2011
For availability of preprints see personal webpage of co-workers
11-001
Matthias Hackl, Tobias Jakobi, Jochen Blom, Daniel Doppmeier, Karina Brinkrolff, Rafael Sczepanowski, Stephan Bernhart, Christian Höner zu Siederdissen, Juan Hernandez-Bort, Matthias Wieser, Renate Kunert, Simon Jeffs, Ivo L.Hofacker, Alexander Goesmann, Alfred Pühler, Nicole Borth, and Johannes Grillari
Next-generation sequencing of the chinese hamster ovary microRNA transcriptome: Identification, annotation and profiling of microRNAs as targets for cellular engineering
Journal of Biotechnology, 153: 62-75, 2011
11-002
Stefan Washietl, Sven Findeiß, Stephan Müller, Stefan Kalkhof, Martin von Bergen, Ivo L. Hofacker, Peter F. Stadler, and Nick Goldman
RNAcode: robust prediction of protein coding regions in comparative genomics data
RNA, 17: 578–594, 2011
11-003
Stephan H. Bernhart, Ulrike Mückstein, and Ivo L. Hofacker
RNA accessibility in cubic time
Algorithms Mol.Biol., 6(1): 3, 2011
11-004
Andreas R Gruber, Jörg Fallmann, Franz Kratochvill, Pavel Kovarik, and Ivo L. Hofacker
AREsite: a database for the comprehensive investigation of AU-rich elements
Nucleic Acids Res., 39: D66–69, 2011
11-005
Florian Eggenhofer, Hakim Tafer, Peter F. Stadler and Ivo L. Hofacker
RNApredator: Fast accessibility-based prediction of sRNA targets
Nucleic Acids Res., 39: W149–W154, 2011
11-006
Hakim Tafer, Fabian Ammann, Florian Eggenhoffer, Peter F. Stadler, and Ivo L. Hofacker
Fast accessibility-based prediction of RNA-RNA interactions
Bioinformatics, 27: 1934-1940, 2011
11-007
Manja Marz, Andreas R. Gruber, Christian Höner zu Siederdissen, Fabian Amman, Stefan Badelt, Sebastian Bartschat, Stephan H. Bernhart, Stephanie Beyer, Kehr, Ronny Lorenz, Andrea Tanzer, Dilmurat Yusuf, Hakim Tafer, Ivo L. Hofacker, and Peter F. Stadler
Animal snoRNAs and scaRNAs with exceptional structures
RNA Biology, 8: 1–9, 2011
11-008
Jan Gorodkin and Ivo L Hofacker
From structure prediction to genomic screens for novel non-coding RNAs
PLoS computational biology, 7(8): e1002100, 2011
11-009
Christian Höner zu Siederdissen, Stephan H. Berhart, Peter F. Stadler, and Ivo L. Hofacker
A folding algorithm for extended RNA secondary structures
Bioinformatics, 27: i129–i136, 2011
11-010
Franz Kratochvill, Christian Machacek, Claus Vogl, Florian Ebner, Vitaly Sedlyarov, Andreas R Gruber, Harald Hartweger, Roland Vielnascher, Marina Karaghiosoff, Thomas Rülicke, Mathias Müller, Ivo L Hofacker, Roland Lang, and Pavel Kovarik
Tristetraprolin-driven regulatory circuit controls quality and timing of mRNA decay in inflammation
Mol.Syst.Biol., 7: 560, 2011
11-011
Alexander Ullrich, Markus Rohrschneider, Gerik Scheuermann, Peter F. Stadler, and Christoph Flamm
In Silico Evolution of Early Metabolism
Artifical Life, 17(2): 87-108, 2011
11-012
Noriko Hiroi, James Lu, Keisuke Iba, Akito Tabira, Shuji Yamashita, Yasunori Okada, Christoph Flamm, Kotaro Oka, Gottfried Köhler and Akira Funahashi
Physiological environment induce quick response - slow exhaustion reactions
Front Physio, 2: 50, 2011
11-013
Ronny Lorenz, Stephan H. Bernhart, Christian Hoener zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, and Ivo L. Hofacker
ViennaRNA Package 2.0
Algorithms for Molecular Biology 2011, 6: 26, 2011
11-014
Leticia Gonzalez, Daniel Escudero, and Luis Serrano-Andras
Progress and Challenges in the Calculation of Electronic Excited States
ChemPhysChem., doi: 10.1002/cphc.201100200, 2011
11-015
Daniel Escudero and Leticia Gonzalez
RASPT2/RASSCF vs Range-Separated/Hybrid DFT Methods: Assessing the Excited States of a Ru(II)bipyridyl Complex
J.Chem.Theory Comput., doi.org/10.1021/ct200640q, 2011
11-016
Daniel Kinzel, Jesus Gonzalez-Vazquezw, and Leticia Gonzalez
H-abstraction is more efficient than cis–trans isomerization in (4-methylcyclohexylidene) fluoromethane. An ab initio molecular dynamics study
Phys.Chem.Chem.Phys., doi: 10.1039/c1cp22646k, 2011
11-017
Daniel Kinzel, Philipp Marquetand, and Leticia Gonzalez
Stark Control of a Chiral Fluoroethylene Derivative
J.Phys.Chem.A, doi.org/10.1021/jp207947x, 2011
11-018
Peter Schuster
Mathematical modeling of evolution. Solved and open problems
Theory Biosci., 130: 71–89, 2011
11-019
Peter Schuster
Power laws in biology. Between fundamental regularities and useful interpolation rules
Complexity, 16(3): 6–9, 2011
11-020
Peter Schuster
Networks in biology. Handling biological complexity requires novel inputs into network theory
Complexity, 16(4): 6-9, 2011
11-021
Peter Schuster
Mit Mathematik und Computer aud Entdeckungsreisen in der Evolutionsbiologie
Nova Acta Leopoldina, NF 110, Nr.377: 167-211, 2011
11-022
Peter Schuster
The Mathematics of Darwin's Theory of Evolution: 1859 and 150 Years Later
The mathematics of Darwin's legacy Book Series: Mathematics and biosciences in interaction,p. 27-66, 2011
11-023
Mario Fasold, David Langenberger, Hans Binder, Peter F. Stadler, and Steve Hoffmann
DARIO: A ncRNA detection and analysis tool for next-generation sequencing experiments
Nucleic Acids Res., doi:10.1093/nar/gkr357, 1-6, 2011
11-024
Sven Findeiß, David Langenberger, Peter F. Stadler, Steve Hoffmann
Traces of Post-Transcriptional RNA Modifications in Deep Sequencing Data
Biol.Chem., 392: , 2011
11-025
Dominic Rose, Michael Hiller, Katharina Schutt, Jörg Hackermüller, Rolf Backofen, and Peter F. Stadler
Computational discovery of human coding and non-coding transcripts with conserved splice sites
Bioinformatics, : , 2011
11-026
Dominic Rose and Peter F. Stadler
Molecular evolution of the non-coding eosinophil granule ontogeny transcript
Frontiers in Genetics, : 2 , 2011
11-027
David Langenberger, Sebastian Bartschat, Jana Hertel, Steve Hoffmann, Hakim Tafer, and Peter F. Stadler
MicroRNA or Not MicroRNA?
BSB 2011. Lecture Notes in Computer Science, Springer Verlag , 2011
11-028
David Langenberger, Sachin Pundhir, Claus T. Ekstrøm, Peter F. Stadler, Steve Hoffmann, and Jan Gorodkin
deepBlockAlign: A tool for aligning RNA-seq profiles of read block patterns
Bioinformatics, doi: 10.1093/bioinformatics/btr598, 2011
11-029
Arli A. Parikesit, Peter F. Stadler, Sonja Prohaska
Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions
Genes, 2(4): 912-924 , 2011
11-030
Sven Findeiß, Jan Engelhardt, Sonja J. Prohaska, and Peter F. Stadler
Protein-coding structured RNAs: A computational survey of conserved RNA secondary structures overlapping coding regions in drosophilids
Biochimie, 93(11): 2019-2023, 2011
11-031
Markus Lechner, Sven Findeiß, Lydia Steiner, Manja Marz, Peter F. Stadler, and Sonja J. Prohaska
Proteinortho: detection of (co-)orthologs in large-scale analysis
BMC Bioinformatics, 12: 124, 2011
11-032
Cornelius Schmidtke, Sven Findeiß, Cynthia M. Sharma, Juliane Kuhfuß, Steve Hoffmann, Jörg Vogel, Peter F. Stadler, and Ulla Bonas
Genome-wide transcriptome analysis of the plant pathogen Xanthomonas identifies sRNAs with putative virulence functions
NAR, doi: 10.1093/nar/gkr904, 2011
11-033
Robert Giegerich and Christian Höner zu Siederdissen
Semantics and Ambiguity of Stochastic RNA Family Models
IEEE-ACM Transactions on Computational Biology and Bioinformatics, 8(2): 499-516, 2011
11-034
M. Courtot, N. Juty, C. Knüpfer, D. Waltemath, A. Zhukova, A. Dräger, M. Dumontier, A. Finney, M. Golebiewski, J. Hastings, S. Hoops, S. Keating, D.B. Kell, S. Kerrien, J. Lawson, A. Lister, J. Lu, R. Machne, P. Mendes, M. Pocock, N. Rodriguez, A. Villeger, D.J. Wilkinson, S. Wimalaratne, C. Laibe, M. Hucka, and N. Le Novere
Controlled vocabularies and semantics in systems biology
Mo.Syst.Biol.7: 543, 2011
11-035
Stephanie Kehr, Sebastian Bartschat, Peter F. Stadler, and Hakim Tafer
PLEXY: efficient target prediction for box C/D snoRNAs
Bioinformatics, 27(2): 279-280, 2011
11-036
Peter Menzel, Peter F. Stadler, and Jan Gorodkin
maxAlike: maximum likelihood-based sequence reconstruction with application to improved primer design for unknown sequences
Bioinformatics, 27(3): 317-325, 2011
11-037
Andrea Tramontano,Alexander Donath, Stephan H. Bernhart, Kristin Reiche, Gudrun Böhmdorfer,Peter F. Stadler, and Andreas Bachmair
Deletion analysis of the 3 ' long terminal repeat sequence of plant retrotransposon Tto1 identifies 125 base pairs redundancy as sufficient for first strand transfer
Virology, 412(1): 75-82, 2011
11-038
Christian Otto, Steve Hoffmann, Jan Gorodkin and Peter F Stadler
Fast local fragment chaining using sum-of-pair gap costs
Algorithms for Molecular Biology, 6: Arti Nr 4, 2011
11-039
Christian M. Reidys, Fenix W. D. Huang, Jorgen E. Andersen, Robert C. Penner, Peter F. Stadler, and Markus E. Nebel
Topology and prediction of RNA pseudoknots
Bioinformatics, 27(8): 1076-1085 , 2011
11-040
Marleen Perseke, Jörg Hetmank, Matthias Bernt, Peter F. Stadler, Martin Schlegel, and Detlef Bernhard
The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria
BMC Evolutionary Biology, 11: Art 134, 2011
11-041
Jeremy D. Raincrow, Ken Dewar, Li-Zhi Gao, Claudia Stocsits, Sonja J. Prohaska, Ken Dewar, Chris T. Amemiya, Peter F. Stadler, and Chi-hua Chiu
Hox Clusters of the Bichir (Actinopterygii, Polypterus senegalus) Highlight Unique Patterns of Sequence Evolution in Gnathostome Phylogeny
Journal of Experimental Zoology Part B, 316B(6): 451-464 , 2011
11-042
Manja Marz and Peter F. Stadler
RNA INTERACTIONS
RNA INFRASTRUCTURE AND NETWORKS Book Series: Advances in Experimental Medicine and Biology , 722: 20-38, 2011
11-043
Nareerat Kitisripanya, Pachareenart Saparpakorn, Peter Wolschann, and Supa Hannongbua
Binding of huperzine A and galanthamine to acetylcholinesterase, based on ONIOM method
Nanotechnology, Biology, and Medicine, 7: 60-68, 2011
11-044
Wanchai Pluempanupat, Michael Abraham, Lothar Brecker, Peter Wolschann, Alfred Karpfen, Vladimir B. Arion, and Michael Widhalm
Synthesis and Conformation of Chiral Biheteroaryls
Journal of Organic Chemistry, 76: 3222-3230, 2011
11-045
Helmut Viernstein and Peter Wolschann
Preface
J.Incl.Phenom.Macrocycl.Chem., 70: 257–258, 2011
11-046
Kanokthip Srisuk Boonyarattanakalin, Peter Wolschann, and Luckhana Lawtrakul
Molecular dynamics of b-CD in water/co-solvent mixtures
J.Incl.Phenom.Macrocycl.Chem., 70: 279–290, 2011
11-047
Patchreenart Saparpakorn, Peter Wolschann, Alfred Karpfen, Pornpan Pungpo, and Supa Hannongbua
Systematic investigation on the binding of GW420867X as HIV-1 reverse transcriptase inhibitor
Monatsh.Chem., 142: 961-971, 2011
11-048
Marcus Seibold, Peter Wolschann, Sabrina Bodevin, and Ole Olsen
Properties of the bubble protein, a defensin and an abundant component of a fungal exudate
Peptides, 32: 1989-1995, 2011
11-049
Marcus Seibold, Peter Wolschann, and Ole Olsen
Joint occurrence of the bubble protein and mycophenolic acid in Penicillium brevicompactum Dierckx
Monatsh.Chem., 142: 1309–1315, 2011
11-050
P. Decha, P. Intharathep, Th. Udommaneethanakit, P. Sompornpisut, S. Hannongbua, Peter Wolschann, V. Parasuk
Theoretical Studies on the Molecular Basis of HIV-1RT/NNRTIs interactions
J. Enzyme Inhibition and Medicinal Chemistry, 26: 29-36, 2011
11-051
S. Avram, D. Duda-Seiman, F. Borcan, Peter Wolschann
QSAR-CoMSIA applied to antipsychotic drugs with their dopamine D-2 and serotonine 5HT(2A) membrane receptors
J.Serb.Chem.Soc., 76: 263-281, 2011
11-052
Bettina Wailzer, Johanna Klocker, Ingrid Lukas, Georg Buchbauer, and Peter Wolschann
Structural Features for Furan-derived Fruity and Meaty Aroma Impression
Flavour & Fragrance Journal, in press, 2011
11-053
Chonticha Suwattanasophon, Roland Faller, Peter Wolschann, and Anna Weinzinger
Molecular dynamics simulations on the function of the transmembrane Cav1.2 channel in dependence of the content of cholesterol in the membrane
European Biophysics Journal, 40: 118, 2011
11-054
Rathawat Daengngern, Nawee Kungwan, Peter Wolschann, Adelia J. A. Aquino, Hans Lischka, and Mario Barbatti
Excited-State Intermolecular Proton Transfer Reactions of 7-Azaindole(MeOH)n (n = 1-3) Clusters in the Gas phase: On-the-Fly Dynamics Simulation
J.Phys.Chem. A, : 115, 14129–14136 , 2011
11-055
Auradee Punkvang, Pharit Kamsri, A. Kumkong, Kodchakon Kunasa, Patchreenart Saparpakorn, Supa Hannongbua, Peter Wolschann, Pornpan Pungpo
The structural requirement of direct InhA inhibitors for high potency against M. Tuberculosis based on computer aided molecular design
Science against microbial pathogens: communicating current research and technological advances. Ed. A. Mendez-Vilas, Formatex, 2011
11-056
Auradee Punkvang, Pharit Kamsri, Kodchakon Kun-asa, Patchreenart Saparpakorn, Supa Hannongbua, Peter Wolschann and Pornpan Pungpo
Insight into the Key Structural Features of Potent Enoyl Acyl Carrier Protein Reductase Inhibitors Based on Computer Aided Molecular Design
Drug Development - A Case Study Based Insight into Modern Strategies, Ed. Chris Rundfeldt, InTech, 2011
11-057
Emil Persson, Markus Pichler, Georg Wachter, Thomas Hisch, Werner Jakubetz, Joachim Burgdörfer, and Stefanie Gräfe
Quantum control of electron wave packets in bound molecules by train of half-cycle pulses
Phys.Rev.A, : 043421 , 2011
11-058
Oliver Skocek, Christoph Uiberacker, and Werner Jakubetz
Dipole-resonance assisted isomerization in the electronic ground state using few-cycle infrared pulses
J.Phys.Chem., 115: 7127-7133, 2011
11-059
Hasan Pasalic, Martina Roeselova, and Hans Lischka
Methyl and Pentyl Chloride in a Microhydrated Environment and at the Liquid Water-Vapor Interface: A Theoretical Study
J.Phys.Chem.B, 115: 1807-1816, 2011
11-060
Tomas Zeleny, Pavel Hobza, Dana Nachtigallova, Matthias Ruckenbauer, and Hans Lischka
Photodynamics of the adenine model 4-aminopyrimidine embedded within double strand of DNA
Collect.Czech.Chem.Commun., 76: 631-643, 2011
11-061
Peter G. Szalay, Adelia J.A. Aquino, Mario Barbatti, and Hans Lischka
Theoretical study of the excitation spectrum of azomethane
Chem.Physics, 380: 9-16, 2011
11-062
Adelia J.A. Aquino1, Daniel Tunega1, Gabriele E. Schaumann, Georg Haberhauer, Martin H. Gerzabek, and Hans Lischka
The Functionality of Cation Bridges for Binding Polar Groups in Soil Aggregates
Int.J.Quant.Chem., 111: 1531-1542, 2011
11-063
Hans Lischka, Thomas Müller, Peter G. Szalay, Isaiah Shavitt, Russell M. Pitzer, and Ron Shepard
COLUMBUS—a program system for advanced multireference theory calculations
Software Focus, Wiley & Sons, 1: 191-199, 2011
11-064
Mario Barbatti, Adelia J.A. Aquino, Jaroslaw J. Szymczak, Dana Nachtigallova, and Hans Lischka
Photodynamical simulations of cytosine: characterization of the ultrafast bi-exponential UV deactivation
Phys.Chem.Chem.Phys., 13: 6145–6155, 2011
11-065
Adelia J.A. Aquino1, Dana Nachtigallova, Pavel Hobza, Donald G. Truhlar, Christof Hättig, and Hans Lischka
The Charge-Transfer States in a Stacked Nucleobase Dimer Complex: A Benchmark Study
J.Comput.Chem., 32: 1217–1227, 2011
11-066
Felix Plasser and Hans Lischka
Semiclassical dynamics simulations of charge transport in stacked π-systems
J.Chem.Phys., 134: 034309, 2011
11-067
Mario Barbatti, Jaroslaw J. Szymczak, Adelia J.A. Aquino, Dana Nachtigallova, and Hans Lischka
The decay mechanism of photoexcited guanine − A nonadiabatic dynamics study
J.Chem.Phys., 134: 014304, 2011
11-068
Sabine Klepsch, Adelia J.A. Aquino, Ursula Haas, Daniel Tunega, Georg Haberhauer, Martin H. Gerzabek, and Hans Lischka
Sorption of Selected Aromatic Substances—Application of Kinetic Concepts and Quantum Mechanical Modeling
Water Air Soil Pollut., 215: 449–464, 2011
11-069
Dana Nachtigallova, Adelia J.A. Aquino, Jaroslaw J. Szymczak, Mario Barbatti, Pavel Hobza, and Hans Lischka
Nonadiabatic Dynamics of Uracil: Population Split among Different Decay Mechanisms
J.Phys.Chem.A, 115: 5247–5255, 2011
11-070
Jaroslaw J. Szymczak, Mario Barbatti, and Hans Lischka
Influence of the Active Space on CASSCF Nonadiabatic Dynamics Simulations
Int. J. of Quantum Chemistry, Vol 111: 3307–3315, 2011
11-071
Lukasz Cwiklik, Adelia J.A. Aquino, Mario Vazdar, Piotr Jurkiewicz, Jiri Pittner, Martin Hof, and Hans Lischka
Absorption and Fluorescence of PRODAN in Phospholipid Bilayers: A Combined Quantum Mechanics and Classical Molecular Dynamics Study
J.Phys.Chem. A, 115: 11428–11437, 2011
11-072
Adelia J.A. Aquino, Daniel Tunega, Hasan Pasalic, Gabriele E. Schaumann, Georg Haberhauer, Martin H. Gerzabek, and Hans Lischka
Molecular Dynamics Simulations of Water Molecule-Bridges in Polar Domains of Humic Acids
Environ.Sci.Technol., 45: 8411–8419, 2011
11-073
Daniel Tunega, Hasan Pasalic, Martin H. Gerzabek, and Hans Lischka
Theoretical study of structural, mechanical and spectroscopic properties of boehmite (γ -AlOOH)
J.Phys.Condens.Matter, 23: 404201, 2011
11-074
Marek Pederzoli and Jiri Pittner, Mario Barbatti, and Hans Lischka
Nonadiabatic Molecular Dynamics Study of the cistrans Photoisomerization of Azobenzene Excited to the S1 State
J.Phys.Chem.A, 115: 11136–11143, 2011
11-075
Adelia J.A. Aquino, Daniel Tunega, Hasan Pasalic, Gabriele E. Schaumann, Georg Haberhauer, Martin H. Gerzabek, and Hans Lischka
Study of solvent effect on the stability of water bridge-linked carboxyl groups in humic acid models
Geoderma, 169: 20–26, 2011
11-076
Roland Solc, Martin H. Gerzabek, Hans Lischka, and Daniel Tunega
Wettability of kaolinite (001) surfaces — Molecular dynamic study
Geoderma, 169: 47–54, 2011
11-077
Daniel Tunega and Ali Zaoui
Understanding of Bonding and Mechanical Characteristics of Cementitious Mineral Tobermorite From First Principles
Journal of Computational Chemistry, 32(2): 306-314, 2011
11-078
Alfred Karpfen
Blue-shifted A-H stretching frequencies in complexes with methanol: the decisive role of intramolecular coupling
Phys.Chem.Chem.Phys., 13: 14194-14201, 2011
11-079
Daniel Lumpi, Berthold Stöger, Christian Hametner, Frank Kubel, Georg Reider, Hans Hagemann, Alfred Karpfen, and Johannes Fröhlich
Modified ene–yne compounds: a novel functional material with nonlinear optical properties
Cryst.Eng.Comm., 13: 7194, 2011
11-080
Mariam Anees, Peter Horak, Ahmed El-Gazzar, Martin Susani, Georg Heinze, Paul Perco, Massimo Loda, Rosina Lis, Michael Krainer, and William K. Oh
Recurrence-Free Survival in Prostate Cancer Is Related to Increased Stromal TRAIL Expression
Cancer, 117(6): 1172-1182, 2011
11-081
Paul Fechete, Andreas Heinzel, Paul Perco, Konrad Mönks, Johannes Söllner, Gil Stelzer, Susanne Eder, Doron Lancet, Rainer Oberbauer, Gert Mayer, Bernd Mayer
Mapping of molecular pathways, biomarkers and drug targets for diabetic nephropathy
Proteomics Clin Appl, 5: 354-366, 2011