% 1990 @article{Stadler:90, author = {Peter F Stadler and Peter Schuster}, title = {Dynamics of Small Autocatalytic Reaction Networks {I}: Bifurcations, Permanence and Exclusion}, journal = {Bull.\ Math.\ Biol.}, volume = {52}, pages = {485-508}, year = {1990}, } % 1991 @article{Stadler:91a, author = {Peter F Stadler}, title = {Dynamics of Small Autocatalytic Reaction Network {IV}: Inhomogeneous Replicator Equations}, journal = {BioSystems}, volume = {26}, pages = {1-19}, year = {1991}, } @article{Stadler:91b, author = {Peter F Stadler}, title = {Complementary Replication}, journal = {Math.\ Biosc.}, volume = {107}, pages = {83-109}, year = {1991}, } @article{Fontana:91, author = {Walter Fontana and Thomas Griesmacher and Wolfgang Schnabl and Peter F Stadler and Peter Schuster}, title = {Statistics of Landscapes Based on Free Energies, Replication and Degradation Rate Constants of {RNA} Secondary Structures}, journal = {Monatsh.\ Chem.}, volume = {122}, pages = {795-819}, year = {1991}, } @article{Schnabl:91, author = {Wolfgang Schnabl and Peter F Stadler and Christian V Forst and Peter Schuster}, title = {Full Characterization of a Strange Attractor. Chaotic Dynamics in Low Dimensional Replicator Systems}, journal = {Physica D}, volume = {48}, pages = {65-90}, year = {1991}, } @article{StadlerB:91, author = {B{\"a}rbel M R Stadler and Peter F Stadler}, title = {Dynamics of Small Autocatalytic Reaction Networks {III}: Monotonous Growth Functions}, journal = {Bull.\ Math.\ Biol.}, volume = {53}, pages = {469-485}, year = {1991}, } % 1992 @article{Stadler:92a, author = {Peter F Stadler and Peter Schuster}, title = {Mutation in Autocatalytic Networks --- An Analysis Based on Perturbation Theory}, journal = {J.\ Math.\ Biol.}, volume = {30}, pages = {597-631}, year = {1992}, } @article{Stadler:92b, author = {Peter F Stadler and Wolfgang Schnabl}, title = {The Landscape of the Travelling Salesman Problem}, journal = {Phys.\ Lett.\ A}, volume = {161}, pages = {337-344}, year = {1992}, } @article{Stadler:92c, author = {Peter F Stadler and Robert Happel}, title = {Correlation Structure of the Landscape of the Graph-Bipartitioning-Problem}, journal = {J.\ Phys.\ A:Math.\ Gen.}, volume = {25}, pages = {3103-3110}, year = {1992}, } @article{Stadler:92d, author = {Peter F Stadler}, title = {Correlation in Landscapes of Combinatorial Optimization Problems}, journal = {Europhys.\ Lett.}, volume = {20}, pages = {479-482}, year = {1992}, } % 1993 @article{Stadler:93a, author = {Peter F Stadler and Robert Happel}, title = {The Probability for Permanence}, journal = {Math.\ Biosc.}, volume = {113}, pages = {25-50}, year = {1993}, } @article{Stadler:93b, author = {Peter F Stadler and Walter Fontana and John H Miller}, title = {Random Catalytic Reaction Networks}, journal = {Physica D}, volume = {63}, pages = {378-392}, year = {1993}, } @article{Stadler:93c, author = {Peter F Stadler and Walter Gr{\"u}ner}, title = {Anisotropy in Fitness Landscapes}, journal = {J.\ Theor.\ Biol.}, volume = {165}, pages = {373-388}, year = {1993}, } @article{Bonhoeffer:93a, author = {Sebastian Bonhoeffer and John S {McCaskill} and Peter F Stadler and Peter Schuster}, title = {{RNA} Multi-Structure Landscapes. A Study Based on Temperature Dependent Partition Functions}, journal = {Eur.\ Biophys.\ J.}, volume = {22}, pages = {13-24}, year = {1993}, } @article{Bonhoeffer:93b, author = {Sebastian Bonhoeffer and Peter F Stadler}, title = {Errorthreshold on Complex Fitness Landscapes}, journal = {J.\ Theor.\ Biol.}, volume = {164}, pages = {359-372}, year = {1993}, } @article{Fontana:93a, author = {Walter Fontana and Peter F Stadler and Erich G Bornberg-Bauer and Thomas Griesmacher and Ivo L Hofacker and Manfred Tacker and Pedro Tarazona and Edward D Weinberger and Peter Schuster}, title = {{RNA} Folding Landscapes and Combinatory Landscapes}, journal = {Phys.\ Rev.\ E}, volume = {47}, pages = {2083-2099}, year = {1993}, } @article{Fontana:93b, author = {Walter Fontana and Daniella A M Konings and Peter F Stadler and Peter Schuster}, title = {Statistics of {RNA} Secondary Structures}, journal = {Biopolymers}, volume = {33}, pages = {1389-1404}, year = {1993}, } @article{Weinberger:93a, author = {Edward D Weinberger and Peter F Stadler}, title = {Why Some Fitness Landscapes are Fractal}, journal = {J.\ Theor.\ Biol.}, volume = {163}, pages = {255-275}, year = {1993}, } % 1994 @article{Stadler:94a, author = {Peter F Stadler}, title = {Linear Operators on Correlated Landscapes}, journal = {J.\ Phys.\ I France}, volume = {4}, pages = {681-696}, year = {1994}, } @article{Stadler:94b, author = {Peter F Stadler and Juan Carlos Nu{\~n}o}, title = {The Influence of Mutation on Autocatalytic Reaction Networks}, journal = {Math.\ Biosci.}, volume = {122}, pages = {127-160}, year = {1994}, } @article{Stadler:94c, author = {Peter F Stadler and Peter Schuster and Alan S Perelson}, title = {Immune Networks Modelled by Replicator Equations}, journal = {J.\ Math.\ Biol.}, volume = {33}, pages = {111-137}, year = {1994}, } @article{Hofacker:94a, author = {Ivo L Hofacker and Walter Fontana and Peter F Stadler and L Sebastian Bonhoeffer and Manfred Tacker and Peter Schuster}, title = {Fast Folding and Comparison of {RNA} Secondary Structures}, journal = {Monatsh.\ Chem.}, volume = {125}, pages = {167-188}, year = {1994}, } @article{Schuster:94a, author = {Peter Schuster and Walter Fontana and Peter F Stadler and Ivo L Hofacker}, title = {From Sequences to Shapes and Back: A case study in {RNA} secondary structures}, journal = {Proc.\ Roy.\ Soc.\ Lond.\ B}, volume = {255}, pages = {279-284}, year = {1994}, } @article{Schuster:94b, author = {Peter Schuster and Peter F Stadler}, title = {Landscapes: Complex Optimization Problems and Biopolymer Structures}, journal = {Computers \& Chem.}, volume = {18}, pages = {295-314}, year = {1994}, } @article{Tacker:94a, author = {Manfred Tacker and Walter Fontana and Peter F Stadler and Peter Schuster}, title = {Statistics of {RNA} Melting Kinetics}, journal = {Eur.\ Biophys.\ J.}, volume = {23}, pages = {29-38}, year = {1994}, } @Misc{Stadler:94d, note = {see Technical Reports}, } %%% 1995 @incollection{Macken:95a, author = {Catherine A. Macken and Peter F. Stadler}, title = {Evolution on Fitness Landscapes}, pages = {43-86}, editor = {L. Nadel and D. L. Stein}, booktitle = {1993 Lectures in Complex Systems}, series = {SFI Studies in the Sciences of Complexity}, volume = {VI}, publisher = {Addison-Wesley}, address = {Reading MA}, year = {1995}, } @incollection{Tacker:95a, author = {Manfred Tacker and Peter F. Stadler}, title = {{RNA}: Genotype and Phenotype}, pages = {579-589}, editor = {L. Nadel and D. L. Stein}, booktitle = {1993 Lectures in Complex Systems}, series = {SFI Studies in the Sciences of Complexity}, volume = {VI}, publisher = {Addison-Wesley}, address = {Reading MA}, year = {1995}, } @article{Stadler:95a, author = {Peter F Stadler and Wolfgang Schnabl and Christian V Forst and Peter Schuster}, title = {Dynamics of Small Autocatalytic Reaction Networks {II}: Replication, Mutation, and Catalysis.}, journal = {Bull.\ Math.\ Biol.}, volume = {57}, pages = {21-61}, year = {1995}, } @article{Stadler:95b, author = {Peter F Stadler}, title = {Random Walks and Orthogonal Functions Associated with Highly Symmetric Graphs}, journal = {Discr.\ Math.}, volume = {145}, pages = {229-238}, year = {1995}, } @inproceedings{Stadler:95c, author = {Peter F. Stadler}, title = {Towards a Theory of Landscapes}, pages = {77-163}, editor = {R. {Lop{\'e}z-Pe{\~n}a} and R. Capovilla and R. Garc{\'\i}a-Pelayo and H. Waelbroeck and F. Zertuche}, booktitle = {Complex Systems and Binary Networks}, publisher = {Springer Verlag}, address = {Berlin, New York}, year = {1995}, series = {Lecture Notes in Physics}, volume = {461}, note = {SFI preprint 95-03-030}, } @inproceedings{Stadler:95d, author = {Peter F. Stadler}, title = {{RNA}: Genotype and Phenotype}, booktitle = {Chemical Evolution: Self-Organization of the Macromolecules of Life}, editor = {J. {Chela-Flores} and M. Chadha and A. {Negron-Mendoza} and T. Oshima}, pages = {159-176}, year = {1995}, note = {Proceedings of the Second Trieste Conference on Chemical Evolution: Self Organization of the Macromolecules of Life 25-29 October 1993}, } @Misc{Hofacker:95a, note = {see Technical Reports} } %% 1996 @article{Gruener:96a, author = {Walter Gruener and Robert Giegerich and Dirk Strothmann and Christian Reidys and Jacqueline Weber and Ivo L. Hofacker and Peter F. Stadler and Peter Schuster}, title = {Analysis of {RNA} Sequence Structure Maps by Exhaustive Enumeration. {I.} Neutral Networks}, journal = {Monath.\ Chem.}, year = {1996}, volume = {127}, pages = {355-374}, note = {SFI preprint 95-10-099}, } @article{Gruener:96b, author = {Walter Gruener and Robert Giegerich and Dirk Strothmann and Christian Reidys and Jacqueline Weber and Ivo L. Hofacker and Peter F. Stadler and Peter Schuster}, title = {Analysis of {RNA} Sequence Structure Maps by Exhaustive Enumeration. {II.} Structures of Neutral Networks and Shape Space Covering}, journal = {Monath.\ Chem.}, year = {1996}, volume = {127}, pages = {375-389}, note = {SFI preprint 95-10-099}, } @article{Reidys:96a, author = {Christian Reidys and Peter F. Stadler}, title = {Bio-Molecular Shapes and Algebraic Structures}, journal = {Computers \& Chem.}, year = {1996}, volume = {20}, pages = {85-94}, note = {SFI preprint 95-10-098}, } @article{Schwienhorst:96a, author = {Andreas Schwienhorst and Andreas Schober and Rolf Guenther and Peter F. Stadler}, title = {Hamming Chromatography}, journal = {Molecular Diversity}, volume = {1}, pages = {187-192}, year = {1996}, note = {SFI preprint 95-10-090}, } @InProceedings{Hofacker:96b, author = {Ivo L. Hofacker and Martijn A. Huynen and Peter F. Stadler and Paul E. Stolorz}, title = {Knowledge Discovery in {RNA} Sequence Families of {HIV} Using Scalable Computers}, year = {1996}, editor = {Evangelos Simoudis and Jiawei Han and Usama Fayyad}, booktitle = {Proceedings of the 2nd International Conference on Knowledge Discovery and Data Mining, Portland, OR}, address = {Menlo Park, CA}, publisher = {AAAI Press}, pages = {20-25}, } @article{Baskaran:96a, author = {Subbiah Baskaran and Peter F. Stadler and Peter Schuster}, title = {Approximate Scaling Properties of {RNA} Free Energy Landscapes}, year = {1996}, pages = {299-310}, volume = {181}, journal = {J.\ Theor.\ Biol.}, note = {SFI preprint 95-10-083}, } @article{Stadler:96a, author = {Peter F. Stadler and B{\"a}rbel Krakhofer}, title = {Local Minima of p-Spin Models}, journal = {Rev.\ Mex.\ Fis.}, volume = {42}, pages = {355-363}, year = {1996}, note = {SFI preprint 95-09-076}, } @article{Stadler:96b, author = {Peter F. Stadler}, title = {Landscapes and Their Correlation Functions}, journal = {J.\ Math.\ Chem.}, pages = {1-45}, volume = {20}, year = {1996}, note = {SFI preprint 95-07-067}, } @article{Happel:96a, author = {Robert Happel and Peter F. Stadler}, title = {Canonical Approximation of Fitness Landscapes}, journal = {Complexity}, year = {1996}, volume = {2}, pages = {53-58}, note = {SFI preprint 95-07-068}, } @article{Happel:96b, author = {Robert Happel and Robert Hecht and Peter F. Stadler}, title = {Autocatalytic Networks with Translation}, journal = {Bull.\ Math.\ Biol.}, volume = {58}, pages = {877-905}, year = {1996}, note = {SFI preprint 95-07-063}, } @article{Huynen:96a, author = {Martijn A. Huynen and Peter F. Stadler and Walter Fontana}, title = {Smoothness within ruggedness: the role of neutrality in adaptation}, journal = {Proc.\ Natl.\ Acad.\ Sci.\ (USA)}, year = {1996}, volume = {93}, pages = {397-401}, note = {SFI preprint 95-01-006, LAUR-94-3763}, } @article{Huynen:96b, author = {Martijn A. Huynen and Alan S. Perelson and Wayne A. Vieira and Peter F. Stadler}, title = {Base Pairing Probabilities in a Complete {HIV-1 RNA}}, journal = {J.\ Comp.\ Biol.}, year = {1996}, volume = {3}, pages = {253-274}, note = {SFI preprint 95-07-057, LAUR-95-1613}, } @article{Stadler:96c, author = {Peter F. Stadler and Peter Schuster}, title = {Permanence of Sparse Autocatalytic Networks}, journal = {Math.\ Biosc.}, volume = {131}, pages = {111-134}, year = {1996}, note = {SFI Preprint 94-05-028}, } @article{Krakhofer:96a, author = {B{\"a}rbel Krakhofer and Peter F. Stadler}, title = {Local Minima in the Graph Bipartitioning Problem}, journal = {Europhys.\ Lett.}, volume = {34}, pages = {85-90}, year = {1996}, note = {SFI preprint 96-02-005}, } @article{Tacker:96a, author = {Manfred Tacker and Peter F. Stadler and Erich G. Bornberg-Bauer and Ivo L. Hofacker and Peter Schuster}, title = {Algorithm Independent Properties of {RNA} Structure Prediction}, journal = {Eur.\ Biophy.\ J.}, pages = {115-130}, volume = {25}, year = {1996}, note = {Santa Fe Institute Preprint 96-04-016} } @InProceedings{Cupal:96, author = {J. Cupal and I. L. Hofacker and P. F. Stadler}, title = {Dynamic Programming Algorithm for the Density of States of {RNA} Secondary Structures}, booktitle = {Computer Science and Biology 96 (Prooceedings of the German Conference on Bioinformatics)}, editor = {R. Hofst{\"a}dt and T. Lengauer and M. L{\"o}ffler and D. Schomburg}, publisher = {Universit{\"a}t Leipzig}, address = {Leipzig, Germany}, pages = {184-186}, year = {1996}, } %%% 1997 @inProceedings{Cupal:97a, author = {Jan Cupal and Christoph Flamm and Alexander Renner and Peter F. Stadler}, title = {Density of States, Metastable States, and Saddle Points. {E}xploring the Energy Landscape of an {RNA} Molecule}, booktitle = {Proceedings of the ISMB-97}, editor = {T. Gaasterland and P. Karp and K. Karplus and Ch. Ouzounis and Ch. Sander and A. Valencia}, publisher = {AAAI Press}, address = {Menlo Park, CA}, year = {1997}, pages = {88-91}, } @article{Hecht:97a, author = {Robert Hecht and Robert Happel and Peter Schuster and Peter F. Stadler}, title = {Autocatalytic networks with intermediates {I}: Irreversible Reactions}, journal = {Math.\ Biosc.}, volume = {140}, pages = {33-74}, year = {1997}, note = {Santa Fe Institute preprint 96-05-024}, } @article{Reidys:97a, author = {Christian Reidys and Peter F. Stadler and Peter Schuster}, title = {Generic Properties of Combinatory Maps: Neutral Networks of {RNA} Secondary Structures}, journal = {Bull.\ Math.\ Biol.}, volume = {59}, pages = {339-397}, note = {SFI preprint 95-07-058}, year = {1997}, } @article{Schuster:97a, author = {Peter Schuster and Peter F. Stadler and Alexander Renner}, title = {{RNA} Structures and Folding: From conventional to new issues in structure predictions}, journal = {Curr.\ Opinions Structural Biol.}, year = {1997}, pages = {229-235}, volume = {7}, } @article{GarciaPelayo:97a, author = {Ricardo Garc{\'\i}a-Pelayo and Peter F. Stadler}, title = {Correlation Length, Isotropy, and Meta-stable States}, journal = {Physica D}, pages = {240-254}, volume = {107}, year = {1997}, note = {Santa Fe Institute Preprint 96-05-034}, } @article{Rauscher:97a, author = {Susanne Rauscher and Christph Flamm and Christian Mandl and Franz X. Heinz and Peter F. Stadler}, title = {Secondary Structure of the 3'-Non-Coding Region of Flavivirus Genomes: Comparative Analysis of Base Pairing Probabilities}, journal = {RNA}, volume = {3}, pages = {779-791}, year = {1997}, note = {Santa Fe Institute Preprint 97-02-010}, } @article{Babajide:97a, author = {Aderonke Babajide and Ivo L. Hofacker and Manfred J. Sippl and Peter F. Stadler}, title = {Neutral Networks in Protein Space: A Computational Study Based on Knowledge-Based Potentials of Mean Force}, journal = {Folding \& Design}, year = {1997}, pages = {261-269}, volume = {2}, note = {Santa Fe Institute Preprint 96-12-085}, } %% 1998 @InCollection{Schuster:98a, author = {Peter Schuster and Peter F. Stadler}, title = {Sequence Redundancy in Biopolymers: A Study on {RNA} and Protein Structures}, pages = {163-186}, booktitle = {Viral Regulatory Structures}, series = {Santa Fe Institute Studies in the Sciences of Complexity}, volume = {XXVIII}, editor = {Gerald Myers}, publisher = {Addison-Wesley}, address = {Reading MA}, year = {1998}, note = {Santa Fe Institute Preprint 97-07-67}, } @article{Stadler:98a, author = {Peter F. Stadler and G{\"u}nter P.\ Wagner}, title = {The Algebraic Theory of Recombination Spaces}, journal = {Evol.\ Comp.}, pages = {241-275}, volume = {5}, year = {1998}, note = {Santa Fe Institute Preprint 96-07-046}, } @article{Mandl:98a, author = {Christian W. Mandl and Heidemarie Holzmann and Tamara Meixner and Susanne Rauscher and Peter F. Stadler and Steven L. Allison and Franz X. Heinz}, title = {Spontaneous and Engineered Deletions in the 3'-Noncoding Region of Tick-Borne Encephalitis Virus: Construction of Highly Attenuated Mutants of Flavivirus}, journal = {J.\ Virology}, volume = {72}, pages = {2132-2140}, year = {1998}, } @article{Leydold:98a, author = {Josef Leydold and Peter F. Stadler}, title = {Minimal Cycle Basis of Outerplanar Graphs}, journal = {Elec.\ J.\ Comb.}, volume = {5}, pages = {209-222 [R16: 14 p.]}, year = {1998}, note = {See {\tt http://www.combinatorics.org/} R16 and Santa Fe Institute Preprint 98-01-011}, } @article{Hofacker:98a, author = {Ivo L. Hofacker and Martin Fekete and Christoph Flamm and Martijn A. Huynen and Susanne Rauscher and Paul E. Stolorz and Peter F. Stadler}, title = {Automatic Detection of Conserved {RNA} Structure Elements in Complete {RNA} Virus Genomes}, journal = {Nucl.\ Acids Res.}, volume = {26}, pages = {3825--3836}, year = {1998}, note = {Santa Fe Institute Preprint 98-03-020}, } @article{Hordijk:98a, author = {Wim Hordijk and Peter F. Stadler}, title = {Amplitude Spectra of Fitness Landscapes}, journal = {J.\ Complex Systems}, volume = {1}, pages = {39-66}, year = {1998}, note = {Santa Fe Institute Preprint 98-03-021}, } @InProceedings{Stadler:98b, author = {Peter F. Stadler}, title = {Generic Properties of the Sequence-Structure Relations of Biopolymers}, editor = {J. {Chela-Flores} and F. Raulin}, booktitle = {Exobiology: Matter, Energy, and Information in the Origin of Life in the Universe}, publisher = {Kluwer}, address = {Dordrecht}, year = {1998}, pages = {149--156}, } @article{Miller:98a, author = {John H. Miller and Peter F. Stadler}, title = {The Dynamics of Adaptive Parties Under Spatial Voting}, journal = {J.\ Econ.\ Dyn.\ \& Control}, pages = {23}, volume = {171--189}, year = {1998}, note = {Santa Fe Institute Preprint 94-06-042}, } @article{Happel:98a, author = {Robert Happel and Peter F. Stadler}, title = {The Evolution of Diversity in Replicator Networks}, journal = {J.\ Theor.\ Biol.}, year = {1998}, volume = {195}, pages = {329--338}, note = {Santa Fe Preprint 97-07-61}, } @article{Wills:98a, author = {Peter R.\ Wills and Stuart A.\ Kauffman and B{\"a}rbel M.R.\ Stadler and Peter F.\ Stadler}, title = {Selection Dynamics in Autocatalytic Systems: Templates Replicating Through Binary Ligation}, journal = {Bull.\ Math.\ Biol.}, volume = {60}, pages = {1073-1098}, year = {1998}, note = {Santa Fe Institute Preprint 97-07-065}, } @article{Hofacker:98d, author = {Ivo L. Hofacker and Peter Schuster and Peter F. Stadler}, title = {Combinatorics of {RNA} Secondary Structures}, journal = {Discr.\ Appl.\ Math.}, volume = {88}, pages = {207--237}, year = {1998}, note = {SFI preprint 94-04-026}, } %%% 1999 @Article{Stadler:99a, author = {Peter F. Stadler}, title = {Fitness Landscapes Arising from the Sequence-Structure Maps of Biopolymers}, journal = {J.\ Mol.\ Struct.\ (THEOCHEM)}, year = {1999}, volume = {463}, pages = {7-19}, note = {Santa Fe Institute Preprint 97-11-082} } @article{Hofacker:99c, author = {Ivo L. Hofacker and Peter F. Stadler}, title = {Automatic Detection of Conserved Base Pairing Patterns in {RNA} Virus Genomes}, journal = {Comp.\ \& Chem.}, volume = {23}, pages = {401-414}, year = {1999}, note = {Santa Fe Institute preprint 98-06-058} } @Article{Flamm:99a, author = {Christoph Flamm and Ivo L. Hofacker and Peter F. Stadler}, title = {{RNA} {\em in silico}: The Computational Biology of {RNA} Secondary Structures}, journal = {Adv.\ Complex Syst.}, volume = {2}, pages = {65-90}, year = 1999, } @article{Happel:99a, author = {Robert Happel and Peter F. Stadler}, title = {Autocatalytic Replication in a {CSTR} and Constant Organization}, journal = {J.\ Math.\ Biol.}, year = {1999}, pages = {422-434}, volume = {38}, note = {SFI preprint 95-07-062}, } @article{Stadler:99b, author = {Peter F. Stadler and Robert Happel}, title = {Random Field Models for Fitness Landscapes}, journal = {J.\ Math.\ Biol.}, year = {1999}, volume = {38}, pages = {435-478}, note = {SFI preprint 95-07-069}, } @article{Haslinger:99a, author = {Christian Haslinger and Peter F. Stadler}, title = {{RNA} Structures with Pseudo-Knots: Graph-Theoretical and Combinatorial Properties}, journal = {Bull.\ Math.\ Biol.}, year = {1999}, volume = {61}, pages = {437-467}, note = {Santa Fe Institute Preprint 97-03-030}, } @InCollection{Schuster:99a, author = {Peter Schuster and Peter F. Stadler}, title = {Nature and Evolution of Early Replicons}, booktitle = {Origin and Evolution of Viruses}, editor = {E. Domingo and R. Webster and J. Holland}, publisher = {Academic Press}, address = {London, UK}, year = {1999}, pages = {1-24}, note = {Santa Fe Preprint 98-11-098}, } @article{WagnerA:99a, author = {Andreas Wagner and Peter F. Stadler}, title = {Viral {RNA} and Evolved Mutational Robustness}, journal = {J.\ Exp.\ Zool./ MDE}, volume = {285}, pages = {119-127}, year = {1999}, note = {Santa Fe Institute preprint 99-02-010}, } @inProceedings{Wagner:99a, author = {G{\"u}nter P.\ Wagner and Peter F. Stadler}, title = {Complex Adaptations and the Structure of Recombination Spaces}, editor = {Chrystopher Nehaniv and Misami Ito}, booktitle = {Algebraic Engineering}, publisher = {World Scientific}, address = {Singapore}, year = {1999}, pages = {96--115}, note = {(Proceedings of the Conference on Semi-Groups and Algebraic Engineering, University of Aizu, Japan); Santa Fe Institute Preprint 97-03-029}, } @InProceedings{Cupal:99b, author = {Jan Cupal and Peter Schuster and Peter F. Stadler}, title = {Topology in Phenotype Space}, booktitle = {Computer Science in Biology}, publisher = {Univ.\ Bielefeld}, address = {Bielefeld, D}, note = {Proceedings of the GCB'99, Hannover, D}, year = {1999}, pages = {9--15}, } @InProceedings{Stocsits:99a, author = {Roman Stocsits and Ivo L. Hofacker and Peter F. Stadler}, title = {Conserved Secondary Structures in Hepatitis {B} Virus {RNA}}, booktitle = {Computer Science in Biology}, publisher = {Univ.\ Bielefeld}, address = {Bielefeld, D}, note = {Proceedings of the GCB'99, Hannover, D}, year = {1999}, pages = {73--79}, } @InProceedings{Weberndorfer:99a, author = {G{\"u}nter Weberndorfer and Ivo L. Hofacker and Peter F. Stadler}, title = {An Efficient Potential for Protein Sequence Design}, booktitle = {Computer Science in Biology}, publisher = {Univ.\ Bielefeld}, address = {Bielefeld, D}, note = {Proceedings of the GCB'99, Hannover, D}, year = {1999}, pages = {107-112}, } @article{Stadler:99c, author = {Peter F. Stadler and Gottfried Tinhofer}, title = {Equitable Partitions, Coherent Algebras and Random Walks: Applications to the Correlation Structure of Landscapes}, journal = {MATCH}, pages = {215-261}, volume = {40}, year = {1999}, } @article{Oliveira:99a, author = {Viviane M. de Oliveira and Jos{\'e} Fernando Fontanari and Peter F. Stadler}, title = {Metastable States in High Order Short-Range Spin Glasses}, journal = {J.\ Phys.\ A: Math.\ Gen.}, volume = {32}, pages = {8793--8802}, year = {1999}, note = {SFI preprint 99-09-62; {\tt xxx.lanl.gov/abs/physics/9908439/}}, } %%% 2000 @article{Campos:00a, author = {Paulo Roberto Ara{\'u}jo Campos and Jos{\'e} Fernando Fontanari and Peter F. Stadler}, title = {Error Propagation in the Hypercycle}, journal = {Phys.\ Rev.\ E}, pages = {2996-3002}, volume = {61}, year = {2000}, note = {SFI preprint 99-09-63; {\tt xxx.lanl.gov/abs/physics/9907049/}}, } @article{Gleiss:00a, author = {Petra M. Gleiss and Josef Leydold and Peter F. Stadler}, title = {Interchangeability of Relevant Cycles in Graphs}, journal = {Elec.\ J.\ Comb.}, volume = {7}, pages = {R16 [16pages]}, year = {2000}, note = {Santa Fe Institute preprint 99-07-046}, } @article{Wimmer:00a, author = {Katharina Wimmer and Markus Eckart and Peter F.\ Stadler and Helga Rehder and Christa Fonatsch}, title = {Three different premature stop codones lead to skipping of exon 7 in {N}eurofibromatosis type {I} patients}, journal = {Human Mutation}, volume = {16}, pages = {90--91}, year = {2000}, note = {Full Text: {\it Mutations in Brief \#341} (7 pages) {\tt http://humu.edoc.com/mutbr1.html} } } @Article{Stadler:00a, author = {Peter F. Stadler and Rudi Seitz and G{\"u}nter P. Wagner}, title = {Evolvability of Complex Characters: Population Dependent {Fourier} Decomposition of Fitness Landscapes over Recombination Spaces}, pages = {399--428}, volume = {62}, journal = {Bull.\ Math.\ Biol.}, year = {2000}, note = {Santa Fe Institute Preprint 99-01-001}, } @Article{Fekete:00a, author = {Martin Fekete and Ivo L. Hofacker and Peter F. Stadler}, title = {Prediction of {RNA} base pairing probabilities using massively parallel computers}, journal = {J.\ Comp.\ Biol.}, volume = {7}, pages = {171--182}, year = {2000}, note = {Santa Fe Institute preprint 98-06-057}, } @Article{Cupal:00a, author = {Jan Cupal and Stefan Kopp and Peter F.\ Stadler}, title = {{RNA} Shape Space Topology}, journal = {Alife}, year = {2000}, volume = {6}, pages = {3-23}, note = {SFI Preprint 99-03-022}, } @article{BMRStadler:00b, author = {B{\"a}rbel M. R. Stadler and Peter F. Stadler and Peter Schuster}, title = {Dynamics of Autocatalytic Replicator Networks Based on Higher Order Ligation Reactions}, journal = {Bull.\ Math.\ Biol.}, pages = {1061-1086}, volume = {62}, year = {2000}, note = {SFI preprint 99-09-65}, } @article{Ferreira:00a, author = {Fernando F. Ferreira and Jos{\'e} F. Fontanari and Peter F Stadler}, title = {Landscape statistics of the low autocorrelated binary string problem}, journal = {J.\ Phys.\ A: Math.\ Gen.}, volume = {33}, pages = {8635--8647}, year = {2000}, note = {Santa Fe Institute Preprint 00-07-033}, } %%% 2001 @Article{Reidys:01a, author = {Christian M. Reidys and Peter F. Stadler}, title = {Neutrality in Fitness Landscapes}, journal = {Appl.\ Math.\ \& Comput.}, volume = {117}, pages = {321--350}, year = {2001}, note = {Santa Fe Institute preprint 98-10-089}, } @article{Flamm:00b, author = {Christoph Flamm and Ivo L. Hofacker and Sebastian Maurer-Stroh and Peter F. Stadler and Martin Zehl}, title = {Design of Multi-Stable {RNA} Molecules}, journal = {RNA}, year = {2000}, volume = {7}, pages = {254--265}, note = {Santa Fe Institute Preprint 00-05-027}, } @Article{Babajide:01a, author = {Aderonke Babajide and Robert Farber and Ivo L. Hofacker and Jeff Inman and Alan S. Lapedes and and Peter F. Stadler}, title = {Exploring Protein Sequence Space Using Knowledge Based Potentials}, journal = {J.\ Theor.\ Biol.}, year = {2001}, volume = {212}, pages = {35-46}, note = {Santa Fe Preprint 98-11-103}, } @article{Davies:01a, author = {E. Brian Davies and Graham M. L. Gladwell and Josef Leydold and Peter F. Stadler}, title = {Discrete Nodal Domain Theorems}, journal = {Lin.\ Alg.\ Appl.}, volume = {336}, pages = {51-60}, year = {2001}, note = {Archive: math.SP/0009120}, } @article{Gleiss:01a, author = {Petra M. Gleiss and Peter F. Stadler and Andreas Wagner and David A. Fell}, title = {Relevant Cycles in Chemical Reaction Network}, journal = {Adv.\ Complex Syst.}, pages = {207-226}, year = {2001}, volume = {4}, } @article{BMRStadler:01a, author = {B{\"a}rbel M. R. Stadler and Peter F. Stadler and G{\"u}nter Wagner and Walter Fontana}, title = {The topology of the possible: Formal spaces underlying patterns of evolutionary change}, journal = {J.\ Theor.\ Biol.}, volume = {213}, pages = {241-274}, year = {2001}, note = {SFI preprint 00-12-070}, } @Article{Witwer:01a, author = {Christina Witwer and Susanne Rauscher and Ivo L. Hofacker and Peter F. Stadler}, title = {Conserved {RNA} Secondary Structures in Picornaviridae Genomes}, journal = {Nucl.\ Acids Res.}, pages = {5079-5089}, volume = {29}, year = {2001}, note = {SFI preprint 01-08-040}, } @Article{Stadler:01a, author = {Peter F. Stadler and Anita Mehta and {Jean-Marc} Luck}, title = {Shaking a Box of Sand}, journal = {Europhys.\ Lett.}, volume = {57}, pages = {46-52}, year = {2001}, } @Article{Stadler:01b, author = {Peter F. Stadler and Anita Mehta and {Jean-Marc} Luck}, title = {Glassy states in a shaken sandbox}, journal = {Adv.\ Complex Syst.}, volume = {4}, pages = {429-439}, year = {2001}, note = {Presented at the research workshop on {\em Challenges in Granular Physics}, ICTP Trieste, Italy, Aug 07-11 (2001)}, } % 2002 @article{Rockmore:02a, author = {Dan Rockmore and Peter Kostelec and Wim Hordijk and Peter F. Stadler}, title = {Fast Fourier Transform for Fitness Landscapes}, journal = {Appl.\ Comput.\ Harmonic Anal.}, volume = {12}, pages = {57-76}, year = {2002}, note = {Santa Fe Institute preprint 99-10-068}, } @Article{BMRStadler:02a, author = {B{\"a}rbel M. R. Stadler and Peter F. Stadler and Peter R. Wills}, title = {Evolution in Systems of Ligation-Based Replicators }, journal = {Z.\ Phys.\ Chem.}, pages = {216}, volume = {21-33}, year = {2001}, } @article{BMRStadler:02b, author = {B{\"a}rbel M. R. Stadler and Peter F. Stadler and Max Shpak and G{\"u}nter P. Wagner}, title = {Recombination Spaces, Metrics, and Pretopologies}, journal = {Z.\ Phys.\ Chem.}, volume = {216}, pages = {217--234}, year = {2002}, note = {SFI preprint 01-02-011}, } @Article{Flamm:02a, author = {Christoph Flamm and Ivo L. Hofacker and Peter F. Stadler and Michael T. Wolfinger }, title = {Barrier Trees of Degenerate Landscapes}, journal = {Z.\ Phys.\ Chem.}, pages = {155-173}, volume = {216}, year = {2002}, } @Article{Fontanari:02a, author = {Jos{\'e} Fernando Fontanari and Peter F. Stadler}, title = {Fractal geometry of spin-glass models}, journal = {J.\ Phys.\ A: Math.\ Gen.}, volume = {35}, pages = {1509-1516}, year = {2002}, note = {SFI preprint 01-06-034}, } @Article{Reidys:02a, author = {Christian M. Reidys and Peter F. Stadler}, title = {Combinatorial Landscapes}, journal = {SIAM Review}, pages = {3-54}, volume = {44}, year = {2002}, note = {SFI preprint 01-03-14}, } @Article{BMRStadler:02c, author = {B{\"a}rbel M. R. Stadler and Peter F. Stadler}, title = {Generalized Topological Spaces in Evolutionary Theory and Combinatorial Chemistry}, journal = {J.\ Chem.\ Inf.\ Comput.\ Sci.}, pages = {577-585}, volume = {42}, year = {2002}, note = {Proceedings MCC 2001, Dubrovnik} } @InProceedings{Stadler:02a, author = {Peter F. Stadler}, title = {Fitness Landscapes}, booktitle = {Biological Evolution and Statistical Physics}, editor = {Michael L{\"a}ssig and Angelo Valleriani}, publisher = {Springer-Verlag}, address = {Berlin}, year = {2002}, pages = {187-207}, } @Article{Hofacker:02a, author = {Ivo L. Hofacker and Martin Fekete and Peter F. Stadler}, title = {Secondary Structure Prediction for Aligned {RNA} Sequences}, journal = {J.\ Mol.\ Biol.}, volume = {319}, pages = {1059-1066}, year = {2002}, note = {SFI Preprint 01-11-067}, } @article{Bastert:02a, author = {Oliver Bastert and Dan Rockmore and Peter F. Stadler and Gottfried Tinhofer}, title = {Landscapes on Spaces of Trees}, journal = {Appl.\ Math.\ Comput.}, volume = {131}, pages = {439-459}, year = {2002}, note = {SFI preprint 01-01-006}, } @Article{Imrich:02a, author = {Wilfried Imrich and Peter F. Stadler}, title = {Minimal Cycle Bases of Product Graphs}, journal = {Australasian J.\ Comb.}, pages = {233-244}, volume = {26}, year = {2002}, note = {SFI preprint 01-08-044} } @Article{Mueckstein:02a, author = {Ulrike M{\"u}ckstein and Ivo L. Hofacker and Peter F. Stadler}, title = {Stochastic Pairwise Alignments}, journal = {Bioinformatics}, pages = {18}, volume = {S153-S160}, year = {2002}, note = {ECCB 2002} } @InProceedings{Stadler:00b, author = {Peter F. Stadler}, title = {Spectral Landscape Theory}, editor = {J. P. Crutchfield and P. Schuster}, booktitle = {Evolutionary Dynamics---Exploring the Interplay of Selection, Neutrality, Accident, and Function}, publisher = {Oxford University Press}, year = {2002}, pages = {231-272}, } @Article{Schuster:02a, author = {Peter Schuster and Peter F. Stadler}, title = {Networks in Molecular Evolutions}, journal = {Complexity}, pages = {34-42}, volume = {8}, year = {2002}, } %%% 2003 @Article{Stadler:03a, author = {Peter F. Stadler and Christoph Flamm}, title = {Barrier Trees on Poset-Valued Landscapes}, journal = {Genetic Prog.\ Evolv.\ Mach.}, pages = {4}, volume = {7-20}, year = {2003}, } @Article{Wagner:03a, author = {Wagner, G{\"u}nter and Stadler, Peter F.}, title = {Quasi-Independence, Homology and the Unity of Type: A Topological Theory of Characters}, journal = {J.\ Theor.\ Biol.}, pages = {505-527}, volume = {220}, year = {2003}, } @Article{Hordijk:03a, author = {Hordijk, Wim and Fontanari, Jos{\'e} F. and Stadler, Peter F.}, title = {Shapes of tree representations of spin-glass landscapes}, journal = {J.\ Phys.\ A: Math.\ Gen.}, volume = {36}, pages = {3671-3681}, year = {2003}, } @article{Stadler:03b, author = {Peter F. Stadler}, title = {Minimal Cycle Bases of {Halin} Graphs}, journal = {J.\ Graph Theory}, year = {2003}, volume = {43}, pages = {150-155 }, } @Article{Stadler:03c, author = {Stadler, Peter F. and Hordijk, Wim and Fontanari, Jos{\'e} F.}, title = {Phase transition and landscape statistics of the number partitioning problem}, journal = {Phys.\ Rev.\ E}, volume = {67}, pages = {056701,1-6}, year = {2003}, } @Article{Wuchty:03a, author = {Wuchty, Stefan and Stadler, Peter F.}, title = {Centers of Complex Networks}, journal = {J.\ Theor.\ Biol.}, volume = {223}, pages = {45-53}, year = {2003}, } @Article{BMRStadler:03a, author = {Stadler, B{\"a}rbel M. R. and Stadler, Peter F.}, title = {Molcular Replicator Dynamics}, journal = {Adv.\ Complex Syst.}, volume = {6}, pages = {47-77}, year = {2003}, note = {presented at \emph{Emergence in Chemical Systems}, Anchorage AK, June 2002; SFI \# 02-09-049} } @Article{Gleiss:03a, author = {Petra M. Gleiss and Josef Leydold and Peter F. Stadler}, title = {Circuit Bases of Strongly Connected Digraphs}, journal = {Discussiones Mathematicae: Graph Theory}, year = {2003}, volume = {23}, pages = {241-260}, note = {Presented at: Recent Trends in Graph Theory, Algebraic Combinatorics, and Graph Algorithms, Bled (Slovenia) Sep 24-27 2001}, } @Article{Benkoe:03b, author = {Benk{\"o}, Gil and Flamm, Christoph and Stadler, Peter F.}, title = {A Graph-Based Toy Model of Chemistry}, journal = {J.\ Chem.\ Inf.\ Comput.\ Sci.}, pages = {1085-1093}, volume = {43}, year = {2003}, note = {presented at \emph{MCC 2002}, Dubrovnik CRO, June 2002; SFI \# 02-09-045}, } @Article{Stadler:03d, author = {Stadler, Peter F. and Stephens, Christopher R.}, title = {Landscapes and Effective Fitness}, journal = {Comments on Theoretical Biology}, volume = {8}, pages = {389-431}, year = {2003}, } @Article{Weberndorfer:03a, author = {G{\"u}nter Weberndorfer and Ivo L. Hofacker and Peter F. Stadler}, title = {On the Evolution of Primitive Genetic Codes}, journal = {Origins Life Evol.\ Biosph.}, year = 2003, volume = {33}, pages = {491-514}, note = {SFI preprint \#02-08-034} } @InProceedings{Benkoe:03c, author = {Benk{\"o}, Gil and Flamm, Christoph and Stadler, Peter F.}, title = {Generic Properties of Chemical Networks: Artificial Chemistry Based on Graph Rewriting}, booktitle = {Advances in Artificial Life}, editor = {Banzhaf, W. and Christaller, T. and Dittrich, P. and Kim, J. T. and Ziegler, J.}, publisher = {Springer-Verlag}, address = {Heidelberg, Germany}, pages = {10-20}, series = {Lecture Notes in Computer Science}, volume = {2801}, year = {2003}, note = {7th European Conference, ECAL 2003, Dortmund, Germany, September 14-17, 2003, Proceedings}, } @Article{Fried:03, author = {Fried, Claudia and Prohaska, Sonja J. and Stadler, Peter F.}, title = {Independent Hox-Cluster Duplications in Lampreys}, journal = {J.\ Exp.\ Zool., Mol.\ Dev.\ Evol}, volume = {299B}, pages = {18-25}, year = {2003}, } @InProceedings{Abfalter:03a, author = {Abfalter, Ingrid and Flamm, Christoph and Stadler, Peter F.}, title = {Design of Multi-Stable Nucleic Acid Sequences}, booktitle = {Proceedings of the German Conference on Bioinformatics. GCB 2003}, volume = {1}, editor = {Mewes, H.-W. and Heun, V. and Frishman, D. and Kramer, S.}, publisher = {belleville Verlag Michael Farin}, address = {M{\"u}nchen, D}, pages = {1-7}, year = 2003, } @Article{Hofacker:03b, author = {Hofacker, Ivo L. and Stocsits, Roman and Stadler, Peter F.}, title = {Conserved {RNA} Secondary Structures in Viral Genomes: A Survey}, journal = {Bioinformatics}, volume = {20}, pages = {1495-1499}, year = {2004}, note = {\textbf{also}: Proceedings of the German Conference on Bioinformatics. GCB 2003 vol.\ \textbf{1}; Mewes, H.-W., Heun, V., Frishman, D. and Kramer, S. (eds.); belleville Verlag Michael Farin, M{\"u}nchen, D (2003), pp. 57-62}, } @InProceedings{Faulstich:03a, author = {Faulstich, Lukas C. and Stadler, Peter F. and Thurner, Caroline and Witwer, Christina}, title = {\texttt{litsift}: Automated Text Categorization in Bibliographic Search}, booktitle = {Data Mining and Text Mining for Bioinformatics: Proceedings of the European Workshop}, editor = {Scheffer, Tobias and Leser, Ulf}, publisher = {Humboldt University}, address = {Berlin}, year = 2003, pages = {20-25}, note = {http://www.informatik.hu-berlin.de/\%7Escheffer/publications/ProceedingsWS2003.pdf} } @Article{BMRStadler:03b, author = {B{\"a}rbel M. R. Stadler and Peter F. Stadler}, title = {Higher Separation Axioms in Generalized Closure Spaces}, journal = {Commentationes Math.\ Warszawa, Ser.\ I}, volume = {43}, pages = {257-273}, year = {2003}, } % 2004 @Article{Chiu:04a, author = {Chiu, Chi-Hua and Dewar, Ken and Wagner, G{\"u}nter P. and Takahashi, Kazuhiko and Ruddle, Frank and Ledje, Christina and Bartsch, Peter and Scemama, Jean-Luc and Stellwag, Edmund and Fried, Claudia and Prohaska, Sonja J. and Stadler, Peter F. and Amemiya, Chris T.}, title = {Bichir \emph{HoxA} Cluster Sequence Reveals Surprising Trends in Ray-Finned Fish Genomic Evolution}, journal = {Genome Res.}, volume = {14}, year = {2004}, pages = {11-17}, } @Article{Rasmussen:04a, author = {Steen Rasmussen and Liaohai Chen and B{\"a}rbel M. R. Stadler and Peter F. Stadler}, title = {Proto-Organism Kinetics: Evolutionary Dynamics of Lipid Aggregates with Genes and Metabolism}, journal = {Orig.\ Life Evol.\ Biosph.}, volume = {34}, pages = {171-180}, year = {2004}, } @Article{Hofacker:04a, author = {Hofacker, Ivo L. and Priwitzer, Barbara and Stadler, Peter F.}, title = {Prediction of Locally Stable {RNA} Secondary Structures for Genome-Wide Surveys}, journal = {Bioinformatics}, year = {2004}, volume = {20}, pages = {191-198}, } @Article{Rasmussen:04b, author = {Rasmussen, Steen and Chen, Liaohai and Deamer, David and Krakauer, David C. and Packard, Norman H.and Stadler, Peter F. and Bedau, Mark A.}, title = {Transitions from Nonliving to Living Matter}, journal = {Science}, pages = {963-965}, year = {2004}, note = {Perspectives}, } @Article{Prohaska:04a, author = {Prohaska, Sonja J. and Fried, Claudia and Amemiya, Chris T. and Ruddle, Frank H. and Wagner, G{\"u}nter P. and Stadler, Peter F.}, title = {The Shark {HoxN} cluster is homologous to the Human {HoxD} cluster}, journal = {J.\ Mol.\ Evol.}, pages = {58}, year = {2004}, note = {212-217}, } @Article{Copeland:04a, author = {Copeland, Claudia S. and Heyers, Oliver and Kalinna, Bernd H. and Bachmair, Andreas and Stadler, Peter F. and Hofacker, Ivo L. and Brindley, Paul J.}, title = {Structural and evolutionary analysis of the transcribed sequence of \emph{Boudicca}, a \emph{Schistosoma mansoni} retrotransposon}, journal = {Gene}, volume = {329}, pages = {103-114}, year = {2004}, } @Article{Berger:04a, author = {Berger, Franziska and Flamm, Christoph and Gleiss, Petra M. and Leydold, Josef and Stadler, Peter F.}, title = {Counterexamples in Chemical Ring Perception}, journal = {J.\ Chem.\ Inf.\ Comput.\ Sci.}, volume = {44}, pages = {323-331}, year = {2004}, } @Article{Fried:04a, author = {Fried, Claudia and Hordijk, Wim and Prohaska, Sonja J. and Stadler, Claus R. and Stadler, Peter F.}, title = {The Footprint Sorting Problem}, journal = {J.\ Chem.\ Inf.\ Comput.\ Sci.}, pages = {332-338}, volume = {44}, year = {2004}, } @Article{Fried:04b, author = {Fried, Claudia and Prohaska, Sonja J. and Stadler, Peter F.}, title = {Exclusion of Repetitive {DNA} Elements from Gnathostome \textsl{Hox} Clusters}, journal = {J.\ Exp.\ Zool., Mol.\ Dev.\ Evol}, volume = {302B}, pages = {165-173}, year = {2004}, } @Article{Prohaska:04b, author = {Prohaska, Sonja and Fried, Claudia and Flamm, Christoph and Wagner, G{\"u}nter and Stadler, Peter F.}, title = {Surveying Phylogenetic Footprints in Large Gene Clusters: Applications to {Hox} Cluster Duplications}, journal = {Mol.\ Phyl.\ Evol.}, volume = {31}, pages = {581-604}, year = {2004}, note = {SFI preprint \#03-02-011}, } @Article{Wolfinger:04a, author = {Wolfinger, Michael T. and Svrcek-Seiler, W. Andreas and Flamm, Christoph and Hofacker, Ivo L. and Stadler, Peter F.}, title = {Exact Folding Dynamics of {RNA} Secondary Structures}, journal = {J.\ Phys.\ A: Math.\ Gen.}, volume = {37}, pages = {4731-4741}, year = {2004}, } @InProceedings{Beck:04a, author = {Beck, Martin and Benk{\"o}, Gil and Eble, Gunther and Flamm, Christoph and M{\"u}ller, Stefan and Stadler, Peter F.}, title = {Graph Grammars as Models for the Evolution of Developmental Pathways}, booktitle = {The Logic of Artificial Life: Abstracting and Synthesizing the Principles of Living Systems}, editor = {H. Schaub and F. Detje and U. Br{\"u}ggemann}, publisher = {IOS Press, Akademische Verlagsgesellschaft}, address = {Berlin}, year = {2004}, note = {presented at GWAL, Bamberg 14-16 April 2004}, pages = {8-15} } @InProceedings{Benkoe:04a, author = {Benk{\"o}, Gil and Flamm, Christoph and Stadler, Peter F.}, title = {Multi-Phase Artificial Chemistry}, booktitle = {The Logic of Artificial Life: Abstracting and Synthesizing the Principles of Living Systems}, editor = {H. Schaub and F. Detje and U. Br{\"u}ggemann}, publisher = {IOS Press, Akademische Verlagsgesellschaft}, address = {Berlin}, year = {2004}, pages = {16-22}, note = {presented at GWAL, Bamberg 14-16 April 2004}, } @Article{Thurner:04a, author = {Thurner, Caroline and Witwer, Christine and Hofacker, Ivo and Stadler, Peter F.}, title = {Conserved {RNA} Secondary Structures in {Flaviviridae} Genomes}, journal = {J.\ Gen.\ Virol.}, volume = {85}, pages = {1113-1124}, year = {2004}, } @Article{Tanzer:04a, author = {Tanzer, Andrea and Stadler, Peter F.}, title = {Molecular Evolution of a Micro{RNA} Cluster}, journal = {J.\ Mol.\ Biol.}, pages = {327-335}, volume = {339}, year = {2004}, } @InProceedings{Hofacker:04c, author = {Hofacker, Ivo L. and Stadler Peter F.}, title = {The Partition Function Variant of {Sankoff's} Algorithm}, booktitle = {Computational Science - ICCS 2004}, editor = {Bubak, Marian and van Albada, Geert Dick and Sloot, Peter M. A. and Dongarra, Jack J. }, year = {2004}, series = {Lecture Notes in Computer Science}, volume = {3039}, pages = {728-735}, note = {Krak{\'o}w, June 6-9, 2004} } @InCollection{Flamm:04x, author = {Flamm, Christoph and Hofacker, Ivo L. and Stadler, Peter F.}, title = {{RNA} folding \emph{in silico}}, editor = {Brakmann, Susanne and Schwienhost, Andreas}, booktitle = {Evolutionary Methods in Biotechnology}, publisher = {Wiley-VCH}, address = {Weinheim, Germany}, year = {2004}, pages = {177-190}, } @InProceedings{BMRStadler:04a, author = {Stadler, B{\"a}rbel M. R. and Stadler, Peter F.}, title = {The Topology of Evolutionary Biology}, booktitle = {Modeling in Molecular Biology}, editor = {Ciobanu}, publisher = {Springer Verlag}, address = {267-286}, year = {2004}, series = {Natural Computing Series}, } @Article{Shpak:04a, author = {Shpak, Max and Stadler, Peter F. and Wagner, G{\"u}nter P. and Hermisson, Joachim}, title = {Aggregation of Variables and System Decomposition: Applications to Fitness Landscape Analysis}, journal = {Th.\ Biosci.}, year = {2004}, volume = {123}, pages = {33-68}, } @Article{Prohaska:04c, author = {Prohaska, Sonja J. and Stadler, Peter F.}, title = {The Duplication of the Hox Gene Clusters in Teleost Fishes}, journal = {Th.\ Biosci.}, volume = {123}, pages = {89-110}, year = {2004}, } @Article{Stadler:04a, author = {Stadler, Peter F. and Fried, Claudia and Prohaska, Sonja J. and Bailey, Wendy J. and Misof, Bernhard Y. and Ruddle, Frank H. and Wagner, G{\"u}nter P.}, title = {Evidence for independent \emph{Hox} gene duplications in the hagfish lineage: A {PCR}-based gene inventory of \emph{Eptatretus stoutii}}, journal = {Mol.\ Phylog.\ Evol.}, volume = {32}, pages = {686-692}, year = {2004}, } @Article{Hofacker:04b, author = {Flamm, Christoph and Hofacker, Ivo L. and Stadler, \ Peter F.}, title = {Computational Chemistry with {RNA} Secondary Structures}, volume = {53}, pages = {315-322}, year = {2004}, journal = {Kemija u industriji}, note = {(Proceedings CECM-2 Vara{\v z}din 2003)}, } @Article{Shpak:04b, author = {Shpak, Max and Stadler, Peter F. and Wagner, G{\"u}nter P. and Altenberg, Lee}, title = {Simon Ando Decomposability and Fitness Landscapes}, journal = {Th. Biosci.}, volume = {123}, pages = {139-180}, year = {2004}, } @Article{Campos:04a, author = {Campos, Paulo R. A. and de Olivera, Viviane M. and Wagner, G{\"u}nter P. and Stadler, Peter F.}, title = {Gene Phylogenies and Protein-Protein Interactions: Possible Artifacts Resulting From Shared Protein Interaction Partners}, journal = {J.\ Theor.\ Biol.}, volume = {231}, pages = {197-202}, year = {2004}, } @Article{Biyikoglu:04a, author = {B{\i}y{\i}ko{\u g}lu, T{\"u}rker and Hordijk, Wim and Leydold, Josef and Pisanski, Toma{\v z} and Stadler, Peter F.}, title = {Graph Laplacians, Nodal Domains, and Hyperplane Arrangements}, journal = {Lin.\ Alg.\ Appl.}, pages = {155-174}, volume = {390}, year = {2004}, note = {SFI \# 02-09-046}, } @Article{Hofacker:04d, author = {Hofacker, Ivo L. and Bernhart, Stephan H. F. and Stadler, Peter F.}, title = {Alignment of {RNA} Base Pairing Probability Matrices}, journal = {Bioinformatics}, volume = {20}, pages = {2222-2227}, year = {2004}, } @InProceedings{Morgenstern:04a, author = {Morgenstern, Burkhard and Prohaska, Sonja J. and Werner, Nadine and Weyer-Menkhoff, Jan and Schneider, Isabelle and Subramanian, Amarendran R. and Stadler, Peter F.}, title = {Multiple sequence alignment with user-defined constraints}, booktitle = {Proceedings of the GCB 2004 (Bielefeld)}, series = {Lecture Notes in Informatics}, editor = {Giegerich, Robert and Stoye, Jens}, volume = {P-53}, year = 2004, pages = {25-36} } @InProceedings{Thurner:04b, author = {Thurner, Caroline and Hofacker, Ivo L. and Stadler, Peter F.}, title = {Conserved {RNA} Pseudoknots}, booktitle = {Proceedings of the GCB 2004 (Bielefeld)}, series = {GI-Edition: Lecture Notes in Informatics}, editor = {Giegerich, Robert and Stoye, Jens}, volume = {P-53}, year = 2004, pages = {207-216}, } @Article{Wagner:04a, author = {Wagner, G{\"u}nter P. and Fried, Claudia and Prohaska, Sonja J. and Stadler, Peter F.}, title = {Divergence of Conserved Non-Coding Sequences: Rate Estimates and Relative Rate Tests}, journal = {Mol.\ Biol.\ Evol.}, volume = {21}, pages = {2116-2121}, year = {2004}, } @Article{Witwer:04a, author = {Witwer, Christina and Hofacker, Ivo L. and Stadler, Peter F.}, title = {Prediction of Consensus {RNA} Secondary Structures Including Pseudoknots}, journal = {IEEE/ACM Trans.\ Comp.\ Biol.\ Bioinf.}, volume = {1}, pages = {65-77}, year = {2004}, } @Article{Binder:04a, author = {Binder, Hans and Kirsten, Toralf and L{\"o}ffler, Markus and Stadler, Peter F.}, title = {The sensitivity of microarray oligonucleotide probes --- variability and the effect of base composition}, journal = {J.\ Phys.\ Chem.}, year = {2004}, volume = {108}, pages = {18003-18014}, } @Article{Binder:04b, author = {Binder, Hans and Kirsten, Toralf and Hofacker, Ivo L. and Stadler, Peter F. and Löffler, Markus}, year = {2004}, title = {Interactions in oligonucleotide hybrid duplexes on microarrays}, journal = {J.\ Phys.\ Chem.}, volume = {108}, pages = {18015-18025}, } @InCollection{Force:04a, author = {Force, Allan and Shashikant, Cooduvalli and Stadler, Peter F. and Amemiya, Chris T.}, title = {Comparative genomics, \emph{cis}-regulatory elements, and gene duplication}, booktitle = {The Zebrafish}, editor = {Detrich~III, H. and Zon, Leonard and Westerfield, Monte}, publisher = {Elsevier}, address = {New York}, year = {2004}, pages = {545-561}, series = {Methods in Cell Biology}, volume = {77}, } @InCollection{Schuster:04a, author = {Peter Schuster and Peter F. Stadler}, title = {Discrete Models of Biopolymers}, booktitle = {Handbook of Computational Chemistry and Biology}, editor = {Crabbe, M. James C. and Konopka, Andrzej}, publisher = {Marcel Dekker}, address = {New York}, year = {2004}, pages = {187-221}, } %% 2005 @Article{Tanzer:05a, author = {Tanzer, Andrea and Amemiya, Chris T. and Kim, Chang-Bae and Stadler, Peter F.}, title = {Evolution of Micro{RNA}s Located Within \emph{Hox} Gene Clusters}, journal = {J.\ Exp.\ Zool.: Mol.\ Dev.\ Evol.}, volume = {304B}, pages = {75-85}, year = {2005}, } @Article{Hackermueller:05a, author = {Hackerm{\"u}ller, J{\"o}rg and Meisner, Nicole-Claudia and Auer, Manfred and Jaritz, Markus and Stadler, Peter F.}, title = {The Effect of {RNA} Secondary Structures on {RNA}-Ligand Binding and the Modifier {RNA} Mechanism: A Quantitative Model}, journal = {Gene}, volume = {345}, pages = {3-12}, year = {2005}, } @Article{Washietl:05a, author = {Stefan Washietl and Ivo L. Hofacker and Peter F. Stadler}, title = {Fast and reliable prediction of noncoding {RNA}s}, journal = {Proc.\ Natl.\ Acad.\ Sci.\ USA}, year = 2005, volume = 102, pages = {2454-2459}, } @Article{Morgenstern:05a, author = {Morgenstern, Burkhard and Werner, Nadine and Prohaska, Sonja J. and Steinkamp, Rasmus and Schneider, Isabelle and Subramanian, Amarendran R. and Stadler, Peter F. and Weyer-Menkhoff, Jan}, title = {Multiple sequence alignment with user-de ned constraints \@ GOBICS}, journal = {Bioinformatics}, volume = {7}, pages = {1271-1273}, year = {2004}, } @Article{Dieterich:05a, author = {Dieterich, Christoph and Grossmann, Steffen and Tanzer, Andrea and Ropcke, Stefan and Arndt, Peter F and Stadler, Peter F and Vingron, Martin}, title = {Comparative promoter region analysis powered by \texttt{CORG}}, journal = {BMC Genomics}, volume = {6}, year = {2005}, pages = {24 [10 pages]}, note = {\texttt{http://www.biomedcentral.com/1471-2164/6/24}}, } @Article{Bompfuenewerer:05, author = {Bompf{\"u}newerer, Athanasius F. and Flamm, Christoph and Fried, Claudia and Fritzsch, Guido and Hofacker, Ivo L. and Lehmann, J{\"o}rg and Missal, Kristin and Mosig, Axel and M{\"u}ller, Bettina and Prohaska, Sonja J. and Stadler, B{\"a}rbel M. R. and Stadler, Peter F. and Tanzer, Andrea and Washietl, Stefan and Witwer, Christina}, title = {Evolutionary Patterns of Non-Coding {RNAs}}, journal = {Th.\ Biosci.}, year = {2005}, pages = {301-369}, volume = {123}, } @Article{Wagner:05a, author = {Wagner, G{\"u}nter P. and Takahashi, Kazuhiko and Lynch, Vincent and Prohaska, Sonja J. and Fried, Claudia and Stadler, Peter F. and Amemiya, Chris T.}, title = {Molecular Evolution of Duplicated Ray Finned Fisch HoxA Clusters: Increased synonymous substitution rate and asymmetrical co-divergence of coding and non-coding sequences}, journal = {J.\ Mol.\ Evol.}, pages = {665-676}, year = {2005}, } @Article{Boehmdorfer:05a, author = {B{\"o}hmdorfer, Gudrun and Hofacker, Ivo L. and Garber, Karin Jelenic, Srecko and Nizhynska, Viktoria and Hirochika, Hirohiko and Stadler, Peter F. and Bachmair, Andreas}, title = {Unorthodox {mRNA} start site to extend the highly structured leader of retrotransposon {Tto1} {mRNA} increases transposition rate}, journal = {RNA}, volume = {11}, pages = {1181-1191}, year = {2005}, } @Article{Stocsits:05a, author = {Stocsits, Roman R. and Hofacker, Ivo L. and Fried, Claudia and Stadler, Peter F.}, title = {Multiple sequence alignments of partially coding nucleic acid sequences}, journal = {BMC Bioinformatics}, year = {2005}, volume = {6}, pages = {160 [epub]}, } @Article{Gleiss:05a, author = {Petra M. Gleiss and Josef Leydold and Peter F. Stadler}, title = {Minimum Path Bases and Relevant Paths}, journal = {Networks}, year = {2005}, volume = {46}, pages = {119-123}, note = {Recent Trends in Graph Theory, Algebraic Combinatorics, and Graph Algorithms, Bled (Slovenia) Sep 24-27 2001; SFI Preprint 01-10-056}, } @InProceedings{Attolini:05a, author = {Stephan-Otto Attolini, Camille and Stadler, Peter F. and Flamm, Christoph}, title = {\texttt{CelloS}: a Multi-level Approach to Evolutionary Dynamics}, booktitle = {Advances in Artificial Life: 8th European Conference, ECAL 2005}, editor = {Mathieu S. Capcarrere and Alex A. Freitas and Peter J. Bentley and Colin G. Johnson and Jon Timmis}, pages = {500-509}, year = 2005, series = {Lect.\ Notes Comp.\ Sci.}, volume = {3630}, publisher = {Springer Verlag}, note = {Canterbury, UK, September 5-9, 2005} } @InProceedings{Benkoe:05b, author = {Benk{\"o}, Gil and Flamm, Christoph and Stadler, Peter F.}, title = {Explicit Collision Simulation of Chemical Reactions in a Graph Based Artifical Chemistry}, booktitle = {Advances in Artificial Life: 8th European Conference, ECAL 2005}, editor = {Mathieu S. Capcarrere and Alex A. Freitas and Peter J. Bentley and Colin G. Johnson and Jon Timmis}, pages = {725-733}, year = 2005, series = {Lect.\ Notes Comp.\ Sci.}, volume = {3630}, publisher = {Springer Verlag}, note = {Canterbury, UK, September 5-9, 2005} } @InCollection{Hofacker:05a, author = {Hofacker, Ivo L. and Stadler, Peter F.}, title = {{RNA} Secondary Structures}, editor = {Meyers, Robert A.}, booktitle = {Encyclopedia of Molecular Cell Biology and Molecular Medicine}, publisher = {Wiley-VCH}, address = {Weinheim}, year = {2005}, edition = {2nd}, volume = {12}, pages = {581-603}, } @Article{Mueckstein:05a, author = {M{\"u}ckstein, Ulrike and Tafer, Hakim and Hackerm{\"u}ller, J{\"o}r and Bernhard, Stephan Bernhard and Stadler, Peter F. and Hofacker, Ivo L}, title = {Thermodynamics of {RNA-RNA} Binding}, journal = {Bioinformatics}, pages = {1177-1182}, volume = {22}, year = {2006}, note = {Earlier version in: \emph{German Conference on Bioinformatics 2005}, Torda, Andrew and Kurtz, Stefan and Rarey, Matthias (eds.), Lecture Notes in Informatics \textbf{P-71}, pp 3-13, Gesellschaft f.\ Informatik, Bonn 2005}, } @Article{Hofacker:05b, author = {Hofacker, Ivo L. and Stadler, Peter F.}, title = {Memory Efficient Folding Algorithms for Circular {RNA} Secondary Structures}, journal = {Bioinformatics}, pages = {1172-1176}, volume = {22}, year = {2006}, note = {Earlier version in: \emph{German Conference on Bioinformatics 2005}, Torda, Andrew and Kurtz, Stefan and Rarey, Matthias (eds.), Lecture Notes in Informatics \textbf{P-71}, pp 3-13, Gesellschaft f.\ Informatik, Bonn 2005}, } @Article{Missal:05a, author = {Missal, Kristin and Rose, Dominic and Stadler, Peter F.}, title = {Non-coding {RNA}s in \emph{Ciona intestinalis}}, journal = {Bioinformatics}, volume = {21 S2}, pages = {i77-i78}, year = {2005}, note = {Proceedings ECCB/JBI'05, Madrid}, } @Article{Washietl:05b, author = {Washietl, Stefan and Hofacker, Ivo L. and Lukasser, Melanie and H{\"u}ttenhofer, Alexander and Stadler, Peter F.}, title = {Mapping of conserved {RNA} Secondary Structures predicts Thousands of functional Non-Coding {RNA}s in the Human Genome}, journal = {Nature Biotech.}, year = {2005}, volume = {23}, pages = {1383-1390}, } @Article{Biyikoglu:05a, author = {B{\i}y{\i}ko{\u g}lu, T{\"u}rker and Leydold, Josef and Stadler, Peter F.}, title = {Nodal Domain Theorems and Bipartite Subgraphs}, journal = {Elec.\ J.\ Lin.\ Algebra}, volume = {13}, pages = {344-351}, year = {2005}, } @Article{Attolini:05b, author = {Stephan-Otto Attolini, Camille and Stadler, Peter F.}, title = {Neutral Networks of Interacting {RNA} Secondary Structures}, journal = {Adv.\ Complex Syst.}, pages = {275-284}, year = 2005, volume = {8}, } % 2006 @Article{Crow:06a, author = {Crow, Karen D. and Stadler, Peter F. and Lynch, Vincent J. and Amemiya, Chris T. and Wagner, G{\"u}nter P.}, title = {The fish specific {Hox} cluster duplication is coincident with the origin of teleosts}, journal = {Mol.\ Biol.\ Evol.}, year = {2006}, pages = {121-136}, volume = {23}, } @Article{Hsu:06a, author = {Hsu, Wei-Che and Huang, Hsien-Da and Hsu, Sheng-Da and Lin, Li-Zen and Tsou, Ann-Ping and Tseng, Ching-Ping and Stadler, Peter F. and Washietl, Stefan and Hofacker, Ivo L.}, title = {\texttt{miRNAMap}: Genomic Maps of Micro{RNA} Genes and Their Target Genes in Mammalian Genomes}, journal = {Nucl.\ Acids Res.}, volume = {34}, pages = {D135-D139}, year = {2006}, note = {Database issue} } @Article{Hertel:06a, author = {Hertel, Jana and Lindemeyer, Manuela and Missal, Kristin and Fried, Claudia and Tanzer, Andrea and Flamm, Christoph and Hofacker, Ivo L. and Stadler, Peter F. and {The Students of Bioinformatics Computer Labs 2004 and 2005}}, title = {The Expansion of the Metazoan Micro{RNA} Repertoire}, journal = {BMC Genomics}, volume = {7}, pages = {15 [epub]}, year = {2006}, } @Article{Forst:06a, author = {Forst, Christian V. and Flamm, Christoph and Hofacker, Ivo L. and Stadler, Peter F.}, title = {Algebraic Comparison of Metabolic Networks, Phylogenetic Inference, and Metabolic Innovation}, journal = {BMC Bioinformatics}, volume = {7}, pages = {67 [epub]}, year = {2006}, } @Article{Klemm:06a, author = {Klemm, Konstantin and Stadler, Peter F.}, title = {Statistics of cycles in large networks}, journal = {Phys.\ Rev.\ E}, volume = {73}, pages = {025101}, year = {2006}, note = {cond-mat/0506493}, } @Article{Bernhart:06a, author = {Bernhart, Stephan and Hofacker, Ivo L. and Stadler, Peter F.}, title = {Local {RNA} Base Pairing Probabilities in Large Sequences}, journal = {Bioinformatics}, volume = {22}, pages = {614-615}, year = {2006} } @Article{Imrich:06a, author = {Imrich, Wilfried and Stadler, Peter F.}, title = {A Prime Factor Theorem for a Generalized Direct Product}, journal = {Discussiones Math.\ Graph Th.}, volume = {26}, pages = {135-140}, year = {2006}, } @Article{Bernhart:06b, author = {Bernhart, Stephan H. and Tafer, Hakim and M{\"u}ckstein, Ulrike and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L.}, title = {Partition Function and Base Pairing Probabilities of {RNA} Heterodimers}, journal = {Algorithms Mol.\ Biol.}, year = {2006}, volume = {1}, pages = {3 [epub]}, } @InCollection{Hofacker:06a, author = {Hofacker, Ivo L. and Stadler, Peter F.}, title = {Modeling {RNA} Folding}, booktitle = {Complex Systems Science in BioMedicine}, editor = {Deisboeck, Thomas S. and Kresh, J. Yasha}, publisher = {Springer}, address = {New York}, year = {2006}, pages = {227-245}, } @Article{Mosig:06a, author = {Mosig, Axel and Sameith, Katrin and Stadler, Peter F.}, title = {\texttt{fragrep}: Efficient Search for Fragmented Patterns in Genomic Sequences}, journal = {Geno.\ Prot.\ Bioinfo.}, volume = {4}, pages = {56-60}, year = {2005}, } @Article{Morgenstern:06, author = {Morgenstern, Burkhard and Prohaska, Sonja J and Pohler, Dirk and Stadler, Peter F}, title = {Multiple sequence alignment with user-defined anchor points}, journal = {Algo.\ Mol.\ Biol.}, year = {2006}, volume = {1}, pages = {6 [epub]}, note = {Updated version of the GCB contribution \protect\cite{Morgenstern:04}}, } @Article{Wolfinger:06a, author = {Wolfinger, Michael T. and Will, Sebastian and Hofacker, Ivo L. and Backofen, Rolf and Stadler, Peter F.}, title = {Exploring the Lower Part of Discrete Polymer Model Energy Landscapes}, journal = {Europhys.\ Lett.}, volume = {74}, pages = {726-732}, year = {2006}, } @Article{Fritzsch:06a, author = {Fritzsch, Guido and Schlegel, Martin and Stadler, Peter F.}, title = {Alignments of Mitochondrial Genome Arrangements: Applications to Metazoan Phylogeny}, journal = {J.\ Theor.\ Biol.}, volume = {240}, pages = {511-520}, year = {2006}, } @Article{StephanOtto:06a, author = {Stephan-Otto Attolini, Camille and Stadler, Peter F.}, title = {Evolving Towards the Hypercycle: A Spatial Model of Molecular Evolution}, journal = {Physica D}, volume = {217}, pages = {134-141}, year = {2006}, } @Article{Missal:06a, author = {Missal, Kirstin and Zhu, Xiaopeng and Rose, Dominic and Deng, Wei and Skogerb{\o}, Geir and Chen, Runsheng and Stadler, Peter F.}, title = {Prediction of Structured Non-Coding {RNA}s in the Genome of the Nematode \emph{Caenorhabitis elegans}}, journal = {J.\ Exp.\ Zool.: Mol.\ Dev.\ Evol.}, volume = {306B}, pages = {379-392}, year = {2006}, } @Article{Hertel:06b, author = {Hertel, Jana and Stadler, Peter F.}, title = {Hairpins in a Haystack: Recognizing {microRNA} Precursors in Comparative Genomics Data}, journal = {Bioinformatics}, volume = {22}, pages = {e197-e202 }, year = {2006}, note = {ISMB 2006 contribution}, } @InCollection{Tanzer:06a, author = {Tanzer, Andrea and Stadler, Peter F.}, title = {Evolution of Micro{RNA}s}, booktitle = {MicroRNA Protocols}, editor = {Ying, Shao Yao}, publisher = {Humana Press}, address = {Totowa, NJ}, series = {Methods in Molecular Biology}, volume = {342}, year = {2006}, pages = {335-350}, } @Article{Prohaska:06a, author = {Prohaska, Sonja J. and Stadler, Peter F.}, title = {Evolution of the Vertebrate Parahox Clusters}, journal = {J.\ Exp.\ Zool.: Mol.\ Dev.\ Evol.}, volume = {306B}, pages = {481-487}, year = {2006}, } @Article{Heine:06a, author = {Heine, Christian and Scheuermann, Gerik and Flamm, Christoph and Hofacker, Ivo L. and Stadler, Peter F.}, title = {Visualization of Barrier Tree Sequences}, journal = {IEEE Trans.\ Vis.\ Comp.\ Graphics}, volume = {12}, pages = {781-788}, year = {2006}, note = {\emph{Info-Vis 2006 contribution}}, } @InProceedings{Poetzsch:06a, author = {P{\"o}tzsch, Sebastian and Scheuermann, Gerik and Wolfinger, Michael T. and Flamm, Christoph and Stadler, Peter F.}, title = {Visualization of Lattice-Based Protein Folding Simulations}, booktitle = {Tenth International Conference on Information Visualization {(IV'06)a}}, year = {2006}, pages = {89-94}, editor = {Banissi, Ebad}, publisher = {IEEE Computer Society Press}, address = {Los Alamitos, CA}, note = {doi: 10.1109/IV.2006.127}, } @InProceedings{Mosig:06b, author = {Mosig, Axel and Hofacker, Ivo L. and Stadler, Peter F.}, title = {Comparative Analysis of Cyclic Sequences: Viroids and other Small Circular {RNAs}}, booktitle = {Proceedings GCB 2006}, series = {Lecture Notes in Informatics}, editor = {Giegerich, Robert and Stoye, Jens}, volume = {P-83}, year = {2006}, pages = {93-102}, } @Article{Stadler:06a, author = {Stadler, Peter F. and Stadler, B{\"a}rbel M. R.}, title = {Genotype Phenotype Maps}, journal = {Biological Theory}, pages = {268-279 }, volume = {3}, year = {2006}, note = {Konrad Lorenz Institute Workshop on Biological Information organized by Werner Callebaut in 2002}, } % 2007 @Article{Conant:07a, author = {Conant, Gavin C. and Wagner, G{\"u}nter P. and Stadler, Peter F.}, title = {Patterns of amino acid substitution in orthologous and paralogous genes}, journal = {Mol.\ Phylog.\ Evol.}, volume = {42}, pages = {298-307}, year = {2007}, } @InCollection{Prohaska:06b, author = {Prohaska, Sonja J. and Stadler, Peter F. and Wagner, G{\"u}nter P.}, title = {Evolutionary Genomics of \emph{Hox} Gene Clusters}, booktitle = {HOX Gene Expression}, editor = {Papageorgiou, Spyros}, publisher = {Landes Bioscience \& Springer}, address = {New York}, year = {2006}, pages = {68-90}, } % 2007 @Article{Bompfuenewerer:07a, author = {{The Athanasius F.\ Bompf{\"u}newerer RNA Consortium:} and Backofen, Rolf and Flamm, Christoph and Fried, Claudia and Fritzsch, Guido and Hackerm{\"u}ller, J{\"o}rg and Hertel, Jana and Hofacker, Ivo L. and Missal, Kristin and Mosig, Axel Prohaska, Sonja J. and Rose, Domininc and Stadler, Peter F. and Tanzer, Andrea and Washietl, Stefan and Will Sebastian}, title = {{RNA}s Everywhere: Genome-Wide Annotation of Structured {RNA}s}, journal = {J.\ Exp.\ Zool.\ B: Mol.\ Dev.\ Evol.}, year = {2007}, pages = {1-25}, volume = {308B}, } @InCollection{Hofacker:07a, author = {Hofacker, Ivo L. and Stadler, Peter F.}, title = {{RNA} Secondary Structures}, booktitle = {Bioinformatics: From Genomes to Therapies}, editor = {Lengauer, Thomas}, publisher = {Wiley-VCH}, address = {Weinheim, Germany}, year = {2007}, volume = {1}, pages = {439--489}, } @Article{Woodhams:07a, author = {Woodhams, Michael D. and Stadler, Peter F. and Penny, David and Collins, Lesley J.}, title = {{RNAse MRP} and the {RNA} Processing Cascade in the Eukaryotic Ancestor}, journal = {BMC Evol.\ Biol.}, volume = {7}, pages = {S13}, year = {2007}, } @Article{Will:07a, author = {Will, Sebastian and Missal, Kristin and Hofacker, Ivo L. and Stadler, Peter F. and Backofen, Rolf}, title = {Inferring Non-Coding {RNA} Families and Classes by Means of Genome-Scale Structure-Based Clustering}, journal = {PLoS Comp.\ Biol.}, volume = {3}, pages = {e65}, year = {2007}, } @Article{Luo:07a, author = {Luo, Jing and Stadler, Peter F. and He, Shunping and Meyer, Axel}, title = {{PCR} Survey of {Hox} Genes in the {G}oldfish \emph{Carassius auratus auratus}}, journal = {J.\ Exp.\ Zool.\ B: (Mol.\ Devel.\ Evol.)}, volume = {308B}, pages = {250-258}, year = {2007}, } @Article{Mosig:07a, author = {Mosig, Axel and Guofeng, Meng and Stadler, B{\"a}rbel M. R. and Stadler, Peter F.}, title = {Evolution of the Vertebrate {Y} {RNA} Cluster}, journal = {Th.\ Biosci.}, volume = {126}, pages = {9-14}, year = {2007}, } @Article{Perseke:07a, author = {Perseke, Madleen and Hankeln, Thomas and Weich, Bettina and Fritzsch, Guido and Stadler, Peter F. and Bernhard, Detlef and Schlegel, Martin}, title = {The Mitochondrial {DNA} of \emph{Xenoturbella bocki}: Genomic Architecture and Phylogenetic Analysis}, journal = {Th.\ Biosci.}, volume = {126}, pages = {35-42}, year = {2007}, } @Article{Kapranov:07a, author = {Kapranov, P and Cheng, J and Dike, S. and Nix, D and Duttagupta, R. and Willingham, A. T. and Stadler, P. F. and Hertel, J. and Hackerm{\"u}ller, J. and Hofacker, I. L. and Bell, I. and Cheung, E. and Drenkow, J. and Dumais, E. and Patel, S. and Helt,G. and Madhavan, G. and Piccolboni, A and Sementchenko, V and Tammana, H. and Gingeras, T. R.}, title = {{RNA} Maps Reveal New {RNA} Classes and a Possible Function for Pervasive Transcription}, journal = {Science}, volume = {316}, pages = {1484-1488}, year = {2007}, } @Article{Reiche:07a, author = {Reiche, Kristin and Stadler, Peter F.}, title = {\texttt{RNAstrand}: Reading Direction of Structured {RNA}s in Multiple Sequence Alignments}, journal = {Alg.\ Mol.\ Biol.}, volume = {1}, pages = {6}, year = {2007}, } @Article{Washietl:07a, author = {Washietl, Stefan and Pedersen, Jakob S. and Korbel, Jan O. and Gruber, Andreas and Hackerm{\"u}ller, J{\"o}rg and Hertel, Jana and Lindemeyer, Manja and Reiche, Kristin and Stocsits, Claudia and Tanzer, Andrea and Ucla, Catherine and Wyss, Carine and Antonarakis, Stylianos E. and Denoeud, France and Lagarde, Julien and Drenkow, Jorg and Kapranov, Philipp and Gingeras, Thomas R. and Guig{\'o}, Roderic and Snyder, Michael and Gerstein, Mark B. and Reymond, Alexandre and Hofacker, Ivo L. and Stadler, Peter F.}, title = {Structured {RNA}s in the {ENCODE} Selected Regions of the Human Genome}, journal = {Gen.\ Res.}, volume = {17}, pages = {852-864}, year = {2007}, } @Article{ENCODE:07a, author = {{The ENCODE Project Consortium}}, title = {Identification and analysis of functional elements in {1\%} of the human genome by the {ENCODE} pilot project}, journal = {Nature}, volume = {447}, pages = {799-816}, year = {2007}, } @Article{Wagner:07a, author = {Wagner, G{\"u}nter P. and Otto, Wolfgang and Lnych, Vincent and Stadler, Peter F.}, title = {The transient probability distribution of $M/M/\infty$: a stochastic model for transcription factor binding site evolution}, journal = {J.\ Theor.\ Biol.}, volume = {247}, pages = {544-553}, year = {2007}, } @Article{Steigele:07a, author = {Steigele, Stephan and Huber, Wolfgang and Fried, Claudia and Stadler, Peter F. and Nieselt, Kay}, title = {Comparative Analysis of Structured {RNA}s in \emph{S.\ cerevisiae} Indicates a Multitude of Different Functions}, journal = {BMC Biology}, volume = {5v}, pages = {25}, year = {2007}, } @Article{Loeffler:07a, author = {L{\"o}ffler, Dennis and Brocke-Heidrich, Katja and Pfeifer, Gabriele and Stocsits, Claudia and Hackerm{\"u}ller, J{\"o}rg and Kretzschmar, Antje and Burger, Renate and Gramatzki, Martin and Blumert, Conny and Bauer, Kay and Cvijic, Helena and Ullmann, Kerstin and Stadler, Peter F. and Horn, Friedemann}, title = {Interleukin-6âdependent survival of multiple myeloma cells involves the {Stat3}-mediated induction of {microRNA-21} through a highly conserved enhancer}, journal = {Blood}, volume = {110}, year = {2007}, pages = {1330-1333}, } @Article{Kruspe:07a, author = {Kruspe, Matthias and Stadler, Peter F.}, title = {Progressive Multiple Sequence Alignments from Triplets}, journal = {BMC Bioinformatics}, volume = {8}, pages = {254}, year = {2007}, note = {doi: doi:10.1186/1471-2105-8-254}, } @InProceedings{Flamm:07a, author = {Flamm, Christoph and Stadler, B{\"a}rbel M. R. and Stadler, Peter F.}, title = {Saddles and Barrier in Landscapes of Generalized Search Operators}, booktitle = {Foundations of Genetic Algortithms IX}, editor = {Stephens, C. R. and Toussaint, M. and Whitley, D. and Stadler, P. F.}, publisher = {Springer}, address = {Berlin, Heidelberg}, year = {2007}, pages = {194-212}, series = {Lecture Notes Comp.\ Sci.}, volume = {4436}, note = {9th International Workshop, FOGA 2007, Mexico City, Mexico, January 8-11, 2007}, } @InCollection{Schuster:07a, author = {Schuster, Peter and Stadler, Peter F.}, title = {Modeling Conformational Flexibility and Evolution of Structure: {RNA} as an Example}, booktitle = {Structural Approaches to Sequence Evolution: Molecules, Networks, Populations}, editor = {Bastolla, Ugo and Porto, Markus and Roman, H. Eduardo and Vendruscolo, Michele}, publisher = {Springer Verlag}, address = {Berlin}, pages = {3-36}, year = {2007}, } @InProceedings{Mosig:07b, author = {Mosig, Axel and Chen, Julian L. and Stadler, Peter F.}, title = {Homology Search with Fragmented Nucleic Acid Sequence Patterns}, booktitle = {Algorithms in Bioinformatics (WABI 2007)}, editor = {Giancarlo, R. and Hannenhalli, S.}, series = {Lecture Notes in Computer Science}, volume = {4645}, pages = {335-345}, publisher = {Springer Verlag}, address = {Berlin, Heidelberg}, year = {2007}, } @InCollection{Prohaska:07a, author = {Prohaska, Sonja J. and Mosig, Axel and Stadler, Peter F.}, title = {Regulatory Signals in Genomic Sequences}, booktitle = {Networks: From Biology to Theory}, editor = {Feng, Jianfeng and Jost, J{\"u}rgen and Qian, Minping}, publisher = {Springer}, address = {New York}, pages = {191-220}, year = {2007}, } @InProceedings{Menzel:07a, author = {Menzel, Peter and Stadler, Peter F. and Mosig, Axel}, title = {{T}animoto's {B}est {B}arbecue: Discovering Regulatory Modules using Tanimoto Scores}, booktitle = {German Conference on Bioinformatics (GCB 2007)}, editor = {Falter, Claudia and Schliep, Alexander and Selbig, Joachim and Vingron, Martin and Walther, Dirk}, publisher = {Gesellschaft f.\ Informatik}, address = {Bonn}, series = {Lecture Notes in Informatics}, volume = {115}, year = {2007}, pages = {68-77}, } @Article{Seemann:07a, author = {Seemann, Stefan E. and Gilchrist, Michael J. and Hofacker, Ivo L. and Stadler, Peter F. and Gorodkin, Jan}, title = {Detection of {RNA} structures in porcine {EST} data and related mammals}, journal = {BMC Genomics}, volume = {8}, pages = {316}, year = {2007}, } @Article{Bernt:07a, author = {Bernt, Matthias and Merkle, Daniel and Rasch, Kai and Fritzsch, Guido and Perseke, Marleen and Bernhard, Detlef and Schlegel, Martin and Stadler, Peter F. and Middendorf, Martin}, title = {\texttt{CREx}: Inferring Genomic Rearrangements Based on Common Intervals}, journal = {Bioinformatics}, volume = {23}, pages = {2957-2958}, year = {2007}, } @Article{Rose:07a, author = {Rose, Dominic Rose and Hackerm\"{u}ller, J\"{o}rg and Washietl, Stefan and Findei{\ss}, Sven and Reiche, Kristin and Hertel, Jana and Stadler, Peter F. and Prohaska, Sonja J.}, title = {Computational {RNomics} of Drosophilids}, journal = {BMC Genomics}, volume = {8}, pages = {406}, year = {2007}, } @Article{Marz:07a, author = {Marz, Manja and Mosig, Axel and Stadler, B{\"a}rbel M. R. and Stadler, Peter F.}, title = {{U7} {snRNAs}: A Computational Survey}, journal = {Geno.\ Prot.\ Bioinf.}, volume = {5}, pages = {187-195}, year = {2007}, } @InCollection{Heine:07a, author = {Heine, Christian and Scheuermann, Gerik and Flamm, Christoph and Hofacker, Ivo and Stadler, Peter F.}, editor = {Linsen, Lars and Hagen, Hans and Hamann, Bernd}, title = {Visualization of Barrier Tree Sequences Revisited}, publisher = {Springer}, address = {Berlin, Heidelberg}, year = {2007}, booktitle = {Visualization in Medicine and Life Sciences}, pages = {275-290}, } % 2008 @Article{Bompfuenewerer:08a, author = {Bompf{\"u}newerer, Athanasius F. and Backofen, Rolf and Berhart, Stephan H. and Hertel, Jana and and Hofacker, Ivo L. and Stadler, Peter F. and Will, Sebastian}, title = {Variations on {RNA} Folding and Alignment: Lessons from {Benasque}}, journal = {J.\ Math.\ Biol.}, pages = {129-144}, volume = {56}, year = {2008}, } @Article{Hertel:08a, author = {Hertel, Jana and Hofacker, Ivo L. and Stadler, Peter F.}, title = {\texttt{snoReport}: Computational identification of {snoRNAs} with unknown targets}, journal = {Bioinformatics}, volume = {24}, pages = {158-164}, year = {2008}, } @Article{Xie:08a, author = {Xie, Mingyi and Mosig, Axel and Qi, Xiaodong and Li, Yang and Stadler, Peter F. and Chen, Julian J.-L.}, title = {Size Variation and Structural Conservation of Vertebrate Telomerase {RNA}}, journal = {J.\ Biol.\ Chem.}, volume = {283}, pages = {2049-2059}, year = {2008}, } @Article{Gruber:08a, author = {Gruber, Andreas R. and Koper-Emde, Dorota and Marz, Manja and Tafer, Hakim and Bernhart, Stephan and Obernosterer, Gregor and Mosig, Axel and Hofacker, Ivo L. and Stadler, Peter F. and Benecke, Bernd-Joachim}, title = {Invertebrate {7SK} {snRNAs}}, journal = {J.\ Mol.\ Evol.}, pages = {66}, volume = {107-115}, year = {2008}, } @Article{Fritzsch:08a, author = {Fritzsch, Guido and B{\"o}hme, Manja U. and Thorndyke, Mike and Nakano, Hiroaki and Israelsson, Olle and Stach, Thomas and Schlegel, Martin and Hankeln, Thomas and Stadler, Peter, F.}, title = {A {PCR} Survey of \emph{Xenoturbella bocki} \emph{Hox} Genes}, journal = {J.\ Exp.\ Zool: Mol.\ Dev.\ Evol.}, volume = {310B}, pages = {278-284}, year = {2008}, } @Article{Krauss:08a, author = {Krauss, Veiko and Th{\"u}mmler, Christian and Georgi, Franziska and Lehmann, J{\"o}rg and Stadler, Peter F. and Eisenhardt, Carina}, title = {Near intron positions are reliable phylogenetic markers: An application to {Holometabolous Insects}}, journal = {Mol.\ Biol.\ Evol.}, volume = {25}, pages = {821-830}, year = {2008}, } @Article{Perseke:08a, author = {Perseke, Marleen and Fritzsch, Guido and Ramsch, Kai and Bernt, Matthias and Merkle, Daniel and Middendorf, Martin and Bernhard, Detlef and Stadler, Peter F. and Schlegel, Martin}, title = {Evolution of Mitochondrial Gene Orders in Echinoderms}, journal = {Mol.\ Phylog.\ Evol.}, volume = {47}, pages = {855-864}, year = {2008}, } @Article{Joechl:08a, author = {J{\"o}chl, Christoph and Rederstorff, Mathieu and Hertel, Jana and Stadler, Peter F. and Hofacker, Ivo L. and Schrettl, Markus and Haas, Hubertus and H{\"u}ttenhofer, Alexander}, title = {Small {ncRNA} transcriptome analysis from \emph{Aspergillus fumigatus} suggests a novel mechanism for regulation of protein-synthesis}, journal = {Nucleic Acids Res.}, volume = {36}, pages = {2677-2689}, year = {2008}, } @Article{Geis:08a, author = {Geis, Michael and Flamm, Christian and Wolfinger, Michael T. and Tanzer, Andrea and Hofacker, Ivo L. and Middendorf, Martin and Mandl, Christian and Stadler, Peter F. and Thurner, Caroline}, title = {Folding kinetics of large {RNA}s}, journal = {J.\ Mol.\ Biol.}, volume = {379}, pages = {160-173}, year = {2008}, } @InProceedings{Prohaska:08a, author = {Prohaska, Sonja J. and Fritzsch, Guido and Stadler, Peter F.}, title = {Rate Variations, Phylogenetics, and Partial Orders}, booktitle = {Fifth International Workshop on Computational Systems Biology, WCSB 2008}, editor = {Ahdesm{\"a}ki, Miika and Strimmer, Korbinian and Radde, Nicole and Rahnenf{\"u}hrer, J{\"o}rg and Klemm, Konstantin and L{\"a}hdesm{\"a}ki, Harri and Yli-Harja, Olli}, publisher = {TU Tampere}, address = {Tampere, FI}, year = {2008}, pages = {133-136}, } @Article{Amemiya:08a, author = {Amemiya, Chris T and Prohaska, Sonja J and Hill-Force, Alicia and Cook, April and Wasserscheid, Jessica and Ferrier David E. K., Pascual-Anaya, Juan and Garcia-Fern{\`a}ndez, Jordi and Dewar, Ken and Stadler, Peter F.}, title = {The amphioxus \emph{Hox} cluster: characterization, comparative genomics, and evolution}, journal = {J.\ Exp.\ Zool.\ B: Mol.\ Dev.\ Evol.}, volume = {310B}, pages = {465-477}, year = {2008}, } @Article{Rose:08a, author = {Rose, Dominic and Hertel, Jana and Reiche, Kristin and Stadler, Peter F. and Hackerm{\"u}ller, J{\"o}rg}, title = {\texttt{NcDNAlign}: Plausible Multiple Alignments of Non-Protein-Coding Genomic Sequences}, journal = {Genomics}, volume = {92}, pages = {65-74}, year = {2008}, } @Article{Klemm:08a, author = {Klemm, Konstantin and Flamm, Christoph and Stadler, Peter F.}, title = {Funnels in Energy Landscapes}, year = {2008}, journal = {Eur.\ Phys.\ J.\ B}, volume = {63}, pages = {387-391}, note = {ECCS 2007 contribution}, } @Article{Dress:08a, author = {Dress, Andreas W. M. and Flamm, Christoph and Fritzsch, Guido and Gr{\"u}newald, Stefan and Kruspe, Matthias and Prohaska, Sonja J. and Stadler, Peter F.}, title = {Identification of Homoplastic Characters in Multiple Sequence Alignments}, journal = {Alg.\ Mol.\ Biol.}, volume = {3}, pages = {7}, year = {2008}, note = {extended abstract accepted at ICMSB 2008}, } @InProceedings{Prohaska:08b, author = {Prohaska, Sonja J. and Stadler, Peter F.}, title = {A story of Growing Confusion: Genes and Their Regulation}, year = {2007}, booktitle = {BIOMAT-2007: International Symposium on Mathematical and Computational Biology}, editor = {Mondaini, Rubem P. and Dil{\~a}o, Rui}, publisher = {World Scientific}, address = {Singapore}, pages = {325-345}, note = {Arma{\c c}{\~a}o dos B{\'u}zios, RJ, Brazil, 24-29 November 2008}, } @Article{Prohaska:08c, author = {Prohaska, Sonja J. and Stadler, Peter F.}, title = {{``Genes''}}, journal = {Th.\ Biosci.}, volume = {127}, pages = {215-221}, year = {2008}, } @Article{Hoffmann:08a, author = {Hoffmann, Steve and Cepok, Sabine and Lehmann-Horn, Klaus and Hackerm{\"u}ller, J{\"o}rg and Stadler, Peter F. and Hartung, Hans-Peter and Berthele, Achim and Deisenhammer, Florian and Wasmuth, Ralf and Hemmer, Bernhard}, title = {{HLA-DRB1*0401} and {HLA-DRB1*0408} are strongly associated with the development of antibodies against interferon-beta therapy in multiple sclerosis}, journal = {Amer.\ J.\ Hum.\ Genet.}, volume = {83}, pages = {219-227}, year = {2008}, } @Article{Gruber:08b, author = {Gruber, Andreas and Kilgus, Carsten and Mosig, Axel and Hofacker, Ivo L. and Hennig, Wolfgang and Stadler, Peter F.}, title = {Arthropod {7SK} {RNA}}, journal = {Mol. Biol.\ Evol.}, pages = {25}, volume = {1923-1930}, year = {2008}, } @Article{Lehmann:08a, author = {Lehmann, J{\"o}rg and Stadler, Peter F. and Prohaska, Sonja J.}, title = {\texttt{SynBlast}: Assisting the Analysis of Conserved Synteny Information}, journal = {BMC Bioinformatics}, volume = {9}, pages = {351}, year = {2008}, note = {doi:10.1186/1471-2105-9-351}, } @InProceedings{Mueckstein:08a, author = {M{\"u}ckstein, Ulrike and Tafer, Hakim and Bernhard, Stephan H. and Hernandez-Rosales, Maribel and Vogel, J{\"o}rg and Stadler, Peter F. and Hofacker, Ivo L.}, title = {Translational Control by {RNA-RNA} Interaction: Improved Computation of {RNA-RNA} Binding Thermodynamics}, booktitle = {BioInformatics Research and Development --- BIRD 2008}, series = {Comm.\ Comp.\ Inf.\ Sci.}, editor = {Elloumi, Mourad and K{\"u}ng, Josef and Linial, Michal and Murphy, Robert F. and Schneider, Kristan and Toma, Cristian Toma}, publisher = {Springer}, address = {Berlin}, volume = {13}, year = {2008}, pages = {114-127}, } @InCollection{Schuster:08a, author = {Peter Schuster and Peter F. Stadler}, title = {Nature and Evolution of Early Replicons}, booktitle = {Origin and Evolution of Viruses}, edition = {2nd}, editor = {Domingo, E. and Parrish, C. R. and Holland, J.}, publisher = {Academic Press}, address = {London, UK}, year = {2008}, pages = {1-41}, note = {completely rewritten from \cite{Schuster:99a}}, } @Article{Sonnleitner:08a, author = {Sonnleitner, Elisabeth and Sorger-Domenigg, Theresa and Madej, Monika J. and Findei{\ss}, Sven and Hackerm{\"u}ller, J{\"o}rg and H{\"u}ttenhofer, Alexander and Stadler, Peter F. and Bl{\"a}si, Udo and Moll, Isabella}, title = {Detection of small non-coding {RNA}s in \emph{Pseudomonas aeruginosa} by {RNomics} and structure-based bioinformatics tools}, journal = {Microbiology}, pages = {3175-3187}, volume = {154}, year = {2008}, } @InCollection{Stadler:08a, author = {Stadler, Peter F. and Stadler, B{\"a}rbel M. R.}, editor = {Rasmussen, Steen and Bedau, Mark A. and Chen, Liaohai and Deamer, David and Krakauer, David C. and Packard, Norman H. and Stadler, Peter F. }, title = {Replicator Dynamics in Protocells}, booktitle = {Protocells: Bridging Nonliving and Living Matter}, publisher = {MIT Press}, year = {2008}, pages = {317-336}, } @InProceedings{Heffel:08a, author = {Heffel, Andreas and Stadler, Peter F. and Prohaska, Sonja J. and Kauer, Gerhard and Kuska, Jens-Peer}, title = {Process Flow for Classification and Clustering of Fruit Fly Gene Expression Patterns}, booktitle = {Proceedings of the 15'th IEEE International Conference on Image Processing, ICIP 2008}, publisher = {IEEE}, year = {2008}, pages = {721-724}, note = {CD Proceedings; ISSN 978-1-4244-1764-3/08/}, } @Article{Rose:08b, author = {Rose, Dominic and J{\"o}ris, Julian and Hackerm{\"u}ller, J{\"o}rg and Reiche, Kristin and Li, Qiang and Stadler, Peter F.}, title = {Duplicated {RNA} Genes in Teleost Fish Genomes}, journal = {J.\ Bioinf.\ Comp.\ Biol.}, volume = {6}, pages = {1157-1175}, year = {2008}, } @Article{Bernhart:08a, author = {Bernhart, Stephan H and Hofacker, Ivo L and Will, Sebastian and Gruber, Andreas R and Stadler, Peter F}, title = {\texttt{RNAalifold}: improved consensus structure prediction for {RNA} alignments}, journal = {BMC Bioinformatics}, year = {2008}, volume = {9}, pages = {474}, } @Article{Marz:08a, author = {Marz, Manuela and Kirsten, Toralf and Stadler, Peter F.}, title = {Evolution of Spliceosomal {snRNA} Genes in Metazoan Animals}, journal = {J.\ Mol.\ Evol.}, pages = {594-607}, volume = {67}, year = {2008}, } % 2009 @Article{Benkoe:09a, author = {Benk{\"o}, Gil and Centler, Florian and Dittrich, Peter and Flamm, Christoph and Stadler, B{\"a}rbel M. R. and Stadler, Peter F.}, title = {A Topological Approach to Chemical Organizations}, journal = {Alife}, volume = {15}, pages = {71-88}, year = {2009}, } @Article{Juehling:09a, author = {J{\"u}hling, Frank and M{\"o}rl, Mario and Hartmann, Roland K and Sprinzl, Mathias and Stadler, Peter F and P{\"u}tz, J{\"o}rn}, title = {\texttt{tRNAdb} 2009: compilation of {tRNA} sequences and {tRNA} genes}, journal = {Nucleic Acids Res.}, year = {2009}, volume = {37}, pages = {D159-D162}, } @Article{Jones:09a, author = {Jones, T A and Otto, Wolfgang and Marz, Manja and Eddy, Sean R and Stadler, Peter F}, title = {A survey of nematode {SmY} {RNA}s}, journal = {RNA Biol.}, volume = {6}, pages = {5-8}, year = {2009} } @Article{Kaczkowski:09a, author = {Kaczkowski, Bogumil and Torarinsson, Elfar and Reiche, Kristin and Havgaard, Jakob Hull and Stadler, Peter F. and Gorodkin, Jan}, title = {Structural profiles of mi{RNA} families from pairwise clustering}, journal = {Bioinformatics}, volume = {25}, pages = {291-294}, year = {2009}, } @Article{Hertel:09a, author = {Hertel, Jana and de Jong, Danielle and Marz, Manja and Rose, Dominic and Tafer, Hakim and Tanzer, Andrea and Schierwater, Bernd and Stadler, Peter F.}, title = {Non-Coding {RNA} Annotation of the Genome of \emph{Trichoplax adhaerens}}, journal = {Nucleic Acids Res.}, volume = {37}, pages = {1602-1615}, year = {2009}, } @Article{ScheibyeAlsing:09, author = {Scheibye-Alsing, Karsten and Hoffmann, Steve and Frankel, Annett M. and Jensen, Peter and Stadler, Peter F. and Mang, Yuan and Tommerup, Niels and Gilchrist, Mike J and Hillig, Ann-Britt N. and Cirera, Susanna and J{\o}rgensen, Claus B and Fredholm, Merete and Gorodkin, Jan}, title = {Sequence Assembly}, journal = {Comp.\ Biol.\ Chem.}, volume = {33}, pages = {121-136}, year = {2009}, } @InProceedings{Heffel:09a, author = {Heffel, Andreas and Prohaska, Sonja J. and Stadler, Peter F. and Kauer, Gerhard and Kuska, Jens-Peer}, title = {Automatic Classification of Embryonic Fruit Fly Gene Expression Patterns}, booktitle = {Bildverarbeitung f{\"u}r die Medizin 2009: Algorithmen -- Systeme -- Anwendungen}, editor = {Meinzer, H.-P. and Deserno, Th. M. and Handels, H. and Tolxdorff, Th.}, year = {2009}, publisher = {Springer}, address = {Heidelberg}, bookseries = {Informatik aktuell}, pages = {415-419} } @Article{Hellmuth:09a, author = {Hellmuth, Marc and Imrich, Wilfried and Kl{\"o}ckl, Werner and Stadler, Peter F.}, title = {Approximate graph products}, journal = {Eur.\ J.\ Comb.}, volume = {30}, pages = {1119-1133}, year = {2009}, } @Article{Chambers:09a, author = {Chambers, Karen E and McDaniell, Ryan and Raincrow, Jeremy D and Deshmukh, Maya and Stadler, Peter F and Chiu, Chi-hua}, title = {{Hox} cluster duplication in the basal teleost \emph{Hiodon alosoides} ({Osteoglossomorpha})}, journal = {Theory Biosci.}, volume = {128}, pages = {109-120}, year = {2009}, } @Article{Conant:09a, author = {Conant, Gavin C. and Stadler, Peter F.}, title = {Solvent exposure imparts similar selective pressures across a range of yeast proteins}, journal = {Mol.\ Biol.\ Evol.}, volume = {26}, pages = {1155-1161}, year = {2009}, } @Article{Klemm:09a, author = {Klemm, Konstantin and Stadler, Peter F.}, title = {A Note on Fundamental, Non-fundamental, and Robust Cycle Bases}, journal = {Discr.\ Appl.\ Math.}, pages = {2432-2438}, volume = {157}, year = {2009}, } @Article{Mosig:09a, author = {Mosig, Axel and B{\i}y{\i}ko{\u g}lu, T{\"u}rker and Prohaska, Sonja J. and Stadler, Peter F.}, title = {Discovering cis-regulatory modules by optimizing barbecues}, pages = {2458-2468}, year = {2008}, volume = {157}, journal = {Discr.\ Appl.\ Math.}, } @Article{Otto:09a, author = {Otto, Wolfang and Stadler, Peter F. and L{\'o}pez-Giald{\'e}z, Francesc and Townsend, Jeffrey P. and Lynch, Vincent J. and Wagner, G{\"u}nter P.}, title = {Measuring Transcription Factor Binding Site Turnover: A Maximum Likelihood Approach using Phylogenies}, journal = {Genome Biol.\ Evol.}, volume = {1}, pages = {85-98}, year = {2009}, } @Article{Hiller:09a, author = {Hiller, Michael and Findei{\ss}, Sven and Lein, Sandro and Marz, Manja and Nickel, Claudia and Rose, Dominic and Schulz, Christine and Backofen, Rolf and Prohaska, Sonja J. and Reuter, Gunter and Stadler, Peter F.}, title = {Conserved Introns Reveal Novel Transcripts in \emph{Drosophila melanogaster}}, journal = {Genome Res.}, volume = {19}, pages = {1289-1300}, year = {2009}, } @Article{Riester:09a, author = {Riester, Markus and Stadler, Peter F. and Klemm, Konstantin}, title = {\texttt{FRANz}: Fast reconstruction of wild pedigrees}, journal = {Bioinformatics}, pages = {2134-2139}, volume = {25}, year = {2009}, note = {Preliminary version in:\newline \emph{German Conference on Bioinformatics GCB 2008}, A.\ Beyer and M.\ Schroeder (eds.), Ges.\ f.\ Informatik, Bonn, \emph{Lect.\ Notes Inf.} \textbf{136}, pp.\ 168-177} } @Article{Stadler:09b, author = {Stadler, Peter F. and Chen, Julian J.-L. and Hackerm{\"u}ller, J{\"o}rg and Hoffmann, Steve and Horn, Friedemann and Khaitovich, Phillip and Kretzschmar, Antje K. and Mosig, Axel and Prohaska, Sonja J. and Qi, Xiaodong and Schutt, Katharina and Ullmann, Kerstin}, title = {Evolution of Vault {RNAs}}, journal = {Mol.\ Biol.\ Evol.}, volume = {26}, year = {2009}, pages = {1975-1991}, } @Article{Langenberger:09a, author = {Langenberger, David and Bermudez-Santana, Clara and Hertel, Jana and Hoffmann, Steve and Khaitovich, Steve and Stadler, Peter F.}, title = {Evidence for Human {microRNA}-Offset {RNA}s in Small {RNA} Sequencing Data}, journal = {Bioinformatics}, volume = {25}, pages = {2298-2301}, year = {2009}, } @Article{Munteanu:09a, author = {Munteanu, Andreea and Stadler, Peter F.}, title = {Mutate Now, Die Later: Evolutionary Dynamics with Delayed Selection}, journal = {J.\ Theor.\ Biol.}, volume = {260}, pages = {412-421}, year = {2009}, } @Article{Hoffmann:09a, author = {Hoffmann, Steve and Otto, Christian and Kurtz, Stefan and Sharma, Cynthia and Khaitovich, Philipp and Vogel, J{\"o}rg and Stadler, Peter F. and Hackerm{\"u}ller, J{\"o}rg}, title = {Fast mapping of short sequences with mismatches, insertions and deletions using index structures}, journal = {PLoS Comp.\ Biol.}, volume = {5}, pages = {e1000502}, year = {2009}, } @InProceedings{Menzel:09b, author = {Menzel, Peter and Gorodkin, Jan and Stadler, Peter F.}, title = {Maximum Likelihood Estimation of Weight Matrices for Targeted Homology Search}, booktitle = {German Conference on Bioinformatics 2009}, editor = {Grosse, Ivo and Neumann, Steffen and Posch, Stefan and Schreiber, Falk and Stadler, Peter F.}, publisher = {Gesellschaft f.\ Informatik}, address = {Bonn}, series = {Lecture Notes in Informatics}, volume = {157}, year = {2009}, pages = {211-220}, } @Article{Mosig:09b, author = {Mosig, Axel and Zhu, Liang and Stadler, Peter F.}, title = {Customized strategies for discovering distant {ncRNA} homologs}, journal = {Brief.\ Funct.\ Genomics Proteomics}, volume = {8}, pages = {451-460}, year = {2009}, } @Article{Marz:09c, author = {Marz, Manja and Donath, Alexander and Verstaete, Nina and Nguyen, Van Trung and Stadler, Peter F. and Bensaude, Olivier}, title = {Evolution of {7SK} {RNA} and its Protein Partners in Metazoa}, journal = {Mol.\ Biol.\ Evol.}, volume = {26}, year = {2009}, pages = {2821-2830}, } @Article{Copeland:09a, author = {Copeland, Claudia S. and Marz, Manja and Rose, Dominic and Hertel, Jana and Brindley, Paul J. and Bermudez Santana, Clara and Kehr, Stephanie and Stephan-Otto Attolini, Camille and Stadler, Peter F.}, title = {Homology-based annotation of non-coding {RNA}s in the genomes of \emph{Schistosoma mansoni} and \emph{Schistosoma japonicum}}, journal = {BMC Genomics}, volume = {10}, pages = {464}, year = {2009}, } @Article{Stocsits:09a, author = {Stocsits, Roman R. and Letsch, Harald and Hertel, Jana and Misof, Berhard and Stadler, Peter F.}, title = {Accurate and efficient reconstruction of deep phylogenies from structured {RNAs}}, journal = {Nucleic Acids Res.}, volume = {37}, pages = {6184-6193}, year = {2009}, } @Article{Stadler:09a, author = {Stadler, Peter F. and Prohaska, Sonja J. and Forst, Christian V. and Krakauer, David C.}, title = {Defining Genes: A Computational Framework}, journal = {Th.\ Biosci.}, volume = {128}, pages = {165-170}, year = {2009}, } @Article{Huang:09a, author = {Huang, Fenix W. D. and Qin, Jing and Reidys, Christian M. and Stadler, Peter F.}, title = {Partition Function and Base Pairing Probabilities for {RNA-RNA} Interaction Prediction}, journal = {Bioinformatics}, volume = {25}, pages = {2646-2654}, year = {2009}, } @Article{Menzel:09a, author = {Menzel, Peter and Gorodkin, Jan and Stadler, Peter F.}, title = {The Tedious Task of Finding Homologous Non-coding {RNA} Genes}, journal = {RNA}, volume = {15}, pages = {2075-2082}, year = {2009}, } @Article{Ostermeier:09a, author = {Ostermeier, Jens-Philipp and Helmuth, Marc and Klemm, Konstantin and Leydold, Josef and Stadler, Peter F.}, title = {A note on quasi-robust cycle bases}, journal = {Acta Math. Contemp.}, pages = {231-240}, volume = {2}, year = {2009}, } @Article{Marz:09b, author = {Marz, Manja and Stadler, Peter F.}, title = {Comparative Analysis of Eukaryotic {U3} {snoRNAs}}, journal = {RNA Biol.}, volume = {6}, pages = {503-507}, year = {2009}, } @Article{Hellmuth:09b, author = {Hellmuth, Marc and Imrich, Wilfried and Kl{\"o}ckl, Werner and Stadler, Peter F.}, title = {Local algorithms for the prime factorization of strong product graphs}, journal = {Math.\ Comp.\ Sci.}, volume = {2}, pages = {653-682}, year = {2009}, } % 2010 @Article{Huang:10a, author = {Huang, Fenix W. D. and Qin, Jing and Reidys, Christian M. and Stadler, Peter F.}, title = {Target prediction and a statistical sampling algorithm for {RNA-RNA} interaction}, journal = {Bioinformatics}, volume = {26}, pages = {175-181}, year = {2010}, } @Article{Langenberger:10a, author = {Langenberger, David and Bermudez-Santana, Clara and Stadler, Peter F. and Hoffmann, Steve}, title = {Identification and classification of small {RNAs} in transcriptome sequence data}, journal = {Pac.\ Symp.\ Biocomput.}, volume = {15}, pages = {80-87}, year = {2010}, } @Article{Gruber:10a, author = {Gruber, Andreas R. and Findei{\ss}, Sven and Washietl, Stefan and Hofacker, Ivo L. and Stadler, Peter F.}, title = {\texttt{RNAz 2.0}: improved noncoding {RNA} detection}, journal = {Pac.\ Symp.\ Biocomput.}, volume = {15}, pages = {69-79}, year = {2010}, } @Article{Marz:10a, author = {Marz, Manja and Vanzo, Nathalie and Stadler, Peter F.}, title = {Temperature-dependent structural variability of {RNA}s: spliced leader {RNA}s and their evolutionary history}, journal = {J.\ Bioinf.\ Comp.\ Biol.}, volume = {8}, pages = {1-17}, year = {2010}, } @Article{Amemiya:10a, author = {Amemiya, Chris T. and Powers, Thomas P. and Prohaska, Sonja J. and Grimwood, Jane and Schmutz, Jeremy and Dickson, Mark and Miyake, Tsutomu and Schoenborn, Michael A. and Myers, Richard M. and Ruddle, Francis H. and Stadler, Peter F.}, title = {Complete {HOX} cluster characterization of the coelacanth provides further evidence for slow evolution of its genome}, journal = {Proc.\ Natl.\ Acad.\ Sci.}, volume = {107}, pages = {3622-3627}, year = {2010}, } @Article{Tafer:10a, author = {Tafer, Hakim and Kehr, Stephanie and Hertel, Jana and Stadler, Peter F.}, title = {\texttt{RNAsnoop}: Efficient target prediction for box {H/ACA} {snoRNAs}}, journal = {Bioinformatics}, volume = {26}, pages = {610-616}, year = {2010}, } @Article{Sharma:10a, author = {Sharma, Cynthia M. and Hoffmann, Steve and Darfeuille, Fabien and Reignier, J{\'e}r{\'e}my and Findei{\ss}, Sven and Sittka, Alexandra and Chabas, Sandrine and Reiche, Kristin and Hackerm{\"u}ller, J{\"o}rg and Reinhardt, Richard Reinhardt and Stadler, Peter F. and Vogel, J{\"o}rg}, title = {The primary transcriptome of the major human pathogen \emph{Helicobacter pylori}}, journal = {Nature}, pages = {250-255}, volume = {464}, year = {2010}, } @Article{Prohaska:10a, author = {Prohaska, Sonja J and Stadler, Peter F. and Krakauer, David C.}, title = {Innovation in Gene Regulation: The Case of Chromatin Computation}, journal = {J.\ Theor.\ Biol.}, volume = {265}, pages = {27-44}, year = {2010}, } @InCollection{Donath:10a, author = {Donath, Alexander and Findei{\ss}, Sven and Hertel, Jana and Marz, Manja and Otto, Wolfgang and Schulz, Christine and Stadler, Peter F. and Wirth, Stefan}, title = {Non-Coding {RNA}s}, booktitle = {Evolutionary Genomics and Systems Biology}, editor = {Caetano-Anolles, Gustavo}, publisher = {Wiley-Blackwell}, address = {Hoboken, NJ}, pages = {251-293}, year = {2010}, } @InCollection{Tanzer:10a, author = {Tanzer, Andrea and Riester, Markus and Hertel, Jana and Bermudez-Santana, Clara Isabel and Gorodkin, Jan and Hofacker, Ivo L. and Stadler, Peter F.}, title = {Evolutionary Genomics of Micro{RNA}s and Their Relatives}, booktitle = {Evolutionary Genomics and Systems Biology}, editor = {Caetano-Anolles, Gustavo}, publisher = {Wiley-Blackwell}, address = {Hoboken, NJ}, pages = {295-327}, year = {2010}, } @Article{Boria:10a, author = {Boria, Ilenia and Gruber, Andreas R. and Tanzer, Andrea and Bernhart, Stephan and Lorenze, Ronny and Mueller, Michael M. and Hofacker, Ivo L. and Stadler, Peter F.}, title = {Nematode {sbRNAs}: homologs of vertebrate {Y} {RNAs}}, journal = {J.\ Mol.\ Evol.}, volume = {70}, pages = {346-358}, year = {2010}, } @Article{Findeiss:10a, author = {Findei{\ss}, Sven and Schubert, Cornelius and Stadler, Peter F. and Bonas, Ulla}, title = {A novel family of plasmid-transferred anti-sense {ncRNAs}}, journal = {RNA Biology}, volume = {7}, pages = {120-124}, year = {2010}, } @Article{Perseke:10a, author = {Perseke, Marleen and Bernhard, Detlef and Fritzsch, Guido and Br{\"u}mmer, Franz and Stadler, Peter F. and Schlegel, Martin}, title = {Mitochondrial genome evolution in {Ophiuroidea}, {Echinoidea}, and {Holothuroidea}: Insights in phylogenetic relationships of {Echinodermata}}, journal = {Mol.\ Phylog.\ Evol.}, volume = {56}, pages = {201-211}, year = {2010}, note = {doi: 10.1016/j.ympev.2010.01.035}, } @Article{Hofacker:10a, author = {Hofacker, Ivo L. and Flamm, Christoph and Heine, Christian and Wolfinger, Michael T. and Scheuermann, Gerik and Stadler, Peter F.}, title = {\texttt{BarMap}: {RNA} Folding on Dynamics Energy Landscapes}, journal = {RNA}, volume = {16}, pages = {1308-1316}, year = {2010}, } @Article{Fasold:10a, author = {Fasold, Mario and Stadler, Peter F. and Binder, Hans}, title = {{G}-stack modulated probe intensities on expression arrays --- sequence corrections and signal calibration}, journal = {BMC Bioinformatics}, volume = {11}, pages = {207}, year = {2010}, } @Article{Bermudez:10a, author = {Bermudez-Santana, Clara and Stephan-Otto Attolini, Camille and Kirsten, Toralf and Engelhardt, Jan and Prohaska, Sonja J. and Steigele, Stephan and Stadler, Peter F.}, title = {Genomic Organization of Eukaryotic {tRNAs}}, journal = {BMC Genomics}, volume = {11}, year = {2010}, pages = {270}, } @Article{Lehmann:10a, author = {Lehmann, J{\"o}rg and Eisenhardt, Carina and Stadler, Peter F. and Krauss, Veiko}, title = {Some novel Intron Positions in conserved Drosophila Genes are caused by Intron Sliding or Tandem Duplications}, journal = {BMC Evol.\ Biol.}, volume = {10}, pages = {156}, year = {2010}, } @Article{Yusuf:10a, author = {Yusuf, Dilmurat and Marz, Manja and Stadler, Peter F. and Hofacker, Ivo L.}, title = {\texttt{Bcheck}: a wrapper tool for detecting {RNase P RNA} genes}, journal = {BMC Bioinformatics}, volume = {11}, pages = {432}, year = {2010}, } @Article{Riester:10a, author = {Riester, Markus and Stadler, Peter F. and Klemm, Konstantin}, title = {Reconstruction of pedigrees in clonal plant populations}, journal = {Theor.\ Pop.\ Biol.}, volume = {78}, pages = {109-117}, year = {2010}, } @Article{Arnold:10a, author = {Arnold, Christian and Stadler, Peter F.}, title = {Polynomial algorithms for the Maximal Pairing Problem: efficient phylogenetic targeting on arbitrary trees}, journal = {Alg.\ Mol.\ Biol.}, volume = {5}, pages = {25}, year = {2010}, } @Article{Flamm:10b, author = {Flamm, Christoph and Ullrich, Alexander and Ekker, Heinz and Mann, Martin and H{\"o}gerl, Daniel and Rohrschneider, Markus and Sauer, Sebastian and Scheuermann, Gerik and Klemm, Konstantin and Hofacker, Ivo L. and Stadler, Peter F.}, title = {Evolution of Metabolic Networks: A Computational Framework}, journal = {J.\ Syst.\ Chem.}, volume = {1}, pages = {4}, year = {2010}, } @InProceedings{Stadler:10a, author = {Stadler, P. F.}, title = {Evolution of the long non-coding {RNAs} {MALAT1} and {MEN}$\beta$/$\epsilon$}, booktitle = {Advances in Bioinformatics and Computational Biology, 5th Brazilian Symposium on Bioinformatics}, editor = {Ferreira, Carlos Eduardo and Miyano, Satoru and Stadler, Peter F.}, series = {Lecture Notes in Computer Science}, volume = {6268}, pages = {1-12}, publisher = {Springer Verlag}, address = {Heidelberg}, year = {2010}, } @Article{Dalloul:10a, author = {Dalloul, Rami A. and Long, Julie A. and Zimin, Aleksey V. and Aslam, Luqman and Beal, Kathryn and Blomberg, Le Ann and Bouffard, Pascal and Burt, David W. and Crasta, Oswald and Crooijmans, Richard P. M. A. Crooijmans and Cooper, Kristal and Coulombe, Roger A. and De, Supriyo and Delany, Mary E. and Dodgson, Jerry B. and Dong, Jennifer J. and Evans, Clive and Frederickson, Karin M. and Flicek, Paul and Florea, Liliana and Folkerts, Otto and Groenen, Martien A. M. and Harkins, Tim T. and Herrero, Javier and Hoffmann, Steve and Megens, Hendrik-Jan and Jiang, Andrew and de Jong, Pieter and Kaiser, Pete and Kim, Heebal and Kim, Kyu-Won and Kim, Sungwon and Langenberger, David and Lee, Mi-Kyung and Lee, Taeheon and Mane, Shrinivasrao and Marcais, Guillaume and Marz, Manja and McElroy, Audrey P. and Modise, Thero and Nefedov, Mikhail and Notredame, C{\'e}dric and Paton, Ian R. and Payne, William S. and Pertea, Geo and Prickett, Dennis and Puiu, Daniela and Qioa, Dan and Raineri, Emanuele and Ruffier, Magali and Salzberg, Steven L. and Schatz, Michael C. and Scheuring, Chantel and Schmidt, Carl J. and Schroeder, Steven and Searle, Stephen M. and Smith, Edward J. and Smith, Jacqueline and Sonstegard, Tad S. and Stadler, Peter F. and Tafer, Hakim and Tu, Zhijian (Jake) and Van Tassel, Curtis P. and Vilella, Albert J. and Williams, Kelly P. and Yorke, James A. and Zhang, Liqing and Zhang, Hong-Bin and Zhang, Xiaojun and Zhang, Yang and Reed, Kent M.}, title = {Multi-Platform Next-Generation Sequencing of the Domestic Turkey (\emph{Meleagris gallopavo}): Genome Assembly and Analysis}, journal = {PLoS Biology}, volume = {8}, pages = {e1000475}, year = {2010}, } @InProceedings{Parikesit:10a, author = {Parikesit, Arli A. and Stadler, Peter F. and Prohaska, Sonja J.}, title = {Quantitative Comparison of Genomic-Wide Protein Domain Distributions}, booktitle = {German Conference on Bioinformatics 2010}, editor = {Schomburg, D. and Grote, A.}, series = {Lecture Notes in Informatics}, volume = {P-173}, year = {2010}, publisher = {Gesellschaft f{\"u}r Informatik}, address = {Bonn}, pages = {93-102}, note = {\begingroup\scriptsize Extended Abstract: \protect\emph{Detection of Protein Domains in Eukaryotic Genome Sequences} in \protect\emph{Advances in Bioinformatics and Computational Biology, 5th Brazilian Symposium on Bioinformatics}, Ferreira, C.\ E., Miyano, S, and Stadler, P.\ F.\ (eds.), Springer, Heidelberg (2010), Lect.\ Notes Comp.\ Sci.\ \textbf{6268}, pp.\ 71-74.\endgroup}, } @InProceedings{Ullrich:10a, author = {Ullrich, Alexander and Stadler, Peter F. and Rohrschneider, Markus and Stadler, Peter F.}, title = {{\em In silico} Evolution of Early Metabolism}, booktitle = {Artificial Life {XII}: Proceedings of the Twelfth International Conference on the Synthesis and Simulation of Living Systems}, editor = {Fellermann, Harold and D{\"o}rr, Mark and Hanczyc, Martin M. and Ladegaard Laursen, Lone and Maurer, Sarah and Merkle, Daniel and Monnard, Pierre-Alain and Stoy, Kasper and Rasmussen, Steen}, pages = {57-64}, publisher = {MIT Press}, address = {Cambridge, MA}, year = {2010}, } @Article{StadlerBMR:10a, author = {Stadler, B{\"a}rbel M. R. and Stadler, Peter F.}, title = {Combinatorial Vector Fields and the Valley Structure of Fitness Landscapes}, journal = {J.\ Math.\ Biol.}, volume = {61}, pages = {877-898}, year = {2010}, } @Article{Jaenicke:10a, author = {J{\"a}nicke, Stefan and Heine, Christian and Hellmuth, Marc and Stadler, Peter F. and Scheuermann, Gerik}, title = {Visualization of Graph Products}, journal = {IEEE Trans.\ Vis.\ Comput.\ Graph.}, volume = {16}, pages = {1082-1089}, year = {2010}, } @InProceedings{Rohrschneider:10a, author = {Rohrschneider, Markus and Ullrich, Alexander and Kerren, Andreas and Stadler, Peter F. and Scheuermann, Gerik}, title = {Visual Network Analysis of Dynamic Metabolic Pathways}, booktitle = {Advances in Visual Computing (ISVC 2010)}, series = {Lect.\ Notes Comp.\ Sci.}, volume = {6453}, editor = {George Bebis and Richard Boyle and Bahram Parvin and Darko Koracin and Ronald Chung and Riad Hammoud and Muhammad Hussain and Tan Kar-Han and Roger Crawfis and Daniel Thalmann and David Kao and Lisa Avila}, publisher = {Springer}, address = {Berlin}, pages = {316-327}, year = {2010}, } @Article{Mueller:10a, author = {M{\"u}ller, Stephan A. and Kohajda, Tibor and Findei{\ss}, Sven and Stadler, Peter F. and Washietl, Stefan and Kellis, Manolis and von Bergen, Martin and Kalkhof, Stefan}, title = {Optimization of parameters for coverage of low molecular weight proteins}, journal = {Anal.\ Bioanal.\ Chem.}, volume = {398}, pages = {2867-2881}, year = {2010}, } %2011 @Article{Kehr:11a, author = {Kehr, Stephanie and Bartschat, Sebastian and Stadler, Peter F. and Tafer, Hakim}, title = {\texttt{PLEXY}: Efficient Target Prediction for Box {C/D} {snoRNAs}}, journal = {Bioinformatics}, volume = {27}, pages = {279-280}, year = {2011}, } @Article{Menzel:11a, author = {Menzel, Peter and Stadler, Peter F. and Gorodkin, Jan}, title = {{maxAlike}: Maximum-likelihood based sequence reconstruction with application to improved primer design for unknown sequences}, journal = {Bioinformatics}, volume = {27}, pages = {317-325}, year = {2011}, } @Article{Findeiss:11a, author = {Findei{\ss}, Sven and Langenberger, David and Stadler, Peter F. and Hoffmann, Steve}, title = {Traces of Post-Transcriptional {RNA} Modifications in Deep Sequencing Data}, journal = {Biol.\ Chem.}, volume = {392}, pages = {305-313}, year = {2011}, } @Article{Washietl:11a, author = {Washietl, Stefan and Findei{\ss}, Sven and M{\"u}ller, Stephan and Kalkhof, Stefan and von Bergen, Martin and Hofacker, Ivo L. and Stadler, Peter F. and Goldman, Nick}, title = {{RNAcode}: robust prediction of protein coding regions in comparative genomics data}, journal = {RNA}, volume = {17}, pages = {578-594}, year = {2011}, } @InCollection{Mosig:11a, author = {Mosig, Axel and Stadler, Peter F.}, title = {Evolution of Vault {RNAs}}, booktitle = {Encyclopedia of Life Sciences}, editor = {N.N.}, pages = {doi: 10.1002/9780470015902.a0022883}, year = {2011}, publisher = {Wiley-Blackwell}, address = {Hoboken, NJ}, } @Article{Tramontano:11a, author = {Tramontano, Andrea and Donath, Alexander and Bernhart, Stephan H. and Reiche, Kristin and B{\"o}hmdorfer, Gudrun and Stadler, Peter F. and Bachmair, Andreas}, title = {Deletion analysis of the 3' long terminal repeat sequence of plant retrotransposon {Tto1} identifies 125 base pairs redundancy as sufficient for first strand transfer}, journal = {Virology}, pages = {412}, volume = {75-82}, year = {2011}, } @Article{Krakauer:11a, author = {Krakauer, David C and Collins, James P and Erwin, Douglas and Flack, Jessica C and Fontana, Walter and Laubichler, Manfred D and Prohaska, Sonja J and West, Geoffrey B and Stadler, Peter F}, title = {The challenges and scope of theoretical biology}, journal = {J. Theor. Biol.}, volume = {276}, pages = {269-276}, year = {2011}, } @InCollection{Prohaska:11a, author = {Prohaska, Sonja J. and Stadler, Peter F.}, title = {The Use and Abuse of -Omes}, booktitle = {Bioinformatics for Omics Data: Methods and Protocols}, editor = {Bernd Mayer}, publisher = {Humana Press}, address = {New York, NY}, year = {2011}, volume = {719}, pages = {173-196}, note = {DOI: 10.1007/978-1-61779-027-0\_8}, } @Article{OttoC:11a, author = {Otto, Christian and Hoffmann, Steve and Gorodkin, Jan and Stadler, Peter F.}, title = {Fast local fragment chaining using sum-of-pair gap costs}, journal = {Alg. Mol. Biol.}, volume = {6}, pages = {4}, year = {2011}, } @Article{Reidys:11a, author = {Reidys, Christian M. and Huang, Fenix W. D. and Andersen, J{\o}rgen E. and Penner, Robert C. and Stadler, Peter F. and Nebel, Markus E.}, title = {Topology and prediction of {RNA} pseudoknots}, journal = {Bioinformatics}, pages = {1076-1085}, volume = {27}, year = {2011}, note = {Addendum in: Bioinformatics 28:300 (2012)} } @Article{Lechner:11a, author = {Lechner, Marcus and Findei{\ss}, Sven and Steiner, Lydia and Marz, Manja and Stadler, Peter F. and Prohaska, Sonja J.}, title = {\texttt{Proteinortho:} Detection of (Co-)Orthologs in Large-Scale Analysis}, journal = {BMC Bioinformatics}, volume = {12}, pages = {124}, year = {2011}, } @Article{Ullrich:11a, author = {Ullrich, Alexander and Rohrschneider, Markus and Scheuermann, Gerik and Stadler, Peter F. and Flamm, Christoph}, title = {\emph{In silico} Evolution of Early Metabolism}, journal = {ALife}, volume = {17}, pages = {87-108}, year = {2011}, } @Article{Hoener:11a, author = {H{\"o}ner zu Siederdissen, Christian and Berhart, Stephan H. and Stadler, Peter F. and Hofacker, Ivo L.}, title = {A Folding Algorithm for Extended {RNA} Secondary Structures}, journal = {Bioinformatics}, volume = {27}, pages = {i129-i137}, year = {2011}, note = {ISMB}, } @Article{Perseke:11a, author = {Perseke, Marleen and Hetmank, Joerg and Bernt, Matthias and Stadler, Peter F. and Schlegel, Martin and Bernhard, Detlef}, title = {The enigmatic mitochondrial genome of \emph{Rhabdopleura compacta} ({PPterobranchia}) reveals insights into selection of an efficient {tRNA} system and supports monophyly of {Ambulacraria}}, journal = {BMC Evol. Biol.}, year = {2011}, volume = {11}, pages = {134}, } @Article{Steiner:11a, author = {Steiner, Lydia and Stadler, Peter F. and Cysouw, Michael}, title = {A Pipeline for Computational Historical Linguistics}, journal = {Language Dynamics \& Change}, volume = {1}, pages = {89-127}, year = {2011}, } @Article{Rose:11a, author = {Rose, Dominic and Hiller, Michael and Schutt, Katharina and Hackerm{\"u}ller, J{\"o}rg and Backofen, Rolf and Stadler, Peter F.}, title = {Computational discovery of human coding and non-coding transcripts with conserved splice sites}, journal = {Bioinformatics}, volume = {27}, pages = {1894-1900}, year = {2011}, } @Article{Tafer:11a, author = {Tafer, Hakim and Ammann, Fabian and Eggenhoffer, Florian and Stadler, Peter F. and Hofacker, Ivo L.}, title = {Fast Accessibility-Based Prediction of {RNA-RNA} Interactions}, journal = {Bioinformatics}, volume = {27}, pages = {1934-1940}, year = {2011}, } @InProceedings{Otto:11a, author = {Otto, Wolfgang and Stadler, Peter F. and Prohaska, Sonja J.}, title = {Phylogenetic Footprinting and Consistent Sets of Local Aligments}, booktitle = {CPM 2011}, editor = {Giancarlo, R. and Manzini, G.}, publisher = {Springer-Verlag}, address = {Heidelberg, Germany}, series = {Lecture Notes in Computer Science}, volume = {6661}, pages = {118-131}, year = {2011}, } @Article{Raincrow:11, author = {Raincrow, Jeremy D. and Dewar, Ken and Stocsits, Claudia and Prohaska, Sonja J. and Amemiya, Chris T. and Stadler, Peter F. and Chiu, Chi-hua}, title = {Hox clusters of the bichir ({Actinopterygii}, \emph{Polypterus senegalus}) highlight unique patterns of sequence evolution in gnathostome phylogeny}, journal = {J. Exp. Zool.}, volume = {316}, pages = {451-464}, year = {2011}, } @InProceedings{Langenberger:11a, author = {Langenberger, David and Bartschat, Sebastian and Hertel, Jana and Hoffmann, Steve and Tafer, Hakim and Stadler, Peter F.}, title = {MicroRNA or Not MicroRNA?}, booktitle = {Advances in Bioinformatics and Computational Biology, 6th Brazilian Symposium on Bioinformatics, BSB 2011}, editor = {de Souza, Osmar Norberto and Telles, Guilherme P. and Palakal, Mathew J.}, series = {Lecture Notes in Computer Science}, volume = {6832}, pages = {1-9}, publisher = {Springer}, address = {Berlin, Heidelberg}, year = {2011} } @Article{Clark:11a, author = {Clark, Michael B. and Amaral, Paulo P. and Schlesinger, Felix J. and Dinger, Marcel E. and Taft, Ryan J. and Rinn, John L. and Ponting, Chris P. and Stadler, Peter F. and Morris, Kevin J. and Morillon, Antonin and Rozowsky, Joel S. and Gerstein, Mark and Wahlestedt, Claes and Hayashizaki, Yoshihide and Carninci, Piero and Gingeras, Thomas R. and Mattick, John S.}, title = {The reality of pervasive transcription}, journal = {PLoS Biology}, volume = {9}, pages = {e1000625}, year = {2011}, } @Article{Fasold:11a, author = {Fasold, Mario and Langenberger, David and Binder, Hans and Stadler, Peter F. and Hoffmann, Steve}, title = {{DARIO}: A {ncRNA} detection and analysis tool for next-generation sequencing experiments}, journal = {Nucleic Acids Res.}, volume = {39}, pages = {W112-W117}, year = {2011}, } @Article{Eggenhofer:11a, author = {Eggenhofer, Florian and Tafer, Hakim and Stadler, Peter F. and Hofacker, Ivo L.}, title = {{RNApredator}: Fast accessibility-Based Prediction of {sRNA} targets}, journal = {Nucleic Acids Res.}, volume = {39}, pages = {W149-W154}, year = {2011}, } @InCollection{Marz:11a, author = {Marz, Manja and Stadler, Peter F.}, title = {{RNA} Interactions}, booktitle = {RNA Infrastructure and Networks}, editor = {Collins, Lesley J.}, publisher = {Landes Biosciences, Springer-Verlag}, address = {Berlin}, series = {Advances in Experimental Medicine and Biology}, volume = {722}, year = {2011}, pages = {20-38}, note = {http://www.landesbioscience.com/curie/chapter/4913/}, } @Article{Findeiss:11b, author = {Findei{\ss}, Sven and Engelhardt, Jan and Prohaska, Sonja P. and Stadler, Peter F.}, title = {Protein-Coding Structured {RNA}s: A Computational Survey of Conserved {RNA} Secondary Structures Overlapping Coding Regions in Drosophilids}, journal = {Biochimie}, volume = {93}, pages = {2019-2023}, year = {2011}, } @Article{Rose:11b, author = {Rose, Dominic and Stadler, Peter F.}, title = {Molecular Evolution of the non-coding Eosinophil Granule Ontogeny Transcript {EGOT}}, journal = {Front. Gene.}, volume = {2}, pages = {69}, year = {2011}, } @Article{Bateman:11a, author = {Bateman, A and Agrawal, S and Birney, E and Bruford, E A and Bujnicki, J M and Cochrane, G and Cole, J R and Dinger, M E and Enright, A J and Gardner, P P and Gautheret, D and Griffiths-Jones, S and Harrow, J and Herrero, J and Holmes, I H and Huang, H D and Kelly, K A and Kersey, P and Kozomara, A and Lowe, T M and Marz, M and Moxon, S and Pruitt, K D and Samuelsson, T and Stadler, P F and Vilella, A J and Vogel, J H and Williams, K P and Wright, M W and Zwieb, C}, title = {{RNAcentral}: A vision for an international database of {RNA} sequences}, journal = {RNA}, volume = {17}, pages = {1941-1946}, year = {2011}, } @Article{Parikesit:11a, author = {Parikesit, Arli A. and Stadler, Peter F. and Prohaska, Sonja, J.}, title = {Evolution and Quantitative Comparison of Genome-Wide Protein Domain Distributions}, journal = {Genes}, volume = {2}, pages = {912-924}, year = {2011}, } @Article{Marz:11b, author = {Marz, Manja and Gruber, Andreas R. and H{\"o}ner zu Siederdissen, Christian and Amman, Fabian and Badelt, Stefan and Bartschat, Sebastian and Bernhart, Stephan H. and Beyer, Kehr, Stephanie and Lorenz, Ronny and Tanzer, Andrea and Yusuf, Dilmurat and Tafer, Hakim and Hofacker, Ivo L. and Stadler, Peter F.}, title = {Animal {snoRNAs} and {scaRNAs} with Exceptional Structures}, journal = {RNA Biology}, volume = {8}, pages = {938-946}, year = {2011}, } @Article{Lorenz:11a, author = {Lorenz, Ronny and Bernhart, Stephan H and H{\"o}ner zu Siederdissen, Christian and Tafer, Hakim and Flamm, Christoph and Stadler, Peter F. and Hofacker, Ivo L.}, title = {{ViennaRNA Package 2.0}}, journal = {Alg.\ Mol.\ Biol.}, volume = {6}, pages = {26}, year = {2011}, } @Article{Lozada:11a, author = {Lozada-Ch{\'a}vez, Irma and Stadler, Peter F. and Prohaska, Sonja J.}, title = {``Hypothesis for the modern {RNA} world'': a pervasive non-coding {RNA}-based genetic regulation is a prerequisite for the emergence 2 of multicellular complexity}, journal = {Orig. Life Evol. Biosph.}, volume = {41}, pages = {587-607}, year = {2011}, } % 2012 @Article{Hofacker:12a, author = {Hofacker, Ivo L. and Reidys, Christian M. and Stadler, Peter F.}, title = {Symmetric circular matchings and {RNA} folding}, journal = {Discr. Math.}, volume = {312}, pages = {100-112}, year = {2012}, } @Article{Hellmuth:12a, author = {Hellmuth, Marc and Ostermeier, Lydia and Stadler, Peter F.}, title = {Diagonalized Cartesian Products of {S}-prime graphs are {S}-prime}, journal = {Discr. Math.}, volume = {312}, pages = {74-80}, year = {2012}, } @Article{Florentz:12a, author = {Florentz, Catherine and J{\"u}hling, Frank and P{\"u}tz, Joern and Sauter, Claude and Stadler, Peter F. and Gieg{\'e}, Richard}, title = {Structure of transfer {RNA}s: a function-driven refined view}, journal = {Wiley Interdiscip Rev RNA}, pages = {37-61}, volume = {3}, year = {2012}, } @Article{Langenberger:12a, author = {Langenberger, David and Pundhir, Sachin and Ekstr{\o}m, Claus T. and Stadler, Peter F. and Hoffmann, Steve and Gorodkin, Jan}, title = {\texttt{deepBlockAlign}: A tool for aligning {RNA-seq} profiles of read block patterns}, journal = {Bioinformatics}, volume = {28}, pages = {17-24}, year = {2012}, } @Article{Hellmuth:12b, author = {Hellmuth, Marc and Ostermeier, Philipp-Jens and Stadler, Peter F.}, title = {Minimum Cycles Bases of Lexicographic Products}, journal = {Ars Math.\ Comptemp.}, volume = {5}, pages = {219-230}, year = {2012}, } @Article{Schmidtke:11a, author = {Schmidtke, Cornelius and Findei{\ss}, Sven and Sharma, Cynthia M. and Kuhfu{\ss}, Juliane and Hoffmann, Steve and Vogel, J{\"o}rg and Stadler, Peter F. and Bonas, Ulla}, title = {Genome-wide transcriptome analysis of the plant pathogen \emph{Xanthomonas} identifies {sRNAs} with putative virulence functions}, journal = {Nucleic Acids Res.}, volume = {40}, pages = {2020-2031}, year = {2012}, } @Article{Hellmuth:12c, author = {Hellmuth, Marc and Ostermeier, Lydia and Stadler, Peter F.}, title = {A Survey on Hypergraph Products}, journal = {Math. Comp. Sci.}, volume = {6}, pages = {132}, year = {2012}, } @Article{Klemm:12b, author = {Klemm, Konstantin and Mehta, Anita and Stadler, Peter F.}, title = {Landscape Encodings Enhance Optimization}, journal = {PLoS ONE}, volume = {7}, pages = {e34780}, year = {2012}, } @Article{OstermeierL:12a, author = {Ostermeier, Lydia and Hellmuth, Marc and Stadler, Peter F.}, title = {The Cartesian Product of Hypergraphs}, journal = {J.\ Graph Th.}, volume = {70}, pages = {180-196}, year = {2012}, } @Article{Engelhardt:12a, author = {Engelhardt, Jan and Stadler, Peter F.}, title = {Hidden treasures in unspliced {EST} data}, journal = {Th. Biosci.}, pages = {49-57}, volume = {131}, year = {2012}, note = {Preliminary version in \emph{Proceedings of HIBIT 2011}, Izmir TR}, } @Article{Juehling:12a, author = {J{\"u}hling, Frank and P{\"u}tz, Joern and Bernt, Matthias and Donath, Alexander and Middendorf, Martin and Florentz, Catherine and Stadler, Peter F.}, title = {Improved systematic {tRNA} gene annotation allows new insights into the evolution of mitochondrial {tRNA} structures and into the mechanisms of mitochondrial genome rearrangements}, journal = {Nucleic Acids Res.}, volume = {40}, pages = {2833-2845}, year = {2012}, } @Article{Will:12a, author = {Will, Sebastian and Joshi, Tejal and Hofacker, Ivo L. and Stadler, Peter F. and Backofen, Rolf}, title = {{LocARNA-P}: Accurate Boundary Prediction and Improved Detection of Structured {RNAs} for Genome-wide Screens}, journal = {RNA}, volume = {18}, pages = {900-914}, year = {2012}, } @Article{Hertel:12a, author = {Hertel, Jana and Bartschat, Sebastian and Wintsche, Axel and Otto, Christian and {The Students of the Bioinformatics Computer Lab 2011} and Stadler, Peter F.}, title = {Evolution of the let-7 {microRNA} Family}, journal = {RNA Biology}, volume = {9}, pages = {231-241}, year = {2012}, } % prepublished @Article{Washietl:12a, author = {Washietl, Stefan and Hofacker, Ivo L. and Stadler, Peter F. and Kellis, Manolis}, title = {{RNA} Folding with Soft Constraints: Reconciliation of Probing Data and Thermodynamic Secondary Structure Prediction}, journal = {Nucleic Acids Res.}, volume = { }, pages = { }, year = {2012}, note = {doi: 10.1093/nar/gks009}, } @Article{Hellmuth:12d, author = {Hellmuth, Marc and Hernandez-Rosales, Maribel and Huber, Katharina T. and Moulton, Vincent and Stadler, Peter F. and Wieseke, Nicolas}, title = {Orthology Relations, Symbolic Ultrametrics, and Cographs}, journal = {J. Math. Biol.}, volume = { }, pages = { }, year = {2012}, note = {doi: 10.1007/s00285-012-0525-x}, } @Article{OttoC:12a, author = {Otto, Christian and Stadler, Peter F and Hoffmann, Steve}, title = {Fast and sensitive mapping of bisulfite-treated sequencing data}, journal = {Bioinformatics}, volume = { }, pages = { }, year = {2012}, note = {doi: 10.1093/bioinformatics/bts254}, } % in press @InCollection{Klemm:12x, author = {Klemm, Konstantin and Stadler, Peter F.}, title = {Elementary Landscapes}, booktitle = {Theory and Principled Methods for Designing Metaheustics}, editor = {Borenstein, Yossi and Moraglio, Alberto}, publisher = {Springer}, pages = { }, address = { }, note = {accepted}, year = {2012} } @Article{Niehuis:12a, author = {Niehuis, Oliver and Hartig, Gerrit Hartig and Garth, Sonja and Pohl, Hans and Lehmann, J{\"o}rg and Tafer, Hakim and Donath, Alexander and Krauss, Veiko and Eisenhardt, Carina and Hertel, Jana and Petersen, Malte and Mayer, Christoph and Meusemann, Karin and Peters, Ralph S. and Stadler, Peter F. and Beutel, Rolf G. and Bornberg-Bauer, Erich and McKenna, Duane D. and Misof, Bernhard}, title = {Genomic and Morphological Evidence Converge to Resolve the Enigma of {Strepsiptera}}, journal = {Current Biol.}, volume = { }, pages = { }, year = {2012}, } @InProceedings{Lorenz:12a, author = {Lorenz, Ronny and Bernhart, Stephan H. and Externbrink, Fabian and Qin, Jing and H{\"o}ner zu Siederdissen, Christian and Amman, Fabian and Hofacker, Ivo L. and Stadler, Peter F.}, title = {{RNA} Folding Algorithms with {G}-Quadruplexes}, booktitle = {BSB 2012}, editor = { }, year = { }, publisher = { }, address = { }, pages = {2012}, note = {accepted}, } %%% under review: @InCollection{Marz:10x, author = {Marz, Manja and Stadler, Peter F.}, title = {Homology Search for Small Structured {ncRNAs}}, booktitle = {Handbook of {RNA} Biochemistry}, pages = {}, publisher = {Wiley VCH}, year = {2010}, editor = {Hartmann, Roland and Bindereif, Albrecht and Sch{\"o}n, Astrid and Westhof, Eric}, address = {Weinheim, D}, note = {submitted}, } @InProceedings{Engelhardt:10a, author = {Engelhardt, Jan and Kirsten, Toralf and Stadler, Peter F. and Prohaska, Sonja J.}, title = {Genome Annotation without Genes}, booktitle = {GI 2010}, editor = { }, pages = { }, publisher = { }, address = { }, year = {2010}, note = {submitted}, } @Article{Lechner:11b, author = {Lechner, Markus and Marz, Manja and Stadler, Peter F. and Krauss, Veiko}, title = {Genome size, methylation rate, and {CpG} depletion in metazoans}, journal = { }, volume = { }, pages = { }, year = {2010}, note = { }, } @Article{Busch:10a, author = {Busch, Anke and Stadler, Peter F.}, title = {Intra-genic Exon Duplications in the Human Transcriptome}, journal = { }, volume = { }, pages = { }, year = {2010}, note = {submitted}, } @Article{Lehmann:11a, author = {Lehmann, J{\"o}rg and Stadler, Peter F. and Krauss, Veiko}, title = {Near Intron Pairs and the Metazoan Tree}, journal = { }, volume = { }, pages = { }, year = {2011}, note = {submitted}, } @Article{Donath:11a, author = {Donath, Alexander and Stadler, Peter F.}, title = {Split-Inducing Indels in Phylogenomic Analysis}, journal = { }, volume = { }, pages = { }, note = {submitted}, year = {2011}, } @InCollection{Stadler:11a, booktitle = {An introduction to {RNA} Bioinformatics}, editor = {Gorodkin, Jan and Ruzzo, Larry}, title = {Class-specific prediction of {ncRNAs}}, author = {Stadler, Peter F.}, series = { }, publisher = { }, address = { }, year = {2011}, note = {submitted}, } @InCollection{Hertel:11a, author = {Hertel, Jana and Langenberger, David and Stadler, Peter F.}, title = {Computational prediction of {microRNA} genes}, booktitle = {An introduction to {RNA} Bioinformatics}, editor = {Gorodkin, Jan and Ruzzo, Larry}, series = { }, publisher = { }, address = { }, year = {2011}, note = {submitted}, } @Article{Long:11a, author = {Long, Yangjing and Yang, Ling and Stadler, Peter F. and Jost, J{\"u}rgen}, title = {Relations Between Graphs}, journal = {Discr.\ Math.}, volume = { }, pages = { }, year = {2011}, note = {submitted}, } @Article{Tafer:12x, author = {Tafer, Hakim and Pedersen, Jan Torleif and Stadler, Peter F. and Gorodkin, Jan}, title = {Accessibility is a significant feature for design of {siRNAs} targeting structured {RNA}}, journal = { }, pages = { }, year = {2012}, note = {submitted} } @InProceedings{Andersen:12a, author = {Andersen, Jakob L and Flamm, Christoph and Merkle, Daniel and Stadler, Peter F.}, title = {Inferring Chemical Reaction Patterns Using Graph Grammar Rule Composition}, booktitle = {ECCB 2012}, editor = { }, publisher = { }, address = { }, pages = { }, year = {2012}, note = {submitted}, } @Article{Bernt:12xa, author = {Bernt, Matthias and Braband, Anke and Schierwater, Bernd and Stadler, Peter F.}, title = {Genetic aspects of mitochondrial genome evolution}, journal = {Mol. Phylog. Evol.}, volume = { }, pages = { }, year = {2012}, note = {submitted}, } @Article{Bernt:12xb, author = {Bernt, Matthias and Donath, Alexander and J{\"u}hling, Frank and Externbrink, Fabian and Florentz, Catherine and Fritzsch, Guido and P{\"u}tz, J{\"o}rn and Middendorf, Martin and Stadler, Peter F.}, title = {\texttt{Mitos}: Improved \emph{de novo} Metazoan Mitochondrial Genome Annotation}, journal = {Mol. Phylog. Evol.}, volume = { }, pages = { }, year = {2012}, note = {submitted}, } @Article{Bernt:12xc, author = {Bernt, Matthias and Braband, Anke and Middendorf, Martin and Misof, Bernhard and Rota-Stabelli, Omar and Stadler, Peter F.}, title = {Bioinformatics Methods for the Comparative Analysis of Metazoan Mitochondrial Genome Sequences}, journal = {Mol. Phylog. Evol.}, volume = { }, pages = { }, year = {2012}, note = {submitted}, } @Article{Smith:12a, author = {Smith, Martin A. and Gesell, Tanja and Stadler, Peter F. and Mattick John S.}, title = {Widespread purifying selection on {RNA} structure in mammals}, journal = { }, volume = { }, pages = { }, year = {2012}, note = {submitted}, } @Article{Lessa:12a, author = {Lessa, Felipe A. and Raiol, Tain{\'a} and Br{\'i}gido, Marcelo M. and Martins Neto, Daniele S. B. and Walter, Maria Em{\'\i}lia M. T. and Stadler, Peter F.}, title = {Clustering {Rfam} 10.1: Clans, Families, and Classes}, journal = {Genes}, volume = { }, pages = { }, year = {2012}, note = {submitted}, } @Article{Li:12a, author = {Li, Yang and Marz, Manja and Qi, Xiaodong and Podlevsky, Joshua D. and Hoffmann, Steve and Stadler, Peter F. and Chen, Julian J.-L.}, title = {Identification of the First Invertebrate Telomerase {RNA} by a Next-Generation Sequencing Based Approach}, journal = { }, volume = { }, pages = { }, year = {2012}, note = {submitted}, } @Article{Richter:12a, author = { }, } @Article{Holdt:12a, author = {Holdt, Lesca M. and Hoffmann, Steve and Sass, Kristina and Langenberger, David and Scholz, Markus and Krohn, Knut and Finstermeier, Knut and Stahringer, Anika and Wilfert, Wolfgang and Beutner, Frank and Gielen, Stephan and Schueler, Gerhard and G{\"a}bel, Gabor and Bergert, Hendrick and Stadler, Peter F. and Thiery, Joachim and Teupser, Daniel}, title = {{ANRIL} regulates genes in trans and affects mechanisms of atherosclerosis at {Chr9p21}}, journal = { }, volume = { }, pages = { }, year = {2012}, note = {submitted}, } %% END SORT