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
Christina Helmling, Anna Wacker, Michael T Wolfinger, Ivo L Hofacker,Martin Hengesbach, Boris Fürtig, and Harald Schwalbe
NMR structural profiling of transcriptional intermediates reveals riboswitch regulation by metastable RNA conformations
Journal of the American Chemical Society, 139:2647, 2017, doi:10.1021/jacs.6b10429
Gesche K Gerresheim, Nadia Dünnes, Anika Nieder-Röhrmann, Lyudmila A Shalamova, Markus Fricke, Ivo Hofacker, Christian Höner zu Siederdissen, Manja Marz, and Michael Niepmann
microRNA-122 target sites in the hepatitis C virus RNA NS5B coding region and 3' untranslated region: function in replication and influence of RNA secondary structure
Cellular and Molecular Life Sciences, 74:747–760, 2017, doi:10.1007/s00018-016-2377-9
Ferhat Alkan, Anne Wenzel, Oana Palasca, Peter Kerpedjiev, Anders Frost Rudebeck, Peter F Stadler, Ivo L Hofacker, and Jan Gorodkin
Risearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets
Nucleic Acids Research, 2017, doi:10.1093/nar/gkw1325
Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
Chemical Graph Transformation with Stereo-Information
de Lara J., Plump D. (eds) Graph Transformation. ICGT 2017. Springer, Cham. LNCS 10373:54-69 (2017), doi:10.1007/978-3-319-61470-0_4
Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
An Intermediate Level of Abstraction for Computational Systems Chemistry
Royal Soc Phil Trans A xxx:xxx-xxx (2017), arXiv:1701.09097
Birgit Märtens, Linlin Hou, Fabian Amman, Michael T. Wolfinger, Elena Evguenieva-Hackenberg, Udo Bläsi
The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts
Nucleic Acids Res gkx437 (2017) PDF, doi:10.1093/nar/gkx437
Panupong Mahalapbutr, Phakawat Chusuth, Nawee Kungwan, Warinthorn Chavasiri, Peter Wolschann, Thanyada Rungrotmongkol
Molecular recognition of naphthoquinone-containing compounds against human DNA topoisomerase IIα ATPase domain: A molecular modeling study
Journal Article published Dec 2017 in Journal of Molecular Liquids volume 247 on pages 374 to 385, doi:10.1016/j.molliq.2017.10.021
Bodee Nutho, Nadtanet Nunthaboot, Peter Wolschann, Nawee Kungwan, Thanyada Rungrotmongkol
Metadynamics supports molecular dynamics simulation-based binding affinities of eucalyptol and beta-cyclodextrin inclusion complexes
Journal Article published 2017 in RSC Advances volume 7 issue 80 on pages 50899 to 50911, doi:10.1039/c7ra09387j
Marwa Al Arab, Christian Höner zu Siederdissen, Kifah Tout, Abdullah H. Sahyoun, Peter F. Stadler, Matthias Bernt
Accurate annotation of protein-coding genes in mitochondrial genomes
Journal Article published Jan 2017 in Molecular Phylogenetics and Evolution volume 106 on pages 209 to 216, doi:j.ympev.2016.09.024
Gesine Domin, Sven Findeiß, Manja Wachsmuth, Sebastian Will, Peter F. Stadler, Mario Mörl
Applicability of a computational design approach for synthetic riboswitches
Journal Article published 19 Dec 2016 in Nucleic Acids Research on page gkw1267, doi:10.1093/nar/gkw1267
Wasinee Khuntawee, Manaschai Kunaseth, Chompoonut Rungnim, Suradej Intagorn, Peter Wolschann, Nawee Kungwan, Thanyada Rungrotmongkol, Supot Hannongbua
Comparison of Implicit and Explicit Solvation Models for Iota-Cyclodextrin Conformation Analysis from Replica Exchange Molecular Dynamics
Journal Article published 23 Mar 2017 in Journal of Chemical Information and Modeling volume 57 issue 4 on pages 778 to 786, doi:10.1021/acs.jcim.6b00595
Anne Nitsche, Peter F. Stadler
Evolutionary clues in lncRNAs
Journal Article published 19 Jul 2016 in Wiley Interdisciplinary Reviews: RNA volume 8 issue 1 on page e1376, doi:10.1002/wrna.1376
Marwa Al Arab, Matthias Bernt, Christian Höner zu Siederdissen, Kifah Tout, Peter F. Stadler
Partially local three-way alignments and the sequence signatures of mitochondrial genome rearrangements
Journal Article published 23 Aug 2017 in Algorithms for Molecular Biology volume 12 issue 1, doi:10.1186/s13015-017-0113-0
Rainer Machné, Douglas B. Murray, Peter F. Stadler
Similarity-Based Segmentation of Multi-Dimensional Signals
Journal Article published 27 Sep 2017 in Scientific Reports volume 7 issue 1, doi:10.1038/s41598-017-12401-8
Stefanie Binder, Nadine Hösler, Diana Riedel, Ivonne Zipfel, Tilo Buschmann, Christoph Kämpf, Kristin Reiche, Renate Burger, Martin Gramatzki, Jörg Hackermüller, Peter F. Stadler, Friedemann Horn
STAT3-induced long noncoding RNAs in multiple myeloma cells display different properties in cancer
Journal Article published 11 Aug 2017 in Scientific Reports volume 7 issue 1, doi:10.1038/s41598-017-08348-5
Sree Rohit Kolora, Rui Faria, Anne Weigert, Stefan Schaffer, Annegret Grimm, Klaus Henle, Abdullah H. Sahyoun, Peter F. Stadler, Katja Nowick, Christoph Bleidorn, Martin Schlegel
The complete mitochondrial genome of Lacerta bilineata and comparison with its closely related congener L. Viridis
Journal Article published 28 Dec 2015 in Mitochondrial DNA Part A volume 28 issue 1 on pages 116 to 118, doi:10.3109/19401736.2015.1111349
Björn A. Grüning, Jörg Fallmann, Dilmurat Yusuf, Sebastian Will, Anika Erxleben, Florian Eggenhofer, Torsten Houwaart, Bérénice Batut, Pavankumar Videm, Andrea Bagnacani, Markus Wolfien, Steffen C. Lott, Youri Hoogstrate, Wolfgang R. Hess, Olaf Wolkenhauer, Steve Hoffmann, Altuna Akalin, Uwe Ohler, Peter F. Stadler, Rolf Backofen
The RNA workbench: best practices for RNA and high-throughput sequencing bioinformatics in Galaxy
Journal Article published 5 Jun 2017 in Nucleic Acids Research volume 45 issue W1 on pages W560 to W566, doi:10.1093/nar/gkx409
Henrike Indrischek, Sonja J. Prohaska, Vsevolod V. Gurevich, Eugenia V. Gurevich, Peter F. Stadler
Uncovering missing pieces: duplication and deletion history of arrestins in deuterostomes
Journal Article published 6 Jul 2017 in BMC Evolutionary Biology volume 17 issue 1, doi:10.1186/s12862-017-1001-4
Bernhard C Thiel, Christoph Flamm, Ivo L Hofacker
RNA structure prediction: from 2D to 3D
Emergent Topics in Life Science/ *ETLS20160027* (2017), doi:10.1042/ETLS20160027
William B. Langdon and Ronny Lorenz
Improving SSE parallel code with grow and graft genetic programming
GECCO '17 Proceedings of the Genetic and Evolutionary Computation, Conference Companion, Pages 1537-1538, doi:10.1145/3067695.3082524
Felix Kühnl, Peter F. Stadler, and Sebastian Will
Tractable Kinetics of Rna–Ligand Interaction
BMC Bioinformatics, 18(Suppl 12):424, 2017, doi:10.1186/s12859-017-1823-5
Jörg Fallmann, Sebastian Will, Jan Engelhardt, Björn Grüning, Rolf Backofen, and Peter F Stadler
Recent advances in Rna folding
Journal of Biotechnology, 2017, doi:10.1016/j.jbiotec.2017.07.007
Hosna Jabbari, Ian Wark, Carlo Montemagno, and Sebastian Will
Sparsification Enables Predicting Kissing Hairpin Pseudoknot Structures of Long RNAs in Practice
In Russell Schwartz and Knut Reinert, editors, 17th International Workshop on Algorithms in Bioinformatics (WABI 2017), volume 88 of Leibniz International Proceedings in Informatics (LIPIcs), pages 12:1–12:13, Dagstuhl, Germany, 2017, doi:10.4230/LIPIcs.WABI.2017.12
Estimation of Retention Time in GC/MS of Volatile Metabolites in Fragrant Rice Using Principle Components of Molecular Descriptors
Journal Article published 2017 in Analytical Sciences volume 33 issue 11 on pages 1211 to 1217, doi:10.2116/analsci.33.1211
Panupong Mahalapbutr, Bodee Nutho, Peter Wolschann, Warinthorn Chavasiri, Nawee Kungwan, Thanyada Rungrotmongkol
Molecular insights into inclusion complexes of mansonone E and H enantiomers with various β-cyclodextrins
Journal Article published Jan 2018 in Journal of Molecular Graphics and Modelling volume 79 on pages 72 to 80, doi:10.1016/j.jmgm.2017.11.006
Muralidhar Tata, Fabian Amman, Vinay Pawar, Michael T. Wolfinger, Siegfried Weiss, Susanne Häussler, Udo Bläsi
The anaerobically induced sRNA PaiI affects denitrification in Pseudomonas aeruginosa PA14
Front. Microbiol. 8 2312 (2017) PDF, doi:10.3389/fmicb.2017.02312
Elisabeth Sonnleitner, Alexander Wulf, Sébastien Campagne Xue-Yuan Pei, Michael T. Wolfinger, Giada Forlani, Konstantin Prindl,Laetitia Abdou, Armin Resch, Frederic H.-T. Allain, Ben F. Luisi Henning Urlaub, Udo Bläsi
Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa
Nucleic Acids Research, gkx1245, doi:10.1093/nar/gkx1245
Chonticha Suwattanasophon, Napat Songtawee, Peter Wolschann, Kiattawee Choowongkomon
Molecular dynamics simulations of asymmetric heterodimers of HER1/HER2 complexes
Journal of Molecular Modeling (2018) 24:30, doi:10.1007/s00894-017-3544-0
Jintawee Kicuntod, Kanyani Sangpheak, Monika Mueller, Peter Wolschann, Helmut Viernstein, Saeko Yanaka, Koichi Kato, Warinthorn Chavasiri, Piamsook Pongsawasdi, Nawee Kungwan, Thanyada Rungrotmongkol
Theoretical and Experimental Studies on Inclusion Complexes of Pinostrobin and β-Cyclodextrins
published 29 Jan 2018 in Sensors volume 18 issue 2 on page 392, doi:10.3390/s18020392