2008
For availability of preprints see personal webpage of co-workers
08-001
Peter Schuster
Modeling in biological chemistry. From biochemical kinetics to systems biology
Monatsh.Chem., 139: 427-446, 2008
08-002
Peter Schuster and Peter Wolschann
Editorial: Computational chemistry
Monatsh.Chem., 139: III-IV, 2008
08-003
Peter Schuster
The mathematics of Darwinian systems
Appendix for the book: Manfred Eigen, From Strange Simplicity to Complex Familiarity, Vol.I, 2008
08-004
Peter Schuster
Was heißt und zu welchem Ende benötigt man eine Akademie der Wissenschaften?
Österreichische Akademie der Wissenschaften 2006-2008
Almanach, 157: 297-310, 2008
08-005
Peter Schuster and Anton Zeilinger
Vom Radiuminstitut zum Forschungsträger
Österreichische Akademie der Wissenschaften 2006-2008
Almanach, 157: 277-282, 2008
08-006
Peter Schuster and Peter F. Stadler
Nature and Evolution of Early Replicons
In: Domingo, E. and Parrish, C. R. and Holland, J.
Nature and Evolution of Early Replicons
Academic Press, London, UK, pages 1-41, 2008
08-007
Christoph Flamm and Ivo L. Hofacker
Beyond energy minimization: Approaches to the kinetic folding of RNA
Monatsh.Chem., 139: 447-457, 2008
08-008
Andreas R. Gruber, Dorota Koper-Emde, Manja Marz, Hakim Tafer, Stephan Bernhart, Gregor Obernosterer, Axel Mosig, Ivo L. Hofacker, Peter F. Stadler, and Bernd-Joachim Benecke
Invertebrate 7SK snRNAs
J.Mol.Evol., 66: 107-115, 2008
08-009
Radka S. Varekova, Ivan Bradac, Martin Plchut, Michal Skrdla, Michael Wacenovsky, Helmuth Mahr, Georg Mayer, Herbert Tanner, Hermann Brugger, Josef Withalm, Peter Lederer, Heinrich Huber, Gerhard Gierlinger, Ronald Graf, Hakim Tafer, Ivo L. Hofacker, Peter Schuster, and Martin Polcik
www.rnaworkbench.com: A new program for analyzing RNA interference
Comput.Methods Programs Biomed., 90: 89-94, 2008
08-010
Andreas R. Gruber, Stefan H. Bernhart, Ivo L. Hofacker, and Stefan Washietl
Strategies for measuring evolutionary conservation of RNA secondary structures
BMC Bioinformatics, 9: 122, 2008
08-011
Jana Hertel, Ivo L. Hofacker, and Peter F. Stadler
SnoReport: Computational identification of snoRNAs with unknown targets
Bioinformatics, 249: 158-164, 2008
08-012
Athanasius F. Bompfünewerer, Rolf Backofen, Stephan H. Bernhart, Jana Hertel, Ivo L. Hofacker, Peter F. Stadler, and Sebastian Will
Variations on RNA folding and alignment: Lessons from benasque
J.Math.Biol., 56: 119-144, 2008
08-013
Hakim Tafer, Stefan L. Ameres, Gregor Obernosterer, Christoph A. Gebeshuber, Renee Schroeder, Javier Martinez, and Ivo L. Hofacker
The impact of target site accessibility on the design of effective siRNAs
Nature Biotech., 26: 578-583, 2008
08-014
Michael Geis, Christoph Flamm, Michael T. Wolfinger, Andrea Tanzer, Ivo L. Hofacker, Martin Middendorf, Christian Mandl, Peter F. Stadler, and Caroline Thurner
Folding kinetics of large RNAs
J.Mol.Biol., 379: 160-173, 2008
08-015
Christoph Jöchl, Mathieu Rederstorff, Jana Hertel, Peter F. Stadler, Ivo L. Hofacker, Markus Schrettl, Hubertus Haas, and Alexander Hüttenhofer
Small ncRNA transcriptome analysis from Aspergillus fumigatus suggests a novel mechanism for regulation of protein-synthesis
Nucleic Acids Res., 36: 2677-2689, 2008
08-016
Ulrike Mückstein, Hakim Tafer, Stephan H. Bernhard, Maribel Hernandez-Rosales, Jörg Vogel, Peter F. Stadler and Ivo L. Hofacker
Translational control by RNA-RNA interaction: Improved computation of RNA-RNA binding thermodynamics
In M. Elloumi, J. Küng, M. Linial, R. Murphy, K. Schneider and C. Toma, eds., Bioinformatics Research and Development
volume 13, pages 114-127, of Communications in Computer and Information Science, Springer Verlag, 2008
08-017
Andreas R. Gruber, Ronny Lorenz, Stephan H Bernhart, Richard Neuböck and Ivo L. Hofacker
The Vienna RNA websuite
Nucl.Acids Res., 36: W70-W74, 2008
08-018
Konstantin Klemm, Christoph Flamm and Peter F. Stadler
Funnels in Energy Landscapes
Eur.J.Phys.B, 63: 387-391, 2008
08-019
Alexander Ullrich and Christoph Flamm
Functional Evolution of Ribozyme-Catalysed Metabolisms in a Graph-Based Toy-Universe
Lecture Notes Bioinf., 5307: 0028, 2008
08-020
Dominic Rose, Jana Hertel, Kristin Reiche, Jörg Hackermüller and Peter F. Stadler
NcDNAlign: Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences
Genomics, 92: 65-74, 2008
08-021
Andreas R. Gruber, Carsten Kilgus, Axel Mosig, Ivo L. Hofacker, Wolfgang Hennig and Peter F. Stadler
Arthropod 7SK RNA
Mol.Biol.Evol., 25: 1923-1930, 2008
08-022
Sonja J. Prohaska and Peter F. Stadler
Genes
Theory Biosci., 127: 215-221, 2008
08-023
Sonja J. Prohaska and Peter F. Stadler
A Story of Growing Confusion: Genes and Their Regulation
In: Rubem P. Mondaini, Rui Dilao Biomat eds., International Symposium on Mathematical and Computational Biology
World Scientific, Singapore , pp.325-345, 2008
08-024
Andreas W.M. Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J. Prohaska and Peter F. Stadler
Noisy: Identification of problematic columns in multiple sequence alignments
Alg.Mol.Biol., 3: 7, 2008
08-025
Sonja J. Prohaska, Guido Fritzsch, Peter F. Stadler
Rate Variations, Phylogenetics, and Partial Orders
In: M. Ahdesmäki, K. Strimmer, N. Radde, J. Rahnenführer, K. Klemm, H. Lähdesmäki, O. Yli-Harja, eds.
Fifth Workshop on Computational System Biology, WCSB 2008, TU Tampere, 2008
08-026
Chris T. Amemiya, Sonja J. Prohaska, Alicia Hill-Force, April Cooke, Jessica Wasserscheid, David E. K. Ferrier, Juan Pacual Anaya, Jordi Garcia-Fern&agrav;ndez, Ken Dewar and Peter F. Stadler
The Amphioxus Hox Cluster: Characterization, Comparative Genomics, and Evolution
J.Exp.Zool.MDE, 310B: 465-477, 2008
08-027
Jörg Lehmann, Peter F. Stadler, Sonja J. Prohaska
SynBlast: Assisting the Analysis of Conserved Synteny Information
BMC Bioinformatics, :9 351, 2008
08-028
Mingyi Xie, Axel Mosig, Xiaodong Qi, Yang Li, Peter F. Stadler and Julian J.-L. Chen
Structure and Function of the Smallest Vertebrate Telomerase RNA from Teleost Fish
J.Biol.Chem., 283: 2049-2059, 2008
08-029
Guido Fritzsch, Manja U. Böhme, Mike Thorndyke, Hiroaki Nakano, Olle Israelsson, Thomas Stach, Martin Schlegel, Thomas Hankeln and Peter F. Stadler
A PCR Survey of Xenoturbella bocki
J.Exp.Zool.B: Mol.Dev.Evol., 310B: 278-284, 2008
08-030
Veiko Krauss, Christian Thümmler, Franziska Georgi, Jörg Lehmann, Peter F. Stadler and Carina Eisenhardt
Near intron positions are reliable phylogenetic markers: An application to Holometabolous Insects
Mol.Biol.Evol, 25:821-830 , 2008
08-031
Marleen Perseke, Guido Fritzsch, Kai Ramsch, Matthias Bernt, Daniel Merkle, Martin Middendorf, Detlef Bernhard, Peter Stadler and Martin Schlegel
Evolution of Mitochondrial Gene Orders in Echinoderms
Mol.Phylog.Evol., 47: 855-864, 2008
08-032
Tanja Gesell and Stefan Washietl
Dinucleotide Controlled Null Models for Comparative RNA Gene Prediction
BMC Bioinformatics, 9: 248, 2008
08-033
Stefan Washietl, Rainer Machne and N. Goldman
Evolutionary Footprints of Nucleosome Positions in Yeast
Trends in Genetics, doi:10.1016/j.tig.2008.09.003, 2008
08-034
V.J. Lynch, Andrea Tanzer, Y. Wang, F.C. Leung, B. Gellersen, D. Emera, Günter P. Wagner
Adaptive Changes in the Transcription Factor HoxA-11 are Essential for the Evolution of Pregnancy in Mammals
Proc.Natl.Acad.Sci.USA, : , 2008
08-035
Gregor Obernosterer, Hakim Tafer and Javier Martinez
Target site effects in the RNA interference and microRNA pathways
Biochem.Soc.Trans., :36 1216-1219, 2008
08-036
Anna Stary, Yinon Shafrir, Steffen Hering, Peter Wolschann and H. Robert Guy
Structural Model of the Cav1.2 Pore
Channels, 2: 210-215, 2008
08-037
Steffen Hering, Stanislav Beyl, Anna Stary, Michaela Kudrnac, Annette Hohaus, Robert H. Guy and Eugen Timin
Pore stability and gating in voltage-activated calcium channels
Channels, 2: 61-69, 2008
08-038
Anna Stary, Michaela Kudrnac, Stanislav Beyl, Annette Hohaus, Eugen Timin, Peter Wolschann, H. Robert Guy and Steffen Hering
Molecular Dynamics and Mutational Analysis of a Channelopathy mutation in the IIS6 Helix of Cav1.2
Channels, 2: 116-223, 2008
08-039
Iris Stappen, Joris Höfinghoff, Susanne Friedl, Claudia Pammer, Peter Wolschann and Gerhard Buchbauer
Structure-activity relationships of sandalwood odorants: Total synthesis and fragrance properties of cyclopropano-β-santalol
Europ.J.med.Chem., 43: 1525-1529, 2008
08-040
Speranta Avram, Heinz Berner, Adina L. Milac, and Peter Wolschann
Quantitative structure-activity relationship studies on membrane receptors inhibition by antipsychotic drugs. Application to schizophrenia treatment
Monatsh.Chem., 139: 407-426, 2008
08-041
Kirsten Knape, Anton Beyer, Anna Stary, Gerhard Buchbauer and Peter Wolschann
Genomics of selected human odorant receptors
Monatsh.Chem., 139: 1537-1544, 2008
08-042
Alfred Karpfen, Elisabeth Liedl, Walter Snor, Helmut Viernstein, Petra Weiss-Greiler, and Peter Wolschann
Density functional calculations on cyclodextrins
Monatsh.Chem., 139: 363-371, 2008
08-043
Alfred Karpfen
Theoretical Characterization of the Trends in Halogen Bonding
Struct.Bond., 126: 1-15, 2008
08-044
Mario Barbatti, Matthias Ruckenbauer, Jaroslaw J. Szymczak, Adelia J.A. Aquino, and Hans Lischka
Nonadiabatic Excited-State Dynamics of Polar -Systems and Related Model Compounds of Biological Relevance
Phys.Chem.Chem.Phys, 10: 482-494, 2008
08-045
H. Köppel, Bernd Schubert, and Hans Lischka
Conical Intersections and Strong Nonadiabatic Coupling Effects in Singlet-Excited Acetylene: an ab initio Quantum Dynamical Study
Chem.Phys., 343: 319-328, 2008
08-046
Ivana Antol, Mario Barbatti, Mirjana Eckert-Maksic, and Hans Lischka
Quantum Chemical Calculations of Electronically Excited States: Formamide, its Protonated Form and Alkali Cation Complexes as Case Studies
Monatsh.Chemie, 139: 319-328, 2008
08-047
Vladimir Lukes, Katarina Matuszna, Peter Rapta, Roland Solc, Lothar Dunsch, Adelia J.A. Aquino, and Hans Lischka
Experimental and theoretical study of model ladder fluoranthenopyracylene with two-dimensional? π-conjugation upon charging: Structure and optical properties
J.Phys.Chem., C 112: 3949-3958, 2008
08-048
Christian Schriever, Mario Barbatti, Kai Stock, Adelia J. A. Aquino, Daniel Tunega, Stefan Lochbrunner, Eberhard Riedle , Regina de Vivie-Riedle and Hans Lischka
The interplay of skeletal deformations and ultrafast excited state intramolecular proton transfer: Experimental and theoretical investigation of 10-hydroxybenzo[h]quinoline
Chem.Phys., 347: 446-461, 2008
08-049
Gunther Zechmann and Mario Barbatti
Ab Initio Study of the Photochemistry of Aminopyrimidine
Int.J.Quant.Chem, 108: 1266-1276, 2008
08-050
Adelia J.A. Aquino, Daniel Tunega, Hasan Pašalic, Georg Haberhauer, Martin H. Gerzabek and Hans Lischka
The thermodynamic stability of hydrogen bonded and cation bridged complexes of humic acid models-A theoretical study
Chem.Phys., 349: 69-76, 2008
08-051
Mario Barbatti, S. Belz, M. Leibscher, Hans Lischka and J. Manz
Sensitivity of femtosecond quantum dynamics and control with respect to non-adiabatic couplings: Model simulations for the cis-trans isomerization of the dideuterated methaniminium cation
Chem.Phys., 350: 145-153, 2008
08-052
Mario Barbatti, Adelia J.A. Aquino and Hans Lischka
Theoretical investigation of the mode-specific induced non-radiative decay in 2-pyridone
Chem.Phys., 349: 278-286, 2008
08-053
Ron Shepard, Gary S. Kedziora, Hans Lischka, Isaiah Shavitt, Thomas Müller, Peter G. Szalay, Mihaly Kallay, Michael Seth
The accuracy of molecular bond lengths computed by multireference electronic structure methods
Chem.Phys., 349: 37-57, 2008
08-054
Jaroslaw J. Szymczak, Mario Barbatti and Hans Lischka
Mechanism of Ultrafast Photodecay in Restricted Motions in Protonated Schiff Bases: The Pentadieniminium Cation
J.Chem.Theory Comput., 4: 1189-1199, 2008
08-055
Mario Barbatti and Hans Lischka
Nonadiabatic Deactivation of 9H-Adenine: A Comprehensive Picture Based on Mixed Quantum-Classical Dynamics
J.Am.Chem.Soc., 130: 6831-6839, 2008
08-056
Adelia J.A. Aquino, Daniel Tunega, Georg Haberhauer, Martin H. Gerzabek, Hans Lischka
Acid-base properties of a goethite surface model: A theoretical view
Geochim.Cosmochim. Acta, 72: 3587-3602, 2008
08-057
Evan B. Wang, Carol A. Parish and Hans Lischka
An extended multireference study of the electronic states of para-benyne
J.Chem.Phys., 129: 044306-1-8, 2008
08-058
Mario Barbatti, Horst Köppel, Ron Shepard and Peter G. Szalay
Electron correlation and molecular dynamics for excited states and photochemistry
Chem.Phys., 349: vii-viii, 2008
08-059
Gunther Zechmann and Mario Barbatti
Photophysics and Deactivation Pathways of Thymine
J.Phys.Chem.A, 112: 8273-8279, 2008
08-060
Mario Barbatti, Bernhard Sellner, Adelia J.A. Aquino and Hans Lischka
Nonadiabatic excited-state dynamics of aromatic heterocycles: Toward the time-resolved simulation of nucleobases
In:Radiation Induced Molecular Phenomena in Nucleic Acids,
Eds.: M.K. Shukla and J. Leszczynski,
Springer Science Business Media B.V., 209-235, 2008
08-061
Daniel Tunega, Martin H. Gerzabek, Georg Haberhauer, Kai U. Totsched and Hans Lischka
Model study on sorption of polycyclic aromatic hydrocarbons to goethite
J. of Colloid and Interface Sci., 330: 244-249, 2008
08-062
Ivana Antol, Mirjana Eckert-Maksic, Milan Oncak, Petr Slavicek and Hans Lischka
Photodissociation Pathways of Acetone upon Excitation into the 3s State: Adiabatic Versus Diabatic Mechanism
Collect.Czech.Chem.Commun., 73: 1475–1494, 2008
08-063
Vladimir Lukes, Roland Solc, Mario Barbatti, Marcus Elstner, Hans Lischka and Harald-Friedrich Kauffmann
Torsional potentials and full-dimensional simulation of electronic absorption and fluorescence spectra of para-phenylene oligomers using the semiempirical self-consistent charge density-functional tight binding approach
J.Chem.Phys., 129: 164905, 2008
08-064
Daniel Tunega, Adelia J.A. Aquino, Georg Haberhauer, Martin H. Gerzabek and Hans Lischka
In: Hydrogen Bonds and Solvent Effects in Soil Processes: A Theoretical View,
S.Canuto (ed.), Solvation Effects on Molecules and Biomolecules, Springer Science+Business Media B.V., pages 321–347, 2008.
08-065
Ivana Antol, Mario Vazdar, Mario Barbatti and Mirjana Eckert-Maksic
The effect of protonation on the photodissociation processes in formamide - An ab initio surface hopping dynamics study
Chem.Phys., 349: 308-318, 2008
08-066
Markus Seidl, Christoph Uiberacker and Werner Jakubetz
Pulse-Train Control of Multiphoton Transitions in Anharmonic Progressions: Resonance Loci and Resonance Ridges
Chem.Phys., 349: 296-307, 2008
08-067
Eva Scholtzova, Lubomir Benco and Daniel Tunega
A Model Study of Dickite Intercalated with Formamide and N-Methylformamide
Phys.Chem.Miner., 35: 299-309, 2008
08-068
Maria Hoffmann-Ostenhof, Thomas Hoffmann-Ostenhof, Ari Laptev, Jesper Tidblom
Many-Particle Hardy Inequalities
J.Lond.Math.Soc., 77:99-114 , 2008
08-069
Soren Fournais, Maria Hoffmann-Ostenhof, Thomas Hoffmann-Ostenhof, Thomas Oestergaard Soerensen
Positivity of the spherically averaged atomic one-electron density
Math. Z., 259: 123-130, 2008
08-070
Ronald Rapberger, Paul Perco, Cornelia Sax, Thomas Panger, Christian Siehs, Dietmar Pils, Andreas Bernthaler, Arno Lukas, Bernd Mayer and Michael Krainer
Linking the ovarian cancer transcriptome and immunome
BMC Systems Biology, 2: 1-15, 2008
08-071
Paul Perco , Julia Wilflingseder , Andreas Bernthaler , Martin Wiesinger , Michael Rudnicki , Barbara Wimmer , Bernd Mayer , Rainer Oberbauer
Biomarker candidates for cardiovascular disease and bone metabolism disorders in chronic kidney disease: a systems biology perspective
J.Cell.Mol.Med., 12: 1-13, 2008
08-072
Johannes Söllner, Rainer Grohmann, Ronald Rapberger, Paul Perco, Arno Lukas and Bernd Mayer
Analysis and prediction of protective continuous B-cell epitopes on pathogen proteins
Immun.Res., 4: 1-17, 2008
08-073
Markus Seidl, Mihajlo Etinski, Christoph Uiberacker and Werner Jakubetz
Pulse-train control of branching processes: Elimination of background- and intruder state population
J.Chem.Phys., 129: 234305, 2008
08-074
James Lu, Stefan Müller, Rainer Machne, Christoph Flamm
SBML ODE Solver Library: Extensions for Inverse Analysis
In: Fifth International Workshop on Computational Systems Biology WCSB 2008 June 11- 13, Leipzig, Germany / M. Ahdesmaki (Ed.) Tampere International Center for Signal
Processing Series, 41: 93-96, 2008.