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Publications

Research Papers

  • Chirico, N.; Gramatica, P. Real External Predictivity of QSAR Models: How To Evaluate It? Comparison of Different Validation Criteria and Proposal of Using the Concordance Correlation Coefficient J. Chem. Inf. Model., 2011, 51 (9), pp 2320–233

  • Iqbal, M.S.; Öberg, T. Description and propagation of uncertainty in input parameters in environmental fate models Submitted

  • Liu, T.; Nicholls, I.; Öberg, T. Comparison of theoretical and experimental models for characterizing solvent properties using reversed phase liquid chromatography (RPLC) Analytica Chimica Acta, 2011, 702, 37-44

  • Sahlin, U.; Filipsson, M.; Öberg, T. A risk assessment perspective of current practice in characterizing uncertainties in QSAR regression predictions Molecular Informatics, 2011, 30, 551-564

  • Öberg, T.; Liu, T. Extension of a prediction model to estimate vapor pressures of perfluorinated compounds (PFCs)s Chemometrics and Intelligent Laboratory Systems, 2011, 107, 59-64

  • Roy, P.P.; Kovarich, S.; Gramatica, P. QSAR model reproducibility and applicability: a case study of rate constants of hydroxy radical reaction models applied to Polybrominated Diphenyl Ethers and (Benzo-)Triazoles J. Computational Chem., 2011, 32, 2386-2396

  • Kovarich, S.; Papa, E.; Gramatica, P. QSAR classification models for the prediction of endocrine disrupting activity of brominated flame retardants J. Hazard. Mater., 2011, 190 (1-3), 106-112

  • Papa E.; Kovarich, S.; Gramatica, P. On the use of local and global QSARs for the prediction of Physico-Chemical Properties of Polybrominated Diphenyl Ethers Molecular Informatics, 2011, 30, 232–240

  • Bhhatarai, B.; Teetz, W.; Liu, T.; Öberg, T.; Jeliazkova, N.; Kochev, N; Pukalov, O.; Tetko, I.; Kovarich, S.; Papa, E.; Gramatica, P. CADASTER QSPR Models for Predictions of Melting and Boiling Points of Perfluorinated Chemicals Molecular Informatics, 2011, 30, 189-203

  • Sushko I.; Novotarskyi S.; Körner R.; Pandey A.K.; Cherkasov A.; Li J.; Gramatica P.; Hansen K.; Schroeter T.; Müller K.R.; Xi L.; Liu H.; Yao X.; Öberg T.; Hormozdiari F.; Dao P.; Sahinalp C.; Todeschini R.; Polishchuk P.; Artemenko A.; Kuz'min V.; Martin T.M.; Young D.M.; Fourches D.; Muratov E.; Tropsha A.; Baskin I.; Horvath D.; Marcou G.; Muller C.; Varnek A.; Prokopenko V.V.; Tetko I.V. Applicability domains for classification problems: benchmarking of distance to models for ames mutagenicity set. J Chem Inf Model, 2010, 50, 2094-2111

  • Bhhatarai, B.; Gramatica, P. Oral LD50 Toxicity Modeling and Prediction of Per- and Polyfluorinated Chemicals on Rat and Mouse Molecular Diversity, 2011, 15 (2), 467-476

  • Bhhatarai, B.; Gramatica, P. Prediction of Aqueous Solubility, Vapor Pressure and Critical Micelle Concentration for Aquatic Partitioning of Perfluorinated Chemicals Environ. Sci. Technol., 2010, 45(19), 8120-8128

  • Bhhatarai, B.; Gramatica, P. Modelling physico-chemical properties of (benzo)triazoles, and screening for environmental partitioning Water Research, 2011, 45, 1463-1471

  • Papa, E.; Kovarich, S.; Gramatica P. Development, Validation and Inspection of the Applicability Domain of QSPR Models for physico-chemical properties of Polybrominated DiphenylEthers QSAR and Combinatorial Science, 2009, 28, 790-796.

  • Papa, E.; Luini, M.; Gramatica, P. QSAR modelling of oral acute toxicity and cytotoxic activity of fragrance materials in rodentsSAR QSAR Environ Res., 2009, 20, 767–779.

  • Bhhatarai, B.; Gramatica P. Per- and Polyfluoro Toxicity (LC50 Inhalation) Study in Rat and Mouse Using QSAR Modeling Chem. Res. Toxicol., 2010, 23, 528-539.

  • Papa, E.; Kovarich, S.; Gramatica, P. QSAR modeling and prediction of the endocrine disrupting potencies of brominated flame retardants Chem. Res. Toxicol., 2010, 23, 946-954.

  • Sushko, I.; Novotarskyi, S.; Körner, R.; Pandey, A.K.; Kovalishyn, V.V.; Prokopenko, V.V.; Tetko, I.V. Applicability domain for in silico models to achieve accuracy of experimental measurements J. Chemometrics., 2010, 24(3-4), 202-208.

    • Conference Presentations

    2011

  • Bhhatarai, B.; Gramatica, P. Physico-chemical property prediction of emerging pollutants: PFCs and (B)TAZs for environmental distribution, 16th International Symposium on Environmental Pollution and its Impact on Life in the Mediterranean Region, Ioannina, Greece September 24-27, 2011, presentation by Paola Gramatica

  • Cassani, S; Kovarich, S.; D’Onofrio, E.; Papa, E.; Roy, P.P.; Gramatica, P. QSAR prediction of aquatic toxicity of triazoles and benzo-triazoles, 16th International Symposium on Environmental Pollution and its Impact on Life in the Mediterranean Region, Ioannina, Greece September 24-27, 2011, presentation by Paola Gramatica

  • Cassani, S.; Kovarich, S.; D’Onofrio, E.; Papa, E.; Roy, P.P.; Gramatica P. QSAR prediction of aquatic toxicity of triazoles and benzo-triazoles, Conferentia Chemometrica 2011, Sümeg, Hungary, September 18-21, 2011, presentation by Stefano Cassani

  • Roy, P.P.; Kovarich, S.; Papa, E.; Gramatica, P. QSAR model reproducibility and applicability: a case study of hydroxyl radical reaction rate constants model, Conferentia Chemometrica 2011, Sümeg, Hungary, September 18-21, 2011, presentation by Partha Pratim Roy

  • Kovarich, S.; Cassani, S.; D’Onofrio, E.; E. Papa, E; Roy, P.P. ; Gramatica. P. QSAR prediction of aquatic toxicity of triazoles and benzo-triazoles, 6th International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, Maribor, Slovenia September 3-7, 2011, presentation by Simona Kovarich

  • Roy, P.P.; Kovarich, S., Papa, E.; Gramatica, P. QSAR model reproducibility and applicability: a case study of hydroxyl radical reaction rate constants model, 6th International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, Maribor, Slovenia September 3-7, 2011, presentation by Simona Kovarich

  • Kovarich, S.; Papa, E.; Bhhatarai, B.; Rahmberg, M.; Nilsson, S.; Liu, T.; Öberg, T.; Jeliazkova, N.; Kochev, N.; Pukalov, O.; Teetz, W.; Brandmaier, S.; Tetko, I.V.; Gramatica, P. QSAR and QSPR models for emerging pollutants: WP3 activities within the FP7 European Project CADASTER, 6th International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, Maribor, Slovenia September 3-7, 2011, presentation by Barun Bhhatarai

  • Bhhatarai, B.; Gramatica, P. Physico-chemical property prediction of emerging pollutants: PFCs and (B)TAZs for environmental distribution, 6th International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, Maribor, Slovenia September 3-7, 2011, presentation by Barun Bhhatarai

  • Chirico, N.; Papa, E.; Gramatica, P. On the agreement of external validation parameters for linear regression QSAR models, 6th International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, Maribor, Slovenia September 3-7, 2011, presentation by Paola Gramatica

  • Gramatica, P. Predictive QSAR modeling for the screening and prioritization of environmental organic pollutants, 6th International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, Maribor, Slovenia September 3-7, 2011, plenary by Paola Gramatica

  • Öberg, T.; Iqbal, M.S. The REACH space of organic chemistry and hazard properties, 6th International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, Maribor, Slovenia September 3-7, 2011, presentation by Tomas Öberg

  • Tetko, I. V. CADASTER & MC ITN ECO, EU-China Environment Research: Looking back and moving forward together, Bejing, China July 2-3, 2011, presentation by Igor V. Tetko, download presentation

  • Brandmaier, S.; Abdelaziz, A.; Sahlin, U.; Öberg, T.; Tetko, I. V. Stepwise D-Optimal design based on latent variables, SETAC Europe annual meeting, Milan, Italy May 15-19, 2011, presentation by Stefan Brandmaier, download poster

  • Brandmaier, S.; Srivastava, V.; Tetko, I. V.; Körner, R.; Teetz, W.; Novotarskyi, S.; Pandey, A.; Sushko, I. MOPAC@home - a structural database for small chemical compounds, SETAC Europe annual meeting, Milan, Italy May 15-19, 2011, presentation by Stefan Brandmaier, download poster

  • Tomas Öberg, T; Iqbal, M. S. Uncertainty in fugacity-based multimedia modeling: probabilistic and non-probabilistic methods, SETAC Europe annual meeting, Milan, Italy May 15-19, 2011, download poster

  • Sahlin, U; Aldenberg, T.; Öberg, T. Towards guidance on how to characterize predictive uncertainty in QSAR regression models, SETAC Europe annual meeting, Milan, Italy May 15-19, 2011, download presentation

  • Sahlin, U; Bhhatarai, B; Papa, E.; Öberg, T.; Gramatica, P. A QSAR-based compound prioritization for lab-testing for chemical safety assessment, SETAC Europe annual meeting, Milan, Italy May 15-19, 2011, download poster

  • Papa, E.; Cassani, S.; D’Onofrio, E.; Kovarich, S.; Roy, P. P.; Rahmberg, M.; Nilsson, S.; Gramatica, P. QSAR prediction of aquatic and mammalian toxicity of triazoles
    and benzo-triazoles, SETAC Europe annual meeting, Milan, Italy May 15-19, 2011, presentation by Ester Papa, download poster

  • Kovarich, S.; Bhhatarai, B,; Papa, E.; Rahmberg, M.; Nilsson, S.; Liu, T.; Öberg, T.; Jeliazkova, N.; Kochev, O.; Teetz, W.; Brandmaier, S.; Tetko, I. V.; Gramatica, P. QSAR and QSPR models for emerging pollutants: WP3 activities within the FP7 European Project CADASTER, SETAC Europe annual meeting, Milan, Italy May 15-19, 2011, presentation by Simona Kovarich, download poster

  • Chirico, N.; Papa, E.; Gramatica, P. On the agreement of external validation parameters for linear regression QSAR models, SETAC Europe annual meeting, Milan, Italy May 15-19, 2011, presentation by Paola Gramatica, download poster

  • Bhhatarai, B,; Gramatica, P. Physico-chemical property prediction of emerging pollutants: PFC and (B)TAZ for environmental distribution, SETAC Europe annual meeting, Milan, Italy May 15-19, 2011, download poster

  • Roy, P. P.; Kovarich, S.; Papa, E.; Gramatica, P. Exploring the QSARs for OH Tropospheric Degradation of VOCs using freely available online descriptors, SETAC Europe annual meeting, Milan, Italy May 15-19, 2011, presentation by Partha Pratim Roy, download poster

  • Peijnenburg, W.; Durjava, M.; Gramatica, P.; Öberg, T.; Rahmberg, M.; Tetko, I.; Jeliaskova, N.; Huijbregts, M.; Comber, M. Exemplification of the integration of tools within REACH: the CADASTER project, SETAC Europe annual meeting, Milan, Italy May 15-19, 2011, presentation by Willie Peijnenburg, download presentation

  • Peijnenburg, W.; Ding, G. Toxicity of poly- and perfluorinated compounds to lettuce (Lactuca sativa) and green algae (Pseudokirchneriella subcapitata), SETAC Europe annual meeting, Milan, Italy May 15-19, 2011, poster by Willie Peijnenburg, download poster

  • Brandmaier, S.; Abdelaziz, A.; Sahlin, U.; Öberg, T.; Tetko, I. V. Stepwise D-Optimal design based on latent variables, interact 2011 Munich, Munich, Germany April 7th, 2011, poster by Stefan Brandmaier, download poster

  • Brandmaier, S.; Abdelaziz, A.; Sahlin, U.; Öberg, T.; Tetko, I. V. Stepwise D-Optimal design based on latent variables, interact 2011 Munich, Munich, Germany April 7th, 2011, presentation by Stefan Brandmaier, download presentation

    • 2010

  • Bhhatarai, B.; Gramatica, P. Rodent Toxicity Studies on Perfluorinated Chemicals for REACH, 18th European Symposium on QSARs (EuroQSAR2010), Rhodes, Greece September 19-24, 2010, plenary lecture of Paola Gramatica

  • Bhhatarai, B.; Teetz, W.; Öberg, T.; Liu, T.; Jeliazkova, N.; Kochev, N.; Pukalov, O.; Tetko, I.V.; Gramatica, P. QSPR Models for Predictions and Data Quality assurances: Melting Poin and Boiling Point of Perfluorinated Chemicals, 18th European Symposium on QSARs (EuroQSAR2010), Rhodes, Greece September 19-24, 2010, poster by Paola Gramatica, download poster

  • Papa, E.; Kovarich, S.; Gramatica, P. CADASTER Models for Brominated Flame Retardants, 18th European Symposium on QSARs (EuroQSAR2010), Rhodes, Greece September 19-24, 2010, poster by Ester Papa, download poster

  • Sahlin, U.; Filipsson, M.; Öberg, T. On the characterization of variability and uncertainty from QSARs for probabilistic environmental risk assessment within REACH. 18th European Symposium on QSARs (EuroQSAR2010), Rhodes, Greece September 19-24, 2010, poster by Ullrika Sahlin

  • Teetz W., Brandmaier S., Pandey A., Tetko I., Modeling of physicochemical properties for perfluorinated chemicals using a data integration approach 2nd international workshop on new developments of fluorinated surfactants. Idstein, Germany, June 17-19, 2010 by Wolfram Teetz, download presentation

  • Bhhatarai B.; Teetz W.; Öberg T.; Liu T.; Jeliazkova N.; Kochev N.; Pukalov O.; Tetko I.; and Gramatica P., SPR Models for Predictions and Data Quality Assurances: Melting Point and Boiling Point of Perfluorinated Chemicals, 2nd international workshop on new developments of fluorinated surfactants. Idstein, Germany, June 17-19, 2010, poster by Wolfram Teetz, download poster.

  • Kovarich, S.; Gramatica, P.; Papa, E. QSAR prediction of the Endocrine Activity of perfluorinated compounds, SETAC-Europe 2010 - 20th Annual Meeting SETAC-Europe, Seville, Spain May 23-27, 2010, poster by Simona Kovarich, download poster.

  • Kovarich, S.; Gramatica, P.; Papa, E. Classification QSAR Models for the prediction of endocrine disruption potencies of brominated flame retardants, SETAC-Europe 2010 - 20th Annual Meeting SETAC-Europe, Seville, Spain May 23-27, 2010, poster by Simona Kovarich, download poster.

  • Kovarich, S.; Gramatica, P.; Papa, E. QSAR models for the prediction of endocrine disruption potencies of brominated flame retardants: a classification approach, 14th International Workshop on QSAR in Environmental and Health Sciences, Montreal, Canada, May 24-28, 2010, poster by Paola Gramatica, download poster.

  • Bhhatarai, B.; Gramatica P. Oral LD50 Toxicity Modeling of Per- and Polyfluorinated Chemicals on Rat and Mouse, 14th International Workshop on QSAR in Environmental and Health Sciences, Montreal, Canada, May 24-28, 2010, poster by Paola Gramatica, download poster,.

  • Gramatica, P.; Bhhatarai, B.; Kovarich, S.; Papa, E. QSAR prediction of physico-chemical properties and biological activities of emerging pollutants: brominated flame retardants and perfluorinated-chemicals, Sixth Indo-US Workshop on Mathematical Chemistry, Kolkata, India 8-10 January; 2010 by Paola Gramatica, download presentation.

    • 2009

  • Öberg, T. Treatment of uncertainty from QSAR models in risk assessment, Annual Meeting of the Society for Risk Analysis, Baltimore, Maryland, United STates December 6-9, 2009, presentation by Tomas Öberg

  • Papa, E.; Kovarich, S.; Gramatica, P. QSPR prediction of physico-chemical properties and endocrine disrupting activity of brominated flame retardants, SETAC 2009 , New Orleans, Louisiana (USA) 19-23 November; 2009 by Paola Gramatica, download presentation.

  • Öberg, T.; Liu, T. Updating existing QSAR models - selection and weighting of new data, 5th German Conference on Chemoinformatics, Goslar, Germany November 8-10, 2009, presentation by Tomas Öberg

  • Bhhatarai, B.; Gramatica, P. Perfluoro Toxicity (LC50 inhalation) in Rattus and Mus species using QSAR , SETAC 2009 , New Orleans, Louisiana (USA) 19-23 November; 2009 by Paola Gramatica, download poster.

    • Tetko, I., In Silico Prediction of ADMET properties with confidence: potential to speed-up drug discovery, presentation, download presentation.

    presented at:

  • Bhhatarai, B.; Gramatica, P. QSPR Studies for Predicting Physico-chemical Properties of Perfluorinated Compounds, Conferentia Chemometrica 2009, Sio`fok, Hungary, September 27-30; 2009 by Barun Bhhatarai, download presentation.

  • Tetko, I., In Silico Prediction of Toxicology - One Can't Embrace Unembraceable, Marcus Evans Predictive Toxicology 2009, Praga, Czech Republic, September 2-4; 2009 by Igor Tetko, download presentation.

  • Poda G.; Ostermann C.; Mannhold R.; McDonald J.; Tetko I., Large Scale Evaluation of log P Prediction Methods: Local Corrections Compensate Insufficient Accuracy and Eliminate the Need of Testing Every Other Compound, ACS Spring National Meeting, Praga, Czech Republic August 16-20; 2009 by Igor Tetko, download presentation.

  • Peijnenburg, W., Chemical Similarity, 4th Summer School AACIMP 2009, Kiev, Ukraine, August 10-13; 2009 by Willie Peijnenburg, download presentation.

  • Tetko, I., Introduction to Chemoinformatics, 4th Summer School AACIMP 2009, Kiev, Ukraine, August 10-13; 2009 by Igor Tetko, download presentation.

  • Bhhatarai, B.; Gramatica, P.; Luini, M.; Papa, E. QSAR modelling of toxicity endpoints of emerging pollutants: Fragrances and Perfluorinated compounds, CMTPI-2009 - Fifth International Symposium on Computational Methods in Toxicology and Pharmacology Integrating Internet Resources, Istanbul, Turkey, July 4-8; 2009 by Paola Gramatica, download presentation.

  • Bhhatarai B.; Papa E.; Gramatica P. QSAR studies on Mouse Inhalation LC50 data of perfluoro- compounds, ICCE 2009 - 12th EuCheMS International Conference on Chemistry & the Environment, Stockholm, Sweden, 14-17 June 2009, , poster, download poster by Barun Bhhatarai.

    • Papa, E.; Kovarich, S.; Gramatica, P. QSAR modelling of the endocrine disrupting activity of  Brominated Flame Retardants (BFRs), poster, download poster.

    presented at:

  • Papa E.; Luini M.; Gramatica P. Chemometrical approaches for the characterization of the environmental behaviour of fragrances, SETAC-Europe 2009 - 19th Annual Meeting SETAC-Europe, Göteborg, Sweden, 31 May – 4 June 2009, poster, download poster by Ester Papa
  • Jeliazkova N., Jeliazkov V., Hierarchical Multi-label Classification of ToxCast Datasets, ToxCast™ Data Analysis Summit, EPA Campus, Research Triangle Park NC, USA, May 14-15; 2009; platform presentation, download presentation.

    • 2008

  • Tetko, I. V.; Sushko, I.; Pandey, A. K.; Zhu, H.; Tropsha, A.; Papa, E.; Oberg, T.; Todeschini, R.; Fourches, D.; Varnek, A. Critical assessment of QSAR models to predict environmental toxicity against T. pyriformis: Applicability domain and overfitting by variable selection, International Symposium on Green Chemistry for Environment and Health, Neuherberg, Germany, October 13-16; 2008; oral report, download oral report.

  • Papa, E.; Kovarich, S.; Gramatica, P. QSPR prediction of physico-chemical properties and endocrine disrupting activity of brominated flame retardants, Euro-QSAR 2008 - 17th European Symposium on Quantitative Structure-Activity Relationships & Omics Technologies and Systems Biology, Uppsala, Sweden, 21-26 September 2008, poster, download poster presented by Paola Gramatica
  • Peijnenburg, W. J. G. M.; Durjava, M.; Gramatica, P.; Furusjo, E.; Oberg, T.; Jeliazkova, N.; Huijbregts, M. A. J.; Comber, M.; Tetko, I. V. CAse studies on the Development and Application of in-Silico Techniques for Environmental hazard (CADASTER), poster, download poster

    • presented at:

  • Papa, E.; Kovarich, S., Gramatica, P. QSPR prediction of physico-chemical properties and degradation of PBDEs, QSAR 2008 - The 13th International Workshop on QSARs in the Environmental Sciences, Syracuse, New York, USA, June 8-12; 2008 by Paola Gramatica, download presentation.

  • Tetko, I. V.; Sushko, I.; Pandey, A. K.; Zhu, H.; Tropsha, A.; Papa, E.; Oberg, T.; Todeschini, R.; Fourches, D.; Varnek, A. Critical assessment of QSAR models to predict environmental toxicity against T. pyriformis: Applicability domain and overfitting by variable selection, The 13th International Workshop on QSARs in the Environmental Sciences, Syracuse, New York, USA, June 8-12; 2008; oral report, download oral report.

  • Papa, E.; Kovarich, S.; Gramatica, P. QSAR prediction of endocrine disruption potencies of brominated flame retardants, poster, download poster.

    • presented at: