> publications <
List of Publications
Google
scholar profile
Scopus Author ID 7004463099
ORCID
0000-0001-5500-2415
![[ORCID iD QR Code]](/~xtof/pic/ORCID-QRCode.png)
Total number of publications: 109
In Journals: 73
In Proceedings: 31
In Books: 2
In Reports: 3
10
# .
o . *
f . * * **
P . * * * *** *
u 5 * * * *** *
b . ** **** **** ** ***
l . ********************* *
s . * ********************* *
1 *****************************
78901234567890123456789012345
9 0 111111111122222
9 0 0 0
1 2 2 2
year
All papers are copyrighted by the authors; revised versions that appeared in print are copyrighted by the respective publisher. Downloadable papers are preprint versions which usually don't correspond exactly to the revised versions published. If you would like to use all or a portion of any paper, please contact the author(s).
Have a look at the TBI preprint server.
Submitted or Accepted
Adittya Pal, Rolf Fagerberg, Jakob Lykke Andersen,
Christoph Flamm, Daniel Merkle
A Thermodynamics based search for Pathways in Reaction
Networks using Mixed Integer Linear Programming.
submitted 12.2024 to CPAIOR 2025
Christoph Flamm, Stefan Müller, Peter F Stadler
Every atom-atom map can be explained by electron pushing diagrams.
submitted 11.2023 to Discrete Mathematical Chemistry
[arXiv:2311.13492]
[math.CO]
Published
2025
Tieu-Long Phan, Klaus Weinbauer, Marcos
E Gonzalez Laffitte, Yingjie Pan, Daniel Merkle, Jakob
L Andersen, Rolf Fagerberg, Christoph Flamm, Peter F Stadler
SynTemp: Efficient Extraction of Graph-Based Reaction Rules
from Large-Scale Reaction Databases.
J Chem Inf Model XX:XXXX, 2025
[doi:10.1021/acs.jcim.4c01795]
[ChemRxiv:chemrxiv-2024-tkm36]
Dominik Scheuer, Frederic Runge, Jörg KH Franke,
Michael T Wolfinger, Christoph Flamm, Frank Hutter
KinPFN: Bayesian Approximation of RNA Folding Kinetics using Prior-Data Fitted Networks.
13th International Conference on Learning Representations
(ICLR) 2025
[OpenReview.net:E1m5yGMOiV]
[bioRxiv:2024.10.15.618378]
Christoph Flamm, Daniel, Merkle, Peter F Stadler
Computation in chemical graph rewriting networks.
Journal of Physics: Complexity, 6(1):015014, 2025
[doi:10.1088/2632-072X/adb7b1]
2024
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, 16:1217, 2024
[doi:10.3390/sym16091217]
2023
Jakob L Andersen, Sissel Banke, Rolf Fagerberg,
Christoph Flamm, Daniel Merkle, Peter F Stadler
On the Realisability of Chemical Pathways.
LNBI 14348, pp 409-419, 2023
[doi:10.1007/978-981-99-7074-2_32]
Sven Findeiß, Christoph Flamm, Yann Ponty
Rational Design of RiboNucleic Acids (Dagstuhl Seminar 22381)
Dagstuhl Reports, 12(9):121–149, 2023
[doi:10.4230/DagRep.12.9.121]
Nino Lauber, Ondřej Ticháček, Rudra Bose, Christoph
Flamm, Luca Leuzzi, T-Y Dora Tang, Kepa Ruiz-Mirazo, Daniele De Martino
Statistical mechanics of biomolecular condensates via cavity methods.
iScience 26:106300, 2023
[doi:10.1016/j.isci.2023.106300]
2022
Jakob L Andersen, Rolf Fagerberg, Christoph Flamm, Walter Fontana,
Juri Kolčák, Christophe VFP Laurent, Daniel Merkle, Nikolai Nøjgaard
Representing catalytic mechanisms with rule
composition.
J Chem Inf Model 62(22):5513-5524, 2022
[doi:10.1021/acs.jcim.2c00426]
[arXiv:2201.04515]
[cs.DM, physics.chm-ph, q-bio.MN]
Stefan Müller, Christoph Flamm, Peter F Stadler
What makes a reaction network "chemical"?
J Cheminfo 14:63, 2022
[doi:10.1186/s13321-022-00621-8]
[arXiv:2201.01646]
[q-bio.MN]
Christoph Flamm, Julia Wielach, Michael T
Wolfinger, Stefan Badelt, Ronny Lorenz, Ivo L Hofacker
Caveats to deep learning approaches to RNA secondary structure prediction.
Front Bioinf 2:835422, 2022
[doi:10.3389/fbinf.2022.835422]
[bioRxiv 2021.12.14.472648]
Christoph Flamm, Marc Hellmuth, Daniel Merkle,
Nikolai Nøjgaard, Peter F Stadler
Generic Context-Aware Group Contributions.
IEEE/ACM Transactions on Computational Biology and
Bioinformatics 19:429-442 (2022)
[doi:10.1109/TCBB.2020.2998948]
2021
Esther Heid, Samuel Goldman, Karthik
Sankaranarayanan, Connor W Coley, Christoph Flamm, William H Green
EHreact: Extended Hasse diagrams for the extraction and scoring of enzymatic reaction templates.
J Chem Inf Model Publication Date:September 29, 2021 Online ahead of print.
[doi:10.1021/acs.jcim.1c00921]
Jakob L Andersen, Rolf Fagerberg, Christoph Flamm,
Walter Fontana, Juraj Kolčák, Christophe VFP Laurent,
Daniel Merkle and Nikolai Nøjgaard
Graph Transformation for Enzymatic Mechanisms.
Bioinformatics 37(1):i392-i400 (2021)
[doi:10.1093/bioinformatics/btab296]
[arXiv:2102.03292]
[q-bio.MN]
Nino Lauber, Christoph Flamm, Kepa Ruiz-Mirazo
Minimal metabolism: a key concept to investigate the
origins and nature of biological systems.
BioEssays, 43:2100103 (2021)
[doi:10.1002/bies.202100103]
Ronny Lorenz, Christoph Flamm, Ivo L Hofacker Peter
F Stadler
Efficient Algorithms for Co-folding of Multiple RNAs.
In: Ye X. et al. (eds) Biomedical Engeneering Systems and
Technologies. BIOSTEC 2020. Communications in Computer and
Information Science, vol 1400, pp 193-214, 2021
ISBN: 978-3-030-72378-1
[doi:10.1007/978-3-030-72379-8_10]
2020
Waldeyr Mendes Cordeiro da Silva, Daniela P. de
Andrade, Jakob L. Andersen, Maria Emília M. T. Walter, Marcelo
Brigido, Peter F. Stadler, Christoph Flamm
Computational Simulations for Cyclizations Catalyzed by Plant Monoterpene Synthases.
In: Advances in Bioinformatics and Computational Biology pp 247-258, 2020
ISBN: 978-3-030-65775-8
[doi:10.1007/978-3-030-65775-8_23]
Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
Defining Autocatalysis in Chemical Reaction Networks.
(Preprint BIOINF 20-004)
J Sys Chem 8:121-133 (2020).
Keating, Sarah M et al (+140 Coauthors)
SBML Level 3: an extensible format for the exchange and reuse of biological models.
Mol Sys Biol 16(8):e9110 (2020).
[10.15252/msb.20199110]
Ronny Lorenz Christoph Flamm, Ivo L Hofacker Peter
F Stadler
Efficient Computation of Base-pairing Probabilities in Multi-strand RNA Folding.
In: n Proceedings of the 13th International Joint Conference on
Biomedical Engineering Systems and Technologies (BIOSTEC 2020) Vol 3,
pp 23-31, 2020
ISBN: 978-989-758-398-8
[doi:10.5220/0008916600230031]
2019
Jakob L Andersen, Christoph Flamm, Daniel Merkle,
Peter F Stadler
Information Processing in Chemical Systems.
In: The Energetics of Computing in Life and Machines, SFI
Press, 2019
[ISBN 1947864076]
Waldeyr MC da Silva, Jakob L Andersen,
Maristela Holanda, Maria Emília MT Walter, Marcelo M Brigido,
Peter F Stadler, Christoph Flamm
Exploring plant sesquiterpene diversity by generating
chemical networks.
(doi:10.3390/pr7040240)
(Preprints 2019, 2019030015)
Processes 7:240 2019
[Pdf]
Jakob L Andersen, Christoph Flamm, Daniel Merkle,
Peter F Stadler
Chemical Transformation Motifs — Modelling Pathways
as Integer Hyperflows.
(doi:10.1109/TCBB.2017.2781724)
IEEE/ACM Trans Comp Biol
Bioinf 16(2):510-523 (2019).
[arXiv:1712.02594]
[q-bio-MN]; [cs.DM]
2018
Michael T Wolfinger, Christoph Flamm, Ivo L Hofacker
Efficient computation of co-transcriptional RNA-ligand interaction dynamics.
(doi:10.1016/j.ymeth.2018.04.036)
Methods 143:70-76 (2018).
[bioRxiv:24850]
Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F Stadler
Rule Composition in Graph Transformation Models of
Chemical Reactions.
MATCH 80(3):661-704 (2018)
[PDF]
Jakob L Andersen, Rolf Fagerberg, Christoph Flamm,
Rojin Kianian, Daniel Merkle, Peter F Stadler
Towards Mechanistic Prediction of Mass Spectra Using Graph
Transformation.
MATCH 80(3):705-731 (2018)
[PDF]
Sven Findeiß, Stefan Hammer, Michael T
Wolfinger, Felix Kühnla, Christoph Flamm, Ivo L Hofacker
In silico design of ligand triggered RNA switches.
(doi:10.1016/j.ymeth.2018.04.003)
Methods 143:90-101 (2018).
Rolf Fagerberg, Christoph Flamm, Rojin Kianian,
Daniel Merkle, Peter F Stadler
Finding the K Best Synthesis Plans.
J Cheminfo 10:19 (2018)
(doi:10.1186/s13321-018-0273-z)
Jakob L Andersen, Christoph Flamm, Daniel Merkle,
Peter F Stadler
Algorithmic Cheminformatics (Dagstuhl Seminar 17452).
(doi:10.4230/DagRep.7.11.28)
Dagstuhl Report 7(11):28-45 (2018)
2017
Bernhard C Thiel, Christoph Flamm, Ivo L Hofacker
RNA structure prediction: from 2D to 3D
(doi:10.1042/ETLS20160027)
Emergent Topics in Life
Science 1(3):275-285
(2017).
Stefan Hammer, Birgit Tschiatschek, Christoph
Flamm, Ivo L. Hofacker, Sven Findeiß
RNAblueprint: flexible multiple target nucleic acid sequence design
(doi:10.1093/bioinformatics/btx263)
Bioinformatics 33(18):2850-2858 (2017).
Jakob L Andersen, Christoph Flamm, Daniel Merkle,
Peter F Stadler
Chemical Graph Transformation with Stereo-Information.
(doi:10.1007/978-3-319-61470-0_4)
In: de Lara J., Plump D. (eds) Graph Transformation. ICGT 2017.
Springer, Cham.
LNCS 10373:54-69 (2017).
Jakob L Andersen, Christoph Flamm, Daniel Merkle,
Peter F Stadler
An Intermediate Level of Abstraction for Computational
Systems Chemistry.
(doi:10.1098/rsta.2016.0354)
Royal Soc Phil Trans A 375(2109):20160354 (2017)
[arXiv:1701.09097]
[q-bio.MN]; [cs.FL]
2016
Stefan Badelt, Christoph Flamm, Ivo L Hofacker
Computational Design of a Circular RNA with Prionlike
Behavior
(doi:10.1162/ARTL_a_00197)
Artificial Life 22(2):172-184 (2016)
Christoph Flamm, Daniel Merkle, Peter F Stadler, Uffe Thorsen
Automatic Inference of Graph Transformation Rules: Using the Cyclic Nature of Chemical Reactions.
(doi:10.1007/978-3-319-40530-8_13)
LNCS 9761:206-222 (2016)
accepted at ICGT 2016
[arXiv:1604.06379] [cs.DM]
Jakob L Andersen, Christoph Flamm, Daniel Merkle,
Peter F Stadler
A Software Package for Chemically Inspired Graph Transformation.
(doi:10.1007/978-3-319-40530-8_5)
LNCS 9761:73-88 (2016)
accepted at ICGT
2016
[arXiv:1603.02481] [cs.FL]
2015
Jakob L Andersen, Christoph Flamm Martin M Hanczyc,
Daniel Merkle
Towards Optimal DNA-Templated Computing.
(doi:10.7551/978-0-262-32621-6-ch090)
Int J Unconv Comput 11(3-4):185-203 (2015)
Yu-Ting Hsiao, Wei-Po Lee, Wei Yang, Stefan
Müller, Christoph Flamm, Ivo L Hofacker, Philipp Kügler
Practical Guidlines for Incorporating Knowledge-Based and
Data-Driven Strategies into the Inference of Gene Regulatory Networks.
(doi:10.1109/TCBB.2015.2465954)
IEEE Trans Comp Biol Bioinf PP(99):1-13 (2015)
Jakob L. Andersen, Christoph Flamm, Daniel Merkle,
Peter F. Stadler.
In silico Support for Eschenmoser's Glyoxylate
Scenario.
(doi:10.1002/ijch.201400187)
Israel Journal of Chemistry 55(8):919-933 (2015)
Sonja Petkovic, Stefan Badelt, Stephan Block,
Christoph Flamm, Mihaela Delcea, Ivo L Hofacker, Sabine Müller.
Sequence-controlled RNA self-processing: computational
design, biochemical analysis, and visualization by ATM.
(doi:10.1261/rna.047670.114)
RNA 21:1-13 (2015)
Stefan Badelt, Stefan Hammer, Christoph Flamm, Ivo
L Hofacker.
Thermodynamic and kinetic folding of Riboswitches.
(doi:10.1016/bs.mie.2014.10.060)
Methods in Enzymology Volume 553, pp 193-213 (2015)
Wolfgang Banzhaf, Christoph Flamm, Daniel Merkle,
Peter F Stadler
Algorithmic Cheminformatics (Dagstuhl Seminar 14452).
(doi:10.4230/DagRep.4.11.22)
Dagstuhl Report 4(11):22-39 2015
2014
Martin Mann, Feras Nahar, Norah Schnorr, Rolf Backofen, Peter F Stadler and Christoph Flamm
Atom mapping with constraint programming
(doi:10.1186/s13015-014-0023-3)
Algo Mol Biol 9:23 (2014)
Jakob L Andersen, Christoph Flamm, Daniel Merkle,
Peter F Stadler
50 Shades of Rule Composition:From Chemical Reactions to Higher Levels of Abstraction
(doi:10.1007/978-3-319-10398-3_9)
In: Proceedings of the 1st Intrnational Conference on Formal
Methods in Macro-Biology
(FMMB
2014). François Fages and Carla Piazza (Eds). Springer, LNCS 8738, pp 117-135, (2014).
[Abstract]
[Pdf]
Jakob L Andersen, Christoph Flamm, Martin M
Hanczyc, Daniel Merkle
Towards an Optimal DNA-Templated Molecular Assembler.
(doi:10.7551/978-0-262-32621-6-ch090)
In: Proceedings of the 14th International Conference on
the Synthesis and Simulation of Living Systems
(ALIFE 14).
Hiroki Sayama, John Rieffel, Sebastian Risi, René Doursat and Hod
Lipson (Eds). MIT Press, pp 557-564, (2014)
[Abstract]
[Pdf]
Stefan Badelt, Christoph Flamm, Ivo L Hofacker
Computational design of a circular RNA with prion-like
behaviour.
(doi:10.7551/978-0-262-32621-6-ch091)
In: Proceedings of the 14th International Conference on
the Synthesis and Simulation of Living Systems
(ALIFe 14).
Hiroki Sayama, John Rieffel, Sebastian Risi, René Doursat and Hod
Lipson (Eds.). MIT Press, pp 565-568, (2014)
[Abstract]
[Pdf]
Martin Mann, Marcel Kucharìk, Christoph
Flamm, Michael T Wolfinger
Memory efficient RNA energy landscape exploration.
(doi:10.1093/bioinformatics/btu337)
Bioinformatics 30(18):2584-2591 (2014)
[Abstract]
arXiv:1404.0270 [q-bio.BM]
Christoph Flamm, Bärbel MR Stadler, Peter F
Stadler
Generalized Topologies: Hypergraphs, Chemical Reactions
and Biological Evolution.
(doi:10.1016/B978-1-68108-053-6.50013-2)
Ebook "Advances in Mathematical Chemistry and Applications", Subash
C Basak and Guillermo Restrepo and Jose L Villaveces (eds.),
Bentham Science Publisher, Vol 2, Chapter 13, pp. 270-297 (2014)
[Abstract]
[PDF]
Jakob L Andersen, Christoph Flamm, Daniel Merkle, Peter F
Stadler
Generic Strategies for Chemical Space Exploration.
(doi:10.1504/IJCBDD.2014.061649)
Int J Comp Biol Drug Des 7(2/3):225-258 (2014)
arXiv:1302.4006 [cs.FL]
2013
Rolf Fagenberg, Christoph Flamm, Daniel Merkle,
Philipp Peters, Peter F Stadler
On the Complexity of Reconstructing Chemical Reaction
Networks.
(doi:10.1007/s11786-013-0160-y)
Math Comput Sci 7(3), 275-292 (2013)
[Abstract]
arXiv:1309.7198 [cs.CC]
Martin Mann, Feras Nahar, Heinz Ekker, Rolf
Backofen, Peter F Stadler, Christoph Flamm
Atom Mapping with Constraint Programming.
(doi:10.1007/978-3-642-40627-0_59)
In: Proceedings of the 19th International Conference on Principles
and Practice of Constraint Programming
(CP 2013). Christian Schulte
(ed.), Springer, LNCS 8124, pp 805-822, (2013).
[Abstract]
[PDF]
Christian Höner zu Siederdissen, Stefan
Hammer, Ingrid Abfalter, Ivo L Hofacker, Christoph Flamm, Peter F
Stadler
Computational Design of RNAs with Complex Energy
Landscapes.
(doi:10.1002/bip.22337)
Biopolymers 99(12):1124-1136 (2013)
[Abstract]
[PDF]
Christoph Flamm, Chris Hemmingsen, Daniel Merkle
Barrier trees for metabolic adjustment landscapes.
(doi:10.7551/978-0-262-31709-2-ch175)
In: Proceedings of the 12th European Conference on the Synthesis
and Simulation of Living systems,
(ECAL 2013).
Liò, Pietro and Miglino, Orazio and Nicosia, Giuseppe and
Nolfi, Stefano and Pavone, Mario (eds), The MIT Press, Advances in
Artifical Life, pp 1151-1158, (2013).
[Abstract]
[PDF]
Jakob L Andersen, Tommy Andersen, Christoph Flamm,
Martin Hanczyc, Daniel Merkle, Peter F Stadler
Navigating the Chemical Space of HCN Polymerization and
Hydrolysis: Guiding Graph Grammars by Mass Spectrometry Data.
(doi:10.3390/e15104066)
Entropy 15(10):4066-4083
[Abstract]
[PDF]
Martin Mann, Heinz Ekker, Christoph Flamm
The Graph Grammar Library - a generic framework
for chemical graph rewrite systems.
(doi:10.1007/978-3-642-38883-5_5)
In: Proceedings of the International Conference on Model
Transformation (ICMT 2013), D. Varro and K. Duddy and
G. Kappel (eds), Springer-Verlag Berlin Heidelberg, LNCS
7909, pp. 52-53, (2013).
[Abstract]
[Pdf]
arXiv:1304.1356 [cs.MS]
Jakob L Andersen, Christoph Flamm, Daniel Merkle,
Peter F Stadler
Inferring chemical reaction patterns using rule composition
in graph grammars.
(doi:10.1186/1759-2208-4-4)
J Sys Chem 4:4 (2013)
[Abstract]
[PDF]
arXiv:1208.3153 [cs.DM]
2012
Fabian Amman, Christoph Flamm , Ivo L Hofacker
Modelling Translation Initiation under the Influence of
sRNA.
(doi:10.3390/ijms131216223)
Int J Mol Sci 13(12):16223-16240 (2012)
Martin Mann, Heinz Ekker, Peter F Stadler,
Christoph Flamm
Atom Mapping with Constraint Programming.
In: Proceedings of the Workshop on Constraint Based Methods for
Bioinformatics
(WCP12),
R. Backofen and S. Will (eds.), pp. 23-29, 2012
[Abstract]
[PDF]
Rolf Fagerberg, Christoph Flamm, Daniel Merkle,
Philipp Peters
Exploring Chemistry Using SMT.
(doi:10.1007/978-3-642-33558-7_64)
In: Proceedings of the 18th International Conference on Principles
and Practice of Constraint Programming
(CP 2012), M. Milano
(eds.), Springer-Verlag Berlin Heidelberg,
LNCS 7514, pp. 900-915, (2012)
[Abstract]
[PDF]
Jakob L Andersen, Christoph Flamm, Daniel Merkle,
Peter F Stadler
Maximizing Output and Recognizing Autocatalysis in Chemical
Reaction Networks is NP-Complete.
(doi:10.1186/1759-2208-3-1)
J Sys Chem 3:1 (2012)
[Abstract]
[PDF]
2011
Ronny Lorenz, Stefan H Bernhart, Christian
Höner zu Siederdissen, Hakim Tafer, Christoph Flamm, Peter F
Stadler, Ivo L Hofacker
ViennaRNA Package 2.0.
(doi:10.1186/1748-7188-6-26)
Algorithms Mol Biol 6:26 (2011)
Noriko Hiroi, James Lu, Keisuke Iba, Akito Tabira,
Shuji Yamashita, Yasunori Okada, Christoph Flamm, Kotaro Oka,
Gottfried Köhler and Akira Funahashi
Physiological environment induce quick response — slow
exhaustion reactions.
(doi:10.3389/fphys.2011.00050)
Front Physio 2:50 (2011)
Alexander Ullrich, Markus Rohrschneider, Gerik
Scheuermann, Peter F. Stadler, Christoph Flamm
In Silico Evolution of Early Metabolism.
(doi:10.1162/artl_a_00021)
Artifical Life 17(2):87-108 (2011)
2010
Christoph Flamm, Alexander Ullrich, Heinz Ekker,
Martin Mann, Daniel Högerl, Markus Rohrschneider, Sebastian Sauer,
Gerik Scheuermann, Konstantin Klemm, Ivo L. Hofacker, Peter
F. Stadler
Evolution of Metabolic Networks: A Computational Framework.
(doi:10.1186/1759-2208-1-4)
J Sys Chem 1:4 (2010)
[Abstract]
[PDF]
[MP4]
Alexander Ullrich, Christoph Flamm, Markus
Rohrschneider, Peter F. Stadler
In silico Evolution of early Metabolism
(Article)
In: Proceedings of Artificial Life XII, Proceedings of the 12th
International Conference on the Synthesis and Simulation of Living
Systems (Alife 12) H.
Fellermann et al. (Eds.); MIT press;
ISBN-13 978-0-262-29075-3 pp. 57-64 (2010).
[PDF]
Ivo L Hofacker, Christoph Flamm, Christian Heine,
Michael T Wolfinger, Gerik Scheuermann, Peter F Stadler
BarMap: RNA Folding on Dynamic Energy Landscapes.
(doi:10.1261/rna.2093310)
RNA 16:1308-1316 (2010)
[Abstract]
[PDF]
2009
Heinz W Engl, Christoph Flamm, Philipp Kügler,
James Lu, Stefan Müller, Peter Schuster
Inverse Problems in Systems Biology.
Inverse Problems
25 123014 (2009)
(doi:10.1088/0266-5611/25/12/123014)
[Abstract]
[PDF]
Alexander Ullrich, Christoph Flamm
A Sequence-to-Function Map for Ribozyme-catalyzed
Metabolisms.
In: Proceedings of the European Conference on Artificial Life
(ECAL
2009)
LNCS in press 2009.
[Abstract]
[PDF]
Ronny Lorenz, Christoph Flamm, Ivo L. Hofacker
2D projections of RNA folding landscapes.
In: Proceedings of German Conference on Bioinformatics
( GCB 2009), I. Grosse et
al. (Eds.); Gesellschaft für Informatik, Bonn;
ISBN 978-3-88579-251-2;
Lecture Notes in Informatik 157:11-20, 2009.
[Abstract]
[PDF]
Gil Benkö, Florian Centler, Peter Dittrich,
Christoph Flamm, Bärbel M. R. Stadler and Peter F. Stadler
A Topological Approach to Chemical Organizations.
Artificial Life,
15(1):71-88 (2009)
(doi:10.1162/artl.2009.15.1.15105)
[Abstract]
[PDF]
2008
Alexander Ullrich, Christoph Flamm
Functional Evolution of Ribozyme-Catalyzed
Metabolisms in a Graph-Based Toy-Universe
In: Proceedings of the 6th International Conference on
Computational Methodes in Systems Biology
(CMSB 2008)
S. Istrail et al. (Eds.); Springer-Verlag Berlin Heidelberg,
LNBI 5307, pp. 28-43, 2008
(doi:10.1007/978-3-540-88562-7_7)
James Lu, Stefan Müller, Rainer Machne,
Christoph Flamm
SBML ODE Solver Library: Extensions for Inverse
Analysis.
In: Fifth International Workshop on Computational Systems Biology
WCSB 2008 June 11- 13, Leipzig, Germany / M. Ahdesmaki (Ed.)
Tampere International Center for Signal Processing Series
#41, pp. 93-96, 2008.
[PDF]
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.,
3:7 (2008)
(doi:10.1186/1748-7188-3-7)
Konstantin Klemm, Christoph Flamm, Peter F. Stadler
Funnels in Energy Landscapes.
Eur. J. Phys. B,
63:3, 387-391 (2008)
(doi:10.1140/epjb/e2008-00136-7)
[Abstract]
[PDF]
Christoph Flamm and Ivo L. Hofacker
Beyond Energy Minimization: Approaches to the
kinetic Folding of RNA.
Chemical Monthly,
139:4, 447-457 (2008)
(doi:10.1007/s00706-008-0895-3)
[Abstract]
[PDF]
Michael Geis, Christoph Flamm, Michael T. Wolfinger,
Andrea Tanzer, Ivo L. Hofacker, Martin Middendorf, Christian Mandl,
Peter F. Stadler and Caroline Thurner
Folding Kinetics of Large RNAs.
J. Mol. Biol.,
379:1, 160-173 (2008)
(doi:10.1016/j.jmb.2008.02.064)
[Abstract]
[PDF]
2007
Christoph Flamm, Ivo L. Hofacker, Bärbel M. R. Stadler and
Peter F. Stadler
Saddles and Barrier in Landscapes of Generalized Search
Operators.
In: Proceedings of the 9th International Workshop of Foundations of
Genetic Algorithms (FOGA
IX) C. Stephens et al, (eds); Springer-Verlag Berlin
Heidelberg, LNCS 4436/2007, pp. 194-212, 2007
(doi:10.1007/978-3-540-73482-6_11)
[Abstract]
[PDF]
Christoph Flamm, Lukas Endler, Stefan Müller,
Stefanie Widder, and Peter Schuster
A minimal and self-consistent in silico cell
model based on macromolecular interactions.
Philos. Trans. R. Soc. Lond. B Biol. Sci.,
362, 1831-1839 (2007)
(doi:10.1098/rstb.2007.2075)
[Abstract]
[Postscript]
[PDF]
The Athanasius F. Bompfünewerer Consortium:
Rolf Backofen, Stephan H. Bernhart, Christoph Flamm, Claudia Fried,
Guido Fritzsch, Jörg Hackermüller, Jana Hertel, Ivo L.
Hofacker, Kristin Missal, Axel Mosig, Sonja J. Prohaska, Dominic
Rose, Peter F. Stadler, Andrea Tanzer, Stefan Washietl and
Sebastian Will
RNAs Everywhere: Genome-Wide Annotation of Structured
RNAs.
J. Exp. Zool. (Mol. Devel. Evol.),
308B:1, 1-25 (2007)
(doi:10.1002/jez.b.21130)
[Abstract]
[Postscript]
[PDF]
The ENCODE Consortium
Identification and analysis of functional elements in 1% of
the human genome by the ENCODE pilot project.
Nature,
447, 799-816 (2007)
(doi:10.1038/nature05874)
2006
Stefan Müller, Josef Hofbauer, Lukas Endler,
Christoph Flamm, Stefanie Widder and Peter Schuster
A Generalized Model of the Repressilator.
J. Math. Biol., 53:6, 905-937 (2006)
(doi:10.1007/s00285-006-0035-9)
[Abstract]
[Postscript]
[PDF]
Sebastian Pötzsch, Gerik Scheuermann, Michael
T. Wolfinger, Christoph Flamm, Peter F. Stadler
Visualization of Lattice-Based Protein Folding
Simulations.
V'06: Proceedings of the Conference on Information Visualization:
89-94 (2006) IEEE Computer Society, Washington, DC, USA
(doi:10.1109/IV.2006.127)
[PDF]
Christian Heine, Gerik Scheuermann, Christoph
Flamm, Ivo L. Hofacker and Peter F. Stadler
Visualization of Barrier Tree Sequences.
IEEE Trans. Vis. Comp. Graphics 12:5 781-788 (2006)
(doi:10.1109/TVCG.2006.196)
[PDF]
Jord H.A. Nagel, Christoph Flamm, Ivo L. Hofacker,
K. Franke M.H. de Smit, Peter Schuster, and Cees W.A. Pleij
Structural parameters affecting the kinetics of RNA
hairpin formation.
Nucl. Acids. Res.,
34:12, 3568-3576 (2006)
(doi:10.1093/nar/gkl445)
[Abstract]
[PDF]
Rainer Machne, Andrew Finney, Stefan Müller,
James Lu, Stefanie Widder and Christoph Flamm
The SBML ODE Solver Library: a native API for symbolic and
fast numerical analysis of reaction networks.
Bioinformatics, 22:11, 1406-1407 (2006)
(doi:10.1093/bioinformatics/btl086)
[Abstract]
[Postscript]
[PDF] [Software]
Stephan Bernhart, Hakim Tafer, Ulrike
Mückstein, Christoph Flamm, Peter F. Stadler and Ivo L.
Hofacker
Partition Function and Base Pairing Probabilities of RNA
Heterodimers.
Alg.Mol.Biol., 1:3 (2006)
(doi:10.1186/1748-7188-1-3)
[Abstract]
[Postscript]
[PDF] [Software]
Christian Forst, Christoph Flamm, Ivo L. Hofacker
and Peter F. Stadler
Algebraic Comparison of Metabolic Networks, Phylogenetic
Inference, and Metabolic Innovation.
BMC Bioinformatics, 7:67 (2006)
(doi:10.1186/1471-2105-7-67)
[Abstract]
[Postscript]
[PDF] [Software]
Jana Hertel, Manuela Lindemeyer, Kristin Missal,
Claudia Fried, Andrea Tanzer, Christoph Flamm, Ivo L. Hofacker,
Peter F. Stadler, and The Students of Bioinformatics Computer Labs
2004 and 2005: Sten Heinze, Alexander "muppet" Donath, Sven
Findeß, Stephanie Keller, Kevin Peter, Julian Jöris,
Jokab Mühmel, Marco Dienelt (in Leipzig), Martina Hödl,
Bernhard Wurzinger, Camille Stephan-Otto Attolini, Ulrich Omasits,
Sebastian Krüttner, Regina Anzengruber, Daniela Lenek, Gregor
Neumayr, Reinhard Wohlfart (in Vienna).
The Expansion of the Metazoan MicroRNA
Repertoire.
BMC Genomics, 7:25 (2006)
(doi:10.1186/1471-2164-7-25)
[Abstract]
[Postscript]
[PDF] [Supplementary
Material]
2005
Gil Benkö, Christoph Flamm and Peter F.
Stadler
Explicit Collision Simulation of Chemical Reactions in a
Graph Based Artificial Chemistry.
In: Proceedings of the 8th European Conference on Artifical
Life
(ECAL 2005) M. Capcarrere et
al. (Eds.); Springer-Verlag Berlin Heidelberg, LNAI 3630, pp.
725-733, 2005
(doi:10.1007/11553090_73)
[Abstract]
[Postscript]
[PDF]
Camille Stephan-Otto Attolini, Peter F. Stadler
and Christoph Flamm
CelloS: a Multi-level Approach to
Evolutionary Dynamics.
In: Proceedings of the 8th European Conference on Artifical
Life
(ECAL 2005) M. Capcarrere et
al. (Eds.); Springer-Verlag Berlin Heidelberg, LNAI 3630, pp.
500-509, 2005
(doi:10.1007/11553090_51)
[Abstract]
[Postscript]
[PDF] [Supplements]
Gil Benkö, Christoph Flamm and Peter F.
Stadler
The ToyChem Package: A Computational Toolkit
Implementing a Realistic Artificial Chemistry Model.
(unpublished Technical Note)
[Abstract]
[Postscript]
[PDF]
Athanasius F. Bompfünewerera, 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 and Christina Witwer
Evolutionary patterns of non-coding RNAs.
(doi:10.1016/j.thbio.2005.01.002)
Theor. Biosci., 123, 301-369 (2005)
[abstract]
[Postscript]
[PDF]
2004
Albert Weixlbaumer, Andreas Werner, Christoph
Flamm,
Eric Westhof and Renée Schroeder
Determination of Thermodynamic Parameters for HIV-1 DIS
Type Loop-Loop Kissing Complexes.
Nucl. Acids Res., 32, 5126-5133
(2004)
[abstract]
[PDF]
Christoph Flamm, Ivo L. Hofacker, and Peter F.
Stadler
Computational Chemistry with RNA Secondary
Structures.
Kemija u indistriji, 53, 315-322
(2004)
[abstract]
[Postscript]
[PDF]
Michael T. Wolfinger, W. Andreas Svrcek-Seiler,
Christoph Flamm,
Ivo L. Hofacker, and Peter F. Stadler
Efficient computation of RNA folding dynamics.
J. Phys. A: Math. Gen., 37, 4731-4741
(2004)
[abstract]
[Postscript]
[PDF]
Sonja Prohaska, Claudia Fried, Christoph Flamm,
Günter P. Wagner
and Peter F. Stadler
Surveying Phylogenetic Footprints in Large Gene Clusters:
Applications to Hox Cluster Duplications.
Mol. Evol. Phylog., 31, 581-604
(2004)
[abstract]
[Postscript]
[PDF]
Martin Beck, Gil Benkö, Gunther J. Eble,
Christoph Flamm, Stefan Müller
and Peter F. Stadler
Graph Grammars as Models for the Evolution of
Developmental Pathways.
In: The Logic of Artificial Life - Proceedings of the 6th German
Workshop on Artificial Life (GWAL 2004)
H. Schaub, F. Detje, U. Brüggemann (Eds.)
Akademische Verlagsgesellschaft Aka GmbH, Berlin, 2004, pp
8-15
[abstract]
[Postscript]
[PDF]
Gil Benkö, Christoph Flamm and Peter F.
Stadler
Multi-Phase Artificial Chemistry.
In: The Logic of Artificial Life - Proceedings of the 6th German
Workshop on Artificial Life (GWAL 2004)
H. Schaub, F. Detje, U. Brüggemann (Eds.)
Akademische Verlagsgesellschaft Aka GmbH, Berlin, 2004, pp.
16-22. ISBN
389838053X
[abstract]
[Postscript]
[PDF]
Franziska Berger, Christoph Flamm Petra M. Gleiss,
Josef Leydold
and Peter F. Stadler
Counterexamples in Chemical Ring Perception.
J. Chem. Inf. Comput. Sci., 44, 323-331
(2004)
[abstract]
[Postscript]
[PDF]
2003
Ingrid Abfalter, Christoph Flamm and Peter F.
Stadler
Design of Multi-Stable Nucleic Acid
Sequences.
In: Proceedings of the German Conference on Bioinformatics.
H.-W. Mewes, V. Heun, D. Frishman, S. Kramer (Eds.)
Belleville Verlag Michael Farin, München, 2003, Vol 1, pp.
1-7.
[abstract]
[Postscript]
[PDF]
Gil Benkö, Christoph Flamm and Peter F.
Stadler
Generic Properties of Chemical Networks:
Artificial Chemistry Based on Graph
Rewriting.
In: Advances in Artificial Life - Proceedings of the 7th European
Conference
on Artificial Life (ECAL 2003)
W. Banzhaf, T. Christaller, P. Dittrich, J. T. Kim, J. Ziegler
(Eds.)
Springer Verlag, 2003, pp. 10-19.
[abstract]
[Postscript]
[PDF]
Gil Benkö, Christoph Flamm and Peter F.
Stadler
A Graph-Based Toy Model of Chemistry.
J. Chem. Inf. Comput. Sci., 43,
1085-1093 (2003)
(doi:10.1021/ci0200570)
[abstract]
[Postscript]
[PDF]
Peter F. Stadler and Christoph Flamm
Barrier Trees on Poset-Valued Landscapes.
J. Gen. Prog. Evol. Machines, 4, 7-20
(2003)
[abstract]
[Postscript]
[PDF]
2002
Christoph Flamm, Ivo L. Hofacker, Peter F. Stadler
and Michael T. Wolfinger
Barrier Trees of Degenerate Landscapes.
Z. Phys. Chem., 216, 1-19 (2002)
[abstract]
[Postscript]
[PDF]
2001
Christoph Flamm, Ivo L. Hofacker, Sebastian
Maurer-Stroh, Peter F. Stadler and Martin Zehl
Design of Multi-Stable RNA Molecules.
RNA, 7, 254-265 (2001)
[abstract]
[Postscript]
[PDF]
2000
Christoph Flamm, Walter Fontana, Ivo L. Hofacker
and Peter Schuster
RNA Folding at Elementary Step Resolution.
RNA, 6, 325-338 (2000)
[abstract]
[Postscript]
[PDF]
1999
Christoph Flamm, Ivo L. Hofacker and Peter F.
Stadler
RNA in silico: The Computational Biology of RNA
Secondary Structures.
Adv. Complex Syst., 2, 65-90 (1999)
[abstract]
[Postscript]
[PDF]
1998
Ivo L. Hofacker, Martin Fekete, Christoph Flamm,
Martijn A. Huynen,
Susanne Rauscher, Paul E. Stolorz and Peter F. Stadler
Automatic Detection of Conserved RNA Structure Elements in
Complete RNA Virus Genomes.
Nucl. Acids Res., 26, 3825-3836
(1998)
[abstract]
[Postscript]
[PDF]
Christoph Flamm
Kinetic Folding of RNA.
PhD Thesis, University of Vienna, Austria (1998)
[Postscript]
[PDF]
1997
Susanne Rauscher, Christoph Flamm, Christian W.
Mandl, Franz X. Heinz and Peter F. Stadler
Secondary Structure of the 3′-Non-Coding Region of
Flavivirus Genomes Comparative Analysis of Base Pairing
Probabilities.
RNA, 3, 779-791, (1997)
[abstract]
[Postscript]
[PDF]
Jan Cupal, Christoph Flamm, Alexander Renner and
Peter F. Stadler
Density of States, Metastable States, and Saddle Points
Exploring the Energy Landscape of an RNA Molecule.
Proceedings of ISMB-97, 88-91 (1997)
[abstract]
[Postscript]
[PDF]
1996
Christoph Flamm
Synthetische Untersuchungen zum Antibiotikum
Nodusmicin.
Master Thesis (in German), University of Vienna, Austria
(1996)
[Postscript]
[PDF]