Mendyk A, Tuszyński P, Polak S, Jachowicz R. In vitro-in vivo relationship (IVIVR) generalized model based on artificial neural networks. Journal of Drug Design, Development and Therapy, 2013;7:223-232.
Fijorek K, Patel N, Klima Ł, Stolarz-Skrzypek K, Kawecka-Jaszcz K, Polak S. Age and gender dependent heart rate circadian model development and performance verification on the proarrhythmic drug case study. Theoretical Biology and Medical Modelling, 2013;10:7.
Polak S. In vitro to human in vivo translation – pharmacokinetics and pharmacodynamics of quinidine. ALTEX, accepted for publication.
Glinka A, Polak S. Wild type and K897T polymorphisms of the hERG gene: modeling the AP in Caucasians. Bioinformation, 2012;8(22):1062-1065.
Polak S, Wisniowska B, Glinka A, Polak M. tox-database.net - data describing the chemicals triggered in vitro cardiac ionic channels inhibition. BMC Pharmacology and Toxicology, 2012;13(6).
Wisniowska B, Mendyk A, Fijorek K, Glinka A, Polak S. Predictive model for the L-type channel inhibition - multichannel block in QT prolongation risk assessment. Journal of Applied Toxicology, 2012;32(10):858-866.
Polak S, Fijorek K. Inter-individual variability in the pre-clinical drug cardiotoxic safety assessment - analysis of the age - cardiomyocytes electric capacitance dependence. Journal of Cardiovascular Translational Research, 2012;5(3):321-332.
Polak S, Wisniowska B, Glinka A, Fijorek K, Mendyk A. Slow delayed rectifying potassium current (IKs) – analysis of the in vitro inhibition data and predictive model development. Journal of Applied Toxicology, Article first published online: 14 FEB 2012 [Epub ehead of print].
Polak S, Fijorek K, Glinka A, Wisniowska B, Mendyk A. Virtual population generator for human cardiomyocytes parameters. In silico drug cardiotoxicity assessment. Toxicology Mechanisms and Methods, 2012;22(1):31-40.
Fijorek K, Fijorek D, Wisniowska B, Polak S. BDTcomparator: a program for comparing binary classifiers. Bioinformatics, 2011;27(24):3439-3440.
Fijorek K, Fijorek D. The effectiveness of best subset variable selection in Firth logistic regression. Applied Informatics Methods, 2012;2(27):15-24.
Polak S, Wisniowska B, Fijorek K, Glinka A, Polak M, Mendyk A. The open-access dataset for in silico cardiotoxicity prediction system. Bioinformation, 2011;6(6):244-245.
Polak S, Wisniowska B, Ahamadi M, Mendyk A. Prediction of the hERG potassium channel inhibition potential with use of Artificial Neural Networks. Applied Soft Computing, 2011;11(2):2611-2617.
Wisniowska B, Mendyk A, Polak M, Szlek J, Polak S. RandomForest based assessment of the hERG channel inhibition potential for the early drug cardiotoxicity testing. Bio-Algorithms and Med-Systems, 2010;6(12):131-136.
Wisniowska B, Polak S. hERG in vitro interchange factors - development and verification. Toxicology Mechanisms and Methods, 2009;19(4):278-284.
Polak S, Wisniowska B, Brandys J. Collation, assessment and analysis of literature in vitro data on hERG receptor blocking potency for subsequent modeling of drugs cardiotoxic properties. Journal of Applied Toxicology, 2009;29(3):183-206.
Books / Proceedings / Conference presentations
Polak S. In Vitro to Human In Vivo Translation – Proarrhythmic Potency of Dofetilide. 8th Annual International Conference on Predictive Human Toxicity and ADME/Tox Studies January 24th - 25th, 2013 Brussels, Belgium.
4th Workshop on using Computational Methods in Pharmaceutical Sciences was a one day long training which took place on 8th of September, 2012 in Krakow, Poland as a part of the Computing in Cardiology Conference - CinC 2012. The main goal of the Workshop was to provide in depth, practical information about design, development, validation and implementation of the computational methods used in the pharmaceutical sciences with focus put on the early drugs cardiotoxicity prediction. Video materials from the event will be available soon.
Polak S, Wisniowska B, Fijorek K, Glinka A, Polak M, Mendyk A. In silico prediction of the drug overdose consequences at the heart electrophysiology level. Computing in Cardiology; September 9-12, 2012; Krakow, Poland. Full text in Computing in Cardiology, 2012;39:889-893.
Polak S, Wisniowska B, Fijorek K, Glinka A, Polak M, Mendyk A. ToxComp ‐ in vitro–in vivo extrapolation system for the drugs proarrhythmic potency assessment. Computing in Cardiology; September 9-12, 2012; Krakow, Poland. Full text in Computing in Cardiology, 2012;39:789-793.
Polak S, Wisniowska B, Fijorek K, Glinka A, Polak M, Mendyk A. Modeling and Simulation Approach for Assessing Proarrhythmic Potency of the Non‐cardiological Drugs. Computing in Cardiology; September 9-12, 2012; Krakow, Poland. Full text in Computing in Cardiology, 2012;39:761-765.
Mendyk A, Wisniowska B, Fijorek K, Glinka A, Polak M, Polak S. Empirical modeling of the sodium channel inhibition caused by drugs. Computing in Cardiology; September 9-12, 2012; Krakow, Poland. Full text in Computing in Cardiology, 2012;39:293-297.
48th EUROTOX Congress took place in Stockholm, Sweden (17-20 of June, 2012). Team achievements were presented as the scientific posters: "Influence of the physiological parameters on the APD90 value simulated by human ventricular tissue model" and "Electrophysiologically inactive drugs - can we predict their cardiotoxicity?". They both were presented during the Session P07 Computational toxicology.
Mishra H, Jamei M. Rostami-Hodjegan M, Polak S. Model-Based Prediction of Domperidone and Ketoconazole Interaction and its Impact on QTc Prolongation. 21st PAGE meeting; June 5th - tth, 2012; Venice, Italy.
11th World Pharma Congress was a one day long training which took place in Philadelphia, PA (5-7 of June, 2012). On Tuesday 5th of June Dr Sebastian Polak gave presentation "In vitro-in vivo Extrapolation of the Cardiotoxic Effect: Inter-Individual Variability Matters!".
Polak S., Wiśniowska B., Polak M., Szlęk J., Glinka A., Fijorek K. Mendyk A., ToxComp 1.2 – an Open Source iv vitro in vivo extrapolation (IVIVE) system for cardiotoxicity prediction with Marvin plugins embedded. ChemAxon UGM Budapest 2012, May 22-23, Budapest.
Polak S, Mishra H. Combining In Vitro-In Vivo Extrapolation (IVIVE) and Physiologically-Based Pharmacokinetics (PBPK) with Drug Related Risk Assessment - Cardiotoxicity prediction. 7th Annual International Conference on Predictive Human Toxicity and ADME/Tox Studies; January 26th - 27th, 2012; Brussels, Belgium.
The 16th Online World Conference on Soft Computing in Industrial Applications (WSC16); December 5th - 16th, 2011 INTERNET! Team achievements were presented during the special session - Special Session on Soft Computing Methods in Pharmaceutical and Medical Sciences.
On-line workshop 3rd International Workshop - Computational Pharmacy; September 22nd, 2011; Krakow, Poland (Internet!).
Polak S, Glinka A, Wisniowska B, Mendyk A. Influence on the physiological parameters on the ADP90 value simulated by human venrticular tissue model. Eurotox 2011, August 28th - 31st; Paris, France.
Half day long workshop Tox IVIVE - inter-individual variability matters! September 14th - 16th 2011; Berlin, Germany. All materials are available for download here.
Polak S. Optimization of the use of information for in vitro and in silico to predict in vivo Computational toxicology - in silico drug safety assessment during the 3rd Annual Predictive Toxicology; September 14th - 16th 2011; Berlin, Germany.
Mini-symposium Computational toxicology - in silico drug safety assessment during the 3rd Annual Predictive Toxicology; 14-16 September 2011; Berlin, Germany.
Mini-symposium Computational toxicology and pharmacology - in silico drug activity and safety assessment (Saturday, July 2, 11:00) during the 8-th European Conference on Mathematical and Theoretical Biology and Annual Meeting of The Society for Mathematical Biology; June 28th - July 2nd 2011, Krakow, Poland.
Sebastian Polak, Aleksander Mendyk. Computational toxicology. In silico assessment of the hERG channel inhibition potential for the early drug cardiotoxicity testing. Chemaxon 2011 European UGM, Training day and Markush Forum, May 16-19, Budapest, Hungary.
Sebastian Polak, Barbara Wisniowska, Kamil Fijorek, Anna Glinka, Miłosz Polak, Aleksander Mendyk. ToxComp - in silico platform for the cardiotoxicity assessment – in vitro-in vivo extrapolation. Applied Pharmaceutical Toxicology Workshop; May 18 - 20 2011; San Francisco, CA, USA.
Sebastian Polak. Combining systems biology and pharmacokinetics - drug cardiotoxicity assessment. 2011 CellML Workshop. Auckland, 11-12.04.2011 (on line presentation).
Sebastian Polak, Barbara Wisniowska, Malidi Ahamadi, Aleksander Mendyk. Prediction of the hERG potassium channel inhibition potential with use of the artificial neural networks. Soft Computing in Industrial Applications. Algorithms, Integration and Success Stories. In Advances in Intelligent and Soft Computing vol. 75 Eds. Gao X-Z, Gaspar-Cunha A., Koeppen M., Schaefer G., Wang J. Springer, Berlin 2010.
Barbara Wisniowska, Aleksander Mendyk, Milosz Polak, Jakub Szlek, Sebastian Polak. RandomForest based assessment of the hERG channel inhibition potential for the early drug cardiotoxicity testing (polish/english). MCSB 2010, Krakow 21-22.05.2010.
Sebastian Polak, Barbara Wisniowska, Malidi Ahamadi, Aleksander Mendyk. Prediction of the hERG potassium channel inhibition potential with use of the artificial neural networks. 14th Online World Conference on Soft Computing in Industrial Applications (WSC14), 17-29.11.2009.
Sebastian Polak. Modelling and simulations in modern pharmacy – bridging regulatory bodies, academia and industry. 3rd BBBB-Bosphorus International Conference on Pharmaceutical Sciences, Antalya, Turkey 26-28.10.2009; European Journal of Pharmaceutical Sciences 2009, vol. 38, Issue 1, Supplement.
Barbara Wisniowska, Sebastian Polak. Cardiotoxicity prediction algorithms. 1st International Workshop Computational Pharmacy, Krakow 19.06.2009.
Sebastian Polak, Barbara Wisniowska, Jerzy Brandys. Decision trees algorithms for the in silico prediction of hERG potassium channels inhibition (in polish). Polish Society of Toxicology Workshop “New trends in toxicology”, Lodz 1-2.06.2009.
Barbara Wisniowska, Sebastian Polak, Jerzy Brandys. Bayesian classification methods for proarrhythmic liability prediction. 5th German-Polish Symposium “New Challenges for Pharmaceutical Sciences”, Poznan 15-16.05.2009.
Sebastian Polak, Barbara Wisniowska, Jerzy Brandys. Modelling and simulation in the drug discovery, research and development. Toxicity prediction. 5th German-Polish Symposium “New Challenges for Pharmaceutical Sciences”, Poznan 15-16.05.2009.
Barbara Wisniowska, Sebastian Polak, Jerzy Brandys. Extrapolating factors for different in vitro hERG systems. Central European Congress of Life Science EUROBIOTECH 2008, Kraków 17-19.10.2008; Acta Biochimica Polonica 2008, vol. 55 suppl. 4.
We will be presenting
Polak S., Tomaszewska D., Patel N., Jamei M., Rostami-Hodjegan A. Pharmacokinetic (PK) and pharmacodynamic (PD) implications of diurnal variation of gastric emptying and small intestinal transit time for quinidine: A mechanistic simulation. PAGE conference, 11-14 June, Glasgow, Scotland.
Video materials from the 4th Workshop on using Computational Methods in Pharmaceutical Sciences will be available soon.
Polak S, Fijorek K, Püsküllüoğlu M, Glinka A, Tomaszewska D, Tomaszewski R. Literature review of the serum potassium, sodium and calcium levels in healthy individuals. Technical Note, 2013; 001.
We were cited
Di Veroli GY, Davies MR, Zhang H, Abi-Gerges N, Boyett MR. High-throughput screening of drug-binding dynamics to HERG improves early drug safety assessment. Am J Physiol Heart Circ Physiol. 2013;304:H104-H117.
Danielsson BR. Maternal Toxicity. Teratogenicity Testing. Methods in Molecular Biology. 2013;947:311-325.
Kireeva N, Kuznetsov SL, Bykow AA, Tsivadze AY. Towards in silico identification of the human ether-a-go-go-related gene channel blockers: discriminative vs. generative classification models. SAR and QSAR in Environmental Research. 2012;24(2).
Wang S, Li Y, Wang J, Chen L, Zhang L, Yu H, Hou T. ADMET Evaluation in Drug Discovery. 12. Development of Binary Classification Models for Prediction of hERG Potassium Channel Blockage. Molecular Pharmaceutics. 2012;9:996-1010.
Mirams GR, Davies MR, Cui Y, Kohl P, Noble D. Application of cardiac electrophysiology simulations to pro-arrhythmic safety testing. British Journal of Pharmacology. 2012;167(5):932-945.
Eichenbaum G, Pugsley MK, Gallacher DJ, Towart R, McIntyre G, Shukla U, Davenport JM, Lu HR, Rohrbacher J, Hillsamer V. Role of Mixed Ion Channel Effects in the Cardiovascular Safety Assessment of the Novel Anti-MRSA Fluoroquinolone JNJ-Q2. British Journal of Pharmacology. 2012; 166(5):1694-1707.
Gleeson MP, Modi S, Bender A, Robinson RL, Kirchmair J, Promkatkaew M, Hannongbua S, Glen RC. The Challenges Involved in Modeling Toxicity Data In Silico: A Review. Current Pharmaceutical Design. 2012;18(9):1266-1291.
Hishigaki H, Kuhara S. hERGAPDbase: a database documenting hERG channel inhibitory potentials and APD-prolongation activities of chemical compounds. Database: The Journal of Biological Databases and Curation. 2011; published online May 17th.
Migliorini C, Lave T, Parrott NJ, Reddy M, Grimm HP, Penland RC, Soubret A, Helmlinger G, Georgieva A, Zuideveld KP. Systems Toxicology Modeling for Prediction in Humans. 2011; in Sahu SC et al. General, Applied and System Toxicology. Chichester, West Sussex, U.K: John Wiley & Sons.
Tan Y, Chen Y, You Q, Sun H, Li M. Predicting the potency of hERG K+ channel inhibition by combining 3D-QSAR pharmacophore and 2D-QSAR models. Journal of Molecular Modeling. 2011; 18(3):1023-1036.
Su Z, Gintant G. Preclinical Drug Safety and Cardiac Ion Channel Screening. Heart Rate and Rhythm. 2011;Part 7:627-638.
Church MK. Safety and efficacy of bilastine: a new H1-antihistamine for the treatment of allergic rhinoconjunctivitis and urticaria. Expert Opinion on Drug Safety. 2011;10(5):779-793.
Schuster AM, Glassmeier G, Bauer CK. Strong activation of erg1 K+ channel isoforms by NS1643 (1,3-bis-(2-hydroxy-5-trifluoromethylphenyl)-urea) in HEK-293 and CHO cells. Molecular Pharmacology. 2011; August 19th: available online.
Schramm A, Baburin I, Hering S, Hamburger M. HERG channel inhibitors in extracts of coptidis rhizoma. Planta Medica. 2011;77(7):692-697.
Taboureau O, Jørgensen FS. In silico Predictions of hERG Channel Blockers in Drug Discovery: From Ligand-Based and Target-Based Approaches to Systems Chemical Biology. Comb Chem High Throughput Screen. 2011;14(5):375-87.
Marchese Robinson RL, Glen RC, Mitchell JBO. Development and Comparison of hERG Blocker Classifiers: Assessment on Different Datasets Yields Markedly Different Results. Molecular Informatics. 2011;30(5):443-458.
Obiol-Pardo C, Gomis-Tena J, Sanz F, Saiz J, Pastor M. A Multiscale Simulation System for the Prediction of Drug-Induced Cardiotoxicity. Journal of Chemical Information and Modeling. 2011;51(2):483-492.
Beyer BK, Chernoff N, Danielsson BR, et al. ILSI/HESI maternal toxicity workshop summary: maternal toxicity and its impact on study design and data interpretation. Birth Defects Research Part B - Developmental and Reproductive Toxicology. 2011;92(1):36-51.
Schmalhofer WA, Swensen AM, Thomas BS, et al. A Pharmacologically Validated, High-Capacity, Functional Thallium Flux Assay for the Human Ether-á-go-go Related Gene Potassium Channel. Assay and Drug Development Technologies. 2010;8(6):714-726
Huang XP, Mangano T, Hufeisen S, Setola V, Roth BL. Identification of human Ether-à-go-go related gene modulators by three screening platforms in an academic drug-discovery setting. Assay and Drug Development Technologies. 2010;8(6):727-42.
Sprous D.G., Palmer R.K., Swanson J.T., Lawless M. QSAR in the pharmaceutical research setting: QSAR models for broad, large problems. Curr. Top. Med. Chem. Current Topics in Medicinal Chemistry. 2010;10(6):619-637.
Sprous D, Palmer K. The T1R2/T1R3 Sweet Receptor and TRPM5 Ion Channel: Taste Targets with Therapeutic Potential. Progress in Molecular Biology and Translational Science. 2010;91:151-208.
Raschi E., De Ponti F., Ceccarini L., Recanatini M. HERG-related drug toxicity and models for predicting hERG liability and QT prolongation. Expert Opinion on Drug Metabolism and Toxicology. 2009;5(9):1005-1021.