Christoph Flamm

Publications

Publications per year 2000 2004 2006 2007 2008 2009 2013 2014 2015 2016 2017 2018 2022 2023

• 59 Article
• 18 Contribution to proceedings
• 5 Chapter
• 3 Meeting abstract/Conference paper
• 3 More
  • 3 Review

Publications per year

Publications per year

Search results

• 2023

  On the Realisability of Chemical Pathways

  Andersen, J. L., Banke, S., Fagerberg, R., Flamm, C., Merkle, D. & Stadler, P., Oct 2023, Bioinformatics Research and Applications - 19th International Symposium, ISBRA 2023, Proceedings. Guo, X., Mangul, S., Patterson, M. & Zelikovsky, A. (eds.). Springer Singapore, p. 409–419 11 p. (Lecture Notes in Computer Science, Vol. 14248).

  Publications: Contribution to book › Contribution to proceedings › Peer Reviewed

  • Pentose Phosphate 100%

• Rational Design of RiboNucleic Acids: Dagstuhl Seminar 22381

  Findeiß, S., Flamm, C. & Ponty, Y., 4 Apr 2023, In: Dagstuhl Reports. 12, 9, p. 121-149

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Statistical mechanics of biomolecular condensates via cavity methods

  Lauber, N., Tichacek, O., Bose, R., Flamm, C., Leuzzi, L., Tang, T. Y. D., Ruiz-Mirazo, K. & De Martino, D., 21 Apr 2023, In: Iscience. 26, 4, 106300.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access
• 2022

  Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction

  Flamm, C., Wielach, J., Wolfinger, M. T., Badelt, S., Lorenz, R. & Hofacker, I. L., 11 Jul 2022, In: Frontiers in bioinformatics. 2, 7 p., 835422.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Generic Context-Aware Group Contributions

  Flamm, C., Hellmuth, M., Merkle, D., Nojgaard, N. & Stadler, P. F., 1 Jan 2022, In: I E E E - A C M Transactions on Computational Biology and Bioinformatics. 19, 1, p. 429-442 14 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Representing Catalytic Mechanisms with Rule Composition

  Anderson, J. L., Fagerberg, R., Flamm, C., Fontana, W., Kolcak, J., Laurent, C. V. F. P., Merkle, D. & Nojgaard, N., 3 Nov 2022, In: Journal of Chemical Information and Modeling. 62, 22, p. 5513-5524 12 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• What makes a reaction network "chemical"?

  Müller, S., Flamm, C. & Stadler, P. F., 19 Sep 2022, In: Journal of Cheminformatics. 14, 1, 24 p., 63.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access
• 2021

  EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates

  Heid, E., Goldman, S., Sankaranarayanan, K., Coley, C. W., Flamm, C. & Green, W. H., 25 Oct 2021, In: Journal of Chemical Information and Modeling. 61, 10, p. 4949-4961 13 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Graph transformation for enzymatic mechanisms

  Andersen, J. L., Fagerberg, R., Flamm, C., Fontana, W., Kolcak, J., Laurent, C. V. F. P., Merkle, D. & Nojgaard, N., Jul 2021, In: Bioinformatics. 37, p. I392-I400 9 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access
• 2020

  Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding

  Lorenz, R., Flamm, C., Hofacker, I. L. & Stadler, P. F., 2020, Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies: Volume 3: BIOINFORMATICS, 23-31, 2020 , Valletta, Malta. DeMaria, E., Fred, A. & Gamboa, H. (eds.). [Sétubal]: SciTePress, p. 23-31 9 p.

  Publications: Contribution to book › Contribution to proceedings › Peer Reviewed

  Open Access

• SBML Level 3: an extensible format for the exchange and reuse of biological models

  SBML Level 3 Community, Keating, S. M., Waltemath, D., König, M., Zhang, F., Dräger, A., Chaouiya, C., Bergmann, F. T., Finney, A., Gillespie, C. S., Helikar, T., Hoops, S., Malik-Sheriff, R. S., Moodie, S. L., Moraru, I. I., Myers, C. J., Naldi, A., Olivier, B. G., Sahle, S., Schaff, J. C., & 32 othersSmith, L. P., Swat, M. J., Thieffry, D., Watanabe, L., Wilkinson, D. J., Blinov, M. L., Begley, K., Faeder, J. R., Gómez, H. F., Hamm, T. M., Inagaki, Y., Liebermeister, W., Lister, A. L., Lucio, D., Mjolsness, E., Proctor, C. J., Raman, K., Rodriguez, N., Shaffer, C. A., Shapiro, B. E., Stelling, J., Swainston, N., Tanimura, N., Wagner, J., Meier-Schellersheim, M., Sauro, H. M., Palsson, B., Bolouri, H., Endler, L., Flamm, C., Machne, R. & Hucka, M., 1 Aug 2020, In: Molecular Systems Biology. 16, 8, 21 p., e9110.

  Publications: Contribution to journal › Review › Peer Reviewed

  Open Access
• 2019

  Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows

  Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., Mar 2019, In: IEEE/ACM Transactions on Computational Biology and Bioinformatics. 16, 2, p. 510-523 14 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Exploring Plant Sesquiterpene Diversity by Generating Chemical Networks

  da Silva, W. M. C., Andersen, J. L., Holanda, M. T., Walter, M. E. M. T., Brigido, M. M., Stadler, P. F. & Flamm, C., Apr 2019, In: Group Processes and Intergroup Relations. 7, 4, 18 p., 240.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Information Processing in Chemical Systems

  Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P., 9 Jun 2019, The Energetics of Computing in Life and Machines. Kempes, C., Stadler, P. F., Grochow, J. A. & Wolpert, D. H. (eds.). SFI Press

  Publications: Contribution to book › Chapter › Peer Reviewed
• 2018

  Efficient computation of co-transcriptional RNA-ligand interaction dynamics

  Wolfinger, M. T., Flamm, C. & Hofacker, I. L., 1 Jul 2018, In: Methods. 143, p. 70-76 7 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Finding the K best synthesis plans

  Fagerberg, R., Flamm, C., Kianian, R., Merkle, D. & Stadler, P. F., 5 Apr 2018, In: Journal of Cheminformatics. 10, 1, 21 p., 19.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• In silico design of ligand triggered RNA switches

  Findeiss, S., Hammer, S., Wolfinger, M. T., Kuehnl, F., Flamm, C. & Hofacker, I. L., 1 Jul 2018, In: Methods. 143, p. 90-101 12 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Rule composition in graph transformation models of chemical reactions

  Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 1 Jan 2018, In: Match. 80, 3, p. 661-704 44 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Towards mechanistic prediction of mass spectra using graph transformation

  Andersen, J. L., Fagerberg, R., Flamm, C., Kianian, R., Merkle, D. & Stadler, P. F., 1 Jan 2018, In: Match. 80, 3, p. 705-731 27 p.

  Publications: Contribution to journal › Article › Peer Reviewed
• 2017

  An intermediate level of abstraction for computational systems chemistry

  Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 28 Dec 2017, In: Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences. 375, 2109, 10 p., 20160354.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Chemical Graph Transformation with Stereo-Information

  Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P., 18 Jul 2017, GRAPH TRANSFORMATION, ICGT 2017: Graph Transformation:Conference Proceedings of the 10th International Conference on Graph Transformation. de Lara, J. & Plump, D. (eds.). SPRINGER INT PUBLISHING AG, Vol. 10373. p. 54-69 16 p.

  Publications: Contribution to book › Contribution to proceedings › Peer Reviewed

• RNAblueprint: flexible multiple target nucleic acid sequence design

  Hammer, S., Tschiatschek, B., Flamm, C., Hofacker, I. L. & Findeiss, S., 15 Sep 2017, In: Bioinformatics. 33, 18, p. 2850-2858 9 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• RNA structure prediction: from 2D to 3D

  Thiel, B., Flamm, C. & Hofacker, I., 15 Sep 2017, In: Emerging Topics in Life Sciences . 1, 3, p. 275-285 11 p.

  Publications: Contribution to journal › Article › Peer Reviewed
• 2016

  A Software Package for Chemically Inspired Graph Transformation

  Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 2016, Graph Transformation. Minas, M. & Echahed, R. (eds.). SPRINGER INT PUBLISHING AG, p. 73-88 16 p. (Lecture Notes in Computer Science, Vol. 9761).

  Publications: Contribution to book › Contribution to proceedings › Peer Reviewed

• Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions

  Flamm, C., Merkle, D., Stadler, P. F. & Thorsen, U., 2016, Graph Transformation - 9th International Conference, ICGT 2016 in Memory of Hartmut Ehrig, Held as Part of STAF 2016, Proceedings. Minas, M. & Echahed, R. (eds.). Cham: SPRINGER INT PUBLISHING AG, p. 206-222 17 p. (Lecture Notes in Computer Science, Vol. 9761).

  Publications: Contribution to book › Contribution to proceedings › Peer Reviewed

• Computational Design of a Circular RNA with Prionlike Behavior

  Badelt, S., Flamm, C. & Hofacker, I. L., 2016, In: Artificial Life. 22, 2, p. 172-184 13 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks

  Hsiao, Y-T., Lee, W-P., Yang, W., Mueller, S., Flamm, C., Hofacker, I. & Kuegler, P., 2016, In: I E E E - A C M Transactions on Computational Biology and Bioinformatics. 13, 1, p. 64-75 12 p.

  Publications: Contribution to journal › Article › Peer Reviewed
• 2015

  Generalized topologies: Hypergraphs, chemical reactions and biological evolution

  Flamm, C., Stadler, B. M. R. & Stadler, P., 2015, Advances in Mathematical Chemistry and Applications. Basak, S. C., Restrepo, G. & Villaveces, J. L. (eds.). Bentham Science Publishers, Vol. 2. p. 300-328

  Publications: Contribution to book › Chapter › Peer Reviewed

• In silico Support for Eschenmoser's Glyoxylate Scenario

  Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P., Aug 2015, In: Israel Journal of Chemistry. 55, 8, p. 919-933 15 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Sequence-controlled RNA self-processing: computational design, biochemical analysis, and visualization by AFM

  Petkovic, S., Badelt, S., Block, S., Flamm, C., Delcea, M., Hofacker, I. & Mueller, S., Jul 2015, In: RNA. 21, 7, p. 1249-1260 12 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Thermodynamic and kinetic folding of riboswitches

  Badelt, S., Hammer, S., Flamm, C. & Hofacker, I. L., 2015, In: Methods in Enzymology. 553, p. 193-213 21 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Towards Optimal DNA-Templated Computing

  Andersen, J. L., Flamm, C., Hanczyc, M. M. & Merkle, D., 2015, In: International Journal of Unconventional Computing. 11, 3-4, p. 185-203 19 p.

  Publications: Contribution to journal › Article › Peer Reviewed
• 2014

  50 Shades of Rule Composition: From Chemical Reactions to Higher Levels of Abstraction

  Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P. F., 2014, Formal Methods in Macro-Biology: First International Conference, FMMB 2014, Nouméa, New Caledonia, September 22-24, 2014. Proceedings. Fages, F. & Piazza, C. (eds.). Cham: SPRINGER INT PUBLISHING AG, p. 117-135 (Lecture Notes in Computer Science, Vol. 8738).

  Publications: Contribution to book › Contribution to proceedings

• Atom mapping with constraint programming

  Mann, M., Nahar, F., Schnorr, N., Backofen, R., Stadler, P. F. & Flamm, C., 29 Nov 2014, In: Algorithms for Molecular Biology. 9, 12 p., 23.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• Computational design of a circular RNA with prion-like behaviour

  Badelt, S., Flamm, C. & Hofacker, I., 2014, Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems. MIT Press, p. 565-568

  Publications: Contribution to book › Contribution to proceedings

• Generic strategies for chemical space exploration

  Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P., 2014, In: International Journal of Computational Biology and Drug Design. 7, 2-3, p. 225-258 34 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Memory-efficient RNA energy landscape exploration

  Mann, M., Kucharik, M., Flamm, C. & Wolfinger, M. T., 15 Sep 2014, In: Bioinformatics. 30, 18, p. 2584-2591 8 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Towards an Optimal DNA-Templated Molecular Assembler

  Andersen, J. L., Flamm, C., Hanczyc, M. M. & Merkle, D., 2014, Proceedings of the 14th International Conference on the Synthesis and Simulation of Living Systems. MIT Press, p. 557-564

  Publications: Contribution to book › Contribution to proceedings
• 2013

  Atom mapping with constraint programming

  Mann, M., Nahar, F., Ekker, H., Backofen, R., Stadler, P. F. & Flamm, C., 1 Jan 2013, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 8124 LNCS. p. 805-822 18 p.

  Publications: Contribution to book › Chapter

• Barrier Trees for Metabolic Adjustment Landscapes

  Flamm, C. & Merkle, D., Sep 2013, Conference Proceedings. Lió, P., Miglino, O., Nicosia, G., Nolfi, S. & Pavone, M. (eds.).

  Publications: Contribution to book › Contribution to proceedings

• Computational Design of RNAs with Complex Energy Landscapes

  Siederdissen, C. H. Z., Hammer, S., Abfalter, I., Hofacker, I. L., Flamm, C. & Stadler, P. F., Dec 2013, In: Biopolymers: original research on biological molecules and assemblies. 99, 12, p. 1124-1136 13 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Exploring Prebiotic Chemistry Space

  Flamm, C., Merkle, D. & Andersen, J. L., Sep 2013, Conference Proceedings. Lió, P., Miglino, O., Nicosia, G., Nolfi, S. & Pavone, M. (eds.).

  Publications: Contribution to book › Contribution to proceedings

• Inferring chemical reaction patterns using rule composition in graph grammars

  Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P., 6 Jun 2013, In: Journal of Systems Chemistry.

  Publications: Contribution to journal › Article › Peer Reviewed

• Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data

  Andersen, J. L., Andersen, T., Flamm, C., Hanczyc, M. M., Merkle, D. & Stadler, P. F., Oct 2013, In: Entropy. 15, 10, p. 4066-4083 18 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access

• The Graph Grammar Library - A Generic Framework for Chemical Graph Rewrite Systems

  Mann, M., Ekker, H. & Flamm, C., 1 Jan 2013, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 7909 LNCS. p. 52-53 2 p.

  Publications: Contribution to book › Chapter

  • Handling Graph 100%
• 2012

  Exploring chemistry using SMT

  Fagerberg, R., Flamm, C., Merkle, D. & Peters, P., 1 Jan 2012, Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). Vol. 7514 LNCS. p. 900-915 16 p.

  Publications: Contribution to book › Chapter

• Maximizing output and recognizing autocatalysis in chemical reaction networks is NP-complete

  Andersen, J. L., Flamm, C., Merkle, D. & Stadler, P., 6 Jan 2012, In: Journal of Systems Chemistry. 3, p. 1-9 9 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Modelling Translation Initiation under the Influence of sRNA

  Amman, F., Flamm, C. & Hofacker, I., 2012, In: International Journal of Molecular Sciences. 13, 12, p. 16223-16240 18 p.

  Publications: Contribution to journal › Article › Peer Reviewed

  Open Access
• 2011

  In Silico Evolution of Early Metabolism

  Ullrich, A., Rohrschneider, M., Scheuermann, G., Stadler, P. & Flamm, C., 2011, In: Artificial Life. 17, 2, p. 87-108 22 p.

  Publications: Contribution to journal › Article › Peer Reviewed

• Physiological Environment Induces Quick Response-Slow Exhaustion Reactions

  Hiroi, N., Lu, J., Iba, K., Tabira, A., Yamashita, S., Okada, Y., Flamm, C., Oka, K., Köhler, G. & Funahashi, A., 2011, In: Frontiers in Physiology. 2

  Publications: Contribution to journal › Article › Peer Reviewed