Publikacje 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. Jurkiewicz Jakub , Nowiński Krzysztof , Bała Piotr , Unicore 6 as a platform for desktop grid W: Computer Science and Information Technology, 2008. IMCSIT 2008. International Multiconference on ed. Ganzha Maria , Paprzycki M , Pełech-Pilkowski T , , 2008, s. 453-457
  3. Jurkiewicz Jakub , Nowiński Krzysztof , Bała Piotr , Prediction of the Jobs Execution on the Community Grid with Added Network Latency W: Distributed and Parallel Systems In Focus: Desktop Grid Computing ed. Kacsuk Péter , Lovas Róbert , Németh Zsolt , , 2008, s. 43-48
  4. Szpindler Maciej , Cytowski Maciej , Numerical Weather Forecasting for Poland, ERCIM News, 2008, 74, s. 19-20
  5. 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
  6. 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
  7. Długosz Maciej , Trylska Joanna , Electrostatic similarity of proteins: Application of three dimensional spherical harmonic decomposition, JOURNAL OF CHEMICAL PHYSICS, 2008, 129, s. 1-10
  8. Trykozko Anna , Brouwer Geert , Zijl Wouter , Downscaling: a complement to homogenization, International Journal of Numerical Analysis and Modeling, 2008, 5, s. 157-170
  9. 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
  10. 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
  11. Wyrwicz Lucjan , Ginalski Krzysztof , Rychlewski Leszek , HSV-1 UL45 encodes a carbohydrate binding C-type lectin protein, Cell Cycle, 2008, 7, s. 269-271
  12. 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
  13. 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
  14. Kutner Jan , Towpik Joanna , Ginalski Krzysztof , Boguta Magdalena , Mitochondrial release factor in yeast: interplay of functional domains, CURRENT GENETICS, 2008, 53, s. 185-192
  15. 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
  16. Romanowski Zbigniew , Jalbout Abraham , Decomposition of Molecular Charge Speeds up the Evaluation of Coulomb Potential, ACTA PHYSICA POLONICA B, 2008, 39, s. 1455-1465
  17. 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
  18. Romanowski Zbigniew , Krukowski Stanisław , Jalbout Abraham , Transformation of Real Spherical Harmonics under Rotations, ACTA PHYSICA POLONICA B, 2008, 39, s. 1985-1991
  19. 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
  20. Romanowski Zbigniew , Numerical calculation of overlap and kinetic integrals in prolate spheroidal coordinates. II, International Journal of Quantum Chemistry, 2008, 108, s. 487-492
  21. Romanowski Zbigniew , Numerical calculation of overlap and kinetic integrals in prolate spheroidal coordinates, International Journal of Quantum Chemistry, 2008, 108, s. 249-256
  22. 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
  23. 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
  24. Romanowski Zbigniew , Krukowski Stanisław , Numerical evaluation of overlap integrals between atomic orbitals, JOURNAL OF MOLECULAR STRUCTURE-THEOCHEM, 2008, 848, s. 34-39
  25. 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
  26. 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
  27. Kulczycka Katarzyna , Długosz Maciej , Trylska Joanna , Molecular Dynamics of Elongation Factors G and Tu W: Bioinformatics 2008 24-27 April, Warsaw Proceedings , Warszawa, 2008
  28. Długosz Maciej , Trylska Joanna , Association of Neamine and its Derivative with Ribosomal A-Site RNA W: From Computational Biophysics to Systems Biology (CBSB08), Symposium 19-21 May 2008 Forschungszentrum Julich Proceedings. , Julich, NIC-Directors, 2008
  29. Voltz Karine , Trylska Joanna , Tozzini Valentina , Kurkal-Siebert Vandana , Smith Jeremy , Langowski Jörg , Global Motions in the Nucleosome Explored Using a Coarse-Grained Model W: From Computational Biophysics to Systems Biology (CBSB08), Symposium 19-21 May 2008 Forschungszentrum Julich Proceedings. , Julich, NIC-Directors, 2008
  30. Kulczycka Katarzyna , Długosz Maciej , Trylska Joanna , Internal Dynamics of Ribosomal elongation Factors G and tu Studied with All-Atom and Coarse-Grained Molecular Dynamics W: From Computational Biophysics to Systems Biology (CBSB08), Symposium 19-21 May 2008 Forschungszentrum Julich Proceedings. , Julich, NIC-Directors, 2008
  31. 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
  32. Plewczyński Dariusz , TVscreen: Rapid screening of large compounds collections using trend vectors W: IARIA BioTechno'2008 Conference Proceedings IEEE Computer Society Digital Library , A, 2008
  33. 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
  34. 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
  35. 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
  36. 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
  37. Mederski Jarosław , Mikulski Łukasz , Bała Piotr , Asynchronous Parallel Molecular Dynamics Simulations, Lecture Notes in Computer Science, 2008, 4967, s. 439-446
  38. Kluszczyński Rafał , Bała Piotr , Supporting NAMD Application on the Grid Using GPE, Lecture Notes in Computer Science, 2008, 4967, s. 762-769
  39. Jurkiewicz Jakub , Nowiński Krzysztof , Bała Piotr , Prediction of the Jobs Execution on the Community Grid W: CGW'07 Proceedings ACC CYFRONET , Kraków, AGH, 2008
  40. Lebioda Paweł , Bała Piotr , Estimating Metabolic Pathways Parameters Using Distributed Monte Carlo Method, Lecture Notes in Computer Science, 2008, 5073, s. 987-999
  41. 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
  42. Zamłyńska Katarzyna , Bolikowski Łukasz , Rosiek Tomasz , Migration of the Mathematical Collection of Polish Virtual Library of Science to the YADDA platform W: DML 2008, Towards Digital Mathematics Library ed. Sojka Petr , , Masaryk University, 2008, s. 127-130
  43. Benedyczak K. , Nowiński A. , Bała P. , Flexible streaming infrastructure for UNICORE, Lecture Notes in Computer Science, 2008, 4854, s. 94-103
  44. Grochowski Paweł , Rotational symmetry of the molecular potential energy in the Cartesian coordinates, THEORETICAL CHEMISTRY ACCOUNTS, 2008, 121, s. 257-266
  45. Benedyczak Krzysztof , Bała Piotr , Flexible streaming infrastructure for Unicore, Lecture Notes in Computer Science, 2008, 4854, s. 94-103
  46. Wróbel Jan , Piechota Jacek , On the structural stability of ZnO phases, SOLID STATE COMMUNICATIONS, 2008, 146, s. 324-329
  47. Bruska Marta , Piechota Jacek , Density functional study of sulphur hexafluoride (SF6) and its hydrogen derivatives, Molecular Simulation, 2008, 34, s. 1041-1050
  48. Romanowska Julia , Setny Piotr , Molecular dynamics study of the ribosomal A-site, JOURNAL OF PHYSICAL CHEMISTRY B, 2008, 112, s. 15227-15243
  49. Grochala Wojciech , Grochala Wojciech , Beyond Fluorides: Extension of Chemistry of Divalent Silver to Oxo Ligands, INORGANIC CHEMISTRY COMMUNICATIONS, 2008, 11, s. 155-158
  50. 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
  51. 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
  52. Grochala Wojciech , Grochala Wojciech , Ligation of Aza Bases to the AgF2 molecule: A Theoretical Study, JOURNAL OF MOLECULAR MODELING, 2008, 14, s. 887-890
  53. Fijałkowski Karol , Grochala Wojciech , Grochala Wojciech , The 'Magic' Electronic State of High-TC Superconductors, DALTON TRANSACTIONS, 2008, 5447-5453, s. 5447-5453
  54. 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
  55. 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
  56. 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
  57. 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
  58. Długosz Maciej , Romanowska Julia , Setny Piotr , Trylska Joanna , Setny Piotr , Association of aminoglycosidic antibiotics with the ribosomal RNA W: Bioinformatics 2008 24-27 April, Warsaw Proceedings , Warszawa, 2008
  59. Szypowski Marcin , Górecki Adam , Górecki Adam , Trylska Joanna , RedMD ‒ a new package for reduced molecular dynamics W: Bioinformatics 2008 24-27 April, Warsaw Proceedings , Warszawa, 2008
  60. Romanowska Julia , Setny Piotr , Molecular Dynamics Study of the Ribosomal A-site W: 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 W: 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 W: From Computational Biophysics to Systems Biology (CBSB08), Symposium 19-21 May 2008 Forschungszentrum Julich Proceedings. , Julich, NIC-Directors, 2008
  63. 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
  64. Herczyński Jan , Herbst Mikołaj , Ре­форма във фи­нанси­ране­то на об­разовани­е­то в Бъл­гария: преглед на те­ку­щи­те проб­ле­ми , Sofia, 2008
  65. Bodnar Marek , Foryś Urszula , Szymańska Zuzanna , Model of AIDS-related tumour with time delay W: Proceedings of the XIV National Conference on Application of Mathematics in Biology and Medicine ed. Bodnar Marek , Foryś Urszula , , Warszawa, Wydział Matematyki Informatyki i Mechaniki, Uniwersytet Warszawski, 2008, s. 153
  66. Kniżewski Łukasz , Ginalski Krzysztof , Jerzmanowski Andrzej , Snf2 proteins in plants: gene silencing and beyond., TRENDS IN PLANT SCIENCE, 2008, 13, s. 557-565
  67. 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
  68. Gruziel Magdalena , Rudnicki Witold , Lesyng Bogdan , Solvation Free Energy - Interpretation of Microscopic Simulations Based on Macroscopic Solvation Models W: 2nd Warsaw School of Statistical Physics, Kazimierz Dolny, Poland, 15-22, June 2007 , Warszawa, Warsaw University Press, 2008
  69. 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
  70. 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
  71. Geller Maciej , Walewski Łukasz , Długosz Maciej , Lesyng Bogdan , Looking for Inhibitors of RIO Kinases W: From Computational Biophysics to System Biology (CBSB08) , Jülich, John von Neumann Institute for Computing (NIC), 2008
  72. Grzelak Janusz , Batorski Dominik , Sułek Antoni , Tymowska Katarzyna , Kotowska Irena , Szumlicz Tadeusz , Social diagnosis 2007 ed. Czapiński Janusz , Panek Tomasz , , Warszawa, Zakład Wydawnictw Statystycznych, 2008