Publications
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Theoretical Biochemistry Group
Institute for Theoretical Chemistry
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2019
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19-001 Khanittha Kerdpol, Jintawee Kicuntod, Peter Wolschann, Seiji Mori, Chompoonut Rungnim, Manaschai Kunaseth, Hisashi Okumura, Nawee Kungwan and Thanyada Rungrotmongkol Cavity Closure of 2-Hydroxypropyl-β-Cyclodextrin: Replica Exchange Molecular Dynamics Simulations Polymers 2019, 11, 145, doi:10.3390/polym11010145 |
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19-002 Kongkaew S, Rungrotmongkol T, Punwong C, Noguchi H, Takeuchi F, Kungwan N, Wolschann P, Hannongbua S Interactions of HLA-DR and Topoisomerase I Epitope Modulated Genetic Risk for Systemic Sclerosis Sci Rep. 2019 Jan 24;9(1):745, doi:10.1038/s41598-018-37038-z |
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19-003 Kanyani Sangpheak, Lueacha Tabtimmai, Supaphorn Seetaha, Chompoonut Rungnim, Warinthorn Chavasiri, Peter Wolschann, Kiattawee Choowongkomon and Thanyada Rungrotmongkol Biological Evaluation and Molecular Dynamics Simulation of Chalcone Derivatives as Epidermal Growth Factor-Tyrosine Kinase Inhibitors Molecules 2019, 24, 1092, doi:10.3390/molecules24061092 |
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19-004 Waldeyr MC da Silva, Jakob L Andersen, Maristela Holanda, Maria Emília MT Walter, Marcelo M Brigido, Peter F Stadler, Christoph Flamm Exploring plant sesquiterpene diversity by generating chemical networks. Processes 7:240 2019, doi:10.3390/pr7040240 |
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19-005 Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler Chemical Transformation Motifs — Modelling Pathways as Integer Hyperflows. IEEE/ACM Trans Comp Biol Bioinf 16(2):510-523 (2019), doi:10.1109/TCBB.2017.2781724 |
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19-006 Adriano de Bernardi Schneider, Michael T. Wolfinger Musashi binding elements in Zika and related Flavivirus 3'UTRs: A comparative study in silico Scientific Reports 9:6911 (2019), doi:10.1038/s41598-019-43390-5 |
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19-007 Roman Ochsenreiter, Ivo L. Hofacker, Michael T. Wolfinger Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses Viruses 11(3):298 (2019), doi:10.3390/v11030298 |
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19-008 Flavia Bassani, Isabelle Anna Zink, Thomas Pribasnig, Michael T. Wolfinger, Alice Romagnoli, Armin Resch, Christa Schleper, Udo Bläsi, Anna La Teana Indications for a moonlighting function of translation factor aIF5A in the crenarchaeum Sulfolobus solfataricus RNA Biology 16(5):675-685 (2019), doi:10.1080/15476286.2019.1582953 |
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19-009 Deforges J, Reis RS, Jacquet P, Sheppard S, Gadekar VP, Tanzer A, Hofacker IL, Iseli C, Xenarios I, Poirier Y Control of cognate sense mRNA translation by cis-natural antisense RNAs in Arabidopsis Plant Physiology (2019), doi:10.1104/pp.19.00043 |
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19-010 Bernhard C. Thiel, Irene K. Beckmann, P. Kerpedjiev and Ivo L. Hofacker 3D based on 2D: Calculating helix angles and stacking patterns using forgi 2.0, an RNA Python library centered on secondary structure elements. F1000Research 2019, 8:287, doi:10.12688/f1000research.18458.1 |
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19-011 Mariam R. Farman, Ivo L. Hofacker, Fabian Amman MSF: Modulated Sub-graph Finder F1000Research 2019, 7:1346, doi:10.12688/f1000research.16005.3 |
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19-012 Sangpheak, K., Müller, M., Darai, N., Wolschann, P., Suwattanasophon, C., Ruga, R., Chavasiri, W., Seetaha, S., Choowongkomon, K., Kungwan, N., Rungnim, C. and Rungrotmongkol, T. Computational screening of chalcones acting against topoisomerase II alpha and their cytotoxicity towards cancer cell lines Journal of Enzyme Inhibition and Medicinal Chemistry. 34, 1, S. 134-143 10 S., doi:10.1080/14756366.2018.1507029 |
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19-013 Kolora, S. R. R., Weigert, A., Saffari, A., Kehr, S., Walter Costa, M. B., Sproeer, C., Indrischek, H., Chintalapati, M., Lohse, K., Doose, G., Overmann, J., Bunk, B., Bleidorn, C., Grimm-Seyfarth, A., Henle, K., Nowick, K., Faria, R., Stadler, P. F. and Schlegel, M. Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation GigaScience. 8, 2, 15 S., 160, doi:10.1093/gigascience/giy160 |
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19-014 Tanzer, A., Hofacker, I. L. and Lorenz, R. RNA modifications in structure prediction – Status quo and future challenges Methods. 156, S. 32-39, doi:10.1016/j.ymeth.2018.10.019 |
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19-015 Sweeney, B. A., Petrov, A. I., Burkov, B., Finn, R. D., Bateman, A., Szymanski, M., Karlowski, W. M., Gorodkin, J., Seemann, S. E., Cannone, J. J., Gutell, R. R., Fey, P., Basu, S., Kay, S., Cochrane, G., Billis, K., Emmert, D., Marygold, S. J. Huntley, R. P., Lovering, R. C., Frankish, A., Chan, P. P., Lowe, T. M., Bruford, E., Seal, R., Vandesompele, J., Volders, P-J., Paraskevopoulou, M., Ma, L., Zhang, Z., Griffiths-Jones, S., Bujnicki, J. M., Boccaletto, P., Blake, J. A., Bult, C. J., Chen, R., Zhao, Y., Wood, V., Rutherford, K., Rivas, E., Cole, J., Laulederkind, S. J. F., Shimoyama, M., Gillespie, M. E., Orlic-Milacic, M., Kalvari, I., Nawrocki, E., Engel, S. R., Cherry, J. M. and Stadler, P. F. RNAcentral: a hub of information for non-coding RNA sequences RNAcentral Consortium Nucleic Acids Research. 47, D1, S. D221-D229 9 S, doi:10.1093/nar/gky1206 |
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19-016 Gatter, T. and Stadler, P. Ryuto: network-flow based transcriptome reconstruction BMC Bioinformatics. 20, 14 S., 190, doi:10.1186/s12859-019-2786-5 |
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19-017 Costa, M. B. W., zu Siederdissen, C. H., Dunjic, M., Stadler, P. F. and Nowick, K. SSS-test: a novel test for detecting positive selection on RNA secondary structure BMC Bioinformatics. 20, 19 S., 151, doi:10.1186/s12859-019-2711-y |
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19-018 Schneider, A. D. B. and Wolfinger, M. T. The role of Arbovirus genome untranslated regions on neurotropism International Journal of Infectious Diseases. 79, S. 142-142 1 S., doi:10.1016/j.ijid.2018.11.347 |
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19-019 Stefan Hammer, Wei Wang, Sebastian Will and Yann Ponty Fixed-parameter tractable sampling for RNA design with multiple target structures BMC Bioinformatics 2019 20:209, doi:10.1186/s12859-019-2784-7 |
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19-020 iparat Hotarat, Sarunya Phunpee, Chompoonut Rungnim, Peter Wolschann, Nawee Kungwan, Uracha Ruktanonchai, Thanyada Rungrotmongkol, Supot Hannongbua Encapsulation of alpha-mangostin and hydrophilic beta-cyclodextrins revealed by all-atom molecular dynamics simulations J Mol Liquids 288, 110965, doi:10.1016/j.molliq.2019.110965 |
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19-021 Adriano de Bernardi Schneider, Roman Ochsenreiter, Reilly Hostager, Ivo L. Hofacker, Daniel Janies, Michael T. Wolfinger Updated phylogeny of Chikungunya virus suggests lineage-specific RNA architecture Viruses 11(9):798 (2019), doi:10.3390/v11090798 |
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19-022 Milad Miladi, Martin Raden, Sebastian Will, and Rolf Backofen Fast and accurate structure probability estimation for simultaneous alignment and folding of RNAs 19th International Workshop on Algorithms in Bioinformatics (WABI 2019) of Leibniz International Proceedings in Informatics (LIPIcs)/, pages 14:1--14:13, Dagstuhl, Germany |
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19-023 Maria Waldl, Sebastian Will, Michael T. Wolfinger, Ivo L. Hofacker, and Peter F. Stadler Bi-Alignments as Models of Incongruent Evolution of RNA Sequence and Structure In 16th International Conference on Computational Intelligence methods for Bioinformatics and Biostatistics (CIBB’19), Bergamo, Italy (September 2019), https://www.biorxiv.org/content/10.1101/631606v2, 2019 |
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19-024 Rick Gelhausen, Sebastian Will, Ivo Hofacker, Rolf Backofen, and Martin Raden Constraint Maximal Inter-molecular Helix Lengths within RNA-RNA Interaction Prediction Improves Bacterial sRNA Target Prediction In 12th International Joint Conference on Biomedical Engineering Systems and Technologies, volume 3 BIONFORMATICS of BIOSTEC, ISBN 978-989-758-353-7, pages 131–140. SciTePress, 2019 |
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19-025 Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler Information Processing in Chemical Systems The Energetics of Computing in Life and Machines, SFI Press, 2019 [ISBN 1947864076] |
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19-026 Michael Kiening, Roman Ochsenreiter, Hans-Jörg Hellinger, Thomas Rattei, Ivo L. Hofacker, and Dmitrij Frishman Conserved secondary structures in viral mRNAs Viruses, 11(5):401, 2019, doi:10.3390/v11050401 |
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19-027 Gärtner, Fabian and Stadler, Peter F. Direct Superbubble Detection Algorithms 12 (4), doi:10.3390/a12040081 |
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19-028 Polina Drozdova, Daria Bedulina, Ekaterina Madyarova, Lorena Rivarola-Duarte, Stephan Schreiber, Peter F. Stadler, Till Luckenbach & Maxim Timofeyev Description of strongly heat-inducible heat shock protein 70 transcripts from Baikal endemic amphipods Scientific Reports volume 9, Article number: 8907 (2019), doi:10.1038/s41598-019-45193-0 |
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19-029 Lieselotte Erber, Anne Hoffmann, Jörg Fallmann, Heike Betat, Peter F. Stadler & Mario Mörl LOTTE-seq (Long hairpin oligonucleotide based tRNA high-throughput sequencing): specific selection of tRNAs with 3’-CCA end for high-throughput sequencing RNA Biology 2019, doi:10.1080/15476286.2019.1664250 |
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19-030 Jörg Fallmann, Pavankumar Videm, Andrea Bagnacani,Berenice Batut, Maria A. Doyle, Tomas Klingstrom, Florian Eggenhofer, Peter F. Stadler, Rolf Backofen and Bjorn Grüning The RNA workbench 2.0: next generation RNA dataanalysis Nucleic Acids Research, 2019, Vol. 47, Web Server issueW511–W515, doi:10.1093/nar/gkz353 |
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19-031 Eugenio J. Llanos, Wilmer Leal, Duc H. Luu, Jürgen Jost, Peter F. Stadler, and Guillermo Restrepo Exploration of the chemical space and its three historical regimes Proceedings of the National Academy of Sciences, doi:10.1073/pnas.1816039116 |
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19-032 Manuela Geiß, Edgar Chávez, Marcos González Laffitte, Alitzel López Sánchez, Bärbel M. R. Stadler, Dulce I. Valdivia, Marc Hellmuth, Maribel Hernández Rosales, Peter F. Stadler Best match graphs Journal of Mathematical Biology, Volume 78, Issue 7, pp 2015–2057, doi:10.1007/s00285-019-01332-9 |
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19-033 Ali M Yazbeck, Peter F Stadler, Kifah Tout, Jörg Fallmann Automatic curation of large comparative animal MicroRNA datasets Bioinformatics Bioinformatics, Volume 35, Issue 22, 15 November 2019, Pages 4553–4559, doi:10.1093/bioinformatics/btz271 |
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19-034 RNAcentral Consortium, SILVA Team, Sweeney, B. A., Petrov, A. I., Burkov, B., Finn, R. D., ... Stadler, P. F. RNAcentral: a hub of information for non-coding RNA sequences Nucleic Acids Research, 47(D1), D221-D229, doi:10.1093/nar/gky1034 |
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19-035 Michael Kiening, Roman Ochsenreiter , Hans-Jörg Hellinger, Thomas Rattei, Ivo Hofacker and Dmitrij Frishman Conserved Secondary Structures in Viral mRNAs Viruses 2019, 11(5), 401, doi:10.3390/v11050401 |
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19-036 Dienstbier, A., Amman, F., Stipl, D., Petrackova, D. & Vecerek, B. Comparative Integrated Omics Analysis of the Hfq Regulon in Bordetella pertussis International Journal of Molecular Sciences. 20, 12, 16 S., 3073, doi:10.3390/ijms20123073 |
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19-037 Drozdova, P., Rivarola-Duarte, L., Bedulina, D., Axenov-Gribanov, D., Schreiber, S., Gurkov, A., Shatilina, Z., Vereshchagina, K., Lubyaga, Y., Madyarova, E., Otto, C., Juhling, F., Busch, W., Jakob, L. Lucassen, M., Sartoris, F. J., Hackermueller, J., Hoffmann, S., Poertner, H-O., Luckenbach, T., Timofeyev, M. & Stadler, P. F. Comparison between transcriptomic responses to short-term stress exposures of a common Holarctic and endemic Lake Baikal amphipods BMC Genomics. 20, 1, 14 S., 712.2019, doi:10.1186/s12864-019-6024-3 |
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19-038 Kolora, S. R. R., Weigert, A., Saffari, A., Kehr, S., Walter Costa, M. B., Sproeer, C., Indrischek, H., Chintalapati, M., Lohse, K., Doose, G., Overmann, J., Bunk, B., Bleidorn, C., Grimm-Seyfarth, A., Henle, K., Nowick, K., Faria, R., Stadler, P. F. & Schlegel, M. Divergent evolution in the genomes of closely related lacertids, Lacerta viridis and L. bilineata, and implications for speciation GigaScience. 8, 2, 15 S., 160.2019, doi:10.1093/gigascience/giy160 |
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19-039 Uxa, S., Bernhart, S. H., Mages, C. F. S., Fischer, M., Kohler, R., Hoffmann, S., Stadler, P. F., Engeland, K. & Mueller, G. A. DREAM and RB cooperate to induce gene repression and cell-cycle arrest in response to p53 activation Nucleic Acids Research. 47, 17, S. 9087-9103 17 S.2019, doi:10.1093/nar/gkz635 |
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19-040 Nowick, K., Walter Costa, M. B., zu Siederdissen, C. H. & Stadler, P. F. Selection Pressures on RNA Sequences and Structures Evolutionary bioinformatics. 15, 4 S., 2019, doi:10.1177/1176934319871919 |
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19-041 Schuster, P. What is special about autocatalysis? Monatshefte für Chemie. 150, 5, S. 763-775 13 S.2019, doi:10.1007/s00706-019-02437-z |
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19-042 Steinparzer, I., Sedlyarov, V., Rubin, J. D., Eislmayr, K., Galbraith, M. D., Levandowski, C. B., Vcelkova, T., Sneezum, L., Wascher, F., Amman, F., Kleinova, R., Bender, H., Andrysik, Z., Espinosa, J. M., Superti-Furga, G., Dowell, R. D., Taatjes, D. J. & Kovarik, P. Transcriptional Responses to IFN-γ Require Mediator Kinase-Dependent Pause Release and Mechanistically Distinct CDK8 and CDK19 Functions Molecular Cell. 76, 3, S. 485-499.e8, doi:10.1016/j.molcel.2019.07.034 |
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19-043 Magan, A., Amman, F., El-Isa, F., Hartl, N., Shamovsky, I., Nudler, E., Schroeder, R. & Sedlyarova, N. iRAPs curb antisense transcription in E. coli Nucleic Acids Research. 47, 20, S. 10894-10905 12 S., doi:10.1093/nar/gkz791 |
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19-044 Licht, K., Hartl, M., Amman, F., Anrather, D., Janisiw, M. P. & Jantsch, M. F. Inosine induces context-dependent recoding and translational stalling Nucleic Acids Research. 47, 10, S. 3-14 gky1163, doi:10.1093/nar/gky1163 |
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19-045 Gelhausen, R., Will, S., Hofacker, I. L., Backofen, R. & Raden, M. INTARNAHELIX-composing RNA-RNA interactions from stable inter-molecular helices boosts bacterial sRNA target prediction Journal of Bioinformatics and Computational Biology (JBCB). 17, 5, 16 S., 1940009, doi:10.1142/S0219720019400092 |
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19-046 Kirsch, R., Olzog, V. J., Bonin, S., Weinberg, C. E., Betat, H., Stadler, P. F., & Mörl, M. A streamlined protocol for the detection of mRNA-sRNA interactions using AMT-crosslinking in vitro. BioTechniques, 67(4), 178-183., doi:10.2144/btn-2019-0047 |
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19-047 Andersen, J. L., Flamm, C., Merkle, D., & Stadler, P. F. Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows Bioinformatics, 16(2), 510-523., doi:10.1109/TCBB.2017.2781724 |
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19-048 da Silva, W. M. C., Andersen, J. L., Holanda, M. T., Walter, M. E. M. T., Brigido, M. M., Stadler, P. F., & Flamm, C. Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks Group Processes and Intergroup Relations, 7 (4), [240], doi:10.3390/pr7040240 |
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19-049 Donath, A., Juehling, F., Al-Arab, M., Bernhart, S. H., Reinhardt, F., Stadler, P. F., ... Bernt, M. Improved annotation of protein-coding genes boundaries in metazoan mitochondrial genomes Nucleic Acids Research, 47(20), 10543-10552, doi:10.1093/nar/gkz833 |
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19-050 Geiss, M., Stadler, P. F., & Hellmuth, M. Reciprocal best match graphs Journal of Mathematical Biology, doi:10.1007/s00285-019-01444-2 |
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19-051 Peter Wolschann, Alfred Karpfen BLUE-SHIFTED FORMYL C-H STRETCHING FREQUENCIES IN HYDROGEN-BONDED AND HALOGEN-BONDED COMPLEXES OF BENZALDEHYDE, N-BENZYLIDENEAMINE AND N-BENZYLIDENEMETHYLAMINE Wiadomosci 2019, 73, 3-4 PL ISSN 0043-5104 |
2018
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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) |
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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) |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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18-032 Farman, Mariam R and Hofacker, Ivo L and Amman, Fabian MSF: Modulated Sub-graph Finder F1000Research, doi:10.12688/f1000research.16005 |
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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 |
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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 |
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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 |
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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 |
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18-037 P. Schuster A mathematical model of evolution MATCH – Communications in Mathematical and in Computer Chemistry, 80:547–585, 2018 |
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18-038 P. Schuster Molecular evolution between chemistry and biology. The interplay of competition, cooperation, and mutation European Biophysics Journal, 47:403–425, 2018 |
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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. |
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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 |
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18-041 Nancy Retzlaff and Peter F. Stadler Phylogenetics beyond biology Th. Biosci., 137:133–143,2018, doi:10.1007/s12064-018-0264-7 |
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18-042 Jakob L. Andersen, Christoph Flamm, Daniel Merkle, and Peter F Stadler Algorithmic Cheminformatics (Dagstuhl Seminar 17452) Dagstuhl Reports , 7:11, 2018 |
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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 |
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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 |
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18-045 Andersen, J. L., & Merkle, D A Generic Framework for Engineering Graph Canonization Algorithms 2018 Proceedings of the Twentieth Workshop on Algorithm Engineering and Experiments (ALENEX) SIAM PUBLICATIONS, doi:10.1137/1.9781611975055.13 |
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18-046 Changat, M., Nezhad, F. H., & Stadler, P. Axiomatic characterization of transit functions of hierarchies Ars Mathematica Contemporanea, 14(1), 117-128, doi:10.26493/2590-9770.1260.989 |
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18-047 Yazbeck, A. M., Tout, K. R., & Stadler, P. F. Detailed secondary structure models of invertebrate 7SK RNAs RNA Biology, 15(2), 158-164, doi:10.1080/15476286.2017.1412913 |
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18-048 Prohaska, S. J., Berkemer, S. J., Gaertner, F., Gatter, T., Retzlaff, N., zu Siederdissen, C. H., & Stadler, P. F. Expansion of gene clusters, circular orders, and the shortest Hamiltonian path problem ournal of Mathematical Biology, 77(2), 313-341, doi:10.1007/s00285-017-1197-3 |
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18-049 Hellmuth, M., Hernandez-Rosales, M., Long, Y., & Stadler, P. F. Inferring phylogenetic trees from the knowledge of rare evolutionary events Journal of Mathematical Biology, 76(7), 1623-1653, doi:10.1007/s00285-017-1194-6 |
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18-050 Mahalapbutr, P., Nutho, B., Wolschann, P., Chavasiri, W., Kungwan, N., & Rungrotmongkol, T. Molecular insights into inclusion complexes of mansonone E and H enantionmers with various ß-dyclodextrins Journal of molecular graphics & modelling, 79, 72-80, doi:10.1016/j.jmgm.2017.11.006 |
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18-051 Donath, A., & Stadler, P. Split-inducing indels in phylogenomic analysis Algorithms for Molecular Biology, 13, [12], doi:10.1186/s13015-018-0130-7 |
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18-052 Costa, M. B. W., Siederdissen, C. H. Z., Tulpan, D., Stadler, P. F., & Nowick, K. Temporal ordering of substitutions in RNA evolution: Uncovering the structural evolution of the Human Accelerated Region 1 Journal of Theoretical Biology, 438, 143-150, doi:10.1016/j.jtbi.2017.11.015 |
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18-053 Canzler, S., Stadler, P. F., & Schor, J. The fungal snoRNAome RNA, 24(3), 342-360, doi:10.1261/rna.062778.117 |
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18-054 Nojgaard, N., Geiss, M., Merkle, D., Stadler, P. F., Wieseke, N., & Hellmuth, M. Time-consistent reconciliation maps and forbidden time travel Algorithms for Molecular Biology, 13, [2], doi:10.1186/s13015-018-0121-8 |
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18-055 Laubichler, M. D., Prohaska, S. J., & Stadler, P. F. Toward a mechanistic explanation of phenotypic evolution: The need for a theory of theory integration Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 330(1), 5-14, doi:10.1002/jez.b.22785 |
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18-056 Lokits, A. D., Indrischek, H., Meiler, J., Hamm, H. E., & Stadler, P. F. Tracing the evolution of the heterotrimeric G protein a subunit in Metazoa BMC Evolutionary Biology, 18, [51], doi:10.1186/s12862-018-1147-8 |
2017
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17-001 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 |
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17-002 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 |
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17-003 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 |
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17-004 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 |
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17-005 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 |
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17-006 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 |
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17-007 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 |
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17-008 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 |
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17-009 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 |
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17-010 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 |
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17-011 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 |
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17-012 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 |
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17-013 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 |
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17-014 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 |
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17-015 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 |
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17-016 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 |
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17-017 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 |
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17-018 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 |
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17-019 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 |
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17-020 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 |
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17-021 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 |
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17-022 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 |
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17-023 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 |
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17-024 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 |
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17-025 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 |
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17-026 Nataporn WIJIT, Sukon PRASITWATTANASEREE, Sugunya MAHATHEERANONT, Peter WOLSCHANN, Supat JIRANUSORNKUL, Piyarat NIMMANPIPUG 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 |
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17-028 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 |
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17-029 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 |
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17-030 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 |
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17-031 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 |
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17-032 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 |
2016
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16-001 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?~@~S98, doi:10.1016/j.jmgm.2015.11.005 |
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16-002 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?~@~S2773, doi:10.3762/bjoc.11.297 |
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16-003 Wasinee Khuntawee, Thanyada Rungrotmongkol, Peter Wolschann, Piamsook Pongsawasdi, Nawee Kungwan, Hisashi Okumura, Supot Hannongbua Conformation study of ?~[-cyclodextrin: Replica exchange molecular dynamics simulations Carbohydrate Polymers 141 (2016) 99?~@~S105, doi:10.1016/j.carbpol.2015.10.018 |
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16-004 Muralidhar Tata, Michael T. Wolfinger, Fabian Amman, Nicole Roschanski, Andreas Dötsch, Elisabeth Sonnleitner, Susanne Häusslerr , 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 |
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16-005 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 |
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16-006 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 |
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16-007 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?~@~S22. Springer-Verlag, Berlin, 2015. |
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16-008 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?~@~S120. Springer-Verlag, Berlin, 2015. |
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16-009 E. Domingo and P. Schuster Quasispecies: From Theory to Experimental Systems Volume 392 of Current Topics in Microbiology and Immunology. Springer-Verlag, Berlin, 2016 |
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16-010 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?~@~S118, doi:10.1016/j.cplett.2016.05.065 |
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16-011 Florian Eggenhofer, Ivo L. Hofacker and Christian Höner zu Siederdissen RNAlien ?~@~S Unsupervised RNA family model construction Nucl. Acids Res. (2016), doi:10.1093/nar/gkw558 |
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16-012 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 |
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16-013 Ronny Lorenz, Ivo L. Hofacker, and Peter F. Stadler RNA folding with hard and soft constraints Alg. Mol. Biol., 11:1?~@~S13, 2016, doi:10.1186/s13015-016-0070-z |
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16-014 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?~@~SD95, 2016, doi:10.1093/nar/gkv1238 |
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16-015 Yu-Ting Hsiao, Wei-Po Lee, Wei Yang, Stefan Mülll er, 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?~@~S75, 2016, doi:10.1109/TCBB.2015.2465954 |
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16-016 Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadll er, and Jing Qin Pseudoknots in RNA folding landscapes Bioinformatics, 32:187?~@~S194, 2016, doi:10.1093/bioinformatics/btv572 |
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16-017 Ronny Lorenz, Dominik Luntzer, Ivo L. Hofacker, Peter F. Stadler, and Michael T. Wolfinger SHAPE directed RNA folding. Bioinformatics, 32:145?~@~S147, 2016 Bioinformatics, 32:145?~@~S147, 2016, doi:10.1093/bioinformatics/btv523 |
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16-018 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 |
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16-019 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 |
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16-020 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 |
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16-021 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 |
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16-022 P. Schuster Major transitions in evolution and in technology. What they have in common and where they differ Complexity, 21(4):7?~@~S13, 2016, doi:10.1002/cplx.21773 |
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16-023 P. Schuster Some mechanistic requirements for major transitions Phil. Trans. Roy. Soc. B, 371:20150439, 2016, doi:10.1098/rstb.2015.0439 |
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16-024 P. Schuster The end of Moore?~@~Ys law. Living without an exponential increase in the efficiency of computational facilities Complexity, 22(1):p?~@~Spp, 2016, doi:10.1002/cplx.21824 |
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16-025 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?~@~S81. The MIT Press, Cambridge, MA, 2016 |
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16-026 Gu, Jiao and Jost, Jürgen and Liu, Shiping and SS tadler, 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 |
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16-027 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 |
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16-028 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 |
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16-029 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 |
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16-030 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 |
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16-031 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 |
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16-032 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 |
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16-033 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 |
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16-034 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 |
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16-035 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?~@~S16, doi:10.1016/j.bpc.2016.09.005 |
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16-036 Martin Hölzer, Verena Krähling, Fabian Amman, EE manuel Barth, Stephan H. Bernhart, Victor A. O. Carmelo, Maximilian Collatz, Gero Doose, Florian Eggenhofer, Jan Ewald, Jörg Fallmann, Lasse M. Feldhahn, Markuu s Fricke, Juliane Gebauer, Andreas J. Gruber, Franziska Hufsky, Henrike Indrischek, Sabina Kanton, Jörg Linde, Nelly Mostajo, Roman Ochsenreiter, Konstantin Rii ege, 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 |
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16-037 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 |
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16-038 P. Schuster Stochasticity in Processes. Fundamentals and Applications to Chemistry and Biology Springer Series in Synergentics, Springer-Verlag, Berlin, 2016 |
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16-039 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 |
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16-040 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 |
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16-041 Cristian A. Velandia-Huerto, Sarah J. Berkemer, Anne Hoffmann, Nancy Retzlaff, Liliana C. Romero Marroquín, Maribel Hernández-RR osales, Peter F. Stadler, Clara I. Bermúdez-Santana>/small> 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 |
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16-042 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 |
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16-043 Frank Jühling, Helene Kretzmer, Stephan H. Bernhh art, 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 |
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16-044 Alexander J. Westermann, Konrad U. Förstner, Fabbian Amman, Lars Barquist, Yanjie Chao, Leon N. Schulte, Lydia Müller, Richard RR einhardt, Peter F. Stadler, Jörg Vogel o Dual RNA-seq unveils noncoding RNA functions in host?~@~Spathogen interactions Nature volume 529 issue 7587 on pages 496 to 501, doi:10.1038/nature16547 |
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16-045 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 |
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16-046 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 |
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16-047 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 Chraa st, 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 |
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16-048 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 |
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16-049 Gesine Domin, Sven Findei?~_, 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 |
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16-050 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 |
2015
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15-001 Wachsmuth M, Domin G, Lorenz R, Serfling R, Findeiß S, Stadler PF, Mörl M. Design criteria for synthetic riboswitches acting on transcription. RNA Biol. 2015 Feb;12(2):221-31. doi:10.1080/15476286.2015.1017235 |
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15-002 Findeiß S, Wachsmuth M, Mörl M, Stadler PF. Design of transcription regulating riboswitches. Methods Enzymol. 2015;550:1-22. Epub 2014 Dec 26, doi:10.1016/bs.mie.2014.10.029 |
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15-003 Sonja Petkovic, Stefan Badelt, Stephan Block, Christoph Flamm, Mihaela Delcea, Ivo L Hofacker, Sabine Müller Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by ATM RNA 21:1-13 (2015), doi:10.1261/rna.047670.114 |
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15-004 Sanja Antic, Michael T. Wolfinger, Anna Skucha, Stefanie Hosiner and Silke Dorner General and miRNA-mediated mRNA degradation occurs on ribosome complexes in Drosophila cells Melecular an Cellular BiologyMCB.01346-14, doi:10.1128/MCB.01346-14 |
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15-005 Michael T. Wolfinger, Jörg Fallmann, Florian Eggenhofer and Fabian Amman ViennaNGS: A toolbox for building efficient next-generation sequencing analysis pipelines F1000Research 4:50 (2015), doi:10.12688/f1000research.6157.1 |
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15-006 Pervouchine DD, Djebali S, Breschi A, Davis Ca, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See L, et al. Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression Nat. Commun. 6 (2015) page(s): 5903, doi:10.1038/ncomms6903 |
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15-007 Hellmuth Marc, Marc Tilen, Ostermeier Lydia, Stadler Peter F. The relaxed square property Australasian Journal of Combinatorics Vol 62: No. 3 240-770 (2015) |
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15-008 Lydia Ostermeier, Peter F. Stadler The Grid Property and Product-Like Hypergraphs Graphs and Combinatorics 31(3): 757-770 (2015), doi:10.1007/s00373-013-1392-y |
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15-009 Peter Kerpedjiev, Christian Höner zu Siederdissen, Ivo L. Hofacke Predicting RNA 3D structure using a coarse-grain helix-centered model RNA 2015. 21: 1110-1121, doi:10.1261/rna.047522.114 |
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15-010 Stephanie Keller-Schmidt, Murat Tuğrul, Víctor M. Eguíluz, Emilio Hernández-García, and Konstantin Klemm Anomalous scaling in an age-dependent branching model Physical Review E 91.2 (2015): 022803, doi:http://dx.doi.org/10.1103/PhysRevE.91.022803 |
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15-011 Marc Hellmuth, Nicolas Wieseke, Marcus Lechner, Hans-Peter Lenhof, Martin Middendorf, and Peter F. Stadler Phylogenomics with paralogs Proceedings of the National Academy of Sciences USA, doi:10.1073/pnas.1412770112 |
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15-012 Jana Hertel, Peter F. Stadler The Expansion of Animal MicroRNA Families Revisited Life (ISSN 2075-1729), doi:10.3390/life5010905 |
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15-013 Anne Nitsche, Dominic Rose, Mario Fasold, Kristin Reiche, and Peter F. Stadler Comparison of splice sites reveals that long non-coding RNAs are evolutionarily well conserved RNA May 2015 21: 801-812; Published in Advance March 23, 2015, doi:10.1261/rna.046342.114. |
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15-014 Peter Kerpedjiev, Stefan Hammer and Ivo L. Hofacker forna (force-directed RNA): Simple and Effective Online RNA Secondary Structure Diagrams Bioinformatics (2015), doi:10.1093/bioinformatics/btv372 |
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15-015 Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler Product grammars for alignment and folding IEEE Trans. Comp. Biol. Bioinf., 12:507–519, 2015, doi:10.1109/TCBB.2014.2326155 |
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15-016 Christopher A. Lavender, Ronny Lorenz, Ge Zhang, Rita Tamayo, Ivo L. Hofacker, and Kevin M. Weeks Model-free RNA sequence and structure alignment informed by SHAPE probing reveals a conserved alternate secondary structure for 16S rRNA PLoS Comput Biol, 11:e1004126, 05 2015, doi:10.1371/journal.pcbi.1004126 |
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15-017 Stefan Badelt, Stefan Hammer, Christoph Flamm, and Ivo L. Hofacker Computational Methods for Understanding Riboswitches volume 553 of Methods in Enzymology, chapter Thermodynamic and Kinetic Folding of Riboswitches, pages 193–213. Elsevier, 2015, doi:10.1016/bs.mie.2014.10.060 |
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15-018 Wasinee Khuntawee, Peter Wolschann, Thanyada Rungrotmongkol, Jirasak Wong-ekkabut and Supot Hannongbua Molecular Dynamics Simulations of the Interaction of Beta Cyclodextrin with a Lipid Bilayer J. Chem. Inf. Model., 2015, 55 (9), pp 1894–1902, doi:10.1021/acs.jcim.5b00152 |
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15-019 Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler and Jing Qin Pseudoknots in RNA folding landscapes Bioinformatics 2015, doi:10.1093/bioinformatics/btv572 |
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15-020 Yu-Ting Hsiao, Wei-Po Lee, Wei Yang, Stefan Müller, Christoph Flamm, Ivo L Hofacker, Philipp Kügler Practical Guidlines for Incorporating Knowledge-Based and Data-Driven Stratewgies into the Inference of Gene Regulatory Networks IEEE Trans Comp Biol Bioinf PP(99): 2015, doi:10.1109/TCBB.2015.2465954 |
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15-021 Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler In silico Support for Eschenmoser's Glyoxylate Scenario Israel Journal of Chemistry 55(8):919-933 (2015), doi:10.1002/ijch.201400187 |
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15-022 Gruber AR, Bernhart SH, Lorenz R The ViennaRNA Web Services RNA Bioinformatics, Methods in Molecular Biology, 1269, (2015) page(s) 307-326, Publisher: Springer New York, Editor(s): Picardi, Ernesto, doi:10.1007/978-1-4939-2291-8_19 |
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15-023 Lorenz R, Luntzer D, Hofacker IL, Stadler PF, Wolfinger MT SHAPE directed RNA folding Bioinformatics (2015), doi:10.1093/bioinformatics/btv523 |
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15-024 Pervouchine DD, Djebali S, Breschi A, Davis Ca, Barja PP, Dobin A, Tanzer A, Lagarde J, Zaleski C, See L, et al. Enhanced transcriptome maps from multiple mouse tissues reveal evolutionary constraint in gene expression Nat. Commun. 6 (2015) page(s): 5903, doi:10.1038/ncomms6903 |
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15-025 Sarah J. Berkemer, Christian Höner zu Siederdissen, Fabian Amman, Axel Wintsche, Sebastian Will, Ivo L. Hofacker, Sonja J. Prohaska, and Peter F. Stadler Processed small RNAs in Archaea and BHB elements Genomics Comp. Biol., 1:e18, 2015, doi:10.18547/gcb.2015.vol1.iss1.e18 |
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15-026 Nikolai Hecker, Mikkel Christensen-Dalsgaard, Stefan E Seemann, Jakob H Havgaard, Peter F Stadler, Ivo L Hofacker, Henrik Nielsen, and Jan Gorodkin Optimizing RNA structures by sequence extensions using RNAcop Nucleic acids research, 43(17):8135–45, 2015, doi:10.1093/nar/gkv813 |
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15-027 Sahyoun, Abdullah H. and Hölzer, Martin and Jühling, Frank and Siederdissen, Christian and Al-Arab, Marwa and Tout, Kifah and Marz, Manja and Middendorf, Martin and Stadler, Peter F. and Bernt, Matthias Towards a Comprehensive Picture of Alloacceptor tRNA Remolding in Metazoan Mitochondrial Genomes Nucl. Acids Res. 43 (16): 8044-8056, doi:10.1093/nar/gkv746 |
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15-028 Berkemer, Sarah and Chaves, Ricardo and Fritz, Adrian and Hellmuth, Marc and Hernandez-Rosales, Maribel and Stadler, Peter F. Spiders can be recognized by counting their legs Math. Comp. Sci., doi:10.1007/s11786-015-0233-1 |
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15-029 Engelhardt, Jan and Stadler, Peter F. Evolution of the unspliced transcriptome BMC Evolutionary Biology 2015, 15:166, doi:10.1186/s12862-015-0437-7 |
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15-030 Angrisani, Alberto and Tafer, Hakim and Stadler, Peter F. and Furia, Maria Unusual Novel snoRNA-like RNAs in Drosophila melanogaster Non-Coding RNA 2015, 1(2), 139-150, doi:10.3390/ncrna1020139 |
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15-031 Fasold, Mario and Burge, Sarah W. and Ninova, Maria and Hertel, Jana and Kehr, Stephanie and Steeves, Tammy E. and Griffiths-Jones, Sam and Stadler, Peter F. Conservation and Losses of Non-Coding RNAs in Avian Genomes PLoS One 10: e0121797, doi:10.1371/journal.pone.0121797 |
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15-032 Hoffmann, Steve and Stadler, Peter F. and Strimmer, Korbinian A Simple Data-Adaptive Probabilistic Variant Calling Model Algorithms for Molecular Biology 2015, 10:10, doi:10.1186/s13015-015-0037-5 |
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15-033 Liu, Xuanshi and Scholz, Markus and Tönjes, Anke and Stumvoll, Michael and Stadler, Peter F. and Böttcher, Yvonne Indications for potential parent of origin effects within the FTO gene PLoS ONE 10: e0119206, doi:10.1371/journal.pone.0119206 |
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15-034 K.Boonyarattanakalin, H. Viernstein, P. Wolschann, L.Lawtrakul Influence of Ethanol as Co-Solvent in Cyclodextrin Inclusion Complexation: A Molecular Dynamics Study Scientia Pharmaceutica 83, 387-399 (2015), doi:10.3797/scipharm.1412-08 |
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15-035 A. Punkvang, P. Kamsri, P. Saparpakorn, S. Hannongbua, P. Wolschann, S. Irle, P. Pungpo Key Structures and Interactions for Binding of Mycobacterium tuberculosis Protein Kinase B Inhibitors from Molecular Dynamics Simulation Chem.Biol Drug Design 86, 91-101 (2015), doi:10.1111/cbdd.12465 |
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15-036 Theis, C., Zirbel, C. L., Höner zu Siederdissen, C., Anthon, C., Hofacker, I. L., Nielsen, H., & Gorodkin, J. RNA 3D Modules in Genome-Wide Predictions of RNA 2D Structure PLoS ONE, 10(10), [0139900], doi:10.1371/journal.pone.0139900 |
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15-037 Betat, H., Mede, T., Tretbar, S., Steiner, L., Stadler, P. F., Moerl, M., & Prohaska, S. J. Holozoa acquired the CCA-adding enzyme from Alphaproteobacteria by horizontal gene transfer Nucleic Acids Research, 43(14), 6739-6746, doi:10.1093/nar/gkv631 |
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15-038 Schuster, P. Ebola-Challenge and Revival of Theoretical Epidemiology Why Extrapolations from Early Phases of Epidemics are Problematic Complexity, 20(5), 7-12, doi:10.1002/cplx.21694 |
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15-039 Schuster, P. Models: From Exploration to Prediction Bad Reputation of Modeling in Some Disciplines Results from Nebulous Goals Complexity, 21(1), 6-9, doi:10.1002/cplx.21729 |
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15-040 Chonticha Suwattanasophon, Peter Wolschann and 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, 34:2, 318-326, doi:10.1080/07391102.2015.1030691 |
2014
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14-001 Amman Fabian, Wolfinger T Michael, Lorenz Ronny, Hofacker L Ivo, Stadler F Peter, Findeiß Sven TSSAR: TSS annotation regime for dRNA-seq data BMC Bioinformatics, doi:10.1186/1471-2105-15-89 |
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14-002 Abdel-Nasser M.A. Alaghaz, Reda A.A. Ammar, Gottfried Koehler, Karl Peter Wolschann, Tarek M. El-Gogary Synthesis, spectral and quantum chemical studies on NO-chelating sulfamonomethoxine–cyclophosph(V)azane and its Er(III) complex Molecular and Biomolecular Spectroscopy 128 (2014) 724–729, doi:10.1016/j.saa.2014.02.061 |
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14-003 Waratchada Sangpheak, Wasinee Khuntawee, Peter Wolschann, Piamsook Pongsawasdi, Thanyada Rungrotmongkol Enhanced stability of a naringenin/2,6-dimethyl ^B-cyclodextrininclusion complex: Molecular dynamics and free energy calculationsbased on MM- and QM-PBSA/GBSA Journal of Molecular Graphics and Modelling 50 (2014) 10–15, doi:10.1016/j.jmgm.2014.03.001 |
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14-004 Manja Marz, Niko Beerenwinkel, Christian Drosten, Markus Fricke, Dmitrij Frishman, Ivo L. Hofacker, Dieter Hoffmann, Martin Middendorf, Thomas Rattei, Peter F. Stadler, and Armin Töpfer Challenges in RNA virus bioinformatics Bioinformatics, 2014, doi:10.1093/bioinformatics/btu105 |
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14-005 Ivo L. Hofacker and Ronny Lorenz Predicting RNA structure: Advances and limitations In Christina Waldsich, editor, RNA Folding, volume 1086 of Methods in Molecular Biology, pages 1–19. Humana Press, 2014, doi:10.1007/978-1-62703-667-2_1 |
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14-006 Haleh Ebadi, Konstantin Klemm Boolean networks with veto functions Physical Review E volume 90 issue 2, doi:10.1103/physreve.90.022815 |
14-007 Backofen R, Amman F, Costa F, Findeiß S, Richter AS and Stadler PF Bioinformatics of Prokaryotic RNAs RNA Biology volume 11 issue 5, doi:10.4161/rna.28647 |
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14-008 P. Schuster Evolution der Molekule. Von der Evolution im Reagenzglas zur Erzeugung von maßgeschneiderten Molekulen In M. Neukamm, editor, Evolutionares Denken. Evolution als Leitbild in den modernen Wissenschaften, chapter 4, Wissenschaftliche Buchgesellschaft – WBG, Darmstadt, DE, 2014 |
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14-009 P. Schuster Are computer scientists the sutlers of modern biology? Bioinformatics is indispensible for progress in molecular life sciences but does not get credit for its contributions Complexity volume 19 issue 4 on pages 10 to 14, doi:10.1002/cplx.21501 |
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14-010 Tanja Gesell, Peter Schuster Phylogeny and Evolution of RNA Structure Methods in Molecular Biology Volume 1097, 2014, pp 319-378, doi:10.1007/978-1-62703-709-9_16 |
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14-011 Hoffmann S, Otto C, Doose G, Tanzer A, Langenberger D, Christ S, Kunz M, Holdt L, Teupser D, Hackermüeller J, Stadler PF A multi-split mapping algorithm for circular RNA, splicing, trans-splicing, and fusion detection Genome Biol. 2014 Feb 10;15(2):R34, doi:10.1186/gb-2014-15-2-r34 |
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14-012 Ivo L. Hofacker Energy-Directed RNA Structure Prediction Methods in Molecular Biology on pages 71 to 84, doi:10.1007/978-1-62703-709-9_4 |
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14-013 Jan Gorodkin, Ivo L. Hofacker, Walter L. Ruzzo Concepts and Introduction to RNA Bioinformatics Methods in Molecular Biology on pages 1 to 31, doi:10.1007/978-1-62703-709-9_1 |
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14-014 Konstantin Klemm, Peter F. Stadler Rugged and Elementary Landscapes Natural Computing Series on pages 41 to 61, doi:10.1007/978-3-642-33206-7_3 |
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14-015 Marc Hellmuth, Lydia Ostermeier, Peter F. Stadler Unique square property, equitable partitions, and product-like graphs Discrete Mathematics volume 320 on pages 92 to 103, doi:10.1016/j.disc.2013.12.012 |
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14-016 Jana Hertel, David Langenberger, Peter F. Stadler Computational Prediction of MicroRNA Genes Methods in Molecular Biology on pages 437 to 456, doi:10.1007/978-1-62703-709-9_20 |
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14-017 Peter F. Stadler Class-Specific Prediction of ncRNAs Methods in Molecular Biology on pages 199 to 213, doi:10.1007/978-1-62703-709-9_10 |
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14-018 Konstantin Klemm, Jing Qin, Peter F. Stadler Geometry and Coarse-Grained Representations of Landscapes Emergence, Complexity and Computation on pages 153 to 176, doi:10.1007/978-3-642-41888-4_6 |
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14-019 Sandra Wende, Edward G. Platzer, Frank Jühling, Joern Pütz, Catherine Florentz, Peter F. Stadler, Mario Mörl Biological evidence for the world's smallest tRNAs Biochimie volume 100 on pages 151 to 158, doi:10.1016/j.biochi.2013.07.034 |
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14-020 Jörg Hackermüller, Kristin Reiche, Christian Otto, Nadine Hösler, Conny Blumert, Katja Brocke-Heidrich, Levin Böhlig, Anne Nitsche, Katharina Kasack, Peter Ahnert, Wolfgang Krupp, Kurt Engeland, Peter F Stadler, Friedemann Horn Cell cycle, oncogenic and tumor suppressor pathways regulate numerous long and macro non-protein-coding RNAs Genome Biology volume 15 issue 3 on page R48, doi:10.1186/gb-2014-15-3-r48 |
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14-021 Bernhard Misof, Karen Meusemann, Björn M von Reumont, Patrick Kück, Sonja J Prohaska, Peter F Stadler A priori assessment of data quality in molecular phylogenetics Algorithms for Molecular Biology volume 9 issue 1 on page 22, doi:10.1186/s13015-014-0022-4 |
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14-022 Peter Kerpedjiev, Jes Frellsen, Stinus Lindgreen, Anders Krogh Adaptable probabilistic mapping of short reads using position specific scoring matrices BMC Bioinformatics volume 15 issue 1 on page 100, doi:10.1186/1471-2105-15-100 |
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14-023 Marcel Kucharík, Ivo L. Hofacker, Peter F. Stadler and Jing Qin Basin Hopping Graph: A computational framework to characterize RNA folding landscapes Bioinformatics 2014, doi:10.1093/bioinformatics/btu156 |
14-024 Martin Mann, Marcel Kucharík, Christoph Flamm and Michael T. Wolfinger Memory-efficient RNA energy landscape exploration Bioinformatics 2014, doi:10.1093/bioinformatics/btu337 |
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14-025 Ebert G, Steininger A, Weißmann R, Boldt V, Lind-Thomsen A, Grune J, Badelt S, Heßler M, Peiser M, Hitzler M, Jensen LR, Müller I, Hu H, Arndt PF, Kuss AW, Tebel K, Ullmann R Distribution of segmental duplications in the context of higher order chromatin organisation of human chromosome 7 BMC Genomics. 2014 Jun 29;15:537, doi:10.1186/1471-2164-15-537 |
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14-026 Marcus Lechner, Maribel Hernandez-Rosales, Daniel Doerr, Nicolas Wieseke, Annelyse Thévenin, Jens Stoye, Roland K. Hartmann, Sonja J. Prohaska, Peter F. Stadler Orthology detection combining clustering and synteny for very large datasets PLoS ONE 9(8): e105015, doi:10.1371/journal.pone.0105015 |
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14-027 Andrew Farmer, Christian Hoener zu Siederdissen, Andy Gill The HERMIT in the stream Proceedings of the ACM SIGPLAN 2014 workshop on Partial evaluation and program manipulation: 97--108 |
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14-028 Marc Hellmuth, Josef Leydold, Peter F Stadler Convex Cycle Bases Acta Math. Con- temp. 7:123–140 (2014) |
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14-029 Arli Aditya Parikesit, Lydia Steiner, Peter F Stadler, Sonja J Prohaska Pitfalls of Ascertainment Biases in Genome Annotations —Computing Comparable Protein Domain Distributions in Eukarya Malaysian Journal of Fundamental and Applied Sciences, Vol 10, No 2 (2014) |
14-030 Jing Qin, Markus Fricke, Manja Marz, Peter F Stadler, Rolf Backofen Graph-distance distribution of the Boltzmann ensemble of RNA secondary structures Algorithms for Molecular Biology volume 9 issue 1 on page 19, doi:10.1186/1748-7188-9-19 |
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14-031 Lorena Rivarola-Duarte, Christian Otto, Frank Jühling, Stephan Schreiber, Daria Bedulina, Lena Jakob, Anton Gurkov, Denis Axenov-Gribanov, Abdullah H. Sahyoun, Magnus Lucassen, Jörg Hackermüller, Steve Hoffmann, Franz Sartoris, Hans-Otto Pörtner, Maxim Timofeyev, Till Luckenbach, Peter F. Stadler A First Glimpse at the Genome of the Baikalian Amphipod Eulimnogammarus verrucosus Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, Volume 322, Issue 3, pages 177–189, May 2014, doi:10.1002/jez.b.22560 |
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14-032 Gerstein MB, Rozowsky J, Yan KK, Wang D, Cheng C, Brown JB, Davis CA, Hillier L, Sisu C, Li JJ, Pei B, Harmanci AO, Duff MO, Djebali S, Alexander RP, Alver BH, Auerbach R, Bell K, Bickel PJ, Boeck ME, Boley NP, Booth BW, Cherbas L, Cherbas P, Di C, Dobin A, Drenkow J, Ewing B, Fang G, Fastuca M, Feingold EA, Frankish A, Gao G, Good PJ, Guigó R, Hammonds A, Harrow J, Hoskins RA, Howald C, Hu L, Huang H, Hubbard TJ, Huynh C, Jha S, Kasper D, Kato M, Kaufman TC, Kitchen RR, Ladewig E, Lagarde J, Lai E, Leng J, Lu Z, MacCoss M, May G, McWhirter R, Merrihew G, Miller DM, Mortazavi A, Murad R, Oliver B, Olson S, Park PJ, Pazin MJ, Perrimon N, Pervouchine D, Reinke V, Reymond A, Robinson G, Samsonova A, Saunders GI, Schlesinger F, Sethi A, Slack FJ, Spencer WC, Stoiber MH, Strasbourger P, Tanzer A, Thompson OA, Wan KH, Wang G, Wang H, Watkins KL, Wen J, Wen K, Xue C, Yang L, Yip K, Zaleski C, Zhang Y, Zheng H, Brenner SE, Graveley BR, Celniker SE, Gingeras TR, Waterston R. Comparative analysis of the transcriptome across distant species Nature. 2014 Aug 28;512(7515):445-8, doi:10.1038/nature13424 |
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14-033 Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler 50 Shades of Rule Composition:From Chemical Reactions to Higher Levels of Abstraction Proceedings of the 1st Intrnational Conference on Formal Methods in Macro-Biology (FMMB 2014). François Fages and Carla Piazza (Eds). Springer, LNCS 8738, pp 117-135, (2014), doi:10.1007/978-3-319-10398-3_9 |
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14-034 Jakob L Andersen, Christoph Flamm, Martin M Hanczyc, Daniel Merkle Towards an Optimal DNA-Templated Molecular Assembler Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems (ALIFe 14). Hiroki Sayama, John Rieffel, Sebastian Risi, René Doursat and Hod Lipson (Eds). MIT Press, pp 557-564, (2014), doi:10.7551/978-0-262-32621-6-ch090 |
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14-035 Stefan Badelt, Christoph Flamm, Ivo L Hofacker Computational design of a circular RNA with prion-like behaviour Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems (ALIFe 14). Hiroki Sayama, John Rieffel, Sebastian Risi, René Doursat and Hod Lipson (Eds.). MIT Press, pp 565-568, (2014), doi:10.7551/978-0-262-32621-6-ch091 |
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14-036 Christoph Flamm, Bärbel MR Stadler, Peter F Stadler Generalized topologies: Hypergraphs, chemical reactions and biological evolution Ebook "Advances in Mathematical Chemistry and Applications", Subash C Basak and Guillermo Restrepo and Jose L Villaveces (eds.), Bentham Science Publisher, Vol 2, Chapter 13, pp. 270-297 (2014), doi: |
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14-037 Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler Generic Strategies for Chemical Space Exploration Int J Comp Biol Drug Des 7(2/3):225-258 (2014), arXiv:1302.4006, doi:10.1504/IJCBDD.2014.061649 |
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14-038 P. Kamsri, N. Koohatammakun, A. Srisupan, P. Meewong, A. Punkvang, P. Saparpakorn, S. Hannongbua, P. Wolschann, S. Prueksaaroon, U. Leartsakulpanich, P. Pungpo Rational design of InhA inhibitors in the class of diphenyl ether derivatives as potential anti-tubercular agents using molecular dynamics simulations SAR and QSAR in Environmental Research, 25, 473-488 (2014), doi:10.1080/1062936x.2014.898690 |
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14-039 Bodee Nutho, Wasinee Khuntawee, Chompoonut Rungnim, Piamsook Pongsawasdi, Peter Wolschann, Alfred Karpfen, Nawee Kungwan and Thanyada Rungrotmongkol Binding mode and free energy prediction of fisetin/β-cyclodextrin inclusion complexes Beilstein J. Org. Chem. 2014, 10, 2789–2799, doi:10.3762/bjoc.10.296 |
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14-040 R. Lehmann, R. Machne, H. Herzel The structural code of cyanobacterial genomes Nucleic Acids Research volume 42 issue 14 on pages 8873, doi:10.1093/nar/gku641 |
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14-041 P. Schuster Are computer scientists the sutlers of modern biology? Bioinformatics is indispensible for progress in molecular life sciences but does not get credit for its contributions. Complexity, 19(4):10–14, 2014 |
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14-042 P. Schuster The dilemma of statistics. Rigorous mathematical methods cannot compensate for lousy data and messy interpretations Complexity, 20(1):11–15, 2014 |
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14-043 Sahyoun, A. H., Bernt, M., Stadler, P. F., Tout, K. GC skew and mitochondrial origins of replication Mitochondrion. 17, S. 56-66, doi:10.1016/j.mito.2014.05.009 |
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14-044 Nitsche A., Doose G., Tafer H., Robinson M., Saha N. R., Gerdol M., Canapa A., Hoffmann S., Amemiya C. T., Stadler P. F. Atypical RNAs in the coelacanth transcriptome Journal of Experimental Zoology Part B: Molecular and Developmental Evolution volume 322 issue 6 on pages 342, doi:10.1002/jez.b.22542 |
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14-045 C. Otto, P. F. Stadler, S. Hoffmann Lacking alignments? The next-generation sequencing mapper segemehl revisited Bioinformatics volume 30 issue 13 on pages 1837, doi:10.1093/bioinformatics/btu146 |
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14-046 S. Kehr, S. Bartschat, H. Tafer, P. F. Stadler, J. Hertel Matching of Soulmates: Coevolution of snoRNAs and Their Targets Molecular Biology and Evolution volume 31 issue 2 on pages 455, doi:10.1093/molbev/mst209 |
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14-047 Hermann Hämmerle, Fabian Amman, Branislav Večerek, Jörg Stülke, Ivo Hofacker, Udo Bläsi Impact of Hfq on the Bacillus subtilis Transcriptome PLoS ONE volume 9 issue 6 on page e98661, doi:10.1371/journal.pone.0098661 |
2013
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13-001 Tarek M. El-Gogary, Abdullah G. Al-Sehemi, Karl Peter Wolschann, Gottfried Koehler Structure and Stability of Chemically Modified DNA Bases: Quantum Chemical Calculations on 16 Isomers of Diphosphocytosine ISRN Physical Chemistry Volume 2013 (2013), Article ID 146401, 10 pages, doi:10.1155/2013/146401 |
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13-002 Rungtiva Palangsuntikul, Heinz Berner, Michael L. Berger, Peter Wolschann Holographic Quantitative Structure-Activity Relationships of Tryptamine Derivatives at NMDA, 5HT1A> and 5HT2A Receptors Molecules 2013, 18, 8799-8811, doi:10.3390/molecules18088799 |
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13-003 Christian Höner zu Siederdissen, Stefan Hammer, Ingrid Abfalter, Ivo L. Hofacker, Christoph Flamm, Peter F. Stadler Computational design of RNAs with complex energy landscapes Wiley Online Library, doi:10.1002/bip.22337 |
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13-004 Gero Doose, Maria Alexis, Rebecca Kirsch, Sven Findeiß, David Langenberger, Rainer Machné, Mario Mörl, Steve Hoffmann, Peter F. Stadler Mapping the RNA-Seq trash bin: Unusual transcripts in prokaryotic transcriptome sequencing data RNA Biology, Volume 10 Issue 7, Research Paper, doi:10.4161/rna.24972 |
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13-005 Müller SA, Findeiß S, Pernitzsch SR, Wissenbach DK, Stadler PF, Hofacker IL, von Bergen M, Kalkhof S Identification of new protein coding sequences and signal peptidase cleavage sites of Helicobacter pylori strain 26695 by proteogenomics J Proteomics. 2013 Jun 28;86:27-42, doi:10.1016/j.jprot.2013.04.036 |
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13-006 Christian Arnold, Peter F. Stadler, Sonja J. Prohaska Chromatin Computation: Epigenetic Inheritance as a Pattern Reconstruction Problem Journal of Theoretical Biology. DOI:10.1016/j.jtbi.2013.07.012, doi:10.1016/j.jtbi.2013.07.012 |
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13-007 Jan Hubička, Jürgen Jost, Yangjing Long and Peter F. Stadler Relations Between Graphs Ars Math Contemp 6: 323-350 (2013)i |
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13-008 David Langenberger, M. Volkan C, Steve Hoffmann, Peter F. Stadler Dicer-Processed Small RNAs: Rules and Exceptions J.Exp.Zool.B Mol.Dev.Evol. 320: 35-46 (2012), doi:jez.b.22481 |
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13-009 Jörg Lehmann, Peter F. Stadler, Veiko Krauss Near Intron Pairs and the Metazoan Tree Mol. Phylogenet. Evol. 66(3):811-823 (2013), doi:10.1016/j.ympev.2012.11.012 |
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13-010 Martin Mann, Feras Nahar, Heinz Ekker, Rolf Backofen, Peter F Stadler, Christoph Flamm Atom Mapping with Constraint Programming In Proceedings of the 19th International Conference on Principles and Practice of Constraint Programming (CP 2013). Christian Schulte (ed.), Springer, LNCS 8124, pp 805-822, (2013), doi:10.1007/978-3-642-40627-0_59 |
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13-011 Pungpo P., Lumlong S., Wolschann K.P., Karpfen A., Baurecht D. Elucidating the structural characteristics of 1,4-Polyisoprene based on quantum chemical calculations Proceedings Pure and Applied Chemistry International Conference 2013, S966-969 4 S. |
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13-012 Christoph Flamm, Chris Hemmingsen, Daniel Merkle Barrier trees for metabolic adjustment landscapes In: Proceedings of the 12th European Conference on the Synthesis and Simulation of Living systems, (ECAL 2013). Liò, Pietro and Miglino, Orazio and Nicosia, Giuseppe and Nolfi, Stefano and Pavone, Mario (eds), The MIT Press, Advances in Artifical Life, pp 1151-1158, (2013), doi:10.7551/978-0-262-31719-2-ch175 |
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13-013 Jakob L Andersen, Tommy Andersen, Christoph Flamm, Martin Hanczyc, Daniel Merkle, Peter F Stadler Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data Entropy 15(10):4066-4083, doi:10.3390/e15104066 |
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13-014 Martin Mann, Heinz Ekker, Christoph Flamm The Graph Grammar Library - a generic framework for chemical graph rewrite systems In: Proceedings of the International Conference on Model Transformation (ICMT 2013), D. Varro and K. Duddy and G. Kappel (eds), Springer-Verlag Berlin Heidelberg, LNCS 7909, pp. 52-53, (2013), doi:10.1007/978-3-642-38883-5_5 |
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13-015 Srisupan A., Kamsri P., Punkvang A., Saparpakorn P., Hannongbua S., Wolschann K.P., Pueksaaroon S., Pungpo P. Computer aided molecular design of diaylpyrimidine derivatives as highly potent HIV-1 NNRTIs active against wild-type and K103N/Y181C HIV-1 RT stains using QSAR approaches Jun 2013 Conference Proceedings, S. 112 |
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13-016 Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler Inferring chemical reaction patterns using rule composition in graph grammars J Sys Chem 4:4 (2013), doi:10.1186/1759-2208-4-4 |
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13-017 Ronny Lorenz, Stephan H. Bernhart, Jing Qin, Christian Höner zu Siederdissen, Andrea Tanzer, Fabian Amman, Ivo L. Hofacker, and Peter F. Stadler 2D meets 4G: G-quadruplexes in RNA secondary structure prediction IEEE Trans. Comp. Biol. Bioinf., 2013, doi:10.1109/TCBB.2013.7 |
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13-018 Florian Eggenhofer, Ivo L. Hofacker, and Christian Höner zu Siederdissen CMCompare webserver: Comparing RNA families via covariance models Nucleic Acids Res., 2013, doi:10.1093/nar/gkt329 |
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13-019 Radhakrishnan Sabarinathan, Hakim Tafer, Stefan Seemann, Ivo L. Hofacker, Peter F. Stadler, and Jan Gorodkin The RNAsnp Web Server: Predicting SNP effects on local RNA secondary structure Nucleic Acids Res., 2013, doi:10.1093/nar/gkt291 |
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13-020 Radhakrishnan Sabarinathan, Hakim Tafer, Stefan E. Seemann, Ivo L. Hofacker, Peter F. Stadler, and Jan Gorodkin RNAsnp: Efficient detection of local RNA secondary structure changes induced by SNPs Human Mutation, 34:546–556, 2013, doi:10.1002/humu.22273 |
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13-021 Julia Reimann1, Dominik Esser, Alvaro Orell, Fabian Amman, Trong Khoa Pham, Josselin Noirel, Ann-Christin Lindas, Rolf Bernander, Phillip C. Wright, Bettina Siebers and Sonja-Verena Albers Archaeal Signal Transduction: Impact of Protein Phosphatase Deletions on Cell Size, Motility and Energy Metabolism in Sulfolobus acidocaldarius mcp.M113.027375, doi:10.1074/mcp.M113.027375 |
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13-022 Birgit Märtens, Fabian Amman, Salim Manoharadas, Lukas Zeichen, Alvaro Orell, Sonja-Verena Albers, Ivo Hofacker, Udo Bläsi Alterations of the Transcriptome of Sulfolobus acidocaldarius by Exoribonuclease aCPSF2 PLoS ONE 8(10): e76569., doi:10.1371/journal.pone.0076569 |
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13-023 Fabian Amman, Stephan H. Bernhart, Gero Doose, Ivo L. Hofacker, Jing Qin, Peter F. Stadler, Sebastian Will The Trouble with Long-Range Base Pairs in RNA Folding Advances in Bioinformatics and Computational Biology, Lecture Notes in Computer Science Volume 8213, 2013, pp 1-11 |
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13-024 Christian Höner zu Siederdissen, Ivo L. Hofacker, and Peter F. Stadler How to Multiply Dynamic Programming Algorithms Lecture Notes in Computer Science Volume 8213, 2013, pp 82-93, doi:10.1007/978-3-319-02624-4_8 |
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13-025 Corinna Theis, Christian Höner zu Siederdissen, Ivo L. Hofacker, and Jan Gorodkin Automated Identification of 3D Modules with Discriminative Power in RNA Structural Alignments 2013. Nucleic Acids Research |
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13-026 Joaquin Vierna, Stefanie Wehner, Christian Höner zu Siederdissen, Andrés Martínez-Lage, and Manja Marz Systematic Analysis and Evolution of 5S Ribosomal DNA in Metazoans 2013. Heredity. 111.(5): 410–21, doi:10.1038/hdy.2013.63 |
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13-027 Bernt, M., Machné, R., Sahyoun, A. H., Middendorf, M. and Stadler, P. F Mitochondrial Genome Evolution eLS. 2013, doi:10.1002/9780470015902.a0025142 |
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13-028 Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ A community-driven global reconstruction of human metabolism Nat Biotechnol. 2013 May;31(5):419-25, doi:10.1038/nbt.2488 |
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13-029 Amariei C, Machne R, Sasidharan K, Gottstein W, Tomita M, Soga T, Lloyd D, Murray DB The dynamics of cellular energetics during continuous yeast culture Conf Proc IEEE Eng Med Biol Soc. 2013 Jul;2013:2708-11, doi:10.1109/EMBC.2013.6610099 |
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13-030 Lehmann R, Machné R, Georg J, Benary M, Axmann I, Steuer R How cyanobacteria pose new problems to old methods: challenges in microarray time series analysis BMC Bioinformatics. 2013, doi:10.1186/1471-2105-14-133 |
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13-031 Sandra Wende, Edward G. Platzer, Frank Jühling, Joern Pütz, Catherine Florentz, Peter F. Stadler, Mario Mörl Biological evidence for the world's smallest tRNAs Biochimie 2013, doi:10.1016/j.biochi.2013.07.034 |
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13-032 Christoph Dieterich and P. F. Stadler Computational biology of RNA interactions Wiley Interdiscip. Rev. RNA, 4:107–120, 2013, doi:10.1002/wrna.1147 |
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13-033 Marc Hellmuth, Maribel Hernandez-Rosales, Katharina T. Huber, Vincent Moulton, Peter F. Stadler, and Nicolas Wieseke Orthology relations, symbolic ultrametrics, and cographs J. Math. Biol., 66:399–420, 2013 |
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13-034 Marcus Lechner, Manja Marz, Christian Ihling, Andrea Sinz, Peter F. Stadler, Veiko Krauss The correlation of genome size and DNA methylation rate in metazoans Theory in Biosciences, March 2013, Volume 132, Issue 1, pp 47-60, doi:10.1007/s12064-012-0167-y |
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13-035 Yinhua Huang, Yingrui Li, David W Burt, Hualan Chen, Yong Zhang, Wubin Qian, Hee-bal Kim, Shangquan Gan, Yiqiang Zhao, Jianwen Li, Kang Yi, Huapeng Feng, Pengyang Zhu, Bo Li, Qiuyue Liu, Suan Fairley, Katharine E Magor, Zhen lin Du, Xiaoxiang Hu, Laurie Goodman, Hakim Tafer, Alain Vignal, Taeheon Lee, Kyu-Won Kim, Zheya Sheng, Yang An, Steve Searle, Javier Herrerol, Martien A M Groenen, Richard P M A Crooijmans, Thomas Faraut, Qingle Cai, Robert G Webster, Jerry R Aldridge, Wesley C Warren, Sebas-tian Bartschat, Stephanie Kehr, Manja Marz, Peter F Stadler, Jacqueline Smith, Robert H S Kraus, Yaofeng Zhao, Liming Ren, Jing Feil, Mireille Morisson, Pete Kaiser, Darren K Grif-fin, Man Rao, Frederique Pitel, Jun Wang, and Ning Li The duck genome and transcriptome provide insight into an avian influenza virus reservoir species Nature Genetics, 45:776–783, 2013 |
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13-036 Rolf Backofen, Markus Fricke, Manja Marz, Jing Qin, and Peter F. Stadler Distribution of graph-distances in Boltzmann ensembles of RNA secondary structures In Aaron Darlin and Jens Stoye, editors, Algorithms in Bioinformatics: WABI 2013, volume 8126 of Lect. Notes Comp. Sci., pages 112–125, Heidelberg, 2013. Springer |
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13-037 Matthias Bernt, Alexander Donath, Frank Juehling, Fabian Externbrink, Catherine Florentz, Guido Fritzsch, Jorn Putz, Martin Middendorf, and Peter F. Stadler MITOS: Improved de novo metazoan mitochondrial genome annotation Mol. Phylog. Evol. 69:313–319, 2013 |
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13-038 Matthias Bernt, Anke Braband, Martin Middendorf, Bernhard Misof, Omar Rota-Stabelli, and Peter F. Stadler Bioinformatics methods for the comparative analysis of metazoan mitochondrial genome sequences Mol. Phylog. Evol., 69:320–327, 2013 |
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13-039 Matthias Bernt, Anke Braband, Bernd Schierwater, and Peter F. Stadler Genetic aspects of mitochondrial genome evolution Mol. Phylog. Evol., 69:328–338, 2013 |
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13-040 Matthias Bernt, Christoph Bleidorn, Anke Braband, Johannes Dambach, Alexander Donath, Guido Fritzsch, Anja Golombek, Heike Hadrys, Frank Juhling, Karen Meusemann, Martin Middendorf, Bernhard Misof, Marleen Perseke, Lars Podsiadlowski, Bjorn von Reumont, Bernd Schierwater, Martin Schlegel, Michael Schrodl, Sabrina Simon, Peter F. Stadler, Isabella Stoger, and Torsten H. Struck A comprehensive analysis of metazoan mitochondrial genomes and animal phylogeny Mol. Phylog. Evol., 69:352–364, 2013 |
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13-041 Kamsri, P., Punkvang, A., Pongprom, N., Srisupan, A., Saparpakorn, P., Hannongbua, S., Wolschann, K. P., Pungpo, P. Key Structural Features of Azanaphthoquinone Annelated Pyrrole Derivative as Anticancer Agents Based on the Rational Drug Design Approaches Molecular Informatics. 32, 5-6, S. 541-554, doi:10.1002/minf.201200132 |
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13-042 Heinzel, A., Fechete, P., Mühlberger, I., Perco, P., Mayer, B., Lukas, A. Molecular models of the cardiorenal syndrome Electrophoresis. 34, 11, S. 1649-1656, doi:10.1002/elps.201200642 |
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13-043 P. Schuster Present Day Biology seen in the Looking Glass of Physics of Complexity Without Bounds: A Scientific Canvas of Nonlinearity and Complex Dynamics Understanding Complex Systems 2013, pp 589-622, doi:10.1007/978-3-642-34070-3_44 |
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13-044 P. Schuster Ursprung des Lebens und Prinzipien der Evolution In P. Wrede and S. Wrede, editors, Charles Darwin. Die Entstehung der Arten, chapter 18, pages 428–443. VCH-Wiley, Weinheim (Bergstraße), DE, 2013 |
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13-045 P. Schuster Eine stille Revolution in der Mathematik Thema – Das Forschungsmagazin der ¨OAW, 14:3, 2013 |
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13-046 P. Schuster Designing living matter. Can we do better than evolution? Complexity, 18(6):21–33, 2013, doi:10.1002/cplx.21461 |
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13-047 P. Schuster A Silent revolution in mathematics. The rise of applications, numerical methods, and computational approaches Complexity, 18(6):7–10, 2013, doi:10.1002/cplx.21464 |
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13-048 P. Schuster Recycling and growth in early evolution and today. Autocatalysis without recycling comes soon to an end – Not only in early evolution Complexity, 19(2):6–9, 2013, doi:10.1002/cplx.21479 |
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13-049 Flamm C., Merkle D., Andersen J.L. Exploring Prebiotic Chemistry Space Sep 2013 Conference Proceedings |
2012
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12-001 Ivo L. Hofacker, Christian M. Reidys, and Peter F. Stadler Symmetric circular matchings and RNA folding Discr. Math., 312: 100–112, 2012, doi:10.1016/j.disc.2011.06.004 |
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12-002 Marc Hellmuth, Lydia Gringmann, Peter F. Stadler Diagonalized Cartesian Products of S-prime graphs are S-prime Discr. Math., 312: 74-80, 2012, doi:10.1016/j.disc.2011.03.033 |
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12-003 Songwut Suramitr, Suphawarat Phalinyot, Peter Wolschann, Ryoichi Fukuda, Masahiro Ehara, and Supa Hannongbua Photophysical Properties and Photochemistry of EE-, EZ-, and ZZ-1, 4-Dimethoxy-2,5-bis[2-(thien-2-yl)ethenyl] Benzene in Solution: Theory and Experiment J.Phys.Chem.A, 116: 924–937, 2012, doi:10.1021/jp206463k |
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12-004 Orathai Sawatdichaikul, Supa Hannongbua, Chak Sangma, Peter Wolschann and Kiattawee Choowongkomon In silico screening of epidermal growth factor receptor (EGFR) in the tyrosine kinase domain through a medicinal plant compound database J.Mol.Model, 18: 1241–1254, 2012, doi:10.1007/s00894-011-1135-z |
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12-005 Konstantin Klemm, Anita Mehta, Peter F. Stadler Landscape Encodings Enhance Optimization PLoS One 7: e34780 (2012), doi:10.1371/journal.pone.0034780 |
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12-006 Songwut Suramitr, Apipol Piriyagagoon, Peter Wolschann and Supa Hannongbua Theoretical study on the structures and electronic properties of oligo(p-phenylenevinylene) carboxylic acid and its derivatives: effects of spacer and anchor groups Theor.Chem.Acc., 131: 1209, 2012, doi:10.1007/s00214-012-1209-8 |
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12-007 Kanjarat Sukrat, Daniel Tunega, Adelia J. A. Aquino, Hans Lischka, Vudhichai Parasuk Proton exchange reactions of C2–C4 alkanes sorbed in ZSM-5 zeolite Theor.Chem.Acc., 131: 1232, 2012, doi:10.1007/s00214-012-1232-9 |
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12-008 Nawee Kungwan, Felix Plasser, Adélia J. A. Aquino, Mario Barbatti, Peter Wolschann and Hans Lischka The effect of hydrogen bonding on the excited-state proton transfer in 2-(20-hydroxyphenyl)benzothiazole: a TDDFT molecular dynamics study Phys. Chem. Chem. Phys., 14, 9016–9025, 2012, doi:10.1039/c2cp23905a |
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12-009 Rainer Machné, Douglas B. Murray The Yin and Yang of Yeast Transcription: Elements of a Global Feedback System between Metabolism and Chromatin PLoS ONE 7(6): e37906, 2012, doi:10.1371/journal.pone.0037906 |
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12-010 Dragoş Alexandru Sorescu, Mathias Möhl, Martin Mann, Rolf Backofen, and Sebastian Will CARNA—alignment of RNA structure ensembles Nucl. Acids Res. first published online June 11, 2012 , doi:10.1093/nar/gks491 |
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12-011 Bela J. Bender, Martin Mann, Rolf Backofen und Heinrich Spiecker Microstructure alignment of wood density profiles: an approach to equalize radial differences in growth rate Trees - Structure and Function, 2012, doi:10.1007/s00468-012-0702-y |
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12-012 M. L. Berger, R. Palangsuntikul, P. Rebernik, P. Wolschann and H. Berner Screening of 64 Tryptamines at NMDA, 5-HT1A and 5-HT2A Receptors: A Comparative Binding and Modeling Study Current Medical Chemistry, 19, 3044-3057, 2012, doi:10.1038/npp.2011.13 |
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12-013 Steuer R, Knoop H, Machné R. Modelling cyanobacteria: from metabolism to integrative models of phototrophic growth J Exp Bot. 2012 Mar;63(6):2259-74, PubMed PMID: 22450165, doi:10.1093/jxb/ers018 |
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12-014 Müller S, Murray DB, Machne R. A new dynamic model for highly efficient mass transfer in aerated bioreactors and consequences for kLa identification. Biotechnol Bioeng. 2012 Jul 5. doi:10.1002/bit.24594 |
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12-015 Ronny Lorenz, Stephan H. Bernhart, Fabian Externbrink, Jing Qin, Christian Höner zu Siederdissen, Fabian Amman, Ivo L. Hofacker and Peter F. Stadler RNA Folding Algorithms with G-Quadruplexes Lecture Notes in Computer Science, 2012, Volume 7409/2012, 49-60, doi:10.1007/978-3-642-31927-3_5 |
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12-016 P. Schuster Ursprung des Lebens und Prinzipien der Evolution. In P. Wrede and S. Wrede, editors, Charles Darwin. Die Entstehung der Arten mit zwei Beiträgen von Alfred Russel Wallace chapter 18, pages 435-449. VCH-Wiley, Weinheim (Bergstraße), DE, 2012 |
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12-017 P. Schuster Optimization of multiple criteria. Pareto efficiency and fast heuristics should be more than they are. Complexity, 18(2):5–7, 2012 |
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12-018 T. Gesell and P. Schuster Phylogeny and evolution of structure. In J. Gorodkin and L. Ruzzo, editors, RNA Structure Prediction. An Introduction to RNA Bioinformatics, pages pp–pp. xxxxxx, ssssss, 2012. |
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12-019 P. Schuster A revival of the landscape paradigm. Large scale data harvesting provides access to fitness landscapes. Complexity, 17(5):6–10, 2012. |
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12-020 P. Schuster Present day biology seen in the looking glass of physics of complexity. In P. Arena, P. Colinet, A. Ferr´us, G. Huang, E. G. Morozov, Y. S. Ryazantsev, R. G. Rubio, V. M. Starov, and U. Thiele, editors, Proceedings of a Week of Science in Madrid, pages pp–pp. Springer-Verlag, Berlin, 2012. |
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12-021 Christian Höner zu Siederdissen Sneaking around concatMap: efficient combinators for dynamic programming. Proceedings of the 17th ACM SIGPLAN international conference on Functional programming. New York, NY, USA: ACM, 2012 (pdf) |
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12-022 Conrad Helm, Stephan H. Bernhart, Christian Höner zu Siederdissen, Birgit Nickel, and Christoph Bleidorn Deep sequencing of small RNAs confirms an annelid affinity of Myzostomida. Molecular Phylogenetics and Evolution 64, 2012, no. 1: 198–203. doi:10.1016/j.ympev.2012.03.017 |
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12-023 Derrien T, Johnson R, Bussotti G, Tanzer A, Djebali S, Tilgner H, Guernec G, Martin D, Merkel A, Knowles DG, Lagarde J, Veeravalli L, Ruan X, Ruan Y, Lassmann T, Carninci P, Brown JB, Lipovich L, Gonzalez JM, Thomas M, Davis CA, Shiekhattar R, Gingeras TR, Hubbard TJ, Notredame C, Harrow J, Guigó R. The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Res. 2012 Sep;22(9):1775-89. doi:10.1101/gr.132159.111 |
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12-024 Harrow J, Frankish A, Gonzalez JM, Tapanari E, Diekhans M, Kokocinski F, Aken BL, Barrell D, Zadissa A, Searle S, Barnes I, Bignell A, Boychenko V, Hunt T, Kay M, Mukherjee G, Rajan J, Despacio-Reyes G, Saunders G, Steward C, Harte R, Lin M, Howald C, Tanzer A, Derrien T, Chrast J, Walters N, Balasubramanian S, Pei B, Tress M, Rodriguez JM, Ezkurdia I, van Baren J, Brent M, Haussler D, Kellis M, Valencia A, Reymond A, Gerstein M, Guigó R, Hubbard TJ. GENCODE: The reference human genome annotation for The ENCODE Project. Genome Res. 2012 Sep;22(9):1760-74 doi:10.1101/gr.135350.111 |
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12-025 Howald C, Tanzer A, Chrast J, Kokocinski F, Derrien T, Walters N, Gonzalez JM, Frankish A, Aken BL, Hourlier T, Vogel JH, White S, Searle S, Harrow J, Hubbard TJ, Guigó R, Reymond A. Combining RT-PCR-seq and RNA-seq to catalog all genic elements encoded in the human genome. Genome Res. 2012 Sep;22(9):1698-710. doi:10.1101/gr.134478.111 |
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12-026 Djebali S, Davis CA, Merkel A, Dobin A, Lassmann T, Mortazavi A, Tanzer A, Lagarde J, Lin W, Schlesinger F, Xue C, Marinov GK, Khatun J, Williams BA, Zaleski C, Rozowsky J, Röder M, Kokocinski F, Abdelhamid RF, Alioto T, Antoshechkin I, Baer MT, Bar NS, Batut P, Bell K, Bell I, Chakrabortty S, Chen X, Chrast J, Curado J, Derrien T, Drenkow J, Dumais E, Dumais J, Duttagupta R, Falconnet E, Fastuca M, Fejes-Toth K, Ferreira P, Foissac S, Fullwood MJ, Gao H, Gonzalez D, Gordon A, Gunawardena H, Howald C, Jha S, Johnson R, Kapranov P, King B, Kingswood C, Luo OJ, Park E, Persaud K, Preall JB, Ribeca P, Risk B, Robyr D, Sammeth M, Schaffer L, See LH, Shahab A, Skancke J, Suzuki AM, Takahashi H, Tilgner H, Trout D, Walters N, Wang H, Wrobel J, Yu Y, Ruan X, Hayashizaki Y, Harrow J, Gerstein M, Hubbard T, Reymond A, Antonarakis SE, Hannon G, Giddings MC, Ruan Y, Wold B, Carninci P, Guigó R, Gingeras TR. Landscape of transcription in human cells. Nature. 2012 Sep 6;489(7414):101-8, doi:10.1038/nature11233 |
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12-027 Pei B, Sisu C, Frankish A, Howald C, Habegger L, Mu XJ, Harte R, Balasubramanian S, Tanzer A, Diekhans M, Reymond A, Hubbard TJ, Harrow J, Gerstein MB. The GENCODE pseudogene resource. Genome Biol. 2012 Sep 5;13(9):R51, doi:10.1186/gb-2012-13-9-r51 |
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12-028 Otto C, Stadler PF, Hoffmann S Fast and sensitive mapping of bisulfite-treated sequencing data. Bioinformatics. (2012) Jul; 28:(13) 1698-1704 doi:10.1093/bioinformatics/bts254 |
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12-029 Lozada-Chavez I, Stadler PF, Prohaska SJ Hypothesis for the modern RNA world: a pervasive non-coding RNA-based genetic regulation is a prerequisite for the emergence of multicellular complexity. Orig Life Evol Biosph. 2011 Dec; 41(6):587-607, doi:10.1007/s11084-011-9262-1 |
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12-030 Jühling F, Pütz J, Bernt M, Donath A, Middendorf M, Florentz C, Stadler PF Improved systematic tRNA gene annotation allows new insights into the evolution of mitochondrial tRNA structures and into the mechanisms of mitochondrial genome rearrangements. Nucleic Acids Res. 2012 Apr 1;40(7):2833-2845. Epub 2011 Dec 1, doi:10.1093/nar/gkr1131 |
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12-031 Washietl S, Hofacker IL, Stadler PF, Kellis M RNA folding with soft constraints: reconciliation of probing data and thermodynamic secondary structure prediction. Nucleic Acids Res. 2012 Jan 28, doi:10.1093/nar/gks009 |
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12-032 Will S, Joshi T, Hofacker IL, Stadler PF, Backofen R LocARNA-P: Accurate boundary prediction and improved detection of structural RNAs RNA. 2012 May;18(5):900-14. Epub 2012 Mar 26, doi:10.1261/rna.029041.111 |
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12-033 Marc Hellmuth, Maribel Hernandez-Rosales, Katharina T. Huber, Vincent Moulton, Peter F. Stadler, Nicolas Wieseke Orthology Relations, Symbolic Ultrametrics, and Cographs J.Math.Biol, doi:10.1007/s00285-012-0525-x |
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12-034 Jana Hertel, Sebastian Bartschat, Axel Wintsche, Christian Otto, The Students of the Bioinformatics Computer Lab 2011, Peter F Stadler Evolution of the let-7 microRNA Family RNA Biology 9: 231-241 (2012), doi:10.4161/rna.18974 |
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12-035 Jan Engelhardt, Peter F. Stadler Hidden treasures in unspliced EST data Th. Biosci. 131: 49-57 (2012), doi:10.1007/s12064-012-0151-6 |
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12-036 Fabian Amman and Hofacker Ivo L. Christoph Flamm Modelling translation initiation under the influence of sRNA. Int. J. Mol. Sci., 13:16223–16240, 2012. doi:10.3390/ijms131216223 |
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12-037 Manja Wachsmuth, Sven Findeiß, Nadine Weissheimer, Peter F Stadler and Mario Mörl De novo design of a synthetic riboswitch that regulates transcription termination. Nucleic Acids Research, 2012, doi:10.1093/nar/gks1330 |
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12-038 Kratochwill K, Boehm M, Herzog R, Lichtenauer AM, Salzer E, Lechner M, Kuster L, Bergmeister K, Rizzi A, Mayer B, Aufricht C. Alanyl-glutamine dipeptide restores the cytoprotective stress proteome of mesothelial cells exposed to peritoneal dialysis fluids. Nephrol Dial Transplant. 2012 Mar;27(3):937-46. , doi:10.1093/ndt/gfr459 |
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12-039 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 (2012) 28 (1): 17-24. doi:10.1093/bioinformatics/btr598 |
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12-040 Panita Kongsune, Thanyada Rungrotmongkol, Nadtanet Nunthaboot, Pathumwadee Yotmanee, Pornthep Sompornpisut, Yong Poovorawan, Peter Wolschann and Supot Hannongbua Molecular insights into the binding affinity and specificity of the hemagglutinin cleavage loop from four highly pathogenic H5N1 isolates towards the proprotein convertase furin Monatshefte für Chemie Springer-Verlag |
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12-041 Lorenz R, Hofacker IL, Bernhart SH Folding RNA/DNA hybrid duplexes. Bioinformatics. 2012 Oct 1;28(19):2530-1. doi:10.1093/bioinformatics/bts466 |
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12-042 Wiesinger M, Mayer B, Jennings P, Lukas A. Comparative analysis of perturbed molecular pathways identified in in vitro and in vivo toxicology studies Toxicol In Vitro. 2012 Sep;26(6):956-62. doi:10.1016/j.tiv.2012.03.018 |
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12-043 Tippmann SC, Ivanek R, Gaidatzis D, Schöler A, Hoerner L, van Nimwegen E, Stadler PF, Stadler MB, Schübeler D. Chromatin measurements reveal contributions of synthesis and decay to steady-state mRNA levels. Mol Syst Biol. 2012 ;8:593. doi:10.1038/msb.2012.23 |
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12-044 Marc Hellmuth, Philipp-Jens Ostermeier, Peter F. Stadler Minimum cycle bases of lexicographic products ARS MATHEMATICA CONTEMPORANEA 5 (2012) 223–234 |
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12-045 Lydia Ostermeier, Marc Hellmuth, Peter F. Stadler The Cartesian product of hypergraphs Journal of Graph Theory Volume 70, Issue 2, pages 180–196, June 2012 doi:10.1002/jgt.20609 |
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12-046 Jühling F, Pütz J, Florentz C, Stadler PF Armless mitochondrial tRNAs in enoplea (nematoda). RNA Biol. 2012 Sep 1;9(9). doi:10.4161/rna.21630 |
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12-047 P. Schuster How universal is Darwin's principle? Physics o Life Reviews, 9:460-461, 2012 |
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12-048 P. Schuster Evolution on "realistic" fitness landscapes. Phase transitions, strong quasispecies, and neutrality. Working Paper #12-06-006, Santa Fe Institut, Santa Fe, NM, 2012 |
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12-049 Martin Mann, Heinz Ekker, Peter F Stadler, Christoph Flamm Atom Mapping with Constraint Programming Proceedings of the Workshop on Constraint Based Methods for Bioinformatics (WCP12), R. Backofen and S. Will (eds.), pp. 23-29, 2012 |
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12-050 Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters Exploring Chemistry Using SMT Proceedings of the 18th International Conference on Principles and Practice of Constraint Programming (CP 2012), M. Milano (eds.), Springer-Verlag Berlin Heidelberg, LNCS 7514, pp. 900-915, (2012), doi:10.1007/978-3-642-33558-7_64 |
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12-051 Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete J Sys Chem 3:1 (2012), doi:10.1186/1759-2208-3-1 |
2011
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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 |
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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 |
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11-003 Stephan H. Bernhart, Ulrike Mückstein, and Ivo L. Hofacker RNA accessibility in cubic time Algorithms Mol.Biol., 6(1): 3, 2011 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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11-018 Peter Schuster Mathematical modeling of evolution. Solved and open problems Theory Biosci., 130: 71–89, 2011 |
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11-019 Peter Schuster Power laws in biology. Between fundamental regularities and useful interpolation rules Complexity, 16(3): 6–9, 2011 |
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11-020 Peter Schuster Networks in biology. Handling biological complexity requires novel inputs into network theory Complexity, 16(4): 6-9, 2011 |
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11-021 Peter Schuster Mit Mathematik und Computer aud Entdeckungsreisen in der Evolutionsbiologie Nova Acta Leopoldina, NF 110, Nr.377: 167-211, 2011 |
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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 |
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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 |
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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 |
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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 |
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11-026 Dominic Rose and Peter F. Stadler Molecular evolution of the non-coding eosinophil granule ontogeny transcript Frontiers in Genetics, : 2 , 2011 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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11-045 Helmut Viernstein and Peter Wolschann Preface J.Incl.Phenom.Macrocycl.Chem., 70: 257–258, 2011 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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11-066 Felix Plasser and Hans Lischka Semiclassical dynamics simulations of charge transport in stacked π-systems J.Chem.Phys., 134: 034309, 2011 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
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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 |
2010
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10-001 Peter Schuster Origins of life: Concepts, data, and debates. Managing complexity seems to be essential for studies on chemical evolution Complexity, 15(3): 7-10, 2010 |
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10-002 Peter Schuster Abschiedsrede des Präsidenten, Österreichische Akademie der Wissenschaften Almanach, 159: 361–377, 2010 |
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10-003 Peter Schuster ... denn wir wissen nicht, wohin die Reise geht. Vier Überlegungen, vier Anregungen zum Nachdenken, Österreichische Akademie der Wissenschaften Almanach, 159: 343–360, 2010 |
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10-004 Peter Schuster Mathematical Modeling of Evolution Solved and Open Problems Theory in Biosci., 110: xx, 2010 |
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10-005 Ivo L. Hofacker and Hakim Tafer Designing optimal siRNA based on target site accessibility In Wei-Ping Min and Thomas Ichim, editors RNA Interference: From Biology to Clinical Applications, volume 623 of Methods in Molecular Biology, chapter 9 Humana Press, Totowa, NJ, 2010 |
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10-006 Stefan Washietl and Ivo L. Hofacker Nucleic acids sequence and structure databases In Oliviero Carugo and Frank Eisenhaber, editors Data Mining Techniques for the Life Sciences, volume 609 of Methods in Molecular Biology, chapter 1, pages 3–16 Humana Press, Totowa, NJ, 2010 |
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10-007 Rolf Backofen, Hamid Chitsaz, Ivo L. Hofacker, S. Cenk Sahinalp and Peter F. Stadler Computational studies of non-coding RNAs Pac.Symp.Biocomput., 15: 54-56, 2010 |
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10-008 Andreas R. Gruber, Sven Findeiß, Stefan Washietl, Ivo L. Hofacker and Peter F. Stadler RNAz 2.0: improved noncoding RNA detection Pac.Symp.Biocomput., 15: 69-79, 2010 |
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10-009 Hakim Tafer, Stephanie Kehr, Jana Hertel, Ivo L. Hofacker and Peter F. Stadler RNAsnoop: efficient target prediction for box H/ACA snoRNAs Bioinformatics, 26: 610-616, 2010 |
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10-010 Yusuf Dilmurat, Manja Marz, Peter F. Stadler and Ivo L. Hofacker bcheck: a wrapper tool for detecting RNase P RNA genes BMC Genomics, 11: 432, 2010 |
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10-011 Ivo L. Hofacker, Christoph Flamm, Christian Heine, Michael T. Wolfinger, Gerik Scheuermann and Peter F. Stadler BarMap: RNA folding on dynamic energy landscapes RNA, 16: 1308–1316, 2010 |
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10-012 Ilenia Boria, Andreas R. Gruber, Andrea Tanzer, Stephan Bernhart, Ronny Lorenz, Michael M. Mueller, Ivo L. Hofacker, and Peter F. Stadler Nematode sbRNAs: Homologs of vertebrate Y RNAs J. Mol. Evol., 70: 346–358, 2010 |
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10-013 Ulrike Mückstein, Germán G. Leparc, Alexandra Posekany, Ivo L. Hofacker, and David P. Kreil Hybridization thermodynamics of nimblegen microarrays BMC Bioinformatics, 11: 35, 2010 |
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10-014 Jan Gorodkin, Ivo L. Hofacker, Elfar Torarinsson, Zizhen Yao, Jakob H. Havgaard, and Walter L. Ruzzo De novo prediction of structured RNAs from genomic sequences Trends in Biotechnology, 28: 9-19, 2010 |
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10-015 Andrea Tanzer, Markus Riester, Jana Hertel, Clara Isabel Bermudez-Santana, Jan Gorodkin, Ivo L. Hofacker, and Peter F. Stadler Evolutionary genomics of microRNAs and their relatives In Gustavo Caetano-Anolles, editor, Evolutionary Genomics and Systems Biology, pages 295–327. Wiley-Blackwell, Hoboken, 2010 |
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10-016 Mathieu Rederstorff, Stephan H. Bernhart, Andrea Tanzer, Marek Zywicki, Katrin Perfler, Melanie Lukasser, Ivo L. Hofacker and Alexander Hüttenhofer RNPomics: Defining the ncRNA transcriptome by cDNA library generation from ribonucleo-protein particles Nuc.Acids Res., doi:10.1093/nar/gkq057: 1-12, 2010 |
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10-017 Christoph Flamm, Alexander Ullrich, Heinz Ekker, Martin Mann, Daniel Högerl, Markus Rohrschneider,Sebastian Sauer, Gerik Scheuermann, Konstantin Klemm, Ivo L. Hofacker and Peter F. Stadler Evolution of Metabolic Networks: A Computational Framework J.Syst.Chem, 1: 4, 2010 |
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10-018 Andreas R. Gruber, Stephan H. Bernhart, You Zhou and Ivo L. Hofacker RNALfoldz: Efficient prediction of thermodynamically stable, local secondary structures In German Conference on Bioinformatics 2010, volume 173 of Lecture Notes in Informatics, pages 12–21, Bonn, Gesellschaft f. Informatik, 2010 |
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10-019 Christian Höner zu Siederdissen and Ivo L. Hofacker Discriminatory power of RNA family models Bioinformatics, 26(18): i453–459, 2010 |
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10-020 Bärbel M. R. Stadler and Peter F. Stadler Combinatorial Vector Fields and the Valley Structure of Fitness Landscapes J.Math.Biol., doi 10.1007/s00285-010-0326-z, 2010 |
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10-021 Fenix Huang, Jing Qin, Christian M. Reidys, Peter F. Stadler Target prediction and a statistical sampling algorithm for RNA-RNA interaction Bioinformatics, 26: 175-181, 2010 |
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10-022 Chris T. Amemiya, Thomas P. Powers, Sonja J. Prohaska, Jane Grimwood, Jeremy Schmutz, Mark Dickson, Tsutomu Miyake, Michael A. Schoenborn, Richard M. Myers, Francis H. Ruddle and Peter F. Stadler Complete HOX cluster characterization of the coelacanth provides further evidence for slow evolution of its genome Proc.Natl.Acad.Sci.USA, doi/10.1073/pnas.0914312107, 2010 |
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10-023 Cynthia M. Sharma, Steve Hoffmann, Fabien Darfeuille, Jeremy Reignier, Sven Findeiß, Alexandra Sittka, Sandrine Chabas, Kristin Reiche, Jörg Hackermüller, Richard Reinhardt, Peter F. Stadler and Jörg Vogel The primary transcriptome of the major human pathogen Helicobacter pylori Nature, doi:10.1038/nature08756, 2010 |
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10-024 Hugo Y.K. Lam, Xinmeng J. Mu, Adrian M. Stütz, Andrea Tanzer, Philip D. Cayting, Michael Snyder, Philip M. Kim, Jan O. Korbe and Mark B. Gerstein Nucleotide-resolution analysis of structural variants using BreakSeq and a breakpoint library Nat.Biotech., 28: 47-55, 2010 |
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10-025 Mario Fasold, Peter F. Stadler and Hans Binder G-stack modulated probe intensities on expression arrays - sequence corrections and signal calibration BMC Bioinformatics 2010, 11: 207, 2010 |
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10-026 Clara Bermudez-Santana, Camille Stephan-Otto Attolini, Toralf Kirsten, Jan Engelhardt, Sonja J. Prohaska, Stephan Steigele, Peter F. Stadler Genomic Organization of Eukaryotic tRNAs BMC Genomics, 11: 270, 2010 |
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10-027 Sven Findeiß, Cornelius Schmidtke, Peter F. Stadler and Ulla Bonas A novel family of plasmid-transferred anti-sense ncRNAs RNA Biol., 7: 120-124, 2010 |
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10-028 Arli A. Parikesit, Peter F. Stadler and Sonja J. Prohaska Quantitative Comparison of Genomic-Wide Protein Domain Distributions In: D. Schomburg, A. Grote (eds.), German Conference on Bioinformatics 2010 Gesellschaft f. Informatik, Bonn, 2010. Lecture Notes in Informatics, vol. P-173, pp. 93-102, 2010 |
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10-029 Peter F. Stadler, Hakim Tafer et all Multi-Platform Next-Generation Sequencing of the Domestic Turkey (Meleagris gallopavo): Genome Assembly and Analysis PLoS Biology, 8: e1000475, 2010 |
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10-030 Peter F. Stadler Evolution of the Long Non-coding RNAs MALAT1 and MENβ/ε In: Advances in Bioinformatics and Computational Biology Carlos E. Ferreira, Satoru Miyano, Peter F. Stadler (eds.), Springer, Heidelberg, Lect. Notes Comp. Sci. 6268 (2010), pp.1-12, 2010 |
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10-031 Christian Arnold and Peter F. Stadler Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees. Alg. Mol. Biol., 5: 25, 2010 |
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10-032 Markus Riester, Peter F. Stadler and Konstantin Klemm Reconstruction of pedigrees in clonal plant populations. Theor. Popul. Biol., 78:109-117 , 2010 |
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10-033 Jörg Lehmann, Carina Eisenhardt, Peter F. Stadler and Veiko Krauss Some novel intron positions in conserved Drosophila genes are caused by intron sliding or tandem duplication BMC Evol Biol., 10: 156, 2010 |
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10-034 Marleen Perseke, Detlef Bernhard, Guido Fritzsch, Franz Brümmer, Peter F. Stadler and Martin Schlegel Mitochondrial genome evolution in Ophiuroidea, Echinoidea, and Holothuroidea: Insights in phylogenetic relationships of Echinodermata. Mol. Phylog. Evol., 56: 201-211, 2010 |
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10-035 Alexander Donath, Sven Findeiß, Jana Hertel, Manja Marz, Wolfgang Otto, Christine Schulz, Peter F. Stadler, Stefan Wirth Non-Coding RNAs In Evolutionary Genomics and Systems Biology, Gustavo Caetano-Anolles, Gustavo (ed.), Wiley-Blackwell, Hoboken NJ, pp. 251-293 , 2010 |
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10-036 Manja Marz, Nathalie Vanzo and Peter F. Stadler Temperature-dependent structural variability of RNAs: spliced leader RNAs and their evolutionary history J. Bioinf. Comp. Biol., 8: 1-17, 2010 |
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10-037 Sonja J Prohaska, Peter F. Stadler and David C. Krakauer Innovation in gene regulation: The case of chromatin computation. J. Theor. Biol., 265: 27-44, 2010 |
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10-038 David Langenberger, Clara Bermudez-Santana, Peter F. Stadler Steve Hoffmann Identification and classification of small RNAs in transcriptome sequence data. Pac. Symp. Biocomput., 15: 80-87, 2010 |
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10-039 Wichanee Meeto , Songwut Suramitr , Vladimir Lukes , Peter Wolschann and Supa Hannongbua Effects of the CN and NH2 substitutions on the geometrical and optical properties of model vinylfluorenes, based on DFT calculations J.Mol.Struct.THEOCHEM, 939: 75-81, 2010 |
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10-040 Songwut Suramitr, Wichanee Meeto, Peter Wolschann and Supa Hannongbua Understanding on absorption and fluorescence electronic transitions of carbazole-based conducting polymers: TD-DFT approaches Theor.Chem.Acc., 125: 35-44, 2010 |
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10-041 Iris Stappena, Joris Höfinghoff, Gerhard Buchbauer and Peter Wolschann Structure-Activity Relationships of Sandalwood Odorants: Synthesis of a New Campholene Derivative Natural Product Communications, 5(9): 1343-1348, 2010 |
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10-042 A.Koll, J.Janski, Alfred Karpfen and Peter Wolschann Bifunctional influence of 3-chloro substitution on structural and energetic characteristics of N-methyl-salicylidene imines J.Mol.Struct., 976: 19–29, 2010 |
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10-043 Auradee Punkvang, Patchreenart Saparpakorn, Supa Hannongbua, Peter Wolschann, Heinz Berner and Pornpan Pungpo Insight into crucial inhibitor–enzyme interaction of arylamides as novel direct inhibitors of the enoyl ACP reductase (InhA) from Mycobacterium tuberculosis: computer-aided molecular design Monatsh.Chem., 141: 1029–1041, 2010 |
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10-044 Auradee Punkvang, Patchreenart Saparpakorn, Supa Hannongbua, Peter Wolschann, Anton Beyer and Pornpan Pungpo Investigating the structural basis of arylamides to improve potency against M. tuberculosis strain through molecular dynamics simulations Europ.J.Med.Chem., 45: 5585-5593, 2010 |
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10-045 Auradee Punkvang, Patchreenart Sarparpakorn, Supa Hannongbua, Peter Wolschann and Pornpan Pungpo Elucidating Drug-Enzyme Interactions and Their Structural Basis for Improving the Affinity and Potency of Isoniazid and Its Derivatives Based on Computer Modeling Approaches Molecules, 15: 2791-2813, 2010 |
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10-046 Dana Nachtigallova, Tomas Zeleny, Matthias Ruckenbauer, Thomas Müller, Mario Barbatti, Pavel Hobza and Hans Lischka Does Stacking Restrain the Photodynamics of Individual Nucleobases? J.Am.Chem.Soc., 132: 8261–8263 9 8261, 2010 |
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10-047 Ivelina Georgieva, Adelia J.A. Aquino, Natasha Trendafilova, Paulo S. Santos and Hans Lischka Solvatochromic and Ionochromic Effects of Iron(II)bis-(1,10-phenanthroline)dicyano: a Theoretical Study Inorg.Chem., 49: 1634–1646, 2010 |
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10-048 Zsolt Gengeliczki, Michael P. Callahan, Nathan Svadlenak, Csaba Istvan Pongor, Balint Sztaray, Leo Meerts, Dana Nachtigallova, Pavel Hobza, Mario Barbatti, Hans Lischka and Mattanjah S. de Vries Effect of substituents on the excited-state dynamics of the modified DNA bases 2,4-diaminopyrimidine and 2,6-diaminopurinew Phys.Chem.Chem.Phys.,12 : 5375–5388, 2010 |
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10-049 Milan Oncak, Hans Lischka and Petr Slavicek Photostability and solvation: photodynamics of microsolvated zwitterionic glycinew Phys.Chem.Chem.Phys., 12: 4906–4914, 2010 |
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10-050 Martin Köhler, Matthias Ruckenbauer, Ivan Janciak, Siegfried Benkner, Hans Lischka and Wilfried N. Gansterer A grid services cloud for molecular modelling workflows Int.J.Web and Grid Services, 6(2), 2010 |
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10-051 Martin Koehler, Matthias Ruckenbauer, Ivan Janciak, Siegfried Benkner, Hans Lischka, and Wilfried N. Gansterer Supporting Molecular Modeling Workflows within a Grid Services Cloud D. Taniar et al. (Eds.): ICCSA 2010, Part IV, LNCS 6019, Springer-Verlag Berlin Heidelberg, pp. 13–28, 2010 |
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10-052 Hasan Pasalic, Adelia J.A. Aquino, Daniel Tunega, Georg Haberbauer, Martin H. Gerzabek, Herbert C. Georg, Tatiane F. Moraes, Kaline Coutinho, Sylvio Canuto and Hans Lischka Thermodynamic Stability of Hydrogen-Bonded Systems in Polar and Nonpolar Environments J.Comput.Chem., 31: 2046–2055, 2010 |
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10-053 Vladimir Lukes, Roland Solc, Mario Barbatti, Hans Lischka and Harald-Friedrich Kauffmann Torsional Potentionals and Full-Dimensional Simulation of Electronic Absorption Spectra of para-Phenylenevinylene Oligomers Using Semiempirical Hamiltonians J.Theor.Computat.Chem., 9(1): 249–263, 2010 |
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10-054 Matthias Ruckenbauer, Mario Barbatti, Thomas Muüller and Hans Lischka Nonadiabatic Excited-State Dynamics with Hybrid ab Initio Quantum-Mechanical/Molecular-Mechanical Methods: Solvation of the Pentadieniminium Cation in Apolar Media J.Phys.Chem.A, 114: 6757–6765, 2010 |
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10-055 Mario Barbatti, Adelia J.A. Aquino and Hans Lischka The UV absorption of nucleobases: semi-classical ab initio spectra simulations Phys.Chem.Chem.Phys., 12: 4959–4967, 2010 |
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10-056 Dana Nachtigallova, Hans Lischka, Jaroslaw J. Szymczak, Mario Barbatti, Pavel Hobza, Zsolt Gengeliczki, Gustavo Pino, Michael P. Callahane and Mattanjah S.de Vries The effect of C5 substitution on the photochemistry of uracil Phys.Chem.Chem.Phys., 12: 4924–4933, 2010 |
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10-057 Mario Barbatti, Jiri Pittner, Marek Pederzoli, Ute Werner, Roland Mitric, Vlasta Bonacic-Koutecky, Hans Lischka Non-adiabatic dynamics of pyrrole: Dependence of deactivation mechanisms on the excitation energy Chem.Phys., : 37526–34 , 2010 |
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10-058 Jaroslaw J. Szymczak, Thomas Müller, Hans Lischka The effect of hydration on the photo-deactivation pathways of 4-aminopyrimidine Chem.Phys., 375: 110–117, 2010 |
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10-059 Bernhard Sellner, Matthias Ruckenbauer, Ivan Stambolic, Mario Barbatti, Adelia J.A. Aquino and Hans Lischka Photodynamics of Azomethane: A Nonadiabatic Surface-Hopping Study J.Phys.Chem.A, 114: 8778–8785, 2010 |
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10-060 Dana Nachtigallova, Mario Barbatti, Jaroslaw J. Szymczak, Pavel Hobza and Hans Lischka The photodynamics of 2,4-diaminopyrimidine in comparison with 4-aminopyrimidine: The effect of amino-substitution Chem.Physics Letters, 497: 129–134, 2010 |
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10-061 Mirjana Eckert-Maksic, Mario Vazdar, Matthias Ruckenbauer, Mario Barbatti, Thomas Muüller and Hans Lischka Matrix-controlled photofragmentation of formamide: dynamics simulation in argon by nonadiabatic QM/MM methodw Phys.Chem.Chem.Phys., 12: 12719–12726, 2010 |
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10-062 Mirjana Eckert-Maksic, Mario Vazdar, Matthias Ruckenbauer, Mario Barbatti, Thomas Muüller and Hans Lischka Matrix-controlled photofragmentation of formamide: dynamics simulation in argon by nonadiabatic QM/MM methodw Phys.Chem.Chem.Phys., 12: 12719–12726, 2010 |
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10-063 Kyoyeon Park, Aaron West, Erica Raheja, Bernhard Sellner, Hans Lischka, Theresa L. Windus and William L. Hase1 Singlet and triplet potential surfaces for the O2+C2H4 reaction J.Chem.Phys., 133: 184306, 2010 |
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10-064 Matthias Ruckenbauer, Mario Barbatti, Bernhard Sellner, Thomas Muller and Hans Lischka Azomethane: Nonadiabatic Photodynamical Simulations in Solution J.Phys.Chem.A, 114: 12585–12590, 2010 |
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10-065 Alfred Karpfen and Eugene S. Kryachko The dimers of glyoxal and acrolein with H2O and HF: Negative intramolecular coupling and blue-shifted C-H stretch Chem.Phys.Lett., 489: 39-43, 2010 |
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10-066 Thomas Hoffmann-Ostenhof and Bernard Helffer On Minimal Partitions: New Properties and Applications to the Disk CRM Proceedings & Lecture NOtes Spectrum and Dynamics Worksop Montreal April 7-11,2008; American Mathematical Society, 52: 119-1363, 2010 |
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10-067 Bernard Helffer, Thomas Hoffmann-Ostenhof and Susanna Terracini Nodal minimal partitions in dimension 3 Discrete Contin. Dyn. Syst., 28: 617-635, 2010 |
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10-068 Bernard Helffer, Thomas Hoffmann-Ostenhof and Susanna Terracini On spectral minimal partitions : the case of the sphere Around the research of Vladimir Maz'ya. III, 153-178, Int.Math.Ser.N.Y. 13, Springer New York, 2010 |
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10-069 A. El-Gazzar, P. Perco, E. Eckelhart, M. Anees, V. Sexl, B. Mayer, Y. Liu, W. Mikulits, R. Horvat, T. Pangerl, D. Zheng and M. Krainer Natural immunity enhances the activity of a DR5 agonistic antibody and carboplatin in the treatment of ovarian cancer Molecular Cancer Therapeutics, 9: 1007-1018, 2010 |
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10-070 A. El-Gazzar, M. Wittinger, P. Perco, M. Anees, R. Horvat, W. Mikulits, T.W. Grunt, B. Mayer, M. Krainer The role of c-FLIPL in ovarian cancer: chaperoning tumor cells from immunosurveillance and increasing their invasive potential Journal of Gynecologic Oncology, 117: 451-459, 2010 |
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10-071 P. Perco, I. Muehlberger, G. Mayer, R. Oberbauer, A. Lukas, B. Mayer Linking transcriptomics and proteomics data on the level of protein interaction networks Electrophoresis, 31: 1780-1789, 2010 |
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10-072 A. Lukas and B. Mayer Data annotation and relations modeling for integrated Omics in clinical research The IIOAB Journal, 1: 15-23, 2010 |
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10-073 J. Söllner, A. Heinzel, G. Summer, R. Fechete, L. Stipkovits, S. Szathmary, B. Mayer Concept and application of a computational vaccinology workflow Immunome Research, 6: S7, 2010 |