Christoph Flamm

Orcid: 0000-0001-5500-2415

Affiliations:
  • University of Vienna, Austria


According to our database1, Christoph Flamm authored at least 71 papers between 1997 and 2024.

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Bibliography

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.
Symmetry, September, 2024

Finding Thermodynamically Favorable Pathways in Reaction Networks using Flows in Hypergraphs and Mixed Integer Linear Programming.
CoRR, 2024

Automated Inference of Graph Transformation Rules.
CoRR, 2024

2023
On the Realisability of Chemical Pathways.
Proceedings of the Bioinformatics Research and Applications - 19th International Symposium, 2023

2022
Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381).
Dagstuhl Reports, September, 2022

Generic Context-Aware Group Contributions.
IEEE ACM Trans. Comput. Biol. Bioinform., 2022

Representing Catalytic Mechanisms with Rule Composition.
J. Chem. Inf. Model., 2022

What makes a reaction network "chemical"?
J. Cheminformatics, 2022

Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction.
Frontiers Bioinform., 2022

Characterizing Catalytic Mechanisms with Overlay Graphs.
CoRR, 2022

2021
EHreact: Extended Hasse Diagrams for the Extraction and Scoring of Enzymatic Reaction Templates.
J. Chem. Inf. Model., 2021

Defining Autocatalysis in Chemical Reaction Networks.
CoRR, 2021

Graph transformation for enzymatic mechanisms.
Bioinform., 2021

2020
Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases.
Proceedings of the Advances in Bioinformatics and Computational Biology, 2020

Efficient Algorithms for Co-folding of Multiple RNAs.
Proceedings of the Biomedical Engineering Systems and Technologies, 2020

Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding.
Proceedings of the 13th International Joint Conference on Biomedical Engineering Systems and Technologies (BIOSTEC 2020), 2020

2019
Chemical Transformation Motifs - Modelling Pathways as Integer Hyperflows.
IEEE ACM Trans. Comput. Biol. Bioinform., 2019

2018
Finding the K best synthesis plans.
J. Cheminformatics, 2018

2017
Algorithmic Cheminformatics (Dagstuhl Seminar 17452).
Dagstuhl Reports, 2017

An Intermediate Level of Abstraction for Computational Systems Chemistry.
CoRR, 2017

RNAblueprint: flexible multiple target nucleic acid sequence design.
Bioinform., 2017

Chemical Graph Transformation with Stereo-Information.
Proceedings of the Graph Transformation - 10th International Conference, 2017

2016
Practical Guidelines for Incorporating Knowledge-Based and Data-Driven Strategies into the Inference of Gene Regulatory Networks.
IEEE ACM Trans. Comput. Biol. Bioinform., 2016

Computational Design of a Circular RNA with Prionlike Behavior.
Artif. Life, 2016

Automatic Inference of Graph Transformation Rules Using the Cyclic Nature of Chemical Reactions.
Proceedings of the Graph Transformation - 9th International Conference, 2016

A Software Package for Chemically Inspired Graph Transformation.
Proceedings of the Graph Transformation - 9th International Conference, 2016

2015
Towards Optimal DNA-Templated Computing.
Int. J. Unconv. Comput., 2015

Support for Eschenmoser's Glyoxylate Scenario.
CoRR, 2015

2014
Generic strategies for chemical space exploration.
Int. J. Comput. Biol. Drug Des., 2014

Algorithmic Cheminformatics (Dagstuhl Seminar 14452).
Dagstuhl Reports, 2014

Memory-efficient RNA energy landscape exploration.
Bioinform., 2014

Atom mapping with constraint programming.
Algorithms Mol. Biol., 2014

50 Shades of Rule Composition - From Chemical Reactions to Higher Levels of Abstraction.
Proceedings of the Formal Methods in Macro-Biology - First International Conference, 2014

Towards an Optimal DNA-Templated Molecular Assembler.
Proceedings of the Fourteenth International Conference on the Simulation and Synthesis of Living Systems, 2014

2013
On the Complexity of Reconstructing Chemical Reaction Networks.
Math. Comput. Sci., 2013

Navigating the Chemical Space of HCN Polymerization and Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data.
Entropy, 2013

A novel method for the identification of synchronization effects in multichannel ECoG with an application to epilepsy.
Biol. Cybern., 2013

The Graph Grammar Library - A Generic Framework for Chemical Graph Rewrite Systems.
Proceedings of the Theory and Practice of Model Transformations, 2013

Automatic ictal HFO detection for determination of initial seizure spread.
Proceedings of the 35th Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2013

Barrier Trees for Metabolic Adjustment Landscapes.
Proceedings of the Twelfth European Conference on the Synthesis and Simulation of Living Systems: Advances in Artificial Life, 2013

Atom Mapping with Constraint Programming.
Proceedings of the Principles and Practice of Constraint Programming, 2013

2012
Inferring Chemical Reaction Patterns Using Rule Composition in Graph Grammars
CoRR, 2012

A physiologically motivated ECoG segmentation method for epileptic seizure onset zone detection.
Proceedings of the Annual International Conference of the IEEE Engineering in Medicine and Biology Society, 2012

Exploring Chemistry Using SMT.
Proceedings of the Principles and Practice of Constraint Programming, 2012

2011
Maximizing Output and Recognizing Autocatalysis in Chemical Reaction Networks is NP-Complete
CoRR, 2011

ViennaRNA Package 2.0.
Algorithms Mol. Biol., 2011

In Silico Evolution of Early Metabolism.
Artif. Life, 2011

2010
In Silico Evolution of Early Metabolism.
Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems, 2010

2009
A Topological Approach to Chemical Organizations.
Artif. Life, 2009

2D Projections of RNA Folding Landscapes.
Proceedings of the German Conference on Bioinformatics 2009, 2009

A Sequence-to-Function Map for Ribozyme-Catalyzed Metabolisms.
Proceedings of the Advances in Artificial Life. Darwin Meets von Neumann, 2009

2008
Noisy: Identification of problematic columns in multiple sequence alignments.
Algorithms Mol. Biol., 2008

Functional Evolution of Ribozyme-Catalyzed Metabolisms in a Graph-Based Toy-Universe.
Proceedings of the Computational Methods in Systems Biology, 6th International Conference, 2008

Using the RNA sequence-to-structure map for functional evolution of ribozyme catalyzed artificial metabolisms.
Proceedings of the Eleventh International Conference on the Synthesis and Simulation of Living Systems, 2008

Visualization of Barrier Tree Sequences Revisited.
Proceedings of the Visualization in Medicine and Life Sciences., 2008

2007
Saddles and Barrier in Landscapes of Generalized Search Operators.
Proceedings of the Foundations of Genetic Algorithms, 9th International Workshop, 2007

2006
Visualization of Barrier Tree Sequences.
IEEE Trans. Vis. Comput. Graph., 2006

Algebraic comparison of metabolic networks, phylogenetic inference, and metabolic innovation.
BMC Bioinform., 2006

The SBML ODE Solver Library: a native API for symbolic and fast numerical analysis of reaction networks.
Bioinform., 2006

Partition function and base pairing probabilities of RNA heterodimers.
Algorithms Mol. Biol., 2006

Visualization of Lattice-Based Protein Folding Simulations.
Proceedings of the 10th International Conference on Information Visualisation, 2006

2005
Evolutionary patterns of non-coding RNAs.
Theory Biosci., 2005

Explicit Collision Simulation of Chemical Reactions in a Graph Based Artificial Chemistry.
Proceedings of the Advances in Artificial Life, 8th European Conference, 2005

CelloS: A Multi-level Approach to Evolutionary Dynamics.
Proceedings of the Advances in Artificial Life, 8th European Conference, 2005

2004
Counterexamples in Chemical Ring Perception.
J. Chem. Inf. Model., 2004

2003
A Graph-Based Toy Model of Chemistry.
J. Chem. Inf. Comput. Sci., 2003

Barrier Trees on Poset-Valued Landscapes.
Genet. Program. Evolvable Mach., 2003

Design of multi-stable nucleid acid sequences.
Proceedings of the German Conference on Bioinformatics, 2003

Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting.
Proceedings of the Advances in Artificial Life, 7th European Conference, 2003

1999
RNA <i>In Silico</i> The Computational Biology of RNA Secondary Structures.
Adv. Complex Syst., 1999

1997
Density of States, Metastable States, and Saddle Points: Exploring the Energy Landscape of an RNA Molecule.
Proceedings of the 5th International Conference on Intelligent Systems for Molecular Biology, 1997


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