Density of States, Metastable States, and Saddle Points: Exploring the Energy Landscape of an RNA Molecule. - Jan Cupal; Christoph Flamm; Alexander Renner; Peter F. Stadler (ISMB, 1997)

RNA In Silico The Computational Biology of RNA Secondary Structures. - Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (Adv. Complex Syst., 1999)

Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting. - Gil Benkö; Christoph Flamm; Peter F. Stadler (ECAL, 2003)

Design of multi-stable nucleid acid sequences. - Ingrid G. Abfalter; Christoph Flamm; Peter F. Stadler (German Conference on Bioinformatics, 2003)

Barrier Trees on Poset-Valued Landscapes. - Peter F. Stadler; Christoph Flamm (Genet. Program. Evolvable Mach., 2003)

A Graph-Based Toy Model of Chemistry. - Gil Benkö; Christoph Flamm; Peter F. Stadler (J. Chem. Inf. Comput. Sci., 2003)

Counterexamples in Chemical Ring Perception. - Franziska Berger; Christoph Flamm; Petra M. Gleiss; Josef Leydold; Peter F. Stadler (J. Chem. Inf. Model., 2004)

CelloS: A Multi-level Approach to Evolutionary Dynamics. - Camille Stephan-Otto Attolini; Peter F. Stadler; Christoph Flamm (ECAL, 2005)

Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry. - Gil Benkö; Christoph Flamm; Peter F. Stadler (ECAL, 2005)

Evolutionary patterns of non-coding RNAs. - 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; et al. (Theory Biosci., 2005)

Visualization of Lattice-Based Protein Folding Simulations. - Sebastian Potzsch; Gerik Scheuermann; Peter F. Stadler; Michael T. Wolfinger; Christoph Flamm (IV, 2006)

Partition function and base pairing probabilities of RNA heterodimers. - Stephan H. Bernhart; Hakim Tafer; Ulrike Mückstein; Christoph Flamm; Peter F. Stadler; Ivo L. Hofacker (Algorithms Mol. Biol., 2006)

The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks. - Rainer Machné; Andrew Finney; Stefan Müller 009; James Lu; Stefanie Widder; Christoph Flamm (Bioinform., 2006)

Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation. - Christian V. Forst; Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (BMC Bioinform., 2006)

Visualization of Barrier Tree Sequences. - Christian Heine 002; Gerik Scheuermann; Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (IEEE Trans. Vis. Comput. Graph., 2006)

Saddles and Barrier in Landscapes of Generalized Search Operators. - Christoph Flamm; Ivo L. Hofacker; Bärbel M. R. Stadler; Peter F. Stadler (FOGA, 2007)

Visualization of Barrier Tree Sequences Revisited. - Christian Heine 002; Gerik Scheuermann; Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (Visualization in Medicine and Life Sciences, 2008)

Using the RNA sequence-to-structure map for functional evolution of ribozyme catalyzed artificial metabolisms. - Alexander Ullrich; Christoph Flamm; Lukas Endler (ALIFE, 2008)

Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe. - Alexander Ullrich; Christoph Flamm (CMSB, 2008)

Noisy: Identification of problematic columns in multiple sequence alignments. - Andreas W. M. Dress; Christoph Flamm; Guido Fritzsch; Stefan Grünewald; Matthias Kruspe; Sonja J. Prohaska; Peter F. Stadler (Algorithms Mol. Biol., 2008)

A Sequence-to-Function Map for Ribozyme-Catalyzed Metabolisms. - Alexander Ullrich; Christoph Flamm (ECAL (2), 2009)

2D Projections of RNA Folding Landscapes. - Ronny Lorenz; Christoph Flamm; Ivo L. Hofacker (GCB, 2009)

A Topological Approach to Chemical Organizations. - Gil Benkö; Florian Centler; Peter Dittrich; Christoph Flamm; Bärbel M. R. Stadler; Peter F. Stadler (Artif. Life, 2009)

In Silico Evolution of Early Metabolism. - Alexander Ullrich; Christoph Flamm; Markus Rohrschneider; Peter F. Stadler (ALIFE, 2010)

In Silico Evolution of Early Metabolism. - Alexander Ullrich; Markus Rohrschneider; Gerik Scheuermann; Peter F. Stadler; Christoph Flamm (Artif. Life, 2011)

ViennaRNA Package 2.0. - Ronny Lorenz; Stephan H. Bernhart; Christian Höner zu Siederdissen; Hakim Tafer; Christoph Flamm; Peter F. Stadler; Ivo L. Hofacker (Algorithms Mol. Biol., 2011)

Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2011)

Exploring Chemistry Using SMT. - Rolf Fagerberg; Christoph Flamm; Daniel Merkle; Philipp Peters (CP, 2012)

A physiologically motivated ECoG segmentation method for epileptic seizure onset zone detection. - Andreas Graef; Christoph Flamm; Susanne Pirker; Manfred Deistler; Christoph Baumgartner (EMBC, 2012)

Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2012)

Atom Mapping with Constraint Programming. - Martin Mann; Feras Nahar; Heinz Ekker; Rolf Backofen; Peter F. Stadler; Christoph Flamm (CP, 2013)

Barrier Trees for Metabolic Adjustment Landscapes. - Christoph Flamm; Chris Hemmingsen; Daniel Merkle (ECAL, 2013)

Automatic ictal HFO detection for determination of initial seizure spread. - Andreas Graef; Christoph Flamm; Susanne Pirker; Christoph Baumgartner; Manfred Deistler; Gerald Matz (EMBC, 2013)

The Graph Grammar Library - A Generic Framework for Chemical Graph Rewrite Systems. - Martin Mann; Heinz Ekker; Christoph Flamm (ICMT, 2013)

A novel method for the identification of synchronization effects in multichannel ECoG with an application to epilepsy. - Andreas Graef; Manfred Martin Hartmann; Christoph Flamm; Christoph Baumgartner; Manfred Deistler; Tilmann Kluge (Biol. Cybern., 2013)

Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data. - Jakob L. Andersen; Tommy Andersen; Christoph Flamm; Martin M. Hanczyc; Daniel Merkle; Peter F. Stadler (Entropy, 2013)

On the Complexity of Reconstructing Chemical Reaction Networks. - Rolf Fagerberg; Christoph Flamm; Daniel Merkle; Philipp Peters; Peter F. Stadler (Math. Comput. Sci., 2013)

Towards an Optimal DNA-Templated Molecular Assembler. - Jakob L. Andersen; Christoph Flamm; Martin M. Hanczyc; Daniel Merkle (ALIFE, 2014)

50 Shades of Rule Composition - From Chemical Reactions to Higher Levels of Abstraction. - Jakob Lykke Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (FMMB, 2014)

Atom mapping with constraint programming. - Martin Mann; Feras Nahar; Norah Schnorr; Rolf Backofen; Peter F. Stadler; Christoph Flamm (Algorithms Mol. Biol., 2014)

Memory-efficient RNA energy landscape exploration. - Martin Mann; Marcel Kucharík; Christoph Flamm; Michael T. Wolfinger (Bioinform., 2014)

Algorithmic Cheminformatics (Dagstuhl Seminar 14452). - Wolfgang Banzhaf; Christoph Flamm; Daniel Merkle; Peter F. Stadler (Dagstuhl Reports, 2014)

Generic strategies for chemical space exploration. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (Int. J. Comput. Biol. Drug Des., 2014)

Support for Eschenmoser's Glyoxylate Scenario. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2015)

Towards Optimal DNA-Templated Computing. - Jakob L. Andersen; Christoph Flamm; Martin M. Hanczyc; Daniel Merkle (Int. J. Unconv. Comput., 2015)

A Software Package for Chemically Inspired Graph Transformation. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (ICGT, 2016)

Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions. - Christoph Flamm; Daniel Merkle; Peter F. Stadler; Uffe Thorsen (ICGT, 2016)

Computational Design of a Circular RNA with Prionlike Behavior. - Stefan Badelt; Christoph Flamm; Ivo L. Hofacker (Artif. Life, 2016)

Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks. - Yu-Ting Hsiao; Wei-Po Lee; Wei Yang; Stefan Müller 009; Christoph Flamm; Ivo L. Hofacker; Philipp Kügler (IEEE ACM Trans. Comput. Biol. Bioinform., 2016)

Chemical Graph Transformation with Stereo-Information. - Jakob Lykke Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (ICGT, 2017)

RNAblueprint: flexible multiple target nucleic acid sequence design. - Stefan Hammer; Birgit Tschiatschek; Christoph Flamm; Ivo L. Hofacker; Sven Findeiß (Bioinform., 2017)

An Intermediate Level of Abstraction for Computational Systems Chemistry. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2017)

Algorithmic Cheminformatics (Dagstuhl Seminar 17452). - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (Dagstuhl Reports, 2017)

Finding the K best synthesis plans. - Rolf Fagerberg; Christoph Flamm; Rojin Kianian; Daniel Merkle; Peter F. Stadler (J. Cheminformatics, 2018)

Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)

Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding. - Ronny Lorenz; Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (BIOINFORMATICS, 2020)

Efficient Algorithms for Co-folding of Multiple RNAs. - Ronny Lorenz; Christoph Flamm; Ivo L. Hofacker; Peter F. Stadler (BIOSTEC (Selected Papers), 2020)

Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases. - Waldeyr Mendes Cordeiro da Silva; Daniela P. de Andrade; Jakob L. Andersen; Maria Emília Telles Walter; Marcelo M. Brigido; Peter F. Stadler; Christoph Flamm (BSB, 2020)

Graph transformation for enzymatic mechanisms. - Jakob L. Andersen; Rolf Fagerberg; Christoph Flamm; Walter Fontana; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (Bioinform., 2021)

Defining Autocatalysis in Chemical Reaction Networks. - Jakob L. Andersen; Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2021)

EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates. - Esther Heid; Samuel Goldman; Karthik Sankaranarayanan; Connor W. Coley; Christoph Flamm; William H. Green Jr. (J. Chem. Inf. Model., 2021)

Characterizing Catalytic Mechanisms with Overlay Graphs. - Jakob L. Andersen; Rolf Fagerberg; Christoph Flamm; Walter Fontana; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (CoRR, 2022)

Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction. - Christoph Flamm; Julia Wielach; Michael T. Wolfinger; Stefan Badelt; Ronny Lorenz; Ivo L. Hofacker (Frontiers Bioinform., 2022)

What makes a reaction network "chemical"? - Stefan Müller 009; Christoph Flamm; Peter F. Stadler (J. Cheminformatics, 2022)

Representing Catalytic Mechanisms with Rule Composition. - Jakob L. Andersen; Rolf Fagerberg; Christoph Flamm; Walter Fontana; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (J. Chem. Inf. Model., 2022)

Generic Context-Aware Group Contributions. - Christoph Flamm; Marc Hellmuth; Daniel Merkle; Nikolai Nøjgaard; Peter F. Stadler (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)

Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381). - Sven Findeiß; Christoph Flamm; Yann Ponty (Dagstuhl Reports, 2022)

On the Realisability of Chemical Pathways. - Jakob L. Andersen; Sissel Banke; Rolf Fagerberg; Christoph Flamm; Daniel Merkle; Peter F. Stadler (ISBRA, 2023)

Automated Inference of Graph Transformation Rules. - Jakob L. Andersen; Akbar Davoodi; Rolf Fagerberg; Christoph Flamm; Walter Fontana; Juraj Kolcák; Christophe V. F. P. Laurent; Daniel Merkle; Nikolai Nøjgaard (CoRR, 2024)

Finding Thermodynamically Favorable Pathways in Reaction Networks using Flows in Hypergraphs and Mixed Integer Linear Programming. - Adittya Pal; Rolf Fagerberg; Jakob Lykke Andersen; Christoph Flamm; Peter Dittrich; Daniel Merkle (CoRR, 2024)

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. - Marcos E. González Laffitte; Klaus Weinbauer; Tieu-Long Phan; Nora Beier; Nico Domschke; Christoph Flamm; Thomas Gatter; Daniel Merkle; Peter F. Stadler (Symmetry, 2024)

KinPFN: Bayesian Approximation of RNA Folding Kinetics using Prior-Data Fitted Networks. - Dominik Scheuer; Frederic Runge; Jörg K. H. Franke; Michael T. Wolfinger; Christoph Flamm; Frank Hutter (ICLR, 2025)

Pathway Realizability in Chemical Networks. - Jakob L. Andersen; Sissel Banke; Rolf Fagerberg; Christoph Flamm; Daniel Merkle; Peter F. Stadler (J. Comput. Biol., 2025)

Finding Thermodynamically Favorable Pathways in Chemical Reaction Networks Using Flows in Hypergraphs and Mixed-Integer Linear Programming. - Adittya Pal; Rolf Fagerberg; Jakob Lykke Andersen; Christoph Flamm; Peter Dittrich; Daniel Merkle (J. Chem. Inf. Model., 2025)

SynTemp: Efficient Extraction of Graph-Based Reaction Rules from Large-Scale Reaction Databases. - Tieu-Long Phan; Klaus Weinbauer; Marcos E. González Laffitte; Yingjie Pan; Daniel Merkle; Jakob L. Andersen; Rolf Fagerberg; Christoph Flamm; Peter F. Stadler (J. Chem. Inf. Model., 2025)

Assembly in Directed Hypergraphs. - Christoph Flamm; Daniel Merkle; Peter F. Stadler (CoRR, 2025)