Christoph Flamm

Publication Activity (10 Years)

Years Active: 1997-2024
Publications (10 Years): 29

Top Topics

Chemical Reactions

Computational Systems

Rna Secondary Structure Prediction

Gene Regulatory

Top Venues

IEEE ACM Trans. Comput. Biol. Bioinform.

Publications

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 (2024)
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
On the Realisability of Chemical Pathways. ISBRA (2023)
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
On the Realisability of Chemical Pathways. CoRR (2023)
Sven Findeiß, Christoph Flamm, Yann Ponty
Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381). Dagstuhl Reports 12 (9) (2022)
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 (2022)
Christoph Flamm, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Peter F. Stadler
Generic Context-Aware Group Contributions. IEEE ACM Trans. Comput. Biol. Bioinform. 19 (1) (2022)
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)
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) (2022)
Stefan Müller, Christoph Flamm, Peter F. Stadler
What makes a reaction network "chemical"? J. Cheminformatics 14 (1) (2022)
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 (2021)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Defining Autocatalysis in Chemical Reaction Networks. CoRR (2021)
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) (2021)
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) (2021)
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)
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Efficient Algorithms for Co-folding of Multiple RNAs. BIOSTEC (Selected Papers) (2020)
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding. BIOINFORMATICS (2020)
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) (2019)
Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F. Stadler
Finding the K best synthesis plans. J. Cheminformatics 10 (1) (2018)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Algorithmic Cheminformatics (Dagstuhl Seminar 17452). Dagstuhl Reports 7 (11) (2017)
Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker, Sven Findeiß
RNAblueprint: flexible multiple target nucleic acid sequence design. Bioinform. 33 (18) (2017)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
An Intermediate Level of Abstraction for Computational Systems Chemistry. CoRR (2017)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. CoRR (2017)
Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Chemical Graph Transformation with Stereo-Information. ICGT (2017)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
A Software Package for Chemically Inspired Graph Transformation. ICGT (2016)
Stefan Badelt, Christoph Flamm, Ivo L. Hofacker
Computational Design of a Circular RNA with Prionlike Behavior. Artif. Life 22 (2) (2016)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
A Software Package for Chemically Inspired Graph Transformation. CoRR (2016)
Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen
Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. CoRR (2016)
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) (2016)
Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen
Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. ICGT (2016)
Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle
Towards Optimal DNA-Templated Computing. Int. J. Unconv. Comput. 11 (3-4) (2015)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Support for Eschenmoser's Glyoxylate Scenario. CoRR (2015)
Wolfgang Banzhaf, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Algorithmic Cheminformatics (Dagstuhl Seminar 14452). Dagstuhl Reports 4 (11) (2014)
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) (2014)
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)
Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle
Towards an Optimal DNA-Templated Molecular Assembler. ALIFE (2014)
Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F. Stadler, Christoph Flamm
Atom mapping with constraint programming. Algorithms Mol. Biol. 9 (2014)
Martin Mann, Marcel Kucharík, Christoph Flamm, Michael T. Wolfinger
Memory-efficient RNA energy landscape exploration. Bioinform. 30 (18) (2014)
Martin Mann, Heinz Ekker, Christoph Flamm
The Graph Grammar Library - A Generic Framework for Chemical Graph Rewrite Systems. ICMT (2013)
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) (2013)
Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler
On the Complexity of Reconstructing Chemical Reaction Networks. Math. Comput. Sci. 7 (3) (2013)
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) (2013)
Martin Mann, Feras Nahar, Heinz Ekker, Rolf Backofen, Peter F. Stadler, Christoph Flamm
Atom Mapping with Constraint Programming. CP (2013)
Andreas Graef, Christoph Flamm, Susanne Pirker, Christoph Baumgartner, Manfred Deistler, Gerald Matz
Automatic ictal HFO detection for determination of initial seizure spread. EMBC (2013)
Martin Mann, Heinz Ekker, Christoph Flamm
The Graph Grammar Library - a generic framework for chemical graph rewrite systems CoRR (2013)
Christoph Flamm, Chris Hemmingsen, Daniel Merkle
Barrier Trees for Metabolic Adjustment Landscapes. ECAL (2013)
Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler
On the Complexity of Reconstructing Chemical Reaction Networks. CoRR (2013)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Generic Strategies for Chemical Space Exploration CoRR (2013)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars CoRR (2012)
Andreas Graef, Christoph Flamm, Susanne Pirker, Manfred Deistler, Christoph Baumgartner
A physiologically motivated ECoG segmentation method for epileptic seizure onset zone detection. EMBC (2012)
Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters
Exploring Chemistry Using SMT. CP (2012)
Alexander Ullrich, Markus Rohrschneider, Gerik Scheuermann, Peter F. Stadler, Christoph Flamm
In Silico Evolution of Early Metabolism. Artif. Life 17 (2) (2011)
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 (2011)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete CoRR (2011)
Alexander Ullrich, Christoph Flamm, Markus Rohrschneider, Peter F. Stadler
In Silico Evolution of Early Metabolism. ALIFE (2010)
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker
2D Projections of RNA Folding Landscapes. GCB (2009)
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) (2009)
Alexander Ullrich, Christoph Flamm
A Sequence-to-Function Map for Ribozyme-Catalyzed Metabolisms. ECAL (2) (2009)
Alexander Ullrich, Christoph Flamm
Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe. CMSB (2008)
Alexander Ullrich, Christoph Flamm, Lukas Endler
Using the RNA sequence-to-structure map for functional evolution of ribozyme catalyzed artificial metabolisms. ALIFE (2008)
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)
Christoph Flamm, Ivo L. Hofacker, Bärbel M. R. Stadler, Peter F. Stadler
Saddles and Barrier in Landscapes of Generalized Search Operators. FOGA (2007)
Sebastian Potzsch, Gerik Scheuermann, Peter F. Stadler, Michael T. Wolfinger, Christoph Flamm
Visualization of Lattice-Based Protein Folding Simulations. IV (2006)
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)
Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. BMC Bioinform. 7 (2006)
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) (2006)
Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
Visualization of Barrier Tree Sequences. IEEE Trans. Vis. Comput. Graph. 12 (5) (2006)
Gil Benkö, Christoph Flamm, Peter F. Stadler
Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry. ECAL (2005)
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) (2005)
Camille Stephan-Otto Attolini, Peter F. Stadler, Christoph Flamm
CelloS: A Multi-level Approach to Evolutionary Dynamics. ECAL (2005)
Franziska Berger, Christoph Flamm, Petra M. Gleiss, Josef Leydold, Peter F. Stadler
Counterexamples in Chemical Ring Perception. J. Chem. Inf. Model. 44 (2) (2004)
Ingrid G. Abfalter, Christoph Flamm, Peter F. Stadler
Design of multi-stable nucleid acid sequences. German Conference on Bioinformatics (2003)
Gil Benkö, Christoph Flamm, Peter F. Stadler
A Graph-Based Toy Model of Chemistry. J. Chem. Inf. Comput. Sci. 43 (4) (2003)
Peter F. Stadler, Christoph Flamm
Barrier Trees on Poset-Valued Landscapes. Genet. Program. Evolvable Mach. 4 (1) (2003)
Gil Benkö, Christoph Flamm, Peter F. Stadler
Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting. ECAL (2003)
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
The Computational Biology of RNA Secondary Structures. Adv. Complex Syst. 2 (1) (1999)
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)