Igor V Tetko

Summary

Affiliation: GSF-National Research Center for Environment and Health
Country: Germany

Publications

  1. doi request reprint Beyond the 'best' match: machine learning annotation of protein sequences by integration of different sources of information
    Igor V Tetko
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Institute of Bioinformatics and Systems Biology, Neuherberg, Germany
    Bioinformatics 24:621-8. 2008
  2. pmc Super paramagnetic clustering of protein sequences
    Igor V Tetko
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    BMC Bioinformatics 6:82. 2005
  3. ncbi request reprint MIPS bacterial genomes functional annotation benchmark dataset
    Igor V Tetko
    Institute for Bioinformatics MIPS, GSF National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, D 85764 Neuherberg, Germany
    Bioinformatics 21:2520-1. 2005
  4. doi request reprint FunCat functional inference with belief propagation and feature integration
    Dimitrij Surmeli
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Institute of Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, Neuherberg, Germany
    Comput Biol Chem 32:375-7. 2008
  5. 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
  6. pmc A systematic approach to infer biological relevance and biases of gene network structures
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 34:e6. 2006
  7. ncbi request reprint A web portal for classification of expression data using maximal margin linear programming
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Bioinformatics 20:3284-5. 2004
  8. doi request reprint Large-scale evaluation of log P predictors: local corrections may compensate insufficient accuracy and need of experimentally testing every other compound
    Igor V Tetko
    Helmholtz Zentrum Munchen, German Research Center for Environmental Health GmbH, Institute for Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, D 85764 Neuherberg
    Chem Biodivers 6:1837-44. 2009
  9. ncbi request reprint Exploiting scale-free information from expression data for cancer classification
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Comput Biol Chem 29:288-93. 2005
  10. ncbi request reprint Gene selection from microarray data for cancer classification--a machine learning approach
    Yu Wang
    Institute for Bioinformatics, German Research Center for Environment and Health, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Comput Biol Chem 29:37-46. 2005

Collaborators

Detail Information

Publications36

  1. doi request reprint Beyond the 'best' match: machine learning annotation of protein sequences by integration of different sources of information
    Igor V Tetko
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Institute of Bioinformatics and Systems Biology, Neuherberg, Germany
    Bioinformatics 24:621-8. 2008
    ..We have developed and compared the automatic annotation of four bacterial genomes employing a 5-fold cross-validation procedure and several machine learning methods...
  2. pmc Super paramagnetic clustering of protein sequences
    Igor V Tetko
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    BMC Bioinformatics 6:82. 2005
    ..The presence of domains in protein families of diverse function, inhomogeneity and different sizes of protein families create considerable difficulties for the application of published clustering methods...
  3. ncbi request reprint MIPS bacterial genomes functional annotation benchmark dataset
    Igor V Tetko
    Institute for Bioinformatics MIPS, GSF National Research Center for Environment and Health, Ingolstaedter Landstrasse 1, D 85764 Neuherberg, Germany
    Bioinformatics 21:2520-1. 2005
    ..Different program settings and incompatible protocols make a comparison of the analyzed methods difficult...
  4. doi request reprint FunCat functional inference with belief propagation and feature integration
    Dimitrij Surmeli
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Institute of Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, Neuherberg, Germany
    Comput Biol Chem 32:375-7. 2008
    ..hRMN consistently outperformed two competitors in annotation of four bacterial genomes. The developed code is available for download at http://mips.gsf.de/proj/bfab/hRMN.html...
  5. 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...
  6. pmc A systematic approach to infer biological relevance and biases of gene network structures
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Nucleic Acids Res 34:e6. 2006
    ..By the analyses of real data we demonstrate that the potential application of BIOREL ranges from various benchmarking purposes to systematic analysis of the network biology...
  7. ncbi request reprint A web portal for classification of expression data using maximal margin linear programming
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Bioinformatics 20:3284-5. 2004
    ..The input data format is the same as that used in most publicly available datasets. This makes the web resource particularly convenient for non-expert machine learning users working in the field of expression data analysis...
  8. doi request reprint Large-scale evaluation of log P predictors: local corrections may compensate insufficient accuracy and need of experimentally testing every other compound
    Igor V Tetko
    Helmholtz Zentrum Munchen, German Research Center for Environmental Health GmbH, Institute for Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, D 85764 Neuherberg
    Chem Biodivers 6:1837-44. 2009
    ....
  9. ncbi request reprint Exploiting scale-free information from expression data for cancer classification
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Comput Biol Chem 29:288-93. 2005
    ..In proposed schema of data analyses only information on relative gene expression levels in each sample is exploited. Testing on publicly available datasets leads to superior classification results...
  10. ncbi request reprint Gene selection from microarray data for cancer classification--a machine learning approach
    Yu Wang
    Institute for Bioinformatics, German Research Center for Environment and Health, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Comput Biol Chem 29:37-46. 2005
    ..This is also the first paper which discusses both computational and biological evidence for the involvement of zyxin in leukaemogenesis...
  11. pmc Online chemical modeling environment (OCHEM): web platform for data storage, model development and publishing of chemical information
    Iurii Sushko
    eADMET GmbH, Ingolstädter Landstraße 1, 85764, Neuherberg, Germany
    J Comput Aided Mol Des 25:533-54. 2011
    ..The ultimate goal of OCHEM is collecting all possible chemoinformatics tools within one simple, reliable and user-friendly resource. The OCHEM is free for web users and it is available online at http://www.ochem.eu...
  12. ncbi request reprint Associative neural network
    Igor V Tetko
    GSF Institute for Bioinformatics, Neuherberg, Germany
    Methods Mol Biol 458:185-202. 2008
    ..The method can be used to estimate a bias and the applicability domain of models. Applications of the ASNN in QSAR and drug design are exemplified. The developed algorithm is available at http://www.vcclab.org...
  13. pmc Development of dimethyl sulfoxide solubility models using 163,000 molecules: using a domain applicability metric to select more reliable predictions
    Igor V Tetko
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Ingolstädter Landstraße 1, D 85764 Neuherberg, Germany
    J Chem Inf Model 53:1990-2000. 2013
    ..The best models developed with the publicly available Enamine data set are freely available online at http://ochem.eu/article/33409 . ..
  14. ncbi request reprint Computing chemistry on the web
    Igor V Tetko
    Institute for Bioinformatics, GSF, Forschungszentrum fuer Umwelt und Gesundheit, Ingolstaedter Landstrasse 1, D 85764 Neuherberg, Germany
    Drug Discov Today 10:1497-500. 2005
    ..The development of on-line software tools is changing the way we traditionally perform our analysis in drug design, but will chemoinformatics be forever behind bioinformatics in this development?..
  15. doi request reprint A comparison of different QSAR approaches to modeling CYP450 1A2 inhibition
    Sergii Novotarskyi
    eADMET GmbH, Ingolstädter Landstrasse 1, D 85764 Neuherberg, Germany
    J Chem Inf Model 51:1271-80. 2011
    ..The applicability domain approach allowed increasing the prediction accuracy to 90% for 78% of the internal and 17% of the external test sets, respectively. The most accurate models are available online at http://ochem.eu/models/Q5747 ...
  16. ncbi request reprint Can we estimate the accuracy of ADME-Tox predictions?
    Igor V Tetko
    Institute for Bioinformatics, GSF National Research Centre for Environment and Health, Neuherberg, D 85764, Germany
    Drug Discov Today 11:700-7. 2006
    ..An analysis of octanol-water distribution coefficients is used to exemplify the consistency of estimated and calculated accuracy of the ALOGPS program (http://www.vcclab.org) to predict in-house and publicly available datasets...
  17. doi request reprint The perspectives of computational chemistry modeling
    Igor V Tetko
    Helmholtz Zentrum Muenchen, German Research Center for Environmental Health and eADMET GmbH, Neuherberg, Germany
    J Comput Aided Mol Des 26:135-6. 2012
    ..The on-line tools for computational chemistry modeling will be increasingly used in the future. This will bring the advantages both for the authors and the readers...
  18. doi request reprint Critical assessment of QSAR models of environmental toxicity against Tetrahymena pyriformis: focusing on applicability domain and overfitting by variable selection
    Igor V Tetko
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Institute of Bioinformatics and Systems Biology, Neuherberg D 85764, Germany
    J Chem Inf Model 48:1733-46. 2008
    ..The developed models are available online at http://www.qspr.org site...
  19. pmc ToxAlerts: a Web server of structural alerts for toxic chemicals and compounds with potential adverse reactions
    Iurii Sushko
    eADMET GmbH, Ingolstädter Landstraße 1, D 85764 Neuherberg, Germany
    J Chem Inf Model 52:2310-6. 2012
    ..The ToxAlerts platform is accessible on the Web at http://ochem.eu/alerts, and it is constantly growing...
  20. ncbi request reprint Calculation of lipophilicity for Pt(II) complexes: experimental comparison of several methods
    Igor V Tetko
    Helmholtz Zentrum Munchen German Research Center for Environmental Health GmbH, Institute of Bioinformatics and Systems Biology, Ingolstadter Landstrasse 1, 85764 Neuherberg, Germany
    J Inorg Biochem 102:1424-37. 2008
    ..46, for the measured molecules. The program was also able to correctly predict errors in calculated logP values. It is freely available for interactive use at http://www.vcclab.org...
  21. pmc Spatiotemporal expression control correlates with intragenic scaffold matrix attachment regions (S/MARs) in Arabidopsis thaliana
    Igor V Tetko
    GSF National Research Center for Environment and Health, MIPS, Institute for Bioinformatics, Neuherberg, Germany
    PLoS Comput Biol 2:e21. 2006
    ..Our findings open new perspectives for the understanding of tissue- and organ-specific regulation of gene expression...
  22. doi request reprint Applicability domains for classification problems: Benchmarking of distance to models for Ames mutagenicity set
    Iurii Sushko
    Institute of Bioinformatics and Systems Biology, Helmholtz Zentrum Muenchen German Research Center for Environmental Health GmbH, Ingolstaedter Landstrasse 1, D 85764 Neuherberg, Germany
    J Chem Inf Model 50:2094-111. 2010
    ..Thus, the in silico predictions can be used to halve the cost of experimental measurements by providing a similar prediction accuracy. The developed model has been made publicly available at http://ochem.eu/models/1 ...
  23. ncbi request reprint Optimization models for cancer classification: extracting gene interaction information from microarray expression data
    Alexey V Antonov
    GSF National Research Center for Environment and Health, Institute for Bioinformatics, Ingolstadter Landstrasse 1, D 85764 Neuherberg, Germany
    Bioinformatics 20:644-52. 2004
    ..Thus, they cannot be detected by simple classification approaches used previously. For these reasons, a classification procedure exploiting information related to changes in gene interactions is needed...
  24. pmc Modeling of non-additive mixture properties using the Online CHEmical database and Modeling environment (OCHEM)
    Ioana Oprisiu
    Institute of Structural Biology, Helmholtz Zentrum Munchen German Research Center for Environmental Health, Ingolstaedter Landstrasse 1b, 60w, D 85764 Neuherberg, Germany
    J Cheminform 5:4. 2013
    ..Thus, we have developed and made publicly available a powerful system for modeling mixtures of chemical compounds on the Web...
  25. ncbi request reprint Predicting the pKa of small molecule
    Matthias Rupp
    Helmholtz Zentrum Munchen, German Research Center for Environmental Health, Neuherberg, Germany
    Comb Chem High Throughput Screen 14:307-27. 2011
    ..We discuss advantages, problems, recent progress, and challenges in the field...
  26. ncbi request reprint The WWW as a tool to obtain molecular parameters
    Igor V Tetko
    Institute for Bioinformatics, GSF, Ingolstaedter Landstrasse 1, D 85764 Neuherberg, Germany
    Mini Rev Med Chem 3:809-20. 2003
    ..Analysis of emerging tools that can be useful to developing new on-line servers for the prediction of molecular parameters and properties is also given...
  27. pmc Eclair--a web service for unravelling species origin of sequences sampled from mixed host interfaces
    Stephen Rudd
    Centre for Biotechnology, Tykistökatu 6 FIN 20521, Turku, Finland
    Nucleic Acids Res 33:W724-7. 2005
    ..In addition to providing an interface for the classification of sequences, users are presented with the opportunity to train a model to suit their preferred species pair. Eclair is freely available at http://eclair.btk.fi...
  28. ncbi request reprint Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage
    Caroline C Friedel
    Institut fuer Informatik, Ludwig Maximilians Universitaet Muenchen, Oettingenstrasse 67, 80538 Muenchen, Germany
    Bioinformatics 21:1383-8. 2005
    ..When using single-pass cDNA sequences difficulties arise from the short sequence length, the lack of sufficient taxonomically relevant sequence data in public databases and ambiguous sequence homology between plant and pathogen genes...
  29. ncbi request reprint Virtual computational chemistry laboratory--design and description
    Igor V Tetko
    Institute of Bioorganic and Petroleum Chemistry, Kyiv, Ukraine
    J Comput Aided Mol Des 19:453-63. 2005
    ..In this article we review the main features and statistics of the developed system that can be used as a prototype for academic and industry models...
  30. ncbi request reprint Application of ALOGPS 2.1 to predict log D distribution coefficient for Pfizer proprietary compounds
    Igor V Tetko
    Biomedical Department, Institute of Bioorganic and Petroleum Chemistry, Ukrainian Academy of Sciences, Murmanskaya 1, Kyiv, 02094, Ukraine
    J Med Chem 47:5601-4. 2004
    ..The self-learning feature of the ALOGPS (LIBRARY mode) remarkably improved the accuracy in log D prediction, and an rmse of 0.64-0.65 was calculated for both data sets...
  31. ncbi request reprint Application of ALOGPS to predict 1-octanol/water distribution coefficients, logP, and logD, of AstraZeneca in-house database
    Igor V Tetko
    Biomedical Department, IBPC, Ukrainian Academy of Sciences, Murmanskaya 1, Kyiv, 02094, Ukraine
    J Pharm Sci 93:3103-10. 2004
    ..We explain and illustrate this result and, moreover, discuss a possible application of the approach to calculate other pharmacokinetic and biological activities of chemicals important for drug development...
  32. ncbi request reprint Separation of sequences from host-pathogen interface using triplet nucleotide frequencies
    Jeppe Emmersen
    Institut for Miljø og Bioteknologi, Aalborg Universitet, Sohngaardsholmsvej 49, 9000 Aalborg, Denmark
    Fungal Genet Biol 44:231-41. 2007
    ..The server to perform classification of EST sequences using triplet frequencies is available at (URL: http://mips.gsf.de/proj/est3)...
  33. ncbi request reprint In silico approaches to prediction of aqueous and DMSO solubility of drug-like compounds: trends, problems and solutions
    Konstantin V Balakin
    Biomedical Department, Institute of Bioorganic and Petrochemistry, Murmanskaya 1, 02094 Kyiv, Ukraine
    Curr Med Chem 13:223-41. 2006
    ..We describe the main tendencies in the field, "booming" approaches and unsolved problems. A critical analysis of the accuracy and applicability of methods is provided...
  34. ncbi request reprint Benchmarking of linear and nonlinear approaches for quantitative structure-property relationship studies of metal complexation with ionophores
    Igor V Tetko
    Institute of Bioorganic and Petrochemistry, Kiev, Ukraine
    J Chem Inf Model 46:808-19. 2006
    ..The current study illustrates the difficulties of quantitative comparison of different methods: conclusions based only on one data set without appropriate statistical tests could be wrong...
  35. ncbi request reprint Volume learning algorithm significantly improved PLS model for predicting the estrogenic activity of xenoestrogens
    Vasyl V Kovalishyn
    Institute of Bioorganic Chemistry and Petrochemistry, Kyiv, Murmanska 1, 02660, Ukraine
    J Mol Graph Model 26:591-4. 2007
    ..Thus, CoMFA/VLA models are successful in prediction of the endocrine disrupting potential of environmental pollutants and can be effectively applied for testing of prospective chemicals prior their exposure to the environment...
  36. ncbi request reprint An unsupervised automatic method for sorting neuronal spike waveforms in awake and freely moving animals
    Tetyana I Aksenova
    Institute of Applied System Analysis, Ukrainian Academy of Sciences, Prospekt Peremogy 37, 03056 Kiev, Ukraine
    Methods 30:178-87. 2003
    ..The new method of spike sorting was tested on simulated and real data and performed better than other approaches currently used in neurophysiology...