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.

2018

18-001
Michael T. Wolfinger, Christoph Flamm, Ivo L Hofacker
Efficient computation of co-transcriptional RNA-ligand interaction dynamics
Methods (2018) PDF, doi:10.1016/j.ymeth.2018.04.036
18-002
Sven Findeiß, Stefan Hammer, Michael T. Wolfinger, Felix Kühnl, Christoph Flamm, Ivo L. Hofacker
In silico design of ligand triggered RNA switches
Methods (2018) PDF, doi:10.1016/j.ymeth.2018.04.003
18-003
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 Res 46(3): 1470-1485 (2018) PDF doi:10.1093/nar/gkx1245
18-004
Florian Eggenhofer, Ivo L. Hofacker, Rolf Backofen and Christian Höner zu Siederdissen
CMV: visualization for RNA and protein family models and their comparisons
Bioinformatics, 2018, 1–3, doi:10.1093/bioinformatics/bty158
18-005
Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F Stadler
Finding the K Best Synthesis Plans
J Cheminfo 10:19 2018, doi:10.1186/s13321-018-0273-z
18-006
Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
Chemical Transformation Motifs — Modelling Pathways as Integer Hyperflows
IEEE/ACM Trans Comp Biol Bioinf 14(x):xxx-xxx 2018, doi:10.1109/TCBB.2017.2781724
18-007
Eva Klopf, Murielle Moes, Fabian Amman, Bob Zimmermann, Frederike von Pelchrzim, Christina Wagner, Renée Schroeder
Nascent RNA signaling to yeast RNA Pol II during transcription elongation
PLOS Published: March 23, 2018, doi:10.1371/journal.pone.0194438
18-008
Anne Hoffmann, Jörg Fallmann, Elisa Vilardo, Mario Mörl, Peter F Stadler, Fabian Amman
Accurate mapping of tRNA reads
Bioinformatics, Volume 34, Issue 7, 1 April 2018, Pages 1116–1124, doi:10.1093/bioinformatics/btx756
18-009
Rolf Backofen, Jan Gorodkin, Ivo L. Hofacker, Peter F. Stadler
Comparative RNA Genomics
Comparative Genomics pp 363-400, doi:10.1007/978-1-4939-7463-4_14
18-010
Stefan Hammer, Yann Ponty, Wei Wang, and Sebastian Will
Fixed-Parameter Tractable Sampling for RNA Design with Multiple Target Structures
Proceedings of RECOMB 2018 – 22nd Annual International Conference on Research in Computational Molecular Biology, France, 2018, PDF
18-011
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
18-012
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
Journal Article published 30 Jan 2018 in Scientia Pharmaceutica volume 86 issue 1 on page 5, doi:10.3390/scipharm86010005
18-013
Chonnikan Hanpaibool, Tipsuda Chakcharoensap, Arifin, Yuh Hijikata, Stephan Irle, Peter Wolschann, Nawee Kungwan, Piamsook Pongsawasdi, Puey Ounjai, Thanyada Rungrotmongkol
Theoretical analysis of orientations and tautomerization of genistein in β-cyclodextrin
Journal Article published Sep 2018 in Journal of Molecular Liquids volume 265 on pages 16 to 23, doi:10.1016/j.molliq.2018.05.109
18-014
Suwannee Sriyab, Kitiya Jorn-Iat, Panida Prompinit, Peter Wolschann, Supa Hannongbua, Songwut Suramitr
Photophysical properties of 1-pyrene-based derivatives for nitroaromatic explosives detection: Experimental and theoretical studies
Journal Article published Nov 2018 in Journal of Luminescence volume 203 on pages 492 to 499, doi:10.1016/j.jlumin.2018.06.070
18-015
Thanyada Rungrotmongkol, Tipsuda Chakcharoensap, Piamsook Pongsawasdi, Nawee Kungwan, Peter Wolschann
The inclusion complexation of daidzein with β-cyclodextrin and 2,6-dimethyl-β-cyclodextrin: a theoretical and experimental study
Journal Article published 11 Aug 2018 in Monatshefte für Chemie - Chemical Monthly volume 149 issue 10 on pages 1739 to 1747, doi:10.1007/s00706-018-2209-8
18-016
Kanyani Sangpheak, Monika Mueller, Nitchakan Darai, Peter Wolschann, Chonticha Suwattanasophon, Ritbey Ruga, Warinthon Chavasiri, Supaporn Seetaha, Kiattawee Choowongkomon, Nawee Kungwan, Chompoonut Rungnim & Thanyada Rungrotmongkol
Computational screening of chalcones acting against topoisomerase IIα and their cytotoxicity towards cancer cell lines
ISSN: 1475-6366 (Print) 1475-6374 (Online) Journal, doi:10.1080/14756366.2018.1507029
18-017
Bernhard C. Thiel, Roman Ochsenreiter, Veerendra P. Gadekar, Andrea Tanzer, and Ivo L. Hofacker
RNA structure elements conserved between mouse and 59 other vertebrates
Genes, 9(8), 2018, doi:10.3390/genes9080392
18-018
Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
Rule Composition in Graph Transformation Models of Chemical Reactions
MATCH 80(3):661-704 (2018)
18-019
Jakob L Andersen, Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F Stadler
Towards Mechanistic Prediction of Mass Spectra Using Graph Transformation
MATCH 80(3):705-731 (2018)
18-020
Langdon WB, Petke J, Lorenz R
Evolving Better RNAfold Structure Prediction
In proceedings, Genetic Programming (2018), doi:10.1007/978-3-319-77553-1_14
18-021
Tanzer A, Hofacker IL, Lorenz R
RNA modifications in structure prediction - status quo and future challenges
Methods (2018), doi:10.1016/j.ymeth.2018.10.019
18-022
Petra Pusic, Elisabeth Sonnleitner, Beatrice Krennmayr, Dorothea Agnes Heitzinger, Michael T. Wolfinger, Armin Resch and Udo Bläsi
Harnessing Metabolic Regulation to increase Hfq-dependent Antibiotic Susceptibility in Pseudomonas aeruginosa
Front Microbiol 9:2709 (2018), doi:10.3389/fmicb.2018.02709
18-023
Maria Waldl, Bernhard C. Thiel, Roman Ochsenreiter, Alexander Holzenleitner, João Victor de Araujo Oliveira, Maria Emília M. T. Walter, Michael T. Wolfinger, Peter F. Stadler
TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes
Genes 9, 372 (2018) PDF, doi:10.3390/genes9080372
18-024
Hosna Jabbari, Ian Wark, Carlo Montemagno, Sebastian Will
Knotty: efficient and accurate prediction of complex RNA pseudoknot structures
Bioinformatics, Volume 34, Issue 22, 15 November 2018, Pages 3849–3856, doi:10.1093/bioinformatics/bty420
18-025
Martin Raden, Syed M Ali, Omer S Alkhnbashi, Anke Busch, Fabrizio Costa, Jason A Davis, Florian Eggenhofer, Rick Gelhausen, Jens Georg, Steffen Heyne, Michael Hiller, Kousik Kundu, Robert Kleinkauf, Steffen C Lott, Mostafa M Mohamed, Alexander Mattheis, Milad Miladi, Andreas S Richter, Sebastian Will, Joachim Wolff, Patrick R Wright, and Rolf Backofen
Freiburg RNA tools: a central online resource for RNA-focused research and teaching
Nucleic Acids Research, 46 no. W1 pp. W25-W29, 2018, doi:10.1093/nar/gky329
18-026
Björn Grüning, Andreas Dale, Ryan Sjödin, Brad A. Chapman, Jillian Rowe, Christopher H. Tomkins-Tinch, Renan Valieris, Bioconda Team, and Johannes Köster
Bioconda: sustainable and comprehensive software distribution for the life sciences
Nature Methods, 15 no. 7 pp. 475-476, 2018. preprint at bioRxiv, doi:10.1101/207092
18-027
Blaesi, Udo and Nguyen, Hue Thi Bach and Romero, A and Amman, Fabian and Sorger-Domenigg, Theresa and Tata, Muralidhar and Sonnleitner, Elisabeth and Bläsi, Udo
Negative control of RpoS synthesis by the sRNA ReaL in Pseudomonas aeruginosa
Frontiers in Microbiology, doi:10.3389/fmicb.2018.02488
18-028
Dienstbier, Ana and Pouchnik, Derek and Wildung, Mark and Amman, Fabian and Hofacker, Ivo L and Parkhill, Julian and Holubova, Jana and Sebo, Peter and Vecerek, Branislav
Comparative genomics of Czech vaccine strains of Bordetella pertussis
Pathogens and disease, doi:10.1093/femspd/fty071
18-029
Czermak, Philipp and Amman, Fabian and Jantsch, Michael F and Cimatti, Laura Organ-wide profiling in mouse reveals high editing levels of Filamin B
mRNA in the musculoskeletal system
RNA biology, doi:10.1080/15476286.2018.1480252
18-030
Keidel, Kristina and Amman, Fabian and Bibova, Ilona and Drzmisek, Jakub and Benes, Vladimir and Hot, David and Vecerek, Branislav
Signal transduction-dependent small regulatory RNA is involved in glutamate metabolism of the human pathogen Bordetella pertussis
RNA, doi:10.1261/rna.067306.118
18-031
Amman, Fabian and D'Halluin, Alexandre and Antoine, Rudy and Huot, Ludovic and Bibova, Ilona and Keidel, Kristina and Slupek, Stéphanie and Bouquet, Peggy and Coutte, Loïc and Caboche, Ségolène and Locht, Camille and Vecerek, Branislav and Hot, David
Primary transcriptome analysis reveals importance of IS elements for the shaping of the transcriptional landscape of Bordetella pertussis
RNA biology, doi:10.1080/15476286.2018.1462655
18-032
Farman, Mariam R and Hofacker, Ivo L and Amman, Fabian
MSF: Modulated Sub-graph Finder
F1000Research, doi:10.12688/f1000research.16005
18-033
Fabian Gärtner, Christian Höner zu Siederdissen, Lydia Müller and Peter F. Stadler
Coordinate systems for supergenomes
Algorithms for Molecular Biology 2018 13:15, doi:10.1186/s13015-018-0133-4
18-034
Skrzypczyk, Aniela and Kehr, Stephanie and Krystel, Ilona and Bernhart, Stephan H and Giri,Shibashish and Bader, Augustinus and Stadler, Peter F
Noncoding RNA Transcripts during Differentiation of Induced Pluripotent Stem Cells into Hepatocytes
Stem Cells International, vol. 2018, Article ID 5692840, 15 pages, doi:10.1155/2018/5692840
18-035
Daniel Wiegreffe, Lydia Müller†, Jens Steuck, Dirk Zeckzer and Peter F. Stadler
The Sierra Platinum Service for generating peak-calls for replicated ChIP-seq experiments
BMC Research Notes 2018 11:512, doi:10.1186/s13104-018-3633-x
18-036
Asna Tungekar, Sumana Mandarthi, Pooja Rajendra Mandaviya, Veerendra P. Gadekar, Ananthajith Tantry, Sowmya Kotian, Jyotshna Reddy, Divya Prabha, Sushma Bhat, Sweta Sahay, Roshan Mascarenhas, Raghavendra Rao Badkillaya, Manoj Kumar Nagasampige, Mohan Yelnadu, Harsh Pawar, Prashantha Hebbar and Manoj Kumar Kashyap
ESCC ATLAS: A population wide compendium of biomarkers for Esophageal Squamous Cell Carcinoma
Scientific Reportsvolume 8, Article number: 12715 (2018), doi:10.1038/s41598-018-30579-3
18-037
P. Schuster
A mathematical model of evolution
MATCH – Communications in Mathematical and in Computer Chemistry, 80:547–585, 2018
18-038
P. Schuster
Molecular evolution between chemistry and biology. The interplay of competition, cooperation, and mutation
European Biophysics Journal, 47:403–425, 2018
18-039
P. Schuster
Darwin gestern und heute
In H. Matis and W.L. Reiter, editors, Darwin in Zentraleuropa. Die wissenschaftliche, weltanschauliche und populäre Rezeption im 19. und frühen 20. Jahrhundert. Pages 449–471. LIT Verlag, Wien, 2018. In German.
18-040
Manuela Geiß, John Anders, Peter F. Stadler, Nicolas Wieseke, and Marc Hellmuth
Reconstructing gene trees from Fitch's xenology relation
J Math Biol. 2018 Nov;77(5):1459-1491, doi:10.1007/s00285-018-1260-8
18-041
Nancy Retzlaff and Peter F. Stadler
Phylogenetics beyond biology
Th. Biosci., 137:133–143,2018, doi:10.1007/s12064-018-0264-7
18-042
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, and Peter F Stadler
Algorithmic Cheminformatics (Dagstuhl Seminar 17452)
Dagstuhl Reports , 7:11, 2018
18-043
Guillermo Restrepo, Peter F. Stadler, and Jurgen Jost
Proceedings of the “mathematics in chemistry meeting”, leipzig, germany, october 26-28 2016
MATCH Commun. Math. Comput. Chem., 80:541–545, 2018
18-044
Langdon W.B., Petke J., Lorenz R.
Evolving Better RNAfold Structure Prediction
In: Castelli M., Sekanina L., Zhang M., Cagnoni S., García-Sánchez P. (eds) Genetic Programming. EuroGP 2018. Lecture Notes in Computer Science, vol 10781. Springer, Cham, doi:10.1007/978-3-319-77553-1_14