2007
For availability of preprints see personal webpage of co-workers
07-001
Peter Schuster, Stefanie Widder, and J. Schicho
Dynamic Patterns of Gene Regulation I: Simple Two Gene Systems
J.Theor.Biol., 241: 395-419, 2007.
07-002
Peter Schuster
Evolution und Design
In: Schöpfung und Evolution, Eds. S. O. Horn, S. Wiedehofer
Eine Tagung mit Papst Benedikt XVI, Castel Gandolfo, IT,
Sankt Ulrich Verlag GmbH, Augsburg, DE, pages 25-56, 2007.
07-003
James Lu, Heinz W. Engl, Rainer Machne, and Peter Schuster
Inverse Bifurcation Analysis of a Model for the Mammalian G1/S Regulatory Module
Lecture Notes in Computer Science, 4414: 168-184, 2007.
07-004
Christoph Flamm, Lukas Endler, Stefan Müller, Stefanie Widder and P. Schuster
A Minimal and Self-Consistent in silico Cell Model Based on Macromolecular Interactions
Phil.Trans.Roy.Soc.B, 362: 1831-1839, 2007.
07-005
Peter Schuster
The Role of Nonlinear Dynamics from Physics to Biology. Selforganization - An old Paradigm Revisited
Complexity, 12(4): 9-11, 2007.
07-006
Peter Schuster
Ursprung des Lebens aus der Sicht der Chemie
In P. Walde and F. Kraus, editors, An den Grenzen des Wissens,
pages 147-184. vdf Hochschulverlag AG der ETH Zürich, Zürich, CH, 2007.
07-007
Peter Schuster
The Beginning of the End of the Holism Versus Reductionism Debate ? Molecular Biology Goes Cellular and Organismic
Complexity, 13(1): 10-13, 2007.
07-008
Ivo L. Hofacker and Peter F. Stadler
RNA Secondary Structure
In: Bioinformatics: From Genomes to Therapies, T. Lengauer (ed),
Wiley-VCH, Weinheim, Germany, pp.439-489, 2007.
07-009
The Athanasius F. Bompfünewerer Consortium: Rolf Backofen, Stephan H. Bernhart, Christoph Flamm, Claudia Fried, Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L. Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Dominic Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl and Sebastian Will
RNAs Everywhere: Genome-Wide Annotation of Structured RNAs
J.Exp.Zool.(Mol.Dev.Evol.), 308B: 1-25, 2007.
07-010
The ENCODE Consortium
Identification and Analysis of Functional Elements in 1% of the Human Genome by the ENCODE Pilot Project
Nature, 447: 799-816, 2007.
07-011
Stefan Washietl, Jakob S. Pedersen, Jan O. Korbel, Andreas Gruber, Jörg Hackermüller, Jana Hertel, Manja Lindemeyer, Kristin Reiche, Claudia Stocsits, Andrea Tanzer, Catherine Ucla, Carine Wyss, Stylianos E. Antonarakis, France Denoeud, Julien Lagarde, Jorg Drenkow, Philipp Kapranov, Thomas R. Gingeras, Roderic Guigó, Michael Snyder, Mark B. Gerstein, Alexandre Reymond, Ivo L. Hofacker, and Peter F. Stadler
Structured RNAs in the ENCODE Selected Regions of the Human Genome
Genome Res., 17: 852-864, 2007.
07-012
Philipp Kapranov, Jill Cheng, Sujit Dike, David A. Nix, Radharani Duttagupta, Aarron T. Willingham, Peter F. Stadler, Jana Hertel, Jörg Hackermüller, Ivo L. Hofacker, Ian Bell, Evelyn Cheung, Jorg Drenkow, Erica Dumais, Sandeep Patel, Gregg Helt, Madhavan Ganesh,Srinka Ghosh, Antonio Piccolboni, Victor Sementchenko, Hari Tammana, and Thomas R. Gingeras
RNA Maps Reveal New RNA Classes and a Possible Function for Pervasive Transcription
Science, 316: 1484-1488, 2007.
07-013
Andreas R. Gruber, Richard Neuböck, Ivo L. Hofacker, and Stefan Washietl
The RNAz Web Server: Prediction of Thermodynamically Stable and Evolutionarily Conserved RNA Structures
Nucl.Acids Res., 447: 799-816, 2007.
07-014
Sebastian Will, Kristin Reiche, Ivo L. Hofacker, Peter F. Stadler, and Rolf Backofen
Inferring Non-Coding RNA Families and Classes by Means of Genome-Scale Structure-Based Clustering
PLoS Comp. Biol., 3: e65, 2007
07-015
Stefan E. Seemann, Michael J. Gilchrist, Ivo L. Hofacker, Peter F. Stadler and Jan Gorodkin
Detection of RNA Structures in Porcine EST Data and Related Mammals
BMC Genomics, 8: 316, 2007
07-016
Ivo L. Hofacker
RNA Consensus Structure Prediction with RNAalifold
In Nicholas Bergman, editor, Comparative Genomics, volume 1 of Methods in Molecular Biology
chapter 33, pages 527-544. Humana Press, Totowa, NJ, 2007
07-017
Christoph Flamm, Ivo L. Hofacker, Bärbel M. R. Stadler and Peter F. Stadler
Saddles and Barrier in Landscapes of Generalized search Operators
In C. R. Stephens, M. Toussaint, D. Whitley, and P. F. Stadler, editors,
Foundations of Genetic Algortithms IX, volume 4436 of Lecture Notes Comp. Sci.,
pages 194-212, Berlin, Heidelberg, 2007
Springer. 9th International Workshop, FOGA 2007, Mexico City, Mexico, January 8-11, 2007
07-018
Ivo L. Hofacker
How MicroRNAs Choose Their Targets
Nature Genetics, 39(10): 1191-1192, 2007
07-019
Stefan Washietl and Ivo L. Hofacker
Identifying Structural Non-Coding RNAs Using RNAz
In A.D. Baxevanis and D.B. Davison, editors, Current Protocols in Bioinformatics,
volume 1. John Wiley & Sons, 2007.
07-020
Hakim Tafer and Ivo L. Hofacker
RNAplex: a Fast and Flexible RNA-RNA Interaction Search Tool
In C. Falter, A. Schliep, J. Selbig, M. Vingron, and D. Walther, editors, German Conference on Bioinformatics (GCB 2007)
Lecture Notes in Informatics, pages 56-67, 2007.
07-021
John Morgan, W. Andreas Svrcek-Seiler and Alexey Onufrievz
Analysis of Integral Expressions for Effective Born Radii
J.Chem.Phys., 127: 185101, 2007.
07-022
Songwut Suramitr, Supa Hannongbua, and Peter Wolschann
Conformational Analysis and Electronic Transition of Carbazole-Based Oligomers as Explained by Density Functional Theory
J.Mol.Struct., 807: 109-119, 2007.
07-023
Rungtiwa Chidthong, Supa Hannongbua, Adelia J.A. Aquino, Peter Wolschann and Hans Lischka
Excited State Properties, Fluorescence Energies, and Lifetime of a (fluorene-pyride) Copolymer, Based on TD-DFT Investigation
J.Comput.Chem., 28: 1735-1742, 2007.
07-024
Anton Beyer, Lawtrakul Luckhana, Pungpo Pornpan and Peter Wolschann
Structural Aspects of Non-Nucleoside HIV-1 Reverse Transcriptase Inhibition
Curr.Comp.-Aided Drug Design, 3: 87-100, 2007.
07-025
Nadtanet Nunthaboot, Somsak Pianwanit, Vudhichai Parasuk, Sirirat Kokpol and Peter Wolschann
Theoretical Study on the HIV-1 Integrase Inhibitor 1-(5-Chloroindol-3-yl)-3-Hydroxy-3-(2H-Tetrazol-5-yl)-Propenone (5CITEP)
J.Mol.Struct., 844-845: 208-214, 2007.
06-026
Aleksander Koll, Alfred Karpfen and Peter Wolschann
The Energy of the Intramolecular Hydrogen Bond in Chloro-Substituted N-Methyl-Salicylidene Imines
J.Mol.Struct., 844-845: 268-277, 2007.
07-027
Walter Snor, Elisabeth Liedl, Petra Weiss-Greiler, Alfred Karpfen, Helmut Viernstein and Peter Wolschann
On the Structure of Anhydrous β-Cyclodextrin
Chem.Phys.Lett., 441: 159-162, 2007.
07-028
Anna Stary, Chonticha Suwattanasophon, Peter Wolschann and Gerhard Buchbauer
Differences in (-)Citronellal Binding to Various Odorant Receptors
Biochem.Biophys.Res.Communicat., 361: 941-945, 2007.
07-029
Philipp Weinzinger, Petra Weiss-Greiler, Walter Snorr, Helmut Viernstein and Peter Wolschannbr
Molecular Dynamics Simulations and Quantum Chemical Calculations on β-cyclodextrin-spironolactone Complex
J.Incl.Phenom.Macrocycl.Chem., 57: 29-33, 2007.
07-030
Stanislav Beyl, Eugen N. Timin, Annette Hohaus, Anna Stary, Michaela Kudrnac, Robert H. Guy and Steffen Hering
Probing the Architecture of an L-type Calcium Channel with a Charged Phenylalkylamine
J.Biol.Chem., 282: 3864-3870, 2007.
07-031
Matthias Ruckenbauer, Ivona Brandic, Siegfried Benker, Wilfried Gansterer, Osvaldo Gervasi, Mario Barbatti and Hans Lischka
Nonadiabatic Ab Initio Surface-Hopping Dynamics Calculation in a Grid Environment - First Experiences
In: ICCSA 2007, LNCS 4705, Part I,
Eds. O. Gervasi and M. Gavrilova
Springer-Verlag, Berlin, pp. 281-294, 2007.
07-032
Ivelina Georgieva, Natasha Trendafilova, Adélia J. A. Aquino and Hans Lischka
Excited State Proton Transfer in 7-Hydroxy-4-methylcoumarin Along a Hydrogen-bonded Water Wire
J.Phys.Chem.A, 111: 127-135, 2007.
07-033
Adélia J. A. Aquino, Daniel Tunega, Georg Haberhauer, Martin H. Gerzabek and Hans Lischka
Quantum Chemical Adsorption Studies on the (110) Surface of the Mineral Goethite
J.Phys.Chem.C, 111: 877-885, 2007.
07-034
Daniel Tunega, Martin H. Gerzabek, Georg Haberbauer and Hans Lischka
Formation of 2,4-D Complexes on Montmorillonites - an ab initio Molecular Dynamics Study
Europ.J.Soil Sci., 58: 680-691, 2007.
07-035
Mario Barbatti, Giovanni Granucci, Maurizio Persico, Matthias Ruckenbauer, Mario Vazdar, Mirjana Eckert-Maksic and Hans Lischka
The on-the-fly Surface-Hopping Program System NEWTON-X: Application to ab initio Simulation of the Nonadiabatic Photodynamics of Benchmark Systems
J.Photochem.Photobiol. A, 190: 228-240, 2007.
07-036
Mario Barbatti and Hans Lischka
Can the Nonadiabatic Photodynamics of Aminopyrimidine be a Model for the Ultrafast Deactivation of Adenine?
J.Phys.Chem. A, 111: 2852-2858, 2007.
07-037
Katarína Matuszna, Vladimír Lukeš, Peter Rapta, Lothar Dunsch, Adelia J. A. Aquino and Hans Lischka
On the Optical Properties of Fluoranthenopyracylene Ladder Type Molecule Series
Synthetic Metals, 157: 214-221, 2007.
07-038
Michael Novoszad, Martin H. Gerzabek, Hans Lischka, Georg Haberhauer and Michael Jakusch
Sorption of Naphthalene Derivatives on to Soils from a Long-Term Field Experiment: A Particle Size Fractionation and Extraction Study
Eur.J.Soil Science, 58: 26-33, 2007.
07-039
Marko Schreiber, Mario Barbatti, Shmuel Zilbergc, Hans Lischka and Leticia Gonzalez
An ab initio Study of the Excited States, Isomerization Energy Profiles and Conical Intersections of a Chiral Cyclohexylidene Derivative
J.Phys.Chem. A, 111: 238-243, 2007.
07-040
Vladimír Lukeš, Katarína Matuszna, Peter Rapta, Lothar Dunsch, Adelia J. A. Aquino and Hans Lischka
Electronic Excitations in a Ladder Type Fluoranthenopyracyclene in its Neutral and Charged States: A Theoretical and Experimental Study
Z.Phys.Chem., 221: 911-928, 2007.
07-041
Ivana Antol, Mirjana Eckert-Maksic, Hans Lischka and Zvonimir B. Maksic
[2.2.2]Propellane Isomerization via Grob Rearrangement - An Ab Initio MR-AQCC Study
Eur.J.Org.Chem., 3137-3178, 2007.
07-042
Adelia J. A. Aquino, Daniel Tunega, Georg Haberhauer, Martin H. Gerzabek and Hans Lischka
Interaction of the 2,4-Dichlorophenoxyacetic Acid Herbicide with Soil Organic Matter Moieties - A Theoretical Study
Eur.J.Soil Science, 58: 889-899, 2007.
07-043
P. Winkler, Michael Novoszad, Martin H. Gerzabek, Georg Haberhauer, Daniel Tunega and Hans Lischka
Interaction of Naphthalene Derivatives with Soil, an Experimental and Theoretical Case Study
Eur.J.Soil Science, 58: 967-977, 2007.
07-044
Daniel Tunega, Bernhard A. Goodman, Georg Haberhauer, Thomas G. Reichenauer, Martin H. Gerzabek and Hans Lischka
Ab initio Calculations of Relative Stabilities of Different Structural Arrangements in Dioctahedral Phyllosilicates
Clay and Clay Minerals, 55: 220-232, 2007.
07-045
Ivan Cernusak, Michal Dallos, Hans Lischka, Thomas Müller and Milan Uhlar
On the Ground and Some Low-Lying Excited States of ScB. A Multiconfigurational Study
J.Chem.Phys., 126: 214311-1-8, 2007.
06-046
Vladimir Lukes, Adelia J.A. Aquino, Hans Lischka and Harald-Friedrich Kauffmann
Dependence of Optical Properties of Oligo-Para-Phenylenes on Torsional Modes and Chain Length
J.Phys.Chem.B, 111: 7954-7962, 2007.
06-047
Ivana Antol, Mirjana Eckert-Maksic, Mario Barbatti and Hans Lischka
Simulation of the Photodeactivation of Formamide in the no-π* and π-π*states: An Ab Intitio On-The-Fly Surface-Hopping Dynamics Study
J.Chem.Phys., 127: 234303, 2007.
06-048
Ivelina Georgieva, Natasha Trendafilova, Adelia J.A. Aquino and Hans Lischka
Theoretical Study of Metal-Ligand Interaction in Sm(III), Eu(III), and Tb(III) Complexes of Coumarin-3-Carboxylic Acid in the Gas Phase and Solution
Inorg.Chem., 46: 10926-10936, 2007.
06-049
Andrea Michalkova and Daniel Tunega
Kaolinite: Dimethylsulfoxide Intercalate - A Theoretical Study
J.Phys.Chem, 111: 11259-11266, 2007.
06-050
Mariana Sladkovicova, Lubomir Smrcok, Pavel Mach, Daniel Tunega, Alexander I. Kolesnikov
Inelastic Neutron Scattering and DFT Study of 2-amino-3-hydroxymethyl-1,3-propane Diol (TRIS)
Chem.Phys., 340: 245-259, 2007.
06-051
Martin H. Gerzabek, Georg Haberhauer, K.-U. Totsche and Daniel Tunega
Editorial: Molecular Modelling in Soil Research
Europ.J. Soil Science, 58: 867-869, 2007.
07-052
Alfred Karpfen, Elisabeth Liedl, Walter Snor, Petra Weiss-Greiler, Helmut Viernstein and Peter Wolschann
Homodromic Hydrogen Bonds in Low-Energy Conformations of Single Molecule Cyclodextrins
J.Incl.Phenom.Macrocycl.Chem., 57: 35-38, 2007.
07-053
Alfred Karpfen and Eugene S. Kryachko
Blue-Shifted A-H Stretching Modes and Cooperative Hydrogen Bonding. 1. Complexes of Substituted Formaldehyde with Cyclic Hydrogen Fluoride and Water Clusters
J.Phys.Chem. A, 111: 8177-8187, 2007.
07-054
Alfred Karpfen and Eugene S. Kryachko
The Concept of Molecular Shape Response Quantified within Force Field Approach
in 'AIP Conference Proceedings 963, Vol.2 Part A, Computation in Modern Science and Engineering:
Proceedings of the International Conference on Computational Methods in Science and Engineering 2007',
eds. T.E. Simos and G. Maroulis, p. 206-209, 2007.
07-055
Avijit Datta, Christoph A. Marx, Christoph Uiberacker and Werner Jakubetz
Dipole Mediated Tunneling: Robust Single-Pulse Population Transfer Across Dipolar Double-Well Systems
Chem.Phys., 338: 237-251, 2007.
07-056
Bernhard Helffer and Thomas Hoffmann-Ostenhof
Converse Spectral Problems for Nodal Domains
Moscow Math.J., 7(1): 67-84, 2007.
07-057
Soren Fournais, Maria Hoffmann-Ostenhof, Thomas Oestergaard Soerensen and Thomas Hoffmann-Ostenhof
Non-Isotropic Cusp Conditions and Regularity of the Electron Density of Molecules the Nuclei
Annales Henri Poincare, 8(4): 731-748, 2007.
07-058
Thomas Hoffmann-Ostenhof
Review of the book: The Mathematics of the Bose Gas and its Condensation
by E.H. Lieb, R. Seiring, J.P. Solovej and J. Yngvason
Bull.Amer.Math.Soc.,44: 494-496, 2007.
07-059
Ronald Rapberger, Arno Lukas and Bernd Mayer
Identification of discontinuous antigenic determinants on proteins based on shape complementarities
J.Mol.Recog.,20: 113-121, 2007.
07-060
Alexander Platzer, Paul Perco, Arno Lukas and Bernd Mayer
Characterization of protein-interaction networks in tumors
BMC Bioinf.,8: 224, 2007.
07-061
Alexander Kainz, Paul Perco, Bernd Mayer, Afschin Soleiman, Rudolf Steininger, Gert Mayer, Christa Mitterbauer, Christoph Schwarz, Timothy W. Meyer, and Rainer Oberbauer
Gene-Expression Profiles and Age of Donor Kidney Biopsies Obtained Before Transplantation Distinguish Medium Term Graft Function
Transplant.,83: 1048-1054, 2007.