane proteins in double-stranded DNA viruses infecting bacteria and archaea. BMC Bioinformatics, 16, 380.
  • Sokolenko A.P., Suspitsin E.N., Kuligina E.Sh., Bizin I.V., Frishman D., Imyanitov EN. (2015) Identification of novel hereditary cancer genes by whole exome sequencing. Cancer Lett., 369, 274-288.
  • Haase, K., Mösch, A., Frishman, D. (2015) Differential expression analysis of human endogenous retroviruses based on ENCODE RNA-seq data, BMC Medical Genomics, 8, 71.
  • Karabulut, P.N., Frishman D. (2015) Tissue-Specific Sequence and Structural Environments of Lysine Acetylation Sites. Journal of Structural Biology191, 39-48.
  • Kaufmann, S., Fuchs, C., Gonik, M., Khrameeva, E.E., Mironov, A.A., Frishman, D.(2015) Inter-chromosomal contact networks provide insights into mammalian chromatin organization. PLoS One, 10, e0126125.
  • Haase, K., Raffegerst, S., Schendel, D.J., Frishman, D. (2015) Expitope: a Web server for epitope expression. Bioinformatics31, 1854-1856.

2014

  • Kaufmann S, Frishman D.(2014)Analysis of micro-rearrangements in 25 eukaryotic species pairs by SyntenyMapper. PLoS One9, e112341.
  • Budziszewska, M., Wieczorek, P., Zhang, Y., Frishman, D., Obrepalska-Steplowska, A. (2014) Genetic variability within the Polish tomato torrado virus Kra isolate caused by deletions in the 3`-untranslated region of genomic RNA1. Virus research, 185:47-52.
  • Marz, M., Beerenwinkel, N., Drosten, C., Fricke, M., Hofacker, I.L., Hoffmann, D., Middendorf, M., Rattei, T., Stadler, P.F., Töpfer, A. (2014) Challenges in RNA virus bioinformatics. Bioinformatics, 30, 1793-1799. 
  • Blohm, P., Frishman, G., Smialowski, P., Goebels, F. Wachinger, B., Ruepp, A., Frishman, D. (2014) Negatome 2.0: a database of non-interacting proteins derived by literature mining, manual annotation, and protein structure analysis. Nucleic Acids Res., 42(1):D396-400.
  • Kolker, E., Ozdemir, V., Martens, L., Hancock, W., Anderson, G., Anderson, N., Aynacioglu, S., Baranova, A., Campagna, S.R., Chen, R., Choiniere, J., Dearth, S.P., Feng, W.C., Ferguson, L., Fox, G., Frishman, D., Grossman, R., Heath, A., Higdon, R., Hutz, M.H., Janko, I., Jiang, L., Joshi, S., Kel, A., Kemnitz, J.W., Kohane, I.S., Kolker, N., Lancet, D., Lee, E., Li, W., Lisitsa, A., Llerena, A., Macnealy-Koch, C., Marshall,, J.C., Masuzzo, P., May, A., Mias, G., Monroe, M., Montague, E., Mooney, S., Nesvizhskii, A., Noronha, S., Omenn, G., Rajasimha, H., Ramamoorthy, P., Sheehan, J., Smarr, L., Smith, C.V., Smith, T., Snyder, M., Rapole, S., Srivastava, S., Stanberry, L., Stewart, E., Toppo, S., Uetz, P., Verheggen, K., Voy, B.H., Warnich, L., Wilhelm, S.W., Yandl, G. (2014) OMICS, 18(1):10-4.

2013

  • Kolker, E., Altintas, I., Bourne, P., Faris, J., Fox, G., Frishman, D., Geraci, C., Hancock, W., Lin, B., Lancet, D., Lisitsa, A., Knight, R., Martens, L., Mesirov, J., Özdemir, V., Schultes, E., Smith, T., Snyder, M., Srivastava, S., Toppo, S., Wilmes, P. (2013) Reproducibility: In praise of open research measures. Nature, 498(7453):170.
  • Goebels, F., Frishman, D. (2013) Prediction of protein interaction types based on sequence and network features, BMC Systems Biology, 7, S5.
  • Neumann, S., Fuchs, A., Hummel, B., Frishman, D. (2013) Classification of alpha-helical membrane proteins using predicted helix architectures, PLoS One8(10):e77491.
  • Chursov, A., Kopetzky, S., Bocharov, G., Frishman, D., Shneider, A. (2013) RNAtips: Analysis of Temperature-induced Changes of RNA Secondary Structure, Nucleic Acids Res., 41(W1):W486-W491.
  • Chursov, A., Frishman, D., Shneider, A. (2013) Conservation of mRNA Secondary Structures May Filter Out Mutations in Escherichia coli Evolution, Nucleic Acids Res., 41, 7854-7860
  • Ivankov, D.N., Bogatyreva, N.S., Hönigschmid, P., Dislich, B., Hogl, S., Kuhn, P.-H., Frishman, D., Lichtenthaler, S.F. (2013) QARIP: a web server for quantitative proteomic analysis of regulated intramembrane proteolysis. Nucleic Acids Res., 41(W1):W459-W464.
  • Ivankov, D.N., Payne, S.H., Galperin, M.Y., Bonissone, S., Pevzner, P.A., Frishman, D. (2013) How many signal peptides are there in bacteria? Environ Microbiol., 15, 983-990.
  • Tyanova, S., Cox, J., Olsen, J., Mann, M., Frishman, D. (2013) Phosphorylation Variation during the Cell Cycle Scales with Structural Propensities of Proteins, PLOS Computational Biology, 9(1):e1002842.

2012

  • Payne S.H., Bonissone, S., Wu, S., Brown, R.Rn, Ivankov, D., Frishman, D., Pasa-Tolic, L., Smith, R.D., Pevzner, P.A. (2012) Unexpected diversity of signal peptides in bacteria and archaea. MBio, 3(6), pii: e00339-12.
  • Chursov, A., Kopetzky, S.J., Leshchiner, I., Kondofersky, I.,Theis, F., Frishman, D., Shneider, A. (2012) Specific Temperature-induced Perturbations of Secondary mRNA Structures are Associated with the Cold-adapted Temperature-sensitive Phenotype of Influenza A Virus. RNA Biology9, 1266-1274.
  • Smialowski,P., Doose, G., Torkler, P., Kaufmann, S., Frishman, D. (2012) PROSO II – a new method for protein solubility prediction. FEBS J.279, 2192-200.
  • Neumann S., Hartmann H., Martin-Galiano A, Fuchs A., Frishman D.  (2012) CAMPS 2.0: exploring the sequence and structure space of prokaryotic, eukaryotic and viral membrane proteins, Proteins80, 839-857.
  • Chursov A, Walter MC, Schmidt T, Mironov A, Shneider A, Frishman D. (2012) Sequence-structure relationships in yeast mRNAs. Nucleic Acids Res., 40, 956-962.

2011

  • Theis, F., Latif, N., Wong, P., Frishman, D. (2011) Complex principal component and correlation structure of 16 yeast genomic variables. Molecular Biology and Evolution, 28, 2501-2512.
  • Mewes HW, Ruepp A, Theis F, Rattei T, Walter M, Frishman D, Suhre K, Spannagl M, Mayer KF, Stümpflen V, Antonov A. (2011) MIPS: curated databases and comprehensive secondary data resources in 2010. Nucleic Acids Res. 39 (Database issue), D220-224.
  • Kuravsky ML, Aleshin VV, Frishman D, Muronetz VI. (2011) Testis-specific glyceraldehyde-3-phosphate dehydrogenase: origin and evolution. BMC Evol Biol. 11, 160.
  • Luo Q, Pagel P, Vilne B, Frishman D. (2011) DIMA 3.0: Domain Interaction Map. Nucleic Acids Res., 39 (Database issue), D724-7299.

2010

  • Gershoni, M., Fuchs, A., Shani, N., Fridman, Y., Corral-Debrinski, M., Aharoni, A., Frishman, D., Mishmar, D. (2010) Co-evolution predicts direct interactions between mtDNA and nuclear DNA-encoded subunits of oxidative phosphorylation complex I. J. Mol. Biol., 404, 158-171.
  • Kowarsch, A., Fuchs, A., Frishman, D., Pagel, P. (2010) Correlated mutations: a hallmark of phenotypic amino acid substitutions. PLoS Computational Biology, 6 (9).
  • Sturm, M., Hackenberg, M., Langenberger, D., and Frishman, D. (2010) TargetSpy: a supervised machine learning approach for microRNA target prediction. BMC Bioinformatics,  11:292.
  • Fuchs A, Frishman D. (2010) Structural comparison and classification of alpha-helical transmembrane domains based on helix interaction patterns. Proteins, 78, 2587-2599.

  • Neumann S., Fuchs A., Mulkidjanian A, and Frishman D. (2010) Current status of membrane protein structure classification. Proteins,  78, 1760-1773.
  • Herrmann, J.R., Fuchs, A., Panitz, J.C., Eckert, T., Unterreitmeier, S., Frishman, D., Langosch, D. (2010) Ionic interactions promote transmembrane helix-helix association depending on sequence context. J. Mol. Biol., 396, 452-461.
  • Smialowski P., Frishman D., Kramer S. (2010) Pitfalls of supervised feature selection. Bioinformatics, 26, 440-443.
  • Smialowski P, Frishman D. (2010) Protein crystallizability. Methods Mol Biol., 609, 385-400.

  • Smialowski P., Pagel P., Wong P., Brauner B., Dunger I., Fobo G., Frishman G., Montrone C., Rattei T., Frishman D., Ruepp A. (2010) The Negatome Database - a reference set of non-interacting protein pairs. Nucleic Acids Res., 38, D540-544.

 

2009

  • Ilyinskii P, Schmidt T, Lukashev D, Meriin A, Thoidi G, Frishman D, Shneider A. (2009) Importance of mRNA structural elements for the expression of Influenza virus genes. Omics  13(5), 421-430.
  • Loewenstein, Y, Raimondo D, Redfern OC, Watson J, Frishman D, Linial M, Orengo C,  Thornton J, and Tramontano A. (2009) Protein function annotation by homology based inference. Genome Biology 10:207.
  • Fuchs, A., Kirschner, A., Frishman D. (2009) Prediction of helix-helix contacts and interacting helices in polytopic membrane proteins using neural networks. Proteins, 74(4), 857-71.
  • Herrmann JR, Panitz JC, Unterreitmeier S, Fuchs A, Frishman D, Langosch D. (2009) Complex Patterns of Histidine, Hydroxylated Amino Acids and the GxxxG Motif Mediate High-affinity Transmembrane Domain Interactions. J. Mol. Biol., 385(3), 912-923.
  • Antranikian G, Ruepp A, Gordon PM, Ballschmiter M, Zibat A, Stark M, Sensen CW, Frishman D, Liebl W, Klenk HP. (2009) Rapid access to genes of biotechnologically useful enzymes by partial genome sequencing: the thermoalkaliphile Anaerobranca gottschalkii. J Mol Microbiol Biotechnol. 16, 81-90.
  • Walter MC, Rattei T, Arnold R, Güldener U, Münsterkötter M, Nenova K, Kastenmüller G, Tischler P, Wölling A, Volz A, Pongratz N, Jost R, Mewes HW, Frishman D. (2009) PEDANT covers all complete RefSeq genomes. Nucleic Acids Res. 37 (Database issue), D408-D411. 

 

2008

  • Wong P., Althammer S., Hildebrand A., Kirschner A., Pagel P., Geissler B., Smialowski P., Bloechl, M., Oesterheld M., Schmidt T., Strack N., Theis, F., Ruepp A., Frishman, D. (2008) An evolutionary and structural characterization of mammalian protein complex organization. BMC Genomics, 9(1), 629.
  • Schmidt, T. and Frishman, D. (2008) Assignment of isochores for all completely sequenced vertebrate genomes using a consensus. Genome Biology, 9(6), R104.
  • Kirschner, A., Frishman D. (2008) Prediction of ?-turns and ?-turn types by a novel bidirectional Elman-type recurrent neural network with multiple output Layers (MOLEBRNN)”, Gene, 422, 22-29.
  • Frishman, D., Albrecht, M., Blankenburg, H., Bork, P., Harrington, E.D., Hermjakob, H., Jensen, L.J., Juan, D.A., Lengauer, T., Pagel., P., Schachter, V., Valencia, A. (2008) Protein-protein interactions: analysis and prediction. In "Modern genome annotation. The BioSapiens network of excellence", Frishman, D. and Valencia, A., Editors, Springer, Vienna.
  • Artamonova, I., Kramer, S., and Frishman, D. (2008) Data mining in genome annotation. In "Modern genome annotation. The BioSapiens network of excellence", Frishman, D. and Valencia, A., Editors, Springer, Vienna.
  • Wong, P., and Frishman, D. (2008) Designability and disease. Methods Mol Biol. 484, 491-504.
  • Smialowski, P. and Frishman, D. (2008) Protein cristallizability, in "Biological data mining", Methods in Molecular Biology, Carugo O. and Eisenhaber F., Eds., Humana Press.
  • Martin-Galiano, A.J., Smialowski, P., Frishman, D. (2008) Predicting experimental properties of integral membrane proteins by a naive bayes approach. Proteins, 70, 1243-1256.
  • Ishihama, Y., Schmidt, T., Rappsilber, J., Mann, M., Hartl, F.U., Kerner, M.J., Frishman, D. (2008) Protein abundance profiling of the Escherichia coli cytosol, BMC Genomics, 9, 102.
  • Grimm, M., Stephan, R., Iversen, C., Manzardo, G.G.G., Rattei, T., Riedel, K., Ruepp, A., Frishman, D., and Lehner, A. (2008) Cellulose as an extra-cellular matrix component present in Enterobacter sakazakii biofilms. Journal of Food protection, 71, 13-18.
  • Mewes, H.W., Dietmann, S., Frishman, D., Gregory, R., Mannhaupt, G., Mayer, K.F., Münsterkötter, M., Ruepp, A., Spannagl, M., Stümpflen, V., Rattei, T. (2008) MIPS: analysis and annotation of genome information in 2007. Nucleic Acids Res., 36, D196-D201.
  • Pagel, P., Oesterheld, M., Tovstukhina, O., Strack, N., Stuempflen, V., Frishman, D. (2008) DIMA 2.0: Predicted and Known Domain Interactions. Nucl. Acids Research, 36, D651-D655.

  

2007

  • Unterreitmeier, S., Fuchs, A., Schäffler, T., Heym, R.G., Frishman, D., and Langosch, D. (2007) Phenylalanine promotes interaction of transmembrane domains via GxxxG motifs. J. Mol. Biol., 374, 705-718.
  • Fuchs, A., Martin-Galiano, A.J., Kalman, M., Fleishman, S., Ben-Tal, S., and Frishman, D. (2007) Co-Evolving Residues in Membrane Proteins. Bioinformatics, 23, 3312-3319.
  • Artamonova, I., Frishman, G., Frishman D. (2007) Applying negative rule mining to improve genome annotation, BMC Bioinformatics, 8, 261.
  • Frishman, D. (2007) Protein annotation at genomic scale: the current status. Chemical Reviews, 107 (8), 3448-3466.
  • Pagel, P., Strack, N., Oesterheld, M., Stümpflen, V., Frishman, D. (2007) Computational prediction of domain interactions. Methods Mol Biol. 396, 3-15.
  • Smialowski, P., Martin-Galiano, A.J., Mikolajka, A., Girschick, T, Holak, T.A., Frishman, D. (2007) Protein solubility: sequence based prediction and experimental verification. Bioinformatics, 23, 2536-2542.
  • Smialowski, P., Martin-Galiano, A.J., Cox, J., Frishman, D. (2007) Predicting experimental properties of proteins from sequence by machine learning. Current Protein and Peptide Science, 8, 121-133.
  • Riley, L., Schmidt, T., Wagner, C., Volz, A., Artamonova, I., Heumann, K., Mewes, H.W., Frishman, D. (2007) PEDANT genome database: ten years online. Nucl. Acids. Res., 35 (Database issue). D354-7.

 

2006

  • Lehner, A., Grimm, M., Rattei, T., Ruepp, A., Frishman, D., Manzardo, G., Stephan, R. (2006) Cloning and characterization of Enterobacter sakazakii pigment genes and in situ spectroscopic analysis of the pigment. FEMS Microbiology Letters, 265, 244-248.
  • Schmidt, T. and Frishman, D. (2006) PROMPT: A protein mapping and comparison tool. BMC Bioinformatics, 7(1),331.
  • Strous, M., Pelletier, E., Mangenot, S., Rattei, T., Lehner, A., Taylor, M.W., 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, B.E., Op den Camp, H.J., van der Drift, C., Cirpus, I., van de Pas-Schoonen, K.T., Harhangi, H.R., van Niftrik, L., Schmid, M., Keltjens, J., van de Vossenberg, J., Kartal, B., Meier, H., Frishman, D., Huynen, M.A., Mewes, H.W., Weissenbach, J., Jetten, M.S., Wagner, M., Le Paslier, D. (2006) Deciphering the evolution and metabolism of an anammox bacterium from a community genome. Nature, 440, 790-794.
  • Frishman, D., Heumann, K., Mewes, H.-W. (2006) The PEDANT genome database. In: Genomics and Proteomics:... ISBN 1-59454-995-8 Editors: Nicola Mulder, Nova Science Publishers, Inc., in press.
  • Martin-Galiano, A.J., Frishman, D. (2006) Defining the Fold Space of Membrane Proteins: the CAMPS Database. PROTEINS: Structure, Function, and Bioinformatics, 64, 906-22.
  • Wong, P., and Frishman, D. (2006) Fold designability, distribution, and disease. PLoS Computational Biology, 2(5):e40.
  • Lehner, A., Riedel, K., Rattei, T., Ruepp, A., Frishman, D., Breeuwer, P., Diep, B., Eberl, L., Stephan, R. (2006) Molecular characterization of the alpha glucosidase activity in Enterobacter sakazakii reveals the presence of a putative gene cluster for palatinose metabolism. Systematic and Applied Microbiology, 29, 609-625.
  • Pagel P., Oesterheld M., Stuempflen V., and Frishman D. (2006) The DIMA Web Resource. Exploring the Protein Domain Network. Bioinformatics, 22, 997-998.
  • Mewes, H.W., Frishman, D., Mayer, K.F.X., Münsterkötter, M., Nobibou, O. , Pagel, P., Rattei, T., Oesterheld, M., Ruepp, A., Stümpflen, V. (2006). MIPS: analysis and annotation of proteins from whole genomes: progress report. Nucleic Acids Res., 34, D169-D72.
  • Ruepp, A., Noubibou Doudieu, O., 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., Mewes, H.-W. (2006) The Mouse Functional Genome Database (MfunGD): functional annotation of proteins in the light of their cellular context. Nucleic Acids Res., 34, D568-D571

 

2005

  • Neverov, A.D., Artamonova, I.I., Nurtdinov, R.N., Frishman, D., Gelfand, M.S., Mironov, A.A. (2005). Alternative splicing and protein function. BMC Bioinformatics, 6, 266.
  • Frishman, D. (2005), Target selection for structural genomics. In Jorde, L.B., Little, P.F.R., Dunn, M.J. and Subramaniam, S. (Eds), Encyclopedia of Genetics, Genomics, Proteomics and Bioinformatics. John Wiley & Sons Ltd: Chichester, pp. 2552-2564.
  • Borodovsky M, Rzhetsky A., 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.
  • Artamonova, I., Frishman, G., Gelfand, M.S., Frishman, D. (2005). Mining sequence annotation databanks for association patterns. Bioinformatics, 21, Suppl_3:iii49-iii57.
  • Smialowski, P., Schmidt, T., Cox, J., Kirschner, A., Frishman, D. (2005). Will my protein crystallize? A sequence-based predictor. Proteins: Structure, FUnction, and Bioinformatics, 62, 343-55.
  • Wong, P. and Frishman. D (2005). Designability, Aggregation Propensity and Duplication of Disease Associated Proteins. Protein Engineering and Design, 18, 503-508.
  • Kerner, M.J., Naylor, D.J., Ishihama, Y., Maier, T., Chang, H.-C., Stines, A.P., Georgopoulos, C., Frishman, D., Hayer-Hartl, M., Mann, M., Hartl, F.U. (2005). Proteome-wide analysis of chaperonin-dependent protein folding in Escherichia coli. Cell, 22,209-220.
  • Pagel, P., Kovac, S., Oesterheld, M., Brauner, B., Dunger-Kaltenbach, I., Frischmann, G., Montrone, C., Mark, P., Stuempflen, V., Mewes, H.W., Ruepp, A., Frishman, D. (2005). The MIPS Mammalian Protein-Protein Interaction Database. Bioinformatics , 21, 832-4.
  • Riley, L., Schmidt, T., Wagner, C., Mewes, H.W., Frishman, D. (2005). The PEDANT genome database in 2005: 334 genomes on the Web. Nucl. Acids. Res. , 33, D308-310.

  

2004

  • Pagel, P., Wong, P., and Frishman, D. (2004). A domain interaction network based on phylogenetic profiling. Journal of Molecular Biology , 344, 1331-1346.
  • Huang, Y., Frishman, D., Muchnik, I. (2004). Predicting Protein-Protein Interactions by a Supervised Learning Classifier. Computational Biology and Chemistry , 28, 4, 291-301.
  • Meyer, T.E., Tsapin, A.I., Vandenberghe, I., De Smet, L., Frishman, D., Nealson, K.H., Cusanovich, M.A., Van Beeumen, J.J. (2004). Identification of 42 Possible Cytochrome C Genes in the Shewanella oneidensis Genome and Characterization of Six Soluble Cytochromes. OMICS 8,57-77.
  • Offman, M., Nurtdinov, R.N., Gelfand, M.S., Frishman, D. (2004). No statistical support for correlation between the positions of protein interaction sites and alternatively spliced regions. BMC Bioinformatics, , 19 41.
  • Heinig, M., Frishman, D. (2004). STRIDE: a Web server for secondary structure assignment from known atomic coordinates of proteins. Nucl. Acids Res. , 32, W500-2.
  • Kolker, E., Makarova, K., Shabalina, S., Picone, A., Purvine, S., Holzman, T., Cherny, T., Armbruster, D., Munson, R., Kolesov, G., Frishman, D., Galperin, M. (2004). Identification and Functional Analysis of "Conserved Hypothetical" Genes Expressed in Haemophilus influenzae. Nucl. Acids Res., 32, 2353-61.
  • Horn, M., Collingro, A., Schmitz-Esser, S., Beier C.L., Purkhold, U., Fartmann, B., Brandt, P., Byakatura, G.J., Droege, M., Frishman, D., Rattei, T., Mewes, H.-W., Wagner, M. (2004). Illuminating the evolutionary history of Chlamydiae via genomic analysis of a Chlamydia-related symbiont of amoebae. Science, 304, 728-730.
  • Frishman, D. (2004). Target selection for structural genomics. In: "Genetics, Genomics, Proteomics and Bioinformatics", Jorde, L.B., Little, P.F.R. Dunn, M.J., Subramaniam, S., eds. , in press.
  • Pagel, P., Mewes, H.W., Frishman, D. (2004) Conservation of protein-protein interactions - lessons from ascomycota. Trends Genet., 20, 72-76.
  • Mewes, H.W., 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.Nucl. Acids Res., 32, D41-D44.

  

2003

  • Frishman, D. (2003) What We Have Learned about Prokaryotes from Structural Genomics. OMICS, A Journal of Integrative Biology, 7, 211-224.
  • Galagan, J.E., Calvo, S.E., Borkovich, K.A., Selker, E.U., Read, D.D., FitzHugh, W., Ma, L.-J., Smirnov, S., Purcell, S., Rehman, B., Elkins, T., Engels, R., Wang, S., Nielsen, C.B., Butler, J., Jaffe, D., Endrizzi, M., Qui, D., Ianakiev, P., Bell-Pedersen, D., Nelson, M.A., Werner-Washburne, M., Selitrennikoff, C.P., Kinsey, J.A., Braun, E.L., Zelter, A., Schulte, U., Kothe, G.O., 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, R.L., Perkins, D.D., Kroken, S., Catcheside, D., Li, W., Pratt, R.J., Osmani, S.A., DeSouza, C.P.C., Glass, L., Orbach, M.J., Berglund, J.A., Voelker, R., Yarden, O., Plamann, M., Seiler, S., Dunlap, J., Radford, A., Aramayo, R., Natvig, D.O., Alex, L.A., Mannhaupt, G., Ebbole, D.J., Freitag, M., Paulsen, I., Sachs, M.S., Lander, E.S., Nusbaum, C., Birren, B. (2003) The Genome Sequence of the Filamentous Fungus Neurospora crassa. Nature, 422, 859-868.
  • Wong, P., Kolesov, G., Frishman, D. and Houry, W.A. (2003) Phylogenetic Web Profiler. Bioinformatics, 19, 782-783.
  • 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., Mewes, H.-W. (2003).The PEDANT genome database.Nucl. Acids Res., 31, 207-211.

  

2002

  • Kolesov, G., Mewes, H.-W., Frishman, D. (2002). SNAPper: gene order predicts gene function. Bioinformatics, 18, 1017-1019.
  • Mewes H.W., Frishman D., Gueldner U., Mannhaupt G., Mayer K., Mokrejs M., Morgenstern B., Muenstekoetter M., Rudd S., Weil B. (2002) MIPS: a database for genomes and protein sequences. Nucl. Acids. Res. 30, 31-34.
  • Frishman, D. (2002). Knowledge-based selection of targets for structural genomics. Protein Engineering 15, 169-183.
  • Frishman, D., Kaps A., Mewes, H.-W. (2002). Online genomics facilities in the new millennium. Pharmacogenomics, 3, 265-271.
  • Kolesov, G., Mewes, H.W., Frishman, D. (2002) SNAPping functionally related genes based on context information: a collinearity-free approach. Ernst Schering Research Foundation Workshop Volume 38: Bioinformatics and Genome Analysis. Editors: H.-W. Mewes, B. Weiss, H. Seidel, Springer-Verlag, Berlin Heidelberg, pp. 29-63.

  

2001

  • Kolesov, D., Mewes, H.-W., Frishman, D. (2001). SNAPping up functionally related genes based on context information: a colinearity-free approach. J.Mol.Biol., 311, 639-656.
  • Frishman D., Albermann K., Hani J., Heumann K., Metanomski A., Zollner A., Mewes H.-W. (2001). Functional and structural genomics using PEDANT. Bioinformatics, 17, 44-57.

  

2000

  • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796-815.
  • Ruepp A., Graml W., Santos-Martinez M.-L., Koretke K.K., Volker C., Mewes H.-W., Frishman D., Stocker S., Lupas A.N., Baumeister W. (2000) The genome of Thermoplasma acidophilum, a scavenger in an extremely acidic environment. Nature, 407, 508-513.
  • Mewes H. W., Frishman D., Gruber C., Geier B., Haase D., Kaps A., Lemcke K., Mannhaupt G., Pfeiffer F., Schüller C., Stocker S., Weil B. (2000). MIPS: a database for genomes and protein sequences. Nucl. Acids Res. , 28, 37-40.
  • R. Wambutt, G. Murphy, G. Volckaert, ..., D. Frishman... (2000) Progress in Arabidopsis genome sequencing and functional genomics. J.Biotechnol. 78, 281-292.
  • Frishman D., Goldstein R.A., Pollock D.D. (2000). Protein Evolution and Structural Genomics. Pacific Symposium on Biocomputing'00. p.3.

 

1999

  • Mayer K., Schueller C., Wambutt R., ..., Frishman D., ... (1999). Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana. Nature 402, 769-777.
  • Houry W.A., Frishman D., Eckerskorn C., Lottspeich F, Hartl F.U. (1999) Identification of in vivo substrates of the chaperonin GroEL. Nature 402, 147-154.
  • Frishman D., Mironov A., and Gelfand M. (1999). Starts of bacterial genes: estimating the reliability of computer predictions. Gene 234, 257-265.
  • Frishman D., Mewes H.W. (1999) Genome Based Structural Biology. Progr. Biophys. Mol. Biol. 72, 1-17.
  • Mewes H.W., Heumann K., Kaps A., Mayer K., Pfeiffer F., Stocker S., Frishman D. (1999) MIPS: a database for genomes and protein sequences. Nucl. Acids. Res. 27, 44-48.
  • Mironov A.A., Frishman D., Gelfand M.S. (1999) Computer analysis of regulatory signals in complete bacterial genomes. Ribosome binding sites. Molecular Biology 33, 133-140.

 

1998

  • Frishman D., Mironov A., Mewes H.W, Gelfand M. (1998) Combining diverse evidence for gene recognition in completely sequenced bacterial genomes. Nucl. Acids Res. 26, 2941-2947.
  • Hartung K., Frishman D., Hinnen A., Woelfl, S. (1998) Single-read sequence tags of a limited number of genomic DNA fragments provide an inexpensive tool for comparative genome analysis. Yeast 14, 1327-1332.
  • Frishman D., Heumann K., Lesk A., Mewes H.-W. (1998) Comprehensive, comprehensible, distributed and intelligent databases: current status. Bioinformatics , 14, 551-561.
  • Muckenthaler M., Gunkel N., Frishman D., Cyrklaff A., Tomancak P., Hentze M.W. (1998) Iron regulatory protein-1 (IRP-1) is highly conserved in the invertebrate species Drosophila Melanogaster and Caenorhabditis elegans. European Journal of Biochemistry , 254, 230-237.
  • Koesel S., Grasbon-Frodl E.M., Mautsch U., Egensperger R., von Eitzen U., Frishman D., Hofmann S., Gerbitz K.-D., Mehraein P., Graeber M.B. (1998) Sequence analysis of mitochondrial complex I genes in pathologically proved Parkinson disease. Neurogenetics 1, 197-204
  • Mewes H.W., Hani J., Pfeiffer F., Frishman D. (1998) MIPS: a database for protein sequences and complete genomes. Nucl. Acids. Res. 26, 33-37.
  • Frishman D. and Mewes H.-W. (1998) The German Conference on Bioinformatics'97. Bioinformatics , 14 , 231.
  • Frishman D. (1998) Intelligent and Distributed Databases (Session Introduction). Pacific Symposium on Biocomputing'98. p.681-682.
  • Mewes H.W., Maierl A. and Frishman D. (1998) Protein sequences and genome databases. Microcharacterization of proteins, (Kellner R., Lottspeich, F., Meyer H.E., eds.), 301-317.
  • Galperin M.Y. and Frishman D. (1998) Toward automated prediction of protein function from microbial genomic sequences. Methods in Microbiol., 28, 245-263.
  • Mewes, H.W., Frishman, D., Zollner, A., Heumann, K. (1998) The bioinformatics of the yeast genome. Meth. Microbiol. 26, 33-51.

 

1997

  • Frishman, D. and Mewes, H.W. (1997) Protein structural classes in five complete genomes. Nature Struct. Biol. 4, 626-628.
  • Frishman, D. and Mewes, H.W. (1997) PEDANTic genome analysis. Trends in Genetics 13, 415-416.
  • Mewes, H.W., Albermann, K., Baehr, M., Frishman, D., Gleissner, A., Hani, J., Heumann, K., Kleine, K., Maierl, A., Oliver, S.G., Pfeiffer, F., Zollner, A. (1997) The yeast genome directory. Nature, 387, 7-65.
  • Boehm S., Frishman D., Mewes H.W. (1997) Variations of the C2Hc zinc finger motif in the yeast genome. Nucl. Acids Res. 25, 2464-2469.
  • Frishman, D. and Argos, P. (1997) The future of the secondary structure prediction accuracy. Folding & Design 2, 159-162
  • Frishman, D. and Argos, P. (1997) 75% accuracy in protein secondary structure prediction. Proteins, 27, 329-335.
  • Argos P., Mewes, H.-W., Frishman D. (1997) Intelligent and Distributed Databases (Session Introduction). Pacific Symposium on Biocomputing'97. p.3.
  • Kaps A., Heumann K., Frishman D., Baehr M., Mewes H.W. (1997) Visuslization and analysis of the complete yeast genome. (1997). Lecture Notes in Computer Science, vol. 1278. Bioinformatics. (Hofestaedt, R., Lengauer T., Loeffler M., and Schomburg, D., eds), pp.178-199.
  • Heringa, J., Frishman, D. and Argos, P. (1997) Computational methods relating protein sequences and structure. In.: "Proteins: a comprehensive treatise", Vol. 1, Principles of Protein Structure, (Allen G, ed.), pp. 171-277, JAI Press, ISBN 1559386711.

 

1996

  • Frishman, D. and Argos, P. (1996) Incorporation of long-distance interactions in a secondary structure prediction algorithm. Prot. Eng. 9, 133-142.
  • Frishman, D. and Hentze, M. (1996) Conservation of aconitase residues revealed by multiple sequence analysis. Implications for structure/function relationships. Eur. J. Biochem. 239, 197-200.
  • Frishman, D. (1996) DSBC protein: a new member of the thioredoxin fold-containing family. Biochem. Biophys. Res. Commun. 219, 686-689.

  

1995

  • Frishman, D. and Argos, P. (1995) Knowledge-based secondary structure assignment. Proteins 23, 566-579.
  • Frishman, D. and Argos, P. (1995) Neural network that recognizes distantly related protein sequences/. In.: Handbook of Neural Computation, Univ. Press. In the press.

 

1994

  • Abagyan, R., Frishman, D. and Argos, P. (1994) Recognition of distantly related proteins through energy calculations. Proteins 19, 132-140.
  • 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.: "Information systems and data analysis", H.H. Bock, W. Lenski and M.M. Richter (eds.). Proc. 17th Annual Conference of the Gesellschaft für Klassification, Springer-Verlag, pp. 397-408.

 

1992

  • Frishman, D. and Argos, P. (1992) Recognition of distantly related protein sequences using conserved motifs and neural networks. J. Mol. Biol. 228, 951-962.
  • Frishman, D. (1992) Signal receptor classification on the basis of their amino acid sequences (review). J. Evol. Physiol. Biochem. 28, 73-83.

 

1991

  • Berman, A.L., Dityatev,A.E. and Frishman, D. (1991) Physicochemical properties of signal receptor domains as the basis for sequence comparison. Comp. Biochem. Physiol. 4, 445-449

 

1990

  • Frishman, D., Berman, A.L. and Kiselev, O.I. (1990) G-proteins have a sequence similar to the ganglioside-binding site of influenza virus hemagglutinins. Mol. Biology 24, 1241-1245.
  • Frishman, D. and Berman, A.L. (1990) Evolution of signal receptor proteins: conserved regions of the polypepdide chain and similarity with GTP-binding proteins. J. Evol. Biochem. Physiol. 26, 14-28.

 

1989

  • Frishman, D. and Berman, A.L. (1989) Similarity between arrestin and octopus rhodopsin. Sensory Systems 3, 428-429.
  • Tsendina, M.B., Frishman, D., Levchenco, W.F. and Berman,A.L. (1988) Primary structure similarity and homology between rhodopsin, b-adrenoreceptor and muscarinic receptor. J. Evol. Biochem. Physiol. 24, 797-806.