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ORCIDChristoph Flamm
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- affiliation: University of Vienna, Austria
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2020 – today
- 2024
[j32]Marcos E. González Laffitte
, Klaus Weinbauer, Tieu-Long Phan, Nora Beier, Nico Domschke, Christoph Flamm, Thomas Gatter, Daniel Merkle, Peter F. Stadler:
Partial Imaginary Transition State (ITS) Graphs: A Formal Framework for Research and Analysis of Atom-to-Atom Maps of Unbalanced Chemical Reactions and Their Completions. Symmetry 16(9): 1217 (2024)- [i18]Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard:
Automated Inference of Graph Transformation Rules. CoRR abs/2404.02692 (2024) - 2023
- [c27]Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
On the Realisability of Chemical Pathways. ISBRA 2023: 409-419 - [i17]Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
On the Realisability of Chemical Pathways. CoRR abs/2309.10629 (2023) - 2022
- [j31]Christoph Flamm, Julia Wielach, Michael T. Wolfinger, Stefan Badelt, Ronny Lorenz, Ivo L. Hofacker:
Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction. Frontiers Bioinform. 2 (2022) - [j30]Stefan Müller, Christoph Flamm, Peter F. Stadler:
What makes a reaction network "chemical"? J. Cheminformatics 14(1): 63 (2022) - [j29]Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard:
Representing Catalytic Mechanisms with Rule Composition. J. Chem. Inf. Model. 62(22): 5513-5524 (2022) - [j28]Christoph Flamm, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Peter F. Stadler:
Generic Context-Aware Group Contributions. IEEE ACM Trans. Comput. Biol. Bioinform. 19(1): 429-442 (2022) - [i16]Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard:
Characterizing Catalytic Mechanisms with Overlay Graphs. CoRR abs/2201.04515 (2022) - [i15]Sven Findeiß, Christoph Flamm, Yann Ponty:
Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381). Dagstuhl Reports 12(9): 121-149 (2022) - 2021
- [j27]Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard:
Graph transformation for enzymatic mechanisms. Bioinform. 37(Supplement): 392-400 (2021) - [j26]Esther Heid, Samuel Goldman, Karthik Sankaranarayanan, Connor W. Coley, Christoph Flamm, William H. Green Jr.:
EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates. J. Chem. Inf. Model. 61(10): 4949-4961 (2021) - [i14]Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard:
Graph Transformation for Enzymatic Mechanisms. CoRR abs/2102.03292 (2021) - [i13]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Defining Autocatalysis in Chemical Reaction Networks. CoRR abs/2107.03086 (2021) - 2020
- [c26]Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding. BIOINFORMATICS 2020: 23-31 - [c25]Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Efficient Algorithms for Co-folding of Multiple RNAs. BIOSTEC (Selected Papers) 2020: 193-214 - [c24]Waldeyr Mendes Cordeiro da Silva, Daniela P. de Andrade, Jakob L. Andersen, Maria Emília Telles Walter, Marcelo M. Brigido, Peter F. Stadler, Christoph Flamm:
Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases. BSB 2020: 247-258
2010 – 2019
- 2019
- [j25]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. IEEE ACM Trans. Comput. Biol. Bioinform. 16(2): 510-523 (2019) - 2018
- [j24]Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F. Stadler:
Finding the K best synthesis plans. J. Cheminformatics 10(1): 19:1-19:21 (2018) - 2017
- [j23]Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker, Sven Findeiß:
RNAblueprint: flexible multiple target nucleic acid sequence design. Bioinform. 33(18): 2850-2858 (2017) - [c23]Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Chemical Graph Transformation with Stereo-Information. ICGT 2017: 54-69 - [i12]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
An Intermediate Level of Abstraction for Computational Systems Chemistry. CoRR abs/1701.09097 (2017) - [i11]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. CoRR abs/1712.02594 (2017) - [i10]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Algorithmic Cheminformatics (Dagstuhl Seminar 17452). Dagstuhl Reports 7(11): 28-45 (2017) - 2016
- [j22]Stefan Badelt, Christoph Flamm, Ivo L. Hofacker:
Computational Design of a Circular RNA with Prionlike Behavior. Artif. Life 22(2): 172-184 (2016) - [j21]Yu-Ting Hsiao, Wei-Po Lee, Wei Yang, Stefan Müller, Christoph Flamm, Ivo L. Hofacker, Philipp Kügler:
Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks. IEEE ACM Trans. Comput. Biol. Bioinform. 13(1): 64-75 (2016) - [c22]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
A Software Package for Chemically Inspired Graph Transformation. ICGT 2016: 73-88 - [c21]Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen:
Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. ICGT 2016: 206-222 - [i9]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
A Software Package for Chemically Inspired Graph Transformation. CoRR abs/1603.02481 (2016) - [i8]Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen:
Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. CoRR abs/1604.06379 (2016) - 2015
- [j20]Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle:
Towards Optimal DNA-Templated Computing. Int. J. Unconv. Comput. 11(3-4): 185-203 (2015) - [i7]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Support for Eschenmoser's Glyoxylate Scenario. CoRR abs/1502.07555 (2015) - 2014
- [j19]Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F. Stadler, Christoph Flamm:
Atom mapping with constraint programming. Algorithms Mol. Biol. 9: 23 (2014) - [j18]Martin Mann, Marcel Kucharík, Christoph Flamm, Michael T. Wolfinger:
Memory-efficient RNA energy landscape exploration. Bioinform. 30(18): 2584-2591 (2014) - [j17]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Generic strategies for chemical space exploration. Int. J. Comput. Biol. Drug Des. 7(2/3): 225-258 (2014) - [c20]Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle:
Towards an Optimal DNA-Templated Molecular Assembler. ALIFE 2014: 557-564 - [c19]Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
50 Shades of Rule Composition - From Chemical Reactions to Higher Levels of Abstraction. FMMB 2014: 117-135 - [i6]Wolfgang Banzhaf, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Algorithmic Cheminformatics (Dagstuhl Seminar 14452). Dagstuhl Reports 4(11): 22-39 (2014) - 2013
- [j16]Andreas Graef, Manfred Martin Hartmann, Christoph Flamm, Christoph Baumgartner, Manfred Deistler, Tilmann Kluge:
A novel method for the identification of synchronization effects in multichannel ECoG with an application to epilepsy. Biol. Cybern. 107(3): 321-335 (2013) - [j15]Jakob L. Andersen, Tommy Andersen, Christoph Flamm, Martin M. 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 (2013) - [j14]Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler:
On the Complexity of Reconstructing Chemical Reaction Networks. Math. Comput. Sci. 7(3): 275-292 (2013) - [c18]Martin Mann, Feras Nahar, Heinz Ekker, Rolf Backofen, Peter F. Stadler, Christoph Flamm:
Atom Mapping with Constraint Programming. CP 2013: 805-822 - [c17]Christoph Flamm, Chris Hemmingsen, Daniel Merkle:
Barrier Trees for Metabolic Adjustment Landscapes. ECAL 2013: 1151-1158 - [c16]Andreas Graef, Christoph Flamm, Susanne Pirker, Christoph Baumgartner, Manfred Deistler, Gerald Matz:
Automatic ictal HFO detection for determination of initial seizure spread. EMBC 2013: 2096-2099 - [c15]Martin Mann, Heinz Ekker, Christoph Flamm:
The Graph Grammar Library - A Generic Framework for Chemical Graph Rewrite Systems. ICMT 2013: 52-53 - [i5]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Generic Strategies for Chemical Space Exploration. CoRR abs/1302.4006 (2013) - [i4]Martin Mann, Heinz Ekker, Christoph Flamm:
The Graph Grammar Library - a generic framework for chemical graph rewrite systems. CoRR abs/1304.1356 (2013) - [i3]Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler:
On the Complexity of Reconstructing Chemical Reaction Networks. CoRR abs/1309.7198 (2013) - 2012
- [c14]Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters:
Exploring Chemistry Using SMT. CP 2012: 900-915 - [c13]Andreas Graef, Christoph Flamm, Susanne Pirker, Manfred Deistler, Christoph Baumgartner:
A physiologically motivated ECoG segmentation method for epileptic seizure onset zone detection. EMBC 2012: 3500-3503 - [i2]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars. CoRR abs/1208.3153 (2012) - 2011
- [j13]Alexander Ullrich, Markus Rohrschneider, Gerik Scheuermann, Peter F. Stadler, Christoph Flamm:
In Silico Evolution of Early Metabolism. Artif. Life 17(2): 87-108 (2011) - [j12]Ronny Lorenz, Stephan H. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker:
ViennaRNA Package 2.0. Algorithms Mol. Biol. 6: 26 (2011) - [i1]Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler:
Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete. CoRR abs/1110.6051 (2011) - 2010
- [c12]Alexander Ullrich, Christoph Flamm, Markus Rohrschneider, Peter F. Stadler:
In Silico Evolution of Early Metabolism. ALIFE 2010: 57-64
2000 – 2009
- 2009
- [j11]Gil Benkö, Florian Centler, Peter Dittrich, Christoph Flamm, Bärbel M. R. Stadler, Peter F. Stadler:
A Topological Approach to Chemical Organizations. Artif. Life 15(1): 71-88 (2009) - [c11]Alexander Ullrich, Christoph Flamm:
A Sequence-to-Function Map for Ribozyme-Catalyzed Metabolisms. ECAL (2) 2009: 19-26 - [c10]Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker:
2D Projections of RNA Folding Landscapes. GCB 2009: 11-20 - 2008
- [j10]Andreas W. M. Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler:
Noisy: Identification of problematic columns in multiple sequence alignments. Algorithms Mol. Biol. 3 (2008) - [c9]Alexander Ullrich, Christoph Flamm, Lukas Endler:
Using the RNA sequence-to-structure map for functional evolution of ribozyme catalyzed artificial metabolisms. ALIFE 2008: 813 - [c8]Alexander Ullrich, Christoph Flamm:
Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe. CMSB 2008: 28-43 - [p1]Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Visualization of Barrier Tree Sequences Revisited. Visualization in Medicine and Life Sciences 2008: 275-290 - 2007
- [c7]Christoph Flamm, Ivo L. Hofacker, Bärbel M. R. Stadler, Peter F. Stadler:
Saddles and Barrier in Landscapes of Generalized Search Operators. FOGA 2007: 194-212 - 2006
- [j9]Stephan H. Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker:
Partition function and base pairing probabilities of RNA heterodimers. Algorithms Mol. Biol. 1 (2006) - [j8]Rainer Machné, Andrew Finney, Stefan Müller, James Lu, Stefanie Widder, Christoph Flamm:
The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. Bioinform. 22(11): 1406-1407 (2006) - [j7]Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinform. 7: 67 (2006) - [j6]Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
Visualization of Barrier Tree Sequences. IEEE Trans. Vis. Comput. Graph. 12(5): 781-788 (2006) - [c6]Sebastian Potzsch, Gerik Scheuermann, Peter F. Stadler, Michael T. Wolfinger, Christoph Flamm:
Visualization of Lattice-Based Protein Folding Simulations. IV 2006: 89-94 - 2005
- [j5]Athanasius F. Bompfünewerer, Christoph Flamm, Claudia Fried, Guido Fritzsch, Ivo L. Hofacker, Jörg Lehmann, Kristin Missal, Axel Mosig, Bettina Müller, Sonja J. Prohaska, Bärbel M. R. Stadler, Peter F. Stadler, Andrea Tanzer, Stefan Washietl, Christina Witwer:
Evolutionary patterns of non-coding RNAs. Theory Biosci. 123(4): 301-369 (2005) - [c5]Camille Stephan-Otto Attolini, Peter F. Stadler, Christoph Flamm:
CelloS: A Multi-level Approach to Evolutionary Dynamics. ECAL 2005: 500-509 - [c4]Gil Benkö, Christoph Flamm, Peter F. Stadler:
Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry. ECAL 2005: 725-733 - 2004
- [j4]Franziska Berger, Christoph Flamm, Petra M. Gleiss, Josef Leydold, Peter F. Stadler:
Counterexamples in Chemical Ring Perception. J. Chem. Inf. Model. 44(2): 323-331 (2004) - 2003
- [j3]Peter F. Stadler, Christoph Flamm:
Barrier Trees on Poset-Valued Landscapes. Genet. Program. Evolvable Mach. 4(1): 7-20 (2003) - [j2]Gil Benkö, Christoph Flamm, Peter F. Stadler:
A Graph-Based Toy Model of Chemistry. J. Chem. Inf. Comput. Sci. 43(4): 1085-1093 (2003) - [c3]Gil Benkö, Christoph Flamm, Peter F. Stadler:
Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting. ECAL 2003: 10-19 - [c2]Ingrid G. Abfalter, Christoph Flamm, Peter F. Stadler:
Design of multi-stable nucleid acid sequences. German Conference on Bioinformatics 2003: 1-7
1990 – 1999
- 1999
- [j1]Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler:
RNA In Silico The Computational Biology of RNA Secondary Structures. Adv. Complex Syst. 2(1): 65-100 (1999) - 1997
- [c1]Jan Cupal, Christoph Flamm, Alexander Renner, Peter F. Stadler:
Density of States, Metastable States, and Saddle Points: Exploring the Energy Landscape of an RNA Molecule. ISMB 1997: 88-91
Coauthor Index
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