chemoinformatics

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2011

  1. Bhhatarai B,Teetz W, Liu T, Öberg T, Jeliazkova N, Kochev N, Pukalov O, Tetko IV, Kovarich S, Papa E, Gramatica P.CADASTER QSPR Models for Predictions of Melting and Boiling Points of Perfluorinated Chemicals Molecular Informatics  30:2-3, 189–204, 2011 DOI: 10.1002/minf.201000133

2010

  1. Rupp M, Körner R, Tetko IV.
    Estimation of Acid Dissociation Constants Using Graph Kernels
    Molecular Informatics 29(10):731–740, 2010.
    DOI:10.1002/minf.201000072
  2. Sushko I, Novotarskyi S, Körner R, Pandey AK, Kovalishyn VV, Prokopenko VV, Tetko IV.
    Applicability domain for in silico models to achieve accuracy of experimental measurements
    Journal of Chemometrics 24:3, 202-208, 2010.
    DOI:10.1002/cem.1296.
  3. Sushko I, Novotarskyi S, Körner R, Pandey AK, Cherkasov A, Li J, Gramatica P, Hansen K, Schroeter T, Müller KR, Xi L, Liu H, Yao X, Öberg T, Hormozdiari F, Dao P, Sahinalp C, Todeschini R, Polishchuk P, Artemenko A, Kuz'min V, Martin TM, Young DM, Fourches D, Muratov E, Tropsha A, Baskin I, Horvath D, Marcou G, Muller C, Varnek A, Prokopenko VV, Tetko IV.
    Applicability domains for classification problems: benchmarking of distance to models for ames mutagenicity set
    J Chem Inf Model 50(12):2094-111, 2010.
    PMID: 21033656
  4. Villa AE, Tetko IV.
    Cross-frequency coupling in mesiotemporal EEG recordings of epileptic patients
    J Physiol Paris 104(3-4):197-202, 2010.
    PMID: 19944158

2009

  1. Arnold R, Brandmaier S, Kleine F, Tischler P, Heinz E, Behrens S, Niinikoski A, Mewes HW, Horn M, Rattei T.
    Sequence-Based Prediction of Type III Secreted Proteins
    Plos Pathog 5(4): e1000376, 2009.
    PMID: 19390696
  2. Mannhold R, Poda GI, Ostermann C, Tetko IV.
    Calculation of molecular lipophilicity: State-of-the-art and comparison of log P methods on more than 96,000 compounds
    J Pharm Sci 98(3):861-93, 2009.
    PMID: 18683876
  3. Tetko IV, Poda GI, Ostermann C, Mannhold R.
    Accurate In Silico log P Predictions: One Can't Embrace the Unembraceable
    QSAR & Combinatorial Science, 28(8):845-849, 2009.
    DOI: 10.1002/qsar.200960003
  4. Tetko IV, Poda GI, Ostermann C, Mannhold R.
    Large-Scale Evaluation of log P Predictors: Local Corrections May Compensate Insufficient Accuracy and Need of Experimentally Testing Every Other Compound
    Chemistry & Biodiversity, 6(11):1837 - 1844, 2009.
    DOI: 10.1002/cbdv.200900075
  5. Varnek A, Gaudin C, Marcou G, Baskin I, Pandey AK, Tetko IV.
    Inductive Transfer of Knowledge: Application of Multi-Task Learning and Feature Net Approaches to Model Tissue-Air Partition Coefficients
    J Chem Inf Model 49(1):133-144, 2009.
    PMID: 19125628

2008

  1. Elstner M, Andreoli C, Ahting U, Tetko I, Klopstock T, Meitinger T, Prokisch H.
    MitoP2: An Integrative Tool for the Analysis of the Mitochondrial Proteome.
    Mol Biotechnol 40(3):306-15, 2008.
    PMID: 18780189
  2. Surmeli D, Ratmann O, Mewes HW, Tetko IV.
    FunCat functional inference with belief propagation and feature integration
    Comput Biol Chem 32(5):375-7, 2008.
    PMID: 18684672
  3. Tetko IV.
    Internet in Drug Design and Discovery
    The Open Applied Informatics Journal 2(1), 2008.
    DOI: 10.2174/1874136300802010018
  4. Tetko IV.
    Associative neural network
    Methods Mol Biol 458:185-202, 2008.
    PMID: 19065811
  5. Tetko IV, Jaroszewicz I, Platts JA, Kuduk-Jaworska J.
    Calculation of lipophilicity for Pt(II) complexes: Experimental comparison of several methods
    J Inorg Biochem 102(7):1424-1437, 2008.
    PMID: 18289687
  6. Tetko IV, Rodchenkov IV, Walter MC, Rattei T, Mewes HW.
    Beyond the "Best" Match: Machine Learning Annotation of Protein Sequences by Integration of Different Sources of Information
    Bioinformatics 24(5):621-8, 2008.
    PMID: 18174184
  7. Tetko IV, Sushko I, Pandey AK, Zhu H, Tropsha A, Papa E, Öberg T, Todeschini R, Fourches D, Varnek A.
    Critical Assessment of QSAR Models of Environmental Toxicity against Tetrahymena pyriformis: Focusing on Applicability Domain and Overfitting by Variable Selection
    J Chem Inf Model 48(9):1733-1746, 2008.
    PMID: 18729318
  8. Varnek A, Fourches D, Horvath D, Klimchuk O, Gaudin C, Vayer P, Solov'ev V, Hoonakker F, Tetko IV, Marcou G.
    ISIDA - Platform for Virtual Screening Based on Fragment and Pharmacophoric Descriptors
    Current Computer - Aided Drug Design 4(3), 4191-198, 2008.
  9. Zhu H, Tropsha A, Fourches D, Varnek A, Papa E, Gramatica P, Öberg T, Dao P, Cherkasov A, Tetko IV.
    Combinatorial QSAR Modeling of Chemical Toxicants Tested against Tetrahymena pyriformis
    J Chem Inf Model 48(4):766-84, 2008.
    PMID: 18311912

2007

  1. Cuomo CA, Güldener U, Xu JR, Trail F, Turgeon BG, Di Pietro A, Walton JD, Ma L, Baker SE, Rep M, Adam G, Antoniw J, Baldwin T, Calvo S, Chang Y, DeCaprio D, Gale LR, Gnerre S, Goswami RS, Hammond-Kosack K, Harris LJ, Hilburn K, Kennell JC, Kroken S, Magnuson JK, Mannhaupt G, Mauceli E, Mewes HW, Mitterbauer R, Muehlbauer G, Münsterkötter M, Nelson D, O'Donnell K, Ouellet T, Qi W, Quesneville H, Roncero MIG, Seong K, Tetko IV, Urban M, Waalwijk C, Ward T, Yao J, Birren BW, and Kistler C.
    The Fusarium graminearum Genome Reveals a Link Between Localized Polymorphism and Pathogen Specialization
    Science 317(5843):1400-1402.
    PMID: 17823352
  2. Emmersen J, Rudd S, Mewes HW, Tetko IV.
    Separation of sequences from host-pathogen interface using triplet nucleotide frequencies.
    Fungal Genet Biol 44(4):231-41, 2007.
    PMID: 17218127
  3. Farre-Castany MA, Schwaller B, Gregory P, Barski J, Mariethoz C, Eriksson JL, Tetko IV, Wolfer D, Celio MR, Schmutz I, Albrecht U, Villa AE.
    Differences in locomotor behavior revealed in mice deficient for the calcium-binding proteins parvalbumin, calbindin D-28k or both.
    Behav Brain Res 178(2):250-61, 2007.
    PMID: 17275105
  4. Varnek A, Kireeva N, Tetko IV, Baskin II, Solov'ev VP.
    Exhaustive QSPR Studies of a Large Diverse Set of Ionic Liquids: How Accurately Can We Predict Melting Points?
    J Chem Inf Model 47(3):1111-22, 2007.
    PMID: 17381081

2006

  1. Antonov AV, Mewes HW.
    BIOREL: The benchmark resource to estimate the relevance of the gene networks.
    FEBS Lett 580(3):844-848, 2006.
    PMID: 16414044
  2. Antonov AV, Tetko IV, Mewes HW.
    A systematic approach to infer biological relevance and biases of gene network structures.
    Nucleic Acids Res 34(1):e6, 2006.
    PMID: 16407322
  3. Balakin KV, Savchuk NP, Tetko IV.
    In Silico Approaches to Prediction of Aqueous and DMSO Solubility of Drug-like Compounds: Trends, Problems and Solutions
    Curr Med Chem 13(2), 223-241, 2006.
    PMID: 16472214

2005

  1. Antonov AV, Tetko IV, Kosykh D, Surmeli D, Mewes HW.
    Exploiting scale-free information from expression data for cancer classification
    Comput Biol Chem 29(4):288-93, 2005.
    PMID: 16039906
  2. Friedel CC, Jahn KH, Sommer S, Rudd S, Mewes HW, Tetko IV.
    Support vector machines for separation of mixed plant-pathogen EST collections based on codon usage.
    Bioinformatics 21(8):1383-8, 2005.
    PMID: 15585526
  3. Rudd S, Tetko IV.
    Eclair--a web service for unravelling species origin of sequences sampled from mixed host interfaces.
    Nucleic Acids Res 33(Web Server issue):W724-7, 2005.
    PMID: 15980572
  4. Tetko IV
    Computing Chemistry on the Web
    Drug Discovery Today 10(22):1497-500, 2005.
    PMID: 16257371
  5. Tetko IV, Abagyan R, Oprea TI.
    Surrogate data - a secure way to share corporate data
    J Comput Aided Mol Des 19(9-10):749-64, 2005.
    PMID: 16267691
  6. Tetko IV, Gasteiger J, Todeschini R, Mauri A, Livingstone D, Ertl P, Palyulin VA, Radchenko EV, Zefirov NS, Makarenko AS, Tanchuk VY, Prokopenko VV.
    Virtual computational chemistry laboratory--design and description
    J Comput Aided Mol Des 19(6):453-63, 2005.
    PMID: 16231203
  7. Tetko IV, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Fobo G, Ruepp A, Antonov AV, Surmeli D, Mewes HW.
    MIPS bacterial genomes functional annotation benchmark dataset.
    Bioinformatics 21(10):2520-1, 2005.
    PMID: 15769832
  8. Tetko IV, Facius A, Ruepp A, Mewes HW.
    Super paramagnetic clustering of protein sequences.
    BMC Bioinformatics 6(1):82, 2005.
    PMID: 15804359
  9. Wang Y, Tetko IV, Hall MA, Frank E, Facius A, Mayer KF, Mewes HW.
    Gene selection from microarray data for cancer classification - a machine learning approach
    Computational Biol and Chem 29(1):37-46, 2005.
    PMID: 15680584

2004

  1. Antonov AV, Tetko IV, Mader MT, Budczies J and Mewes HW.
    Optimization models for cancer classification: extracting gene interaction information from microarray expression data.
    Bioinformatics 20(5):644-52. Jan 22, 2004.
    PMID: 15033871
  2. Antonov AV, Tetko IV, Prokopenko VV, Kosykh D, Mewes HW.
    Web portal for classification of expression data using maximal margin linear programming.
    Bioinformatics 2004 Jun 24
    PMID: 15217811
  3. Ruepp A, Zollner A, Maier D, Albermann K, Hani J, Mokrejs M, Tetko I, Guldener U, Mannhaupt G, Munsterkotter M and Mewes HW.
    The FunCat, a functional annotation scheme for systematic classification of proteins from whole genomes.
    Nucleic Acids Res 32(18):5539-45, 2004.
    PMID: 15486203

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