➞ Publications ➞ 2008

2008

  1. Plewczyński Dariusz, Rychlewski Leszek Meta-basic estimates the size of druggable human genome, JOURNAL OF MOLECULAR MODELING, 2008, 1, s. 1-5
  2. Benedyczak K., Nowiński A., Bała P. Flexible streaming infrastructure for UNICORE, Lecture Notes in Computer Science, 2008, 4854, s. 94-103
  3. Rada-Iglesias Alvaro, Ameur Adam, Kapranov Philipp, Enroth Stefan, Komorowski Jan, Gingeras Thomas, Wadelius Claes Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders, Genome Research, 2008, 18, s. 380-392
  4. Andersson Robin, Bruder Carl, Piotrowski Arkadiusz, Menzel Uwe, Nord Helena, Sandgren Johanna, Hvidsten Torgeir, Diaz de Stahl Teresita, Dumanski Jan, Komorowski Jan A segmental maximum a posteriori approach to genome-wide copy number profiling, BIOINFORMATICS, 2008, 24, s. 751-758
  5. Trykozko Anna, Brouwer Geert, Zijl Wouter Downscaling: a complement to homogenization, International Journal of Numerical Analysis and Modeling, 2008, 5, s. 157-170
  6. Dramiński Michał, Rada-Iglesias Alvaro, Enroth Stefan, Wadelius Claes, Koronacki Jacek, Komorowski Jan Monte Carlo feature selection for supervised classification, BIOINFORMATICS, 2008, 24, s. 110-117
  7. Kontijevskis Aleksejs, Komorowski Jan, Wikberg Jarl Generalized Proteochemometric Model of Multiple Cytochrome P450 Enzymes and Their Inhibitors, Journal of Chemical Information and Modeling, 2008, 48, s. 1840-1850
  8. Wyrwicz Lucjan, Ginalski Krzysztof, Rychlewski Leszek HSV-1 UL45 encodes a carbohydrate binding C-type lectin protein, Cell Cycle, 2008, 7, s. 269-271
  9. Jimenez Jose, Canales Angeles, Jimenez-Barbero Jesus, Ginalski Krzysztof, Rychlewski Leszek, Garcia Jose, Diaz Eduardo Reply to Behrman: ‘N-Formylmaleamic acid: An intermediate in nicotinic acid metabolism’, Proceedings of the National Academy of Sciences of the United States of America, 2008, 105, s. 89
  10. Jimenez Jose, Canales Angeles, Jimenez-Barbero Jesus, Ginalski Krzysztof, Rychlewski Leszek, Garcia Jose, Diaz Eduardo Deciphering the genetic determinants for aerobic nicotinic acid degradation: the nic cluster from Pseudomonas putida KT2440, Proceedings of the National Academy of Sciences of the United States of America, 2008, 105, s. 11329-11334
  11. Kutner Jan, Towpik Joanna, Ginalski Krzysztof, Boguta Magdalena Mitochondrial release factor in yeast: interplay of functional domains, CURRENT GENETICS, 2008, 53, s. 185-192
  12. Gruziel Magdalena, Gruziel Magdalena, Grochowski Paweł, Trylska Joanna The Poisson-Boltzmann model for tRNA: Assessment of the calculation set-up and ionic concentration cutoff, JOURNAL OF COMPUTATIONAL CHEMISTRY, 2008, 29, s. 1970-1981
  13. Voltz Karine, Trylska Joanna, Tozzini Valentina, Kurkal-Siebert Vandana, Langowski Jörg, Smith Jeremy Coarse-grained force field for the nucleosome from self-consistent multiscaling, JOURNAL OF COMPUTATIONAL CHEMISTRY, 2008, 29, s. 1429-1439
  14. Voltz Karine, Trylska Joanna, Tozzini Valentina, Kurkal-Siebert Vandana, Smith Jeremy, Langowski Jörg Global Motions in the Nucleosome Explored Using a Coarse-Grained Model From Computational Biophysics to Systems Biology (CBSB08), Symposium 19-21 May 2008 Forschungszentrum Julich Proceedings., Julich, NIC-Directors, 2008
  15. Plewczyński Dariusz, Słabiński Łukasz, Ginalski Krzysztof, Rychlewski Leszek Prediction of signal peptides in protein sequences by neural networks, Acta Biochimica Polonica, 2008, 55, s. 261-267
  16. Orzechowski Westholm Jakub, Xu Feifei, Ronne Hans, Komorowski Jan Genome-scale study of the importance of binding site context for transcription factor binding and gene regulation, BMC BIOINFORMATICS, 2008, 9, s. 1-38
  17. Romanowski Zbigniew, Jalbout Abraham Representation of Kohn-Sham free atom eigenfunctions by Slater-type orbitals, International Journal of Quantum Chemistry, 2008, 108, s. 1465-1476
  18. Romanowski Zbigniew Numerical calculation of overlap and kinetic integrals in prolate spheroidal coordinates. II, International Journal of Quantum Chemistry, 2008, 108, s. 487-492
  19. Romanowski Zbigniew Numerical calculation of overlap and kinetic integrals in prolate spheroidal coordinates, International Journal of Quantum Chemistry, 2008, 108, s. 249-256
  20. Jalbout A.F, Romanowski Zbigniew, Contrerras-Torres .F, de Leon A Stabilization of Excess Electrons in Molecular Charge Pockets on Nano-Surfaces, Journal of Computational and Theoretical Nanoscience, 2008, 5, s. 1263-1268
  21. Romanowski Zbigniew, Jalbout Abraham Two-center overlap integrals, three dimensional adaptive integration, and prolate ellipsoidal coordinates, JOURNAL OF MATHEMATICAL CHEMISTRY, 2008, 1-11, s. 1-11
  22. Romanowski Zbigniew, Krukowski Stanisław Numerical evaluation of overlap integrals between atomic orbitals, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 2008, 848, s. 34-39
  23. Plewczyński Dariusz TVscreen: Rapid screening of large compounds collections using trend vectors IARIA BioTechno’2008 Conference Proceedings IEEE Computer Society Digital Library, A, 2008
  24. Plewczyński Dariusz kNNsim: k-Nearest neighbors similarity with genetic algorithm features optimization enhances the prediction of activity classes for small molecules, JOURNAL OF MOLECULAR MODELING, 2008, 1, s. 1-6
  25. Plewczyński Dariusz, Tkacz Adrian, Wyrwicz Lucjan, Rychlewski Leszek, Ginalski Krzysztof AutoMotif Server for prediction of phosphorylation sites in proteins using support vector machine: 2007 update, JOURNAL OF MOLECULAR MODELING, 2008, 14, s. 69-76
  26. Grochowski Paweł, Trylska Joanna Continuum molecular electrostatics, salt effects, and counterion binding – A review of the Poisson-Boltzmann theory and its modifications, BIOPOLYMERS, 2008, 89, s. 93-113
  27. Zamłyńska Katarzyna, Bolikowski Łukasz, Rosiek Tomasz Migration of the Mathematical Collection of Polish Virtual Library of Science to the YADDA platform DML 2008, Towards Digital Mathematics Library, Sojka Petr , Masaryk University, 2008
  28. Grochowski Paweł Rotational symmetry of the molecular potential energy in the Cartesian coordinates, THEORETICAL CHEMISTRY ACCOUNTS, 2008, 121, s. 257-266
  29. Schuller Bernd, Demuth Bastian, Mix Hartmut, Rasch Katharina, Romberg Mathilde, Sild Sulev, Maran Uko, Bała Piotr, del Grosso Enrico, Casalegno Mosé, Piclin Nadège, Pintore Marco, Sudholt Wibke, Baldridge Kim Chemomentum – UNICORE 6 based infrastructure for complex applications in science and technology, Lecture Notes in Computer Science, 2008, 4854, s. 82-93
  30. Benedyczak Krzysztof, Bała Piotr Flexible streaming infrastructure for Unicore, Lecture Notes in Computer Science, 2008, 4854, s. 94-103
  31. Lebioda Paweł, Bała Piotr Estimating Metabolic Pathways Parameters Using Distributed Monte Carlo Method, Lecture Notes in Computer Science, 2008, 5073, s. 987-999
  32. Mederski Jarosław, Mikulski Łukasz, Bała Piotr Asynchronous Parallel Molecular Dynamics Simulations, Lecture Notes in Computer Science, 2008, 4967, s. 439-446
  33. Kluszczyński Rafał, Bała Piotr Supporting NAMD Application on the Grid Using GPE, Lecture Notes in Computer Science, 2008, 4967, s. 762-769
  34. Romanowski Zbigniew, Jalbout Abraham Decomposition of Molecular Charge Speeds up the Evaluation of Coulomb Potential, Acta Physica Polonica B, 2008, 39, s. 1455-1465
  35. Romanowski Zbigniew, Jalbout Abraham Overlap Integrals Between Atomic Orbitals with Piecewise Polynomial Radial Part Evaluated in Prolate Spheroidal Coordinates, Acta Physica Polonica B, 2008, 39, s. 923-939
  36. Romanowski Zbigniew, Krukowski Stanisław, Jalbout Abraham Transformation of Real Spherical Harmonics under Rotations, Acta Physica Polonica B, 2008, 39, s. 1985-1991
  37. Długosz Maciej, Trylska Joanna Electrostatic similarity of proteins: Application of three dimensional spherical harmonic decomposition, JOURNAL OF CHEMICAL PHYSICS, 2008, 129, s. 1-10
  38. Kulczycka Katarzyna, Długosz Maciej, Trylska Joanna Molecular Dynamics of Elongation Factors G and Tu Bioinformatics 2008 24-27 April, Warsaw Proceedings, Warszawa, 2008
  39. Długosz Maciej, Trylska Joanna Association of Neamine and its Derivative with Ribosomal A-Site RNA From Computational Biophysics to Systems Biology (CBSB08), Symposium 19-21 May 2008 Forschungszentrum Julich Proceedings., Julich, NIC-Directors, 2008
  40. Kulczycka Katarzyna, Długosz Maciej, Trylska Joanna Internal Dynamics of Ribosomal elongation Factors G and tu Studied with All-Atom and Coarse-Grained Molecular Dynamics From Computational Biophysics to Systems Biology (CBSB08), Symposium 19-21 May 2008 Forschungszentrum Julich Proceedings., Julich, NIC-Directors, 2008
  41. Jurkiewicz Jakub, Nowiński Krzysztof, Bała Piotr Prediction of the Jobs Execution on the Community Grid CGW’07 Proceedings ACC CYFRONET, Kraków, AGH, 2008
  42. Jurkiewicz Jakub, Nowiński Krzysztof, Bała Piotr Numerical simulations of the resource utilization in the community grids., Polish Journal of Environmental Studies, 2008, 17, s. 130-134
  43. Bruska Marta, Piechota Jacek Density functional study of sulphur hexafluoride (SF6) and its hydrogen derivatives, Molecular Simulation, 2008, 34, s. 1041-1050
  44. Wróbel Jan, Piechota Jacek On the structural stability of ZnO phases, SOLID STATE COMMUNICATIONS, 2008, 146, s. 324-329
  45. Szpindler Maciej, Cytowski Maciej Numerical Weather Forecasting for Poland, ERCIM News, 2008, 74, s. 19-20
  46. Jurkiewicz Jakub, Nowiński Krzysztof, Bała Piotr Unicore 6 as a platform for desktop grid Computer Science and Information Technology, 2008. IMCSIT 2008. International Multiconference on, Ganzha Maria, Paprzycki M, Pełech-Pilkowski T , 2008
  47. Jurkiewicz Jakub, Nowiński Krzysztof, Bała Piotr Prediction of the Jobs Execution on the Community Grid with Added Network Latency Distributed and Parallel Systems In Focus: Desktop Grid Computing, Kacsuk Péter, Lovas Róbert, Németh Zsolt , 2008
  48. Chlebiej Michał, Nowiński Krzysztof, Scisło Piotr, Bała Piotr Development of heart motion reconstruction framework based on 4D echocardiographic data, Annales Universitatis Mariae Curie-Skłodowska Sectio AI Informatica, 2008, 8, s. 43-50
  49. Romanowska Julia, Setny Piotr Molecular dynamics study of the ribosomal A-site, JOURNAL OF PHYSICAL CHEMISTRY B, 2008, 112, s. 15227-15243
  50. Grochala Wojciech, Grochala Wojciech Greedy Ag(II) Oxidizer: Can Any Inorganic Ligand Except Fluoride Endure Its Presence in Simple Ionic Solids?, JOURNAL OF FLUORINE CHEMISTRY, 2008, 129, s. 82-90
  51. Jaroń Tomasz, Grochala Wojciech, Grochala Wojciech Prediction of Giant Antiferromagnetic Coupling in Exotic Fluorides of AgII, Physica Status Solidi-Rapid Research Letters, 2008, 2, s. 71-73
  52. Grochala Wojciech, Grochala Wojciech Beyond Fluorides: Extension of Chemistry of Divalent Silver to Oxo Ligands, INORGANIC CHEMISTRY COMMUNICATIONS, 2008, 11, s. 155-158
  53. Kurzydłowski Dominik, Grochala Wojciech, Grochala Wojciech Elusive AuF in the Solid State As Accessed via High Pressure Comproportionation, CHEMICAL COMMUNICATIONS, 2008, 1073-1075, s. 1073-1075
  54. Kurzydłowski Dominik, Grochala Wojciech, Grochala Wojciech Xenon as a Mediator of Chemical Reactions? Case of Elusive Gold Monofluoride, AuF, and Its Adduct With Xenon, XeAuF, ZEITSCHRIFT FUR ANORGANISCHE UND ALLGEMEINE CHEMIE, 2008, 634, s. 1082-1086
  55. Grochala Wojciech, Grochala Wojciech Ligation of Aza Bases to the AgF2 molecule: A Theoretical Study, JOURNAL OF MOLECULAR MODELING, 2008, 14, s. 887-890
  56. Fijałkowski Karol, Grochala Wojciech, Grochala Wojciech The ‘Magic’ Electronic State of High-TC Superconductors, DALTON TRANSACTIONS, 2008, 5447-5453, s. 5447-5453
  57. Grzybowska Dorota, Malinowski Przemysław, Mazej Zoran, Grochala Wojciech, Grochala Wojciech Probing Reactivity of the Potent AgF2 Oxidizer. Part 1: Organic Compounds, Collection of Czechoslovak Chemical Communications, 2008, 73, s. 1729-1746
  58. Malinowski Przemysław, Mazej Zoran, Grochala Wojciech, Grochala Wojciech Probing Reactivity of the Potent AgF2 Oxidizer. Part 2: Inorganic Compounds, ZEITSCHRIFT FUR ANORGANISCHE UND ALLGEMEINE CHEMIE, 2008, 634, s. 2608-2616
  59. Szypowski Marcin, Górecki Adam, Górecki Adam, Trylska Joanna RedMD ‒ a new package for reduced molecular dynamics Bioinformatics 2008 24-27 April, Warsaw Proceedings, Warszawa, 2008
  60. Romanowska Julia, Setny Piotr Molecular Dynamics Study of the Ribosomal A-site Bioinformatics 2008 24-27 April, Warsaw Proceedings, Warszawa, 2008
  61. Długosz Maciej, Romanowska Julia, Setny Piotr, Setny Piotr, Trylska Joanna Association of Aminoglycosidic Antibiotics. Molecular and Brownian Dynamics Study Struktura a funkcja białek i kwasów nukleinowych. XXXV Szkoła Zimowa Wydziału Biochemii, Biofizyki i Biotechnologii Uniwersytetu Jagiellońskiego, Zakopane 23-27.02.2008, Kraków, Wydawnictwo EJB, 2008
  62. Szypowski Marcin, Górecki Adam, Górecki Adam, Trylska Joanna RedMD – A New Package for reduced Molecular Dynamics From Computational Biophysics to Systems Biology (CBSB08), Symposium 19-21 May 2008 Forschungszentrum Julich Proceedings., Julich, NIC-Directors, 2008
  63. Kurzydłowski Dominik, Grochala Wojciech Elusive AuF in the solid state as accessed via high pressure comproportionation., CHEMICAL COMMUNICATIONS, 2008, 1, s. 1073-5
  64. Kurzydłowski Dominik, Grochala Wojciech Xenon as a mediator of Chemical Reactions ? Case of scarce gold monofluoride, Auf, and Its Adduct With Xenon XeAuf, ZEITSCHRIFT FUR ANORGANISCHE UND ALLGEMEINE CHEMIE, 2008, 634, s. 1082-1086
  65. Długosz Maciej, Romanowska Julia, Setny Piotr, Trylska Joanna, Setny Piotr Association of aminoglycosidic antibiotics with the ribosomal RNA Bioinformatics 2008 24-27 April, Warsaw Proceedings, Warszawa, 2008
  66. Herczyński Jan, Herbst Mikołaj Ре­форма във фи­нанси­ране­то на об­разовани­е­то в Бъл­гария: преглед на те­ку­щи­те проб­ле­ми, Sofia, 2008
  67. Kowalczyk Remigiusz, Szymańska Zuzanna On the global existence of solution to an aggregation model, JOURNAL OF MATHEMATICAL ANALYSIS AND APPLICATIONS, 2008, 343, s. 379-398
  68. Bodnar Marek, Foryś Urszula, Szymańska Zuzanna Model of AIDS-related tumour with time delay Proceedings of the XIV National Conference on Application of Mathematics in Biology and Medicine, Bodnar Marek, Foryś Urszula , Warszawa, Wydział Matematyki Informatyki i Mechaniki, Uniwersytet Warszawski, 2008
  69. Kniżewski Łukasz, Ginalski Krzysztof, Jerzmanowski Andrzej Snf2 proteins in plants: gene silencing and beyond., TRENDS IN PLANT SCIENCE, 2008, 13, s. 557-565
  70. Kniżewski Łukasz, Steczkiewicz Kamil, Kuchta Krzysztof, Wyrwicz Lucjan, Plewczyński Dariusz, Koliński Andrzej, Rychlewski Leszek, Ginalski Krzysztof Uncharacterized DUF1574 leptospira proteins are SGNH hydrolases, Cell Cycle, 2008, 7, s. 542-544
  71. Długosz Maciej, Antosiewicz Jan, Trylska Joanna Association of Aminoglycosidic Antibiotics with the Ribosomal A-Site Studied with Brownian Dynamics, Journal of Chemical Theory and Computation, 2008, 4, s. 549-559
  72. Gruziel Magdalena, Rudnicki Witold, Lesyng Bogdan Solvation Free Energy – Interpretation of Microscopic Simulations Based on Macroscopic Solvation Models 2nd Warsaw School of Statistical Physics, Kazimierz Dolny, Poland, 15-22, June 2007, Warszawa, Warsaw University Press, 2008
  73. Gruziel Magdalena, Rudnicki Witold, Lesyng Bogdan Hydration free energy of a Model Lennard-Jones solute particle: Microscopic Monte Carlo simulation studies, and interpretation based on mesoscopic models, JOURNAL OF CHEMICAL PHYSICS, 2008, 128, s. 1-13
  74. Grzelak Janusz, Batorski Dominik, Sułek Antoni, Tymowska Katarzyna, Kotowska Irena, Szumlicz Tadeusz Social diagnosis 2007, Czapiński Janusz, Panek Tomasz , Warszawa, Zakład Wydawnictw Statystycznych, 2008
  75. Geller Maciej, Walewski Łukasz, Długosz Maciej, Lesyng Bogdan Looking for Inhibitors of RIO Kinases From Computational Biophysics to System Biology (CBSB08), Jülich, John von Neumann Institute for Computing (NIC), 2008
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