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List of
Publications
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
Ivo L Hofacker, Christoph Flamm, Christian Heine,
Michael T Wolfinger, Gerik Scheuermann, Peter F Stadler
BarMap: RNA Folding on Dynamic Energy Landscapes.
RNA submitted 2009.
[Abstract]
[PDF]
Published
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]
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.
[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)
[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]
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