2006
For availability of preprints see personal webpage of co-workers
06-001Peter Schuster
Evolution and Design - The Darwinian View of Evolution is a Scientific Fact and Not an Ideology
Complexity, 11 (1): 12-15, 2006.
06-002
Peter F. Stadler and Peter Schuster
Modelling Conformational Flexibility and Evolution of Structure - RNA as an Example
In: Structural Approaches to Sequence Evolution: Molecules, Networks, Populations
Eds. U. Blastolla, M. Porto, H. Eduardo Roman, M. Vendruscolo
Series: Biological and Medical Physics, Biomedical Engineering
Springer-Verlag, Berlin, pp. 1-34, 2006.
06-003
Peter Schuster
Less is More and the Art of Modeling Complex Phenomena -Simplification May but Need not be the Key to Handle Large Networks
Complexity, 11 (2): 11-13, 2006.
06-004
Peter Schuster
Prediction of RNA Secondary Structures: From Theory to Models and Real Molecules
Reports on Progress in Physics, 69: 1419-1477, 2006.
06-005
Jord H.A. Nagel, Christoph Flamm, Ivo L. Hofacker, Kai Franke, Maarten H. de Smit, Peter Schuster, and Cornelis W.A. Pleij
Structural Parameters Affecting the Kinetics of RNA Hairpin Formation
Nucl.Acids Res., 34: 3568-3576, 2006.
06-006
James Lu, Heinz W. Engl, and Peter Schuster
Inverse Bifurcation Analysis: Application to Simple Gene Systems
AMB-Algorithms Mol.Biol., 1: (11), 2006.
06-007
Peter Schuster
Untamable Curiosity, Innovation, Discovery, and Bricolage. Are we Doomed to Progress to Ever Increasing Complexity?
Complexity, 11 (5): 9-11, 2006.
06-008
Peter Schuster
Boltzmann, Atomism, Evolution, and Statistics. Contuinity Versus Discreteness in Biology
Complexity, 11 (6): 9-11, 2006.
06-009
Stefan Müller, Josef Hofbauer, Lukas Endler, Christoph Flamm, Stefanie Widder and Peter Schuster
A Generalized Model of the Repressilator
J.Math.Biol., 53: 905–937, 2006.
06-010
Paul E. Phillipson and Peter Schuster
Analytical Dynamics of Neuron Pulse Propagation
Int.J.of Bifurcation and Chaos, 16: 3605–3616, 2006.
06-011
Wei-Che Hsu, Hsien-Da Huang, Sheng-Da Hsu, Li-Zen Lin, Ann-Ping Tsou, Ching-Ping Tseng, Peter F. Stadler, Stefan Washietl and Ivo L. Hofacker
miRNAMap: Genomic Maps of MicroRNA Genes and Their Target Genes in Mammalian Genomes
Nucleic Acids Res., 34: D135-D139, 2006.
06-012
Ulrike Mückstein, Hakim Tafer, Jörg Hackermüller, Stephan Bernhard, Peter F. Stadler and Ivo L. Hofacker
Thermodynamics of RNA-RNA Binding
Bioinformatics, 22: 1177-1182, 2006.
06-013
Ivo L. Hofacker and Peter F. Stadler
Memory Efficient Folding Algorithms for Circular RNA Secondary Structures
Bioinformatics, 22: 1172-1176, 2006.
06-014
Michael T. Wolfinger, Sebastian Will, Ivo L. Hofacker, Rolf Backofen and Peter F. Stadler
Exploring the Lower Part of Discrete Polymer Model Energy Landscapes
Europhys.Lett., 74: 726-732, 2006.
06-015
Stephan Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F. Stadler and Ivo L. Hofacker
Partition Function and Base Pairing Probabilities of RNA Heterodimers
AMB-Algorithms Mol.Biol., 1: 3, 2006.
06-016
Ivo L. Hofacker and Peter F. Stadler
Modeling RNA Folding
In: Complex Systems Science in BioMedicinei
Thomas S. Deisboeck, J. Yasha Kresh (eds.)
pp. 227-245, Springer Verlag, New York, NY, 2006.
06-017
Stephan Bernhart, Ivo L. Hofacker and Peter F. Stadler
Local Base Pairing Probabilities in Large RNAs
Bioinformatics, 22: 614-615, 2006.
06-018
Christian V. Forst, Christoph Flamm, Ivo L. Hofacker and Peter F. Stadler
Algebraic Comparison of Metabolic Networks, Phylogenetic Inference, and Metabolic Innovation
BMC Bioinformatics, 7: 67, 2006.
06-019
Jana Hertel, Manuela Lindemeyer, Kristin Missal, Claudia Fried, Andrea Tanzer, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler, and The Students of Bioinformatics Computer Labs 2004 and 2005
The Expansion of the Metazoan MicroRNA Repertoire
BMC Genomics, 7: 15, 2006.
06-020
Camille Stephan-Otto Attolini and Peter F. Stadler
Evolving Towards the Hypercycle: A Spatial Model of Molecular Evolution
Physica D, 217: 143-141, 2006.
06-021
Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, and Peter F. Stadler
Visualization of Barrier Tree Sequences
IEEE Trans., Visualization and Computer Graphics, 12, in press, 2006.
06-022
Axel Mosig, Ivo L. Hofacker, and Peter F. Stadler
Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular RNAs
In Robert Giegerich and Jens Stoye, editors,
Proceedings GCB 2006, Lecture Notes in Informatics, in press, 2006.
06-023
Sonja J. Prohaska and Peter F. Stadler
Evolution of the Vertebrate Parahox Clusters
J.Exp.Zool B(Mol.Dev.Evol.), 306B: 481-487, 2006.
06-024
Sebastian Pötzsch, Gerik Scheuermann, Michael T. Wolfinger, Christoph Flamm and Peter F. Stadler
Visualization of Lattice-Based Protein Folding Simulations
Tenth International Conference on Information Visualization (IV'06), 89-94, 2006.
06-025
Peter F. Stadler and Bärbel M. R. Stadler
Genotype-Phenotype Maps
Bio.Theory, 3: 268-279, 2006.
06-026
Suporn Charumanee, Aurawan Titwan, Jakkapan Sirithunyalug, Petra Weiß-Greiler, Peter Wolschann, Helmut Viernstein and Siriporn Okonogi
Thermodynamics of the Encapsulation by Cyclodextrins
J.Chem Tech.Biotech., 81: 523-529, 2006.
06-027
Ornjira Aruksankunwong, Supa Hannongbua, and Peter Wolschann
Hydrogen Bonding in Molecular Recognition by HIV-1 Protease
J. Mol.Struct., 790: 174-182, 2006.
06-028
J. Hönighoff, Gerhard Holzer, Peter Wolschann, and Gerhard Buchbauer
Syntheses and Odor of "bulky-group"-Modified Sandalwood Odorants: Isophorono-β-santalol Analogues
Europ.J.Med.Chem., 41: 905-913,2006.
06-029
Ornjira Aruksankunwong, Peter Wolschann, Supot Hannongbua and Pornthep Sompornpisut
Molecular Dynamic and Free Energy Studies of Primary Resistance Mutations in HIV-1 Protease-Ritonavir Complexes
J.Chem.Inf.Model., 46: 2085-2092, 2006.
06-030
Pornpan Pungpo, Patchardenat Saparpakorn, Peter Wolschann, and Supa Hannongbua
Computer-Aided Molecular Design of Highly Potent HIV-1 RT Inhibitors: 3D QSAR and Molecular Docking Studies of Efavirenz Derivates
SAR & QSAR in Environmental Research, 17: 353-370, 2006.
06-031
Nadtanet Nunthaboot, Somsak Tonmunphean, Vudhichai Parasuk, Sirirat Kokpol, and Peter Wolschann
Three-Dimensional Quantitative Structure Activity Relationships Studies on Diverse Structural Classes of HIV-1 Integrase Inhibitors using CoMFa and CoMSIA
Europ.J.Med.Chem., 41: 1359-1372, 2006.
06-032
Aleksander Koll, Alfred Karpfen and Peter Wolschann
Structural and Energetic Consequences of the Formation of Intramolecular Hydrogen Bonds
J.Mol.Struct., 790: 55-64, 2006.
06-033
Gunther Zechmann, Mario Barbatti, Hans Lischka, Jiri Pittner and Vlasta Bonacic-Koutecky
Multiple Pathways in the Photodynamics of a polar π-bond: A Case Study of Silaethylene
Chem.Phys.Lett., 418: 377-382, 2006.
06-034
Wilfried N. Gansterer, Wolfgang Kreuzer and Hans Lischka
Data Reduction Schemes in Davidson Subspace Diagonalization for MR-CI
LSSC 2005, LNCS 3743: 564-571, 2006.
06-035
Mario Barbatti, Adelia J.A. Aquino, and Hans Lischka
Ultrafast Two-Step Process in the Non-Adiabatic Relaxation of the CH2NH2+Molecule
Mol.Phys., 104: 1053-1060, 2006.
06-036
Mirjana Eckert-Maksic, Mario Vazdar, Mario Barbatti, Hans Lischka, and Zvonimir B. Maksic
Automerization Reaction of Cyclobutadiene and its Barrier Height – an ab initio Benchmark Multireference Average-Quadratic Coupled Cluster Study
J.Chem.Phys., 125: 064310-1-9, 2006.
06-037
Adélia J. A. Aquino, Mario Barbatti, and Hans Lischka
Excited-state properties and environmental effects for protonated Schiff bases: A Theoretical Study
Chem.Phys.Chem., 7: 2089-2096, 2006.
06-038
Roland Mitric, Vlasta Bonacic-Koutecky, Jiri Pittner, and Hans Lischka
Ab initio Nonadiabatic Dynamics Study of Ultrafast Radiationless Decay Over Conical Intersections Illustrated on the Na3F Cluster
J.Chem.Phys., 125: 024303-1-7, 2006.
06-039
Mario Barbatti, Mario Vazdar, Adélia J. A. Aquino, Mirjana Eckert-Maksic and Hans Lischka
The Nonadiabatic Deactivation Paths of Pyrrole
J.Chem.Phys., 125: 164323-1-7, 2006.
06-040
Mihajlo Etinski, Christoph Uiberacker and Werner Jakubetz
Counterdiabatic Suppression of Background State Population in Resonance Leaking by Controlling Intermediate Branching
J.Chem.Phys., 124: 124110, 2006.
06-041
Vojtek Szocs, Tibor Palszegi, Vladimir Lukes, Jaroslaw Sperling, Franz Milota, Werner Jakubetz and, Harald F. Kauffmann
Two-Dimensional Electronic Spectra of Symmetric Dimers: Intermolecular Coupling and Conformational States
J.Chem.Phys., 124: 124511, 2006.
06-042
Christoph A. Marx and Werner Jakubetz
Phase-sensitive Stimulated Raman Adiabatic Passage in Dipolar Extended Lambda Systems
J.Chem.Phys., 125: 234103, 2006.
06-043
Werner Jakubetz
Peter Schuster zum 65. Geburtstag
Deut.Bunseng., 8: 73-74, 2006.
06-044
Alfred Karpfen and Ajit J. Thakkar
Does the Most Stable Formic Acid Tetramer Have π Stacking or C-H•••O Interactions?
J.Chem.Phys., 124: 224313, 2006.
06-045
Juan Carlos Sancho-Garcia and Alfred Karpfen
Conformational Analysis of 2,2’-Bifuran: Correlated High Level ab initio and DFT Results
Theor.Chem.Acc., 115: 427-433, 2006.
06-046
Eugene S. Kryachko and Alfred Karpfen
Theoretical Force-Field Model for Blue-Shifted Hydrogen Bonds with Fluoromethanes
Chem.Phys., 329: 313-328, 2006.
06-047
Alfred Karpfen and Eugene S. Kryachko
On Blue-Shifts of C-H Stretching Modes of Dimethyl Ether in Hydrogen- and Halogen-Bonded Complexes
Chem.Phys.Lett., 431: 428-433, 2006.
06-048
Paul Perco and Ronald Rapberger and Christian Siehs and Arno Lukas and Rainer Oberbauer and Gert Mayer and Bernd Mayer
Transforming Omics Data Into Context: Bioinformatics on Genomics and Proteomics Raw Data
Electrophoresis.Rev., 27: 2659-2675, 2006.
06-049
Johannes Söllner and Bernd Mayer
Machine Learning Approaches for Prediction of Linear B-Cell Epitopes on Proteins
J.Mol.Recognit., 19: 200-208, 2006.
06-050
Paul Perco, Clara Pleban, Alexander Kainz, Arno Lukas, Gert Mayer, Bernd Mayer and Rainer Oberbauer
Protein biomarkers associated with acute renal failure and chronic kidney disease
Europ.J.Cli.Invest., 36: 753-763, 2006.
06-051
Paul Perco, Clara Pleban, Alexander Kainz, Arno Lukas, Bernd Mayer, and Rainer Oberbauer
Gene expression and biomarkers in renal transplant ischemia reperfusion injury
Transplant Int., 20: 2-11, 2006.