Christoph Flamm

83 papers A* 1A 4B 3C 4Journal 54Unranked 16
YearRankTypeTitle / Venue / Authors
2025 J jnl
Assembly in Directed Hypergraphs.
CoRR
Christoph Flamm, Daniel Merkle, Peter F. Stadler
2025 J jnl
Finding Thermodynamically Favorable Pathways in Chemical Reaction Networks Using Flows in Hypergraphs and Mixed-Integer Linear Programming.
J. Chem. Inf. Model.
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen, Christoph Flamm, Peter Dittrich, Daniel Merkle
2025 A* conf
KinPFN: Bayesian Approximation of RNA Folding Kinetics using Prior-Data Fitted Networks.
ICLR
Dominik Scheuer, Frederic Runge, Jörg K. H. Franke, Michael T. Wolfinger, Christoph Flamm, Frank Hutter
2025 J jnl
Pathway Realizability in Chemical Networks.
J. Comput. Biol.
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2024 J jnl
Automated Inference of Graph Transformation Rules.
CoRR
Jakob L. Andersen, Akbar Davoodi, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2024 J jnl
Finding Thermodynamically Favorable Pathways in Reaction Networks using Flows in Hypergraphs and Mixed Integer Linear Programming.
CoRR
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen, Christoph Flamm, Peter Dittrich, Daniel Merkle
2024 J jnl
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
Marcos E. González Laffitte, Klaus Weinbauer, Tieu-Long Phan, Nora Beier, Nico Domschke, Christoph Flamm, Thomas Gatter, Daniel Merkle, Peter F. Stadler
2023 — conf
On the Realisability of Chemical Pathways.
ISBRA
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2023 J jnl
On the Realisability of Chemical Pathways.
CoRR
Jakob L. Andersen, Sissel Banke, Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2022 J jnl
Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction.
Frontiers Bioinform.
Christoph Flamm, Julia Wielach, Michael T. Wolfinger, Stefan Badelt, Ronny Lorenz, Ivo L. Hofacker
2022 J jnl
Characterizing Catalytic Mechanisms with Overlay Graphs.
CoRR
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2022 J jnl
Generic Context-Aware Group Contributions.
IEEE ACM Trans. Comput. Biol. Bioinform.
Christoph Flamm, Marc Hellmuth, Daniel Merkle, Nikolai Nøjgaard, Peter F. Stadler
2022 J jnl
Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381).
Dagstuhl Reports
Sven Findeiß, Christoph Flamm, Yann Ponty
2022 J jnl
Representing Catalytic Mechanisms with Rule Composition.
J. Chem. Inf. Model.
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2022 J jnl
What makes a reaction network "chemical"?
J. Cheminformatics
Stefan Müller, Christoph Flamm, Peter F. Stadler
2021 J jnl
Defining Autocatalysis in Chemical Reaction Networks.
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2021 J jnl
EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates.
J. Chem. Inf. Model.
Esther Heid, Samuel Goldman, Karthik Sankaranarayanan, Connor W. Coley, Christoph Flamm, William H. Green Jr.
2021 J jnl
Graph Transformation for Enzymatic Mechanisms.
CoRR
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2021 J jnl
Graph transformation for enzymatic mechanisms.
Bioinform.
Jakob L. Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana, Juraj Kolcák, Christophe V. F. P. Laurent, Daniel Merkle, Nikolai Nøjgaard
2020 — conf
Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases.
BSB
Waldeyr Mendes Cordeiro da Silva, Daniela P. de Andrade, Jakob L. Andersen, Maria Emília Telles Walter, Marcelo M. Brigido, Peter F. Stadler, Christoph Flamm
2020 — conf
Efficient Algorithms for Co-folding of Multiple RNAs.
BIOSTEC (Selected Papers)
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2020 — conf
Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding.
BIOINFORMATICS
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2019 J jnl
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows.
IEEE ACM Trans. Comput. Biol. Bioinform.
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2018 J jnl
Finding the K best synthesis plans.
J. Cheminformatics
Rolf Fagerberg, Christoph Flamm, Rojin Kianian, Daniel Merkle, Peter F. Stadler
2017 J jnl
Algorithmic Cheminformatics (Dagstuhl Seminar 17452).
Dagstuhl Reports
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2017 J jnl
An Intermediate Level of Abstraction for Computational Systems Chemistry.
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2017 B conf
Chemical Graph Transformation with Stereo-Information.
ICGT
Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2017 J jnl
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows.
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2017 J jnl
RNAblueprint: flexible multiple target nucleic acid sequence design.
Bioinform.
Stefan Hammer, Birgit Tschiatschek, Christoph Flamm, Ivo L. Hofacker, Sven Findeiß
2016 B conf
A Software Package for Chemically Inspired Graph Transformation.
ICGT
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2016 J jnl
A Software Package for Chemically Inspired Graph Transformation.
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2016 B conf
Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions.
ICGT
Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen
2016 J jnl
Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions.
CoRR
Christoph Flamm, Daniel Merkle, Peter F. Stadler, Uffe Thorsen
2016 J jnl
Computational Design of a Circular RNA with Prionlike Behavior.
Artif. Life
Stefan Badelt, Christoph Flamm, Ivo L. Hofacker
2016 J jnl
Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks.
IEEE ACM Trans. Comput. Biol. Bioinform.
Yu-Ting Hsiao, Wei-Po Lee, Wei Yang, Stefan Müller, Christoph Flamm, Ivo L. Hofacker, Philipp Kügler
2015 J jnl
Support for Eschenmoser's Glyoxylate Scenario.
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2015 J jnl
Towards Optimal DNA-Templated Computing.
Int. J. Unconv. Comput.
Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle
2014 — conf
50 Shades of Rule Composition - From Chemical Reactions to Higher Levels of Abstraction.
FMMB
Jakob Lykke Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2014 J jnl
Algorithmic Cheminformatics (Dagstuhl Seminar 14452).
Dagstuhl Reports
Wolfgang Banzhaf, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2014 J jnl
Atom mapping with constraint programming.
Algorithms Mol. Biol.
Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F. Stadler, Christoph Flamm
2014 J jnl
Generic strategies for chemical space exploration.
Int. J. Comput. Biol. Drug Des.
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2014 J jnl
Memory-efficient RNA energy landscape exploration.
Bioinform.
Martin Mann, Marcel Kucharík, Christoph Flamm, Michael T. Wolfinger
2014 C conf
Towards an Optimal DNA-Templated Molecular Assembler.
ALIFE
Jakob L. Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle
2013 J jnl
A novel method for the identification of synchronization effects in multichannel ECoG with an application to epilepsy.
Biol. Cybern.
Andreas Graef, Manfred Martin Hartmann, Christoph Flamm, Christoph Baumgartner, Manfred Deistler, Tilmann Kluge
2013 A conf
Atom Mapping with Constraint Programming.
CP
Martin Mann, Feras Nahar, Heinz Ekker, Rolf Backofen, Peter F. Stadler, Christoph Flamm
2013 — conf
Automatic ictal HFO detection for determination of initial seizure spread.
EMBC
Andreas Graef, Christoph Flamm, Susanne Pirker, Christoph Baumgartner, Manfred Deistler, Gerald Matz
2013 — conf
Barrier Trees for Metabolic Adjustment Landscapes.
ECAL
Christoph Flamm, Chris Hemmingsen, Daniel Merkle
2013 J jnl
Generic Strategies for Chemical Space Exploration
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2013 J jnl
Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data.
Entropy
Jakob L. Andersen, Tommy Andersen, Christoph Flamm, Martin M. Hanczyc, Daniel Merkle, Peter F. Stadler
2013 J jnl
On the Complexity of Reconstructing Chemical Reaction Networks.
CoRR
Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler
2013 J jnl
On the Complexity of Reconstructing Chemical Reaction Networks.
Math. Comput. Sci.
Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters, Peter F. Stadler
2013 — conf
The Graph Grammar Library - A Generic Framework for Chemical Graph Rewrite Systems.
ICMT
Martin Mann, Heinz Ekker, Christoph Flamm
2013 J jnl
The Graph Grammar Library - a generic framework for chemical graph rewrite systems
CoRR
Martin Mann, Heinz Ekker, Christoph Flamm
2012 — conf
A physiologically motivated ECoG segmentation method for epileptic seizure onset zone detection.
EMBC
Andreas Graef, Christoph Flamm, Susanne Pirker, Manfred Deistler, Christoph Baumgartner
2012 A conf
Exploring Chemistry Using SMT.
CP
Rolf Fagerberg, Christoph Flamm, Daniel Merkle, Philipp Peters
2012 J jnl
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2011 J jnl
In Silico Evolution of Early Metabolism.
Artif. Life
Alexander Ullrich, Markus Rohrschneider, Gerik Scheuermann, Peter F. Stadler, Christoph Flamm
2011 J jnl
Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete
CoRR
Jakob L. Andersen, Christoph Flamm, Daniel Merkle, Peter F. Stadler
2011 J jnl
ViennaRNA Package 2.0.
Algorithms Mol. Biol.
Ronny Lorenz, Stephan H. Bernhart, Christian Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker
2010 C conf
In Silico Evolution of Early Metabolism.
ALIFE
Alexander Ullrich, Christoph Flamm, Markus Rohrschneider, Peter F. Stadler
2009 — conf
2D Projections of RNA Folding Landscapes.
GCB
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker
2009 — conf
A Sequence-to-Function Map for Ribozyme-Catalyzed Metabolisms.
ECAL (2)
Alexander Ullrich, Christoph Flamm
2009 J jnl
A Topological Approach to Chemical Organizations.
Artif. Life
Gil Benkö, Florian Centler, Peter Dittrich, Christoph Flamm, Bärbel M. R. Stadler, Peter F. Stadler
2008 — conf
Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe.
CMSB
Alexander Ullrich, Christoph Flamm
2008 J jnl
Noisy: Identification of problematic columns in multiple sequence alignments.
Algorithms Mol. Biol.
Andreas W. M. Dress, Christoph Flamm, Guido Fritzsch, Stefan Grünewald, Matthias Kruspe, Sonja J. Prohaska, Peter F. Stadler
2008 C conf
Using the RNA sequence-to-structure map for functional evolution of ribozyme catalyzed artificial metabolisms.
ALIFE
Alexander Ullrich, Christoph Flamm, Lukas Endler
2008 — ch.
Visualization of Barrier Tree Sequences Revisited.
Visualization in Medicine and Life Sciences
Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2007 A conf
Saddles and Barrier in Landscapes of Generalized Search Operators.
FOGA
Christoph Flamm, Ivo L. Hofacker, Bärbel M. R. Stadler, Peter F. Stadler
2006 J jnl
Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation.
BMC Bioinform.
Christian V. Forst, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2006 J jnl
Partition function and base pairing probabilities of RNA heterodimers.
Algorithms Mol. Biol.
Stephan H. Bernhart, Hakim Tafer, Ulrike Mückstein, Christoph Flamm, Peter F. Stadler, Ivo L. Hofacker
2006 J jnl
The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks.
Bioinform.
Rainer Machné, Andrew Finney, Stefan Müller, James Lu, Stefanie Widder, Christoph Flamm
2006 J jnl
Visualization of Barrier Tree Sequences.
IEEE Trans. Vis. Comput. Graph.
Christian Heine, Gerik Scheuermann, Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
2006 C conf
Visualization of Lattice-Based Protein Folding Simulations.
IV
Sebastian Potzsch, Gerik Scheuermann, Peter F. Stadler, Michael T. Wolfinger, Christoph Flamm
2005 — conf
CelloS: A Multi-level Approach to Evolutionary Dynamics.
ECAL
Camille Stephan-Otto Attolini, Peter F. Stadler, Christoph Flamm
2005 J jnl
Evolutionary patterns of non-coding RNAs.
Theory Biosci.
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
2005 — conf
Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry.
ECAL
Gil Benkö, Christoph Flamm, Peter F. Stadler
2004 J jnl
Counterexamples in Chemical Ring Perception.
J. Chem. Inf. Model.
Franziska Berger, Christoph Flamm, Petra M. Gleiss, Josef Leydold, Peter F. Stadler
2003 J jnl
A Graph-Based Toy Model of Chemistry.
J. Chem. Inf. Comput. Sci.
Gil Benkö, Christoph Flamm, Peter F. Stadler
2003 J jnl
Barrier Trees on Poset-Valued Landscapes.
Genet. Program. Evolvable Mach.
Peter F. Stadler, Christoph Flamm
2003 — conf
Design of multi-stable nucleid acid sequences.
German Conference on Bioinformatics
Ingrid G. Abfalter, Christoph Flamm, Peter F. Stadler
2003 — conf
Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting.
ECAL
Gil Benkö, Christoph Flamm, Peter F. Stadler
1999 J jnl
RNA
Adv. Complex Syst.
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
1997 A conf
Density of States, Metastable States, and Saddle Points: Exploring the Energy Landscape of an RNA Molecule.
ISMB
Jan Cupal, Christoph Flamm, Alexander Renner, Peter F. Stadler