Theoretical Biochemistry Group

Institute for Theoretical Chemistry

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Recent Publications

All our recent publications (from this year) are on display right here on this page. For older publications choose a period from the menu.

Preliminary versions of most of our work can be found on our pre-print server.


Sven Findeiß, Maja Etzel, Sebastian Will, Mario Mörl, Peter Stadler
Design of Artificial Riboswitches as Biosensors
Sensors volume 17 issue 9 on page 1990, doi:10.3390/s17091990
Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker, Sven Findeiß
RNAblueprint: flexible multiple target nucleic acid sequence design
Bioinformatics, doi:10.1093/bioinformatics/btx263


Jintawee Kicuntod, Wasinee Khuntawee, Peter Wolschann, Piamsook Pongsawasdi, Warinthorn Chavasiri, Nawee Kungwan, Thanyada Rungrotmongkol
Inclusion complexation of pinostrobin with various cyclodextrin derivatives
Journal of Molecular Graphics and Modelling 63 (2016) 91–98, doi:10.1016/j.jmgm.2015.11.005
Waratchada Sangpheak, Jintawee Kicuntod, Roswitha Schuster, Thanyada Rungrotmongkol, Peter Wolschann, Nawee Kungwan, Helmut Viernstein, Monika Mueller and Piamsook Pongsawasdi
Physical properties and biological activities of hesperetin and naringenin in complex with methylated β-cyclodextrin
Beilstein J. Org. Chem. 2015, 11, 2763–2773, doi:10.3762/bjoc.11.297
Wasinee Khuntawee, Thanyada Rungrotmongkol, Peter Wolschann, Piamsook Pongsawasdi, Nawee Kungwan, Hisashi Okumura, Supot Hannongbua
Conformation study of ɛ-cyclodextrin: Replica exchange molecular dynamics simulations
Carbohydrate Polymers 141 (2016) 99–105, doi:10.1016/j.carbpol.2015.10.018
Muralidhar Tata, Michael T. Wolfinger, Fabian Amman, Nicole Roschanski, Andreas Dötsch, Elisabeth Sonnleitner, Susanne Häussler, Udo Bläsi
RNA-seq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium
PLoS ONE 11(1): e0147811, doi:10.1371/journal.pone.0147811
Martina Sauert, Michael T. Wolfinger, Oliver Vesper, Christian Müller, Konstantin Byrgazov, Isabella Moll
The MazF-regulon: a toolbox for the post-transcriptional stress response in Escherichia coli
Nucl. Acids Res. (2016), doi:10.1093/nar/gkw115
Chompoonut Rungnim, Rungroj Chanajaree, Thanyada Rungrotmongkol, Supot Hannongbua, Nawee Kungwan, Peter Wolschann, Alfred Karpfen, Vudhichai Parasuk
How strong is the edge effect in the adsorption of anticancer drugs on a graphene cluster?
J Mol Model (2016) 22:85, doi:10.1007/s00894-016-2937-9
E. Domingo and P. Schuster
What is a quasispecies? Historical origins and current scope.
In E. Domingo and P. Schuster, editors, Quasispecies: From Theory to Experimental Systems, volume 392 of Current topics in Microbiology and Immunology, chapter 1, pages 1–22. Springer-Verlag, Berlin, 2015.
P. Schuster
Quasispecies on fitness landscapes.
In E. Domingo and P. Schuster, editors, Quasispecies: From Theory to Experimental Systems, volume 392 of Current topics in Microbiology and Immunology, chapter 4, pages 61–120. Springer-Verlag, Berlin, 2015.
E. Domingo and P. Schuster
Quasispecies: From Theory to Experimental Systems
Volume 392 of Current Topics in Microbiology and Immunology. Springer-Verlag, Berlin, 2016
Rathawat Daengngern, Chanatkran Prommin, Thanyada Rungrotmongkol, Vinich Promarak, Peter Wolschann, Nawee Kungwan
Theoretical investigation of 2-(iminomethyl)phenol in the gas phase as a prototype of ultrafast excited-state intramolecular proton transfer
Chemical Physics Letters 657 (2016) 113–118, doi:10.1016/j.cplett.2016.05.065
Florian Eggenhofer, Ivo L. Hofacker and Christian Höner zu Siederdissen
RNAlien – Unsupervised RNA family model construction
Nucl. Acids Res. (2016), doi:10.1093/nar/gkw558
Ronny Lorenz, Michael T. Wolfinger, Andrea Tanzer, and Ivo L. Hofacker
Predicting RNA Secondary Structures from Sequence and Probing Data
Methods, 2016. in press, doi:10.1016/j.ymeth.2016.04.004
Ronny Lorenz, Ivo L. Hofacker, and Peter F. Stadler
RNA folding with hard and soft constraints
Alg. Mol. Biol., 11:1–13, 2016, doi:10.1186/s13015-016-0070-z
Jörg Fallmann, Vitaly Sedlyarov, Andrea Tanzer, Pavel Kovarik, and Ivo L Hofacker
AREsite2: an enhanced database for the comprehensive investigation of AU/GU/U-rich elements
Nucleic Acids Res, 44(D1):D90–D95, 2016, doi:10.1093/nar/gkv1238
Yu-Ting Hsiao, Wei-Po Lee, Wei Yang, Stefan Müller, Christoph Flamm, Ivo L. Hofacker, and Philipp Kugler
Practical guidelines for incorporating knowledge-based and data-driven strategies into the inference of gene regulatory networks
IEEE Trans. Comp. Biol. Bioinf., 13:64–75, 2016, doi:10.1109/TCBB.2015.2465954
Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler, and Jing Qin
Pseudoknots in RNA folding landscapes
Bioinformatics, 32:187–194, 2016, doi:10.1093/bioinformatics/btv572
Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, and Michael T. Wolfinger
SHAPE directed RNA folding. Bioinformatics, 32:145–147, 2016
Bioinformatics, 32:145–147, 2016, doi:10.1093/bioinformatics/btv523
Stefan Badelt, Christoph Flamm, and Ivo L. Hofacker
Computational design of a circular RNA with prion-like behavior
Artificial Life, 2016. early access, doi:10.1162/ARTL_a_00197
Christoph Flamm, Daniel Merkle, Peter F Stadler, Uffe Thorsen
Automatic Inference of Graph Transformation Rules: Using the Cyclic Nature of Chemical Reactions
LNCS 9761:206-222 (2016), doi:10.1007/978-3-319-40530-8_13
Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
A Software Package for Chemically Inspired Graph Transformation
LNCS 9761:73-88 (2016), doi:10.1007/978-3-319-40530-8_5
Sedlyarov V, Fallmann J, Ebner F, Huemer J, Sneezum L, Ivin M, Kreiner K, Tanzer A, Vogl C, Hofacker I, et al.
Tristetraprolin binding site atlas in the macrophage transcriptome reveals a switch for inflammation resolution
Molecular Systems Biology 12:5 (2016), doi:10.15252/msb.20156628
P. Schuster
Major transitions in evolution and in technology. What they have in common and where they differ
Complexity, 21(4):7–13, 2016, doi:10.1002/cplx.21773
P. Schuster
Some mechanistic requirements for major transitions
Phil. Trans. Roy. Soc. B, 371:20150439, 2016, doi:10.1098/rstb.2015.0439
P. Schuster
The end of Moore’s law. Living without an exponential increase in the efficiency of computational facilities
Complexity, 22(1):p–pp, 2016, doi:10.1002/cplx.21824
R. Axtell, A. Kirman, I. D. Couzin, D. Fricke, T. Hens, M. E. Hochberg, J. E. Mayfield, P. Schuster, and R. Sethi
Challenges integrating complexity and evolution into economics
In D. S. Wilson and A. Kirman, editors, Complexity and Evolution. Towards a New Systhesis for Economics, Stungmann Forum Reports, chapter 5, pages 65–81. The MIT Press, Cambridge, MA, 2016
Gu, Jiao and Jost, Jürgen and Liu, Shiping and Stadler, Peter F
Spectral classes of regular, random, and empirical graphs
Linear Algebra and its Applications 489: 30--49, doi:10.1016/j.laa.2015.08.038
Indrischek, Henrike and Wieseke, Nicolas and Stadler, Peter F and Prohaska, Sonja J
The paralog-to-contig assignment problem: high quality gene models from fragmented assemblies
Algorithms for Molecular Biology 11: 1, doi:10.1186/s13015-016-0063-y
Riechert, M., Siederdissen, C. H. Z. and Stadler, P. F.
Algebraic dynamic programming for multiple context-free grammars
Theoretical Computer Science. 639, S. 91-109 19 S., doi:10.1016/j.tcs.2016.05.032
Jorjani, H., Kehr, S., Jedlinski, D. J., Gumienny, R., Hertel, J., Stadler, P. F., Zavolan, M. and Gruber, A. R.
An updated human snoRNAome
Acids Research. 44, 11, S. 5068-5082 15 S., doi:10.1093/nar/gkw386
Restrepo, G. and Stadler, P. F.
Assessing Greenness of Chemical Reactions and Synthesis Plans through Posetic Landscapes
ACS Sustainable Chemistry and Engineering. 4, 4, S. 2191-2199 9 S., doi:10.1021/acssuschemeng.5b01649
Perez, T., Klemm, K. and Eguiluz, V. M.
Competition in the presence of aging: dominance, coexistence, and alternation between states
Scientific Reports. 6, 8 S., 21128, doi:10.1038/srep21128
Canzler, S., Stadler, P. F. and Hertel, J.
U6 snRNA intron insertion occurred multiple times during fungi evolution
RNA Biology. 13, 2, S. 119-127 9 S., doi:10.1080/15476286.2015.1132139
Juehling, F., Kretzmer, H., Bernhart, S. H., Otto, C., Stadler, P. F. and Hoffmann, S.
metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data
Genome Research. 26, 2, S. 256-262 7 S., doi:10.1101/gr.196394.115
Westermann, A. J., Foerstner, K. U., Amman, F., Barquist, L., Chao, Y., Schulte, L. N., Mueller, L., Reinhardt, R., Stadler, P. F. & Vogel, J.
Dual RNA-seq unveils noncoding RNA functions in host-pathogen interactions
Nature. 529, 7587, S. 496-+ 23 S., doi:10.1038/nature16547
W. Jetsadawisut, B. Nutho, A. Meeprasert, T. Rungrotmongkol, N. Kungwan, P. Wolschann, S. Hannongbua
Susceptibility of inhibitors against 3C protease of coxsackievirus A16 and enterovirus A71 causing hand, foot and mouth disease: A molecular dynamics study
Biophysical Chemistry 219 (2016) 9–16, doi:10.1016/j.bpc.2016.09.005
Martin Hölzer, Verena Krähling, Fabian Amman, Emanuel Barth, Stephan H. Bernhart, Victor A. O. Carmelo, Maximilian Collatz, Gero Doose, Florian Eggenhofer, Jan Ewald, Jörg Fallmann, Lasse M. Feldhahn, Markus Fricke, Juliane Gebauer, Andreas J. Gruber, Franziska Hufsky, Henrike Indrischek, Sabina Kanton, Jörg Linde, Nelly Mostajo, Roman Ochsenreiter, Konstantin Riege, Lorena Rivarola-Duarte, Abdullah H. Sahyoun, Sita J. Saunders, Stefan E. Seemann, Andrea Tanzer, Bertram Vogel, Stefanie Wehner, Michael T. Wolfinger, Rolf Backofen, Jan Gorodkin, Ivo Grosse, Ivo Hofacker, Steve Hoffmann, Christoph Kaleta, Peter F. Stadler, Stephan Becker, Manja Marz
Differential transcriptional responses to Ebola and Marburg virus infection in bat and human cells
Scientific Reports 6, 34589 (2016) PDF, doi:10.1038/srep34589
Bettina Wailzer, Johanna Klocker, Peter Wolschann and Gerhard Buchbauer
Structural Features for Furan-Derived Fruity and Meaty Aroma Impressions
NPC 2016 Vol. 11, No. 10, 1475 - 1479
P. Schuster
Stochasticity in Processes. Fundamentals and Applications to Chemistry and Biology
Springer Series in Synergentics, Springer-Verlag, Berlin, 2016
Hammack RH, Hellmuth M, Ostermeier L, Stadler PF
Associativity and Non-Associativity of Some Hypergraph Products
Mathematics in Computer Science, Volume 10, Issue 3, Pages 403-408, doi:10.1007/s11786-016-0276-y
Cristian A. Velandia-Huerto, Adriaan A. Gittenberger, Federico D. Brown, Peter F. Stadler, Clara I. Bermúdez-Santana
Automated detection of ncRNAs in the draft genome sequence of a colonial tunicate: the carpet sea squirt Didemnum vexillum
BMC Genomics volume 17 issue 1, doi:10.1186/s12864-016-2934-5
Cristian A. Velandia-Huerto, Sarah J. Berkemer, Anne Hoffmann, Nancy Retzlaff, Liliana C. Romero Marroquín, Maribel Hernández-Rosales, Peter F. Stadler, Clara I. Bermúdez-Santana
Orthologs, turn-over, and remolding of tRNAs in primates and fruit flies
BMC Genomics volume 17 issue 1, doi:10.1186/s12864-016-2927-4
Sebastian Canzler, Peter F. Stadler, Jana Hertel
U6 snRNA intron insertion occurred multiple times during fungi evolution
RNA Biology volume 13 issue 2 on pages 119 to 127, doi:10.1080/15476286.2015.1132139
Frank Jühling, Helene Kretzmer, Stephan H. Bernhart, Christian Otto, Peter F. Stadler, Steve Hoffmann
metilene: fast and sensitive calling of differentially methylated regions from bisulfite sequencing data
Genome Research volume 26 issue 2 on pages 256 to 262, doi:10.1101/gr.196394.115
Alexander J. Westermann, Konrad U. Förstner, Fabian Amman, Lars Barquist, Yanjie Chao, Leon N. Schulte, Lydia Müller, Richard Reinhardt, Peter F. Stadler, Jörg Vogel
Dual RNA-seq unveils noncoding RNA functions in host–pathogen interactions
Nature volume 529 issue 7587 on pages 496 to 501, doi:10.1038/nature16547
Kuehnl Felix, Stadler Peter F., Will, Sebastian
Tractable Kinetics of RNA-Ligand Interaction
Bioinformatics Research and Applications, ISBRA 2016, Lecture Notes in Bioinformatics, Volume 9683, Pages 337-338
Mansoureh Tajaddod, Andrea Tanzer, Konstantin Licht, Michael T. Wolfinger, Stefan Badelt, Florian Huber, Oliver Pusch, Sandy Schopoff, Michael Janisiw, Ivo Hofacker, Michael F. Jantsch
Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity
Genome Biology volume 17 issue 1, doi:10.1186/s13059-016-1083-0
ulien Lagarde, Barbara Uszczynska-Ratajczak, Javier Santoyo-Lopez, Jose Manuel Gonzalez, Electra Tapanari, Jonathan M. Mudge, Charles A. Steward, Laurens Wilming, Andrea Tanzer, Cédric Howald, Jacqueline Chrast, Alicia Vela-Boza
Extension of human lncRNA transcripts by RACE coupled with long-read high-throughput sequencing (RACE-Seq)
Nature Communications volume 7 on page 12339, doi:10.1038/ncomms12339
Chonticha Suwattanasophon, Peter Wolschann, Roland Faller
Molecular dynamics simulations on the interaction of the transmembrane Na v Ab channel with cholesterol and lipids in the membrane
Journal of Biomolecular Structure and Dynamics volume 34 issue 2 on pages 318 to 326, doi:10.1080/07391102.2015.1030691
Gesine Domin, Sven Findeiß, Manja Wachsmuth, Sebastian Will, Peter F. Stadler, Mario Mörl
Applicability of a computational design approach for synthetic riboswitches
Nucleic Acids Research, doi:10.1093/nar/gkw1267
Klug Christoph, Hemmer Wolfgang, Focke Margarete, Quirce S., Boyano-Martinez T., Gaubitzer E., Wank Herbert, Swoboda Ines
Myosin essential light chain (Gal d 7), a major poultry meat allergen
Allergy, Volume 71, August 2016, Supplement S102, doi:10.1111/all.12979