Plasticity, Evolvability, and Modularity in RNA © 2000 WILEY-LISS, INC. (2009)
Lauren W. Ancel, Walter Fontana
ABSTRACT RNA folding from sequences into secondary structures is a simple yet powerful, biophysically grounded model of a genotype–phenotype map in which concepts like plasticity, evolvability,...
Scalable simulation of cellular signaling networks (2009)
Vincent Danos, Jérôme Feret, Walter Fontana, Jean Krivine, Plectix Biosystems, ...
Abstract. Given the combinatorial nature of cellular signalling pathways, where biological agents can bind and modify each other in a large number of ways, concurrent or agent-based languages seem...
Rule-based modelling, symmetries, refinements (2009)
Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer
Abstract. Rule-based modelling is particularly effective for handling the highly combinatorial aspects of cellular signalling. The dynamics is described in terms of interactions between partial...
Investigation of a biological repair scheme (2009)
Vincent Danos, Jérôme Féret, Walter Fontana, Russell Harmer
Abstract. This note details an interaction pattern for the allocation of a scarce biological resource where and when it is needed. It is entirely based on a mass action stochastic dynamics....
J. Arjan, G. M. Visser, Joachim Hermisson, Günter P. Wagner, Ancel Meyers, Homayoun Bagheri-chaichian, ...
1 23-12-02 Abstract. – Robustness is the invariance of phenotypes in the face of perturbation. The robustness of phenotypes appears at various levels of biological organization, including gene...
Abstract interpretation of cellular signalling networks (2008)
Vincent Danos, Jérôme Feret, Walter Fontana, Jean Krivine, Plectix Biosystems, École Polytechnique
Abstract. Cellular signalling pathways, where proteins can form complexes and undergo a large array of post translational modifications are highly combinatorial systems sending and receiving...
Abstract Systems Biology, Models, and Concurrency ∗ (2008)
Models will play a central role in the representation, storage, manipulation, and communication of knowledge in systems biology. Models capable of fulfilling such a role will likely differ from the...
an der Formal- und Naturwissenschaftlichen (2008)
Martin Fekete, Walter Fontana, Thomas Griesmacher, Judith Jakubetz, Bärbel Krakhofer, ...
First of all I want to mention Peter Schuster for giving me the chance to join his group and his tremendous support. It always has been a pleasure for me to discuss with him. Ivo Hofacker the great...
The barrier of objects: From dynamical systems to bounded organizations
Submitted to Journal of Experimental Zoology (Molecular and Developmental Evolution) (2008)
Lauren W. Ancel, Walter Fontana, L. Ancel, W. Fontana Plasticity
RNA folding from sequences into secondary structures is a simple yet powerful, biophysically grounded model of a genotype-phenotype map in which concepts like plasticity, evolvability, epistasis and...
2 Research examples....................... 3 2.1 RNA folding and evolutionary dynamics: Evolution and development at the level of a single
Systems Analysis (IIASA) (2008)
Walter Fontana, Leo W. Buss, John Casti, Anders Karlqvist
The barrier of objects: From dynamical systems to bounded organizations
Copyright © 2000 RNA Society+ RNA folding at elementary step resolution (2008)
Christoph Flamm, Walter Fontana, Ivo L. Hofacker, Peter Schuster
We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss...
Mag Susanne Rauscher, Molekulare Strukturbiologie, Im Juni, Peter Schuster, Peter Stadler, ...
Dank an alle,
Copyright © 2000 RNA Society+ RNA folding at elementary step resolution (2008)
Christoph Flamm, Walter Fontana, Ivo L. Hofacker, Peter Schuster
We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss...
Walter Fontana Theoretical, Walter Fontana
n of the Social Siences) "The Dynamic Emergence of Individuals and Cognition". This is joint work with Leo W. Buss, Department of Biology and Department of Geology and Geophysics, Yale...
Chance and Necessity in Evolution: (2008)
Lessons From Rna, Peter Schuster, Walter Fontana
The RNA folding map, understood as the relationship between sequences and secondary structures or shapes, exhibits robust statistical properties summarized by three notions: (1) the notion of a...
Modelling `evo-devo' with RNA (2008)
Walter Fontana Summary, Walter Fontana
Introduction Phenotype refers to the physical, organizational and behavioral expression of an organism during its lifetime. Genotype refers to a heritable repository of information that instructs the...
Rule-based modelling and model perturbations (2008)
Danos, Vincent, Feret, Jérôme, Fontana, Walter, Harmer, Russ, Krivine, Jean
Rule-based modelling has already proved successful for taming the combinatorial complexity, typical of cellular signalling, caused by the combination of physical protein-protein interactions and...
Rule-based modelling and model perturbations (2008)
Danos, Vincent, Feret, Jérôme, Fontana, Walter, Harmer, Russ, Krivine, Jean
Rule-based modelling has already proved successful for taming the combinatorial complexity, typical of cellular signalling, caused by the combination of physical protein-protein interactions and...
Visto che siete cani, Walter Fontana. . - Milano. NALUAF00001079, Rizzoli. NAEDAF00005357. 2008.
and Necessity in Organizational Change 1 (2007)
Marine records of sedimented wind-borne dust plumes indicate a shift in African climate from closed canopy forests toward more arid conditions about 2:8 million years ago [2]. This shift seems to...
Plasticity, Evolvability, and Modularity in RNA © 2000 WILEY-LISS, INC. (2007)
Lauren W. Ancel, Walter Fontana
ABSTRACT RNA folding from sequences into secondary structures is a simple yet powerful, biophysically grounded model of a genotype–phenotype map in which concepts like plasticity, evolvability,...
Peter F. Stadler, Walter Fontana
The topology of the possible: Formal spaces underlying patterns of evolutionary change B arbel M. R. Stadler
Martijn Huynen, Peter Stadler, Walter Fontana
RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure. On such networks evolving populations split into subpopulations which...
Theoretical Chemistry, Walter Fontana
iology and Department of Geology and Geophysics, Yale University, New Haven CT 06520-8104 USA. 2 or vice versa recognized that the synthesis of natural selection and genetics need not await a...
ion A x [ fx : ø 0 g ` e : ø A ` x:e : ø 0 ! ø Let A ` e : oe A x [ fx : oeg ` e 0 : ø A ` (let x = e in e 0 ) : ø The meaning of the Taut-rule is simply that a free variable has the type...
Evolution of lambda-expressions through Genetic Programming (2007)
Dorothea Heiss-Czedik, Walter Fontana
We illustrate a minimal version of Genetic Programming operating with -calculus by evolving the predecessor function. The expression obtained works differently than the original version of Kleene. In...
Fast Folding and Comparison of RNA Secondary Structures (2007)
The Vienna, Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. Sebastian Bonhoeffer, Manfred Tacker, ...
Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures...
On the Emergence of Organization (2007)
and Department of Geology and Geophysics, Yale University, New Haven CT 06520-8104 USA. 2 or vice versa recognized that the synthesis of natural selection and genetics need not await a "theory...
What Would Be Conserved If "the Tape Were Played Twice"? (2007)
Evolution Organization, Walter Fontana, Leo W. Buss
We develop an abstract chemistry, implemented in a -calculus based modelling platform, and argue that the following features are generic to this particular abstraction of chemistry, hence would be...
1996, at the University of Chicago on the occasion of the Dean's Symposium 1996 (Division of the Social Siences) "The Dynamic Emergence of Individuals and Cognition". This is joint...
Expressions Through, Dorothea Heiss-czedik, Walter Fontana
We illustrate a minimal version of Genetic Programming operating with -calculus by evolving the predecessor function. The expression obtained works differently than the original version of Kleene. In...
Walter Fontana, Gunter Wagner, Leo W. Buss
The success of Artificial Life depends on whether it will help solving the conceptual problems of biology. Biology may be viewed as the science of the transformation of organizations. And, yet,...
Peter F. Stadler, Walter Fontana
The topology of the possible: Formal spaces underlying patterns of evolutionary change B arbel M. R. Stadler
Lauren W. Ancel, Walter Fontana
Modularity is a hallmark of biological organization and a important source of evolutionary novelty 1-3. Yet, the origin of modules remains a problem for evolutionary biology, even in the case of the...
The stochastic behavior of a molecular switching circuit with feedback (2007)
Krishnamurthy, Supriya, Smith, Eric, Krakauer, David, Fontana, Walter
Abstract Background Using a statistical physics approach, we study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. The circuit...
Biological signalling and causality (2007)
Danos, Vincent, Fontana, Walter, Harmer, Russ, Krivine, Jean
Modelling is becoming a necessity in studying biological signalling pathways, because the combinatorial complexity of such systems rapidly overwhelms intuitive and qualitative forms of reasoning....
Biological signalling and causality (2007)
Danos, Vincent, Fontana, Walter, Harmer, Russ, Krivine, Jean
Modelling is becoming a necessity in studying biological signalling pathways, because the combinatorial complexity of such systems rapidly overwhelms intuitive and qualitative forms of reasoning....
Rule-based Modelling of Cellular Signalling (2007)
Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Jean Krivine, Plectix Biosystems, ...
Abstract. Modelling is becoming a necessity in studying biological signalling pathways, because the combinatorial complexity of such systems rapidly overwhelms intuitive and qualitative forms of...
Rule-based Modelling of Cellular Signalling (2007)
Vincent Danos, Jérôme Feret, Walter Fontana, Russell Harmer, Plectix Biosystems, École Normale Supérieure, ...
Abstract. Modelling is becoming a necessity in studying biological signalling pathways, because the combinatorial complexity of such systems rapidly overwhelms intuitive and qualitative forms of...
Rules for Modeling Signal-Transduction Systems (2006)
William S. Hlavacek, James R. Faeder, Michael L. Blinov, Richard G. Posner, Michael Hucka, Walter Fontana
Formalized rules for protein-protein interactions have recently been introduced to represent the binding and enzymatic activities of proteins in cellular signaling. Rules encode an understanding of...
John F. Padgett, Paul D. Mclean, Ron Burt, William Caferro, Samuel Cohn, Nick Collier, ...
Acknowledgements: We are very grateful for the stimulating criticism and support we have received over a number of years about this research from Andy Abbott, Skye Bender-deMoll,
Walter W. Powell, Douglas R. White, Kenneth W. Koput, Jason Owen-smith, Tim Bresnahan, Paul David, ...
where these ideas were initially discussed and much of the work was done. We are especially grateful to John Padgett, organizer of the States and Markets group at SFI for his support and insights. We...
Neutrality in Technological Landscapes (2004)
Jose Lobo, John H. Miller, Walter Fontana
Searching for technological and organizational innovations is a fundamental activity in social systems. Recent work in this area has focused on the notion of firms locally searching for high points...
Evolutionary lock-in and the origin of modularity in RNA structure (2004)
Lauren W. Ancel, Walter Fontana
Modularity is a hallmark of biological organization and a important source of evolutionary novelty 1–3. Yet, the origin of modules remains a problem for evolutionary biology, even in the case of...
Non ho problemi di comunicazione (2004)
Non ho problemi di comunicazione, Walter Fontana. . - Milano. NALUAF00001079, Rizzoli. NAEDAF004331, 2004.
The stochastic behavior of a molecular switching circuit with feedback (2003)
Krishnamurthy, Supriya, Smith, Eric, Krakauer, David, Fontana, Walter
Background: Using a statistical physics approach, we study the stochastic switching behavior of a model circuit of multisite phosphorylation and dephosphorylation with feedback. The circuit consists...
PERSPECTIVE:EVOLUTION AND DETECTION OF GENETIC ROBUSTNESS (2003)
Joachim Hermisson, Günter P. Wagner, Lauren Ancel Meyers, Homayoun Bagheri-Chaichian, Jeffrey L. Blanchard, ...
Robustness is the invariance of phenotypes in the face of perturbation. The robustness of phenotypes appears at various levels of biological organization, including gene expression, protein folding,...
this paper. The important message is that accessibi ity is not a distance. A distance re ation is a ways a symmetric re ation, whi e accessibi ity is not as iuj--q-jl in Figu- 7B. The RNA phenotype...
The Assica Framework, Walter Fontana
this paper. The important message is that accessibility is not a distance. A distance relation is always a symmetric relation, while accessibility is not asillujfilz"" in Figuj 6B. The RNA...
Modelling ’evo-devo’ with RNA (2002)
Introduction Phenotype refers to the physica , organizationa and behaviora expression of an organismduani its ifetime. Genotype refers to a heritab e repository of information that instruYl the...
Contents 1 Novelty in Evolution..................... 1 (2001)
Ine Green Paper, Walter Fontana
Chemistry: Organization as a self-maintaining network of transformations ..................... 14 4.3 Self-rewiring signaling networks: Organization as distributed control ........ 16 5 References...
RNA folding at elementary step resolution (2000)
Christoph Flamm Walter, Walter Fontana, Ivo L. Hofacker, Peter Schuster
We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss...
RNA Folding at Elementary Step Resolution (2000)
Christoph Flamm, Walter Fontana, Ivo L. Hofacker, Peter Schuster
We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss...
RNA Folding at Elementary Step Resolution (2000)
Christoph Flamm, Walter Fontana, Ivo L. Hofacker, Peter Schuster
A algorithm based one three classes of elementary steps for folding RNA sequences into secondary structures is presented. It is formulated as a stochastic process on the discrete confomational space...
Plasticity, Evolvability and Modularity in RNA (2000)
Lauren W. Ancel, Walter Fontana, L. Ancel, W. Fontana Plasticity
this paper weaves together several seemingly diverse concepts, we begin with an overview.
Plasticity, Evolvability and Modularity in RNA (2000)
Lauren W. Ancel, Walter Fontana, L. Ancel, W. Fontana Plasticity
this paper weaves together several seemingly diverse concepts, we begin with an overview.
Chance and Necessity in Evolution: Lessons from RNA (1999)
Peter Schuster, Walter Fontana
The RNA folding map, understood as the relationship between sequences and secondary structures or shapes, exhibits robust statistical properties summarized by three notions: (1) the notion of a...
Chance and Necessity in Evolution: Lessons from RNA (1999)
Peter Schuster And, Peter Schuster, Walter Fontana
The RNA folding map, understood as the relationship between sequences and secondary structures or shapes, exhibits robust statistical properties summarized by three notions: (1) the notion of a...
Chance and Necessity in Evolution: Lessons from RNA (1999)
Peter Schuster And, Peter Schuster, Walter Fontana
The RNA folding map, understood as the relationship between sequences and secondary structures or shapes, exhibits robust statistical properties summarized by three notions: (1) the notion of a...
Chance and Necessity in Evolution: Lessons from RNA (1999)
Peter Schuster And, Peter Schuster, Walter Fontana
The RNA folding map, understood as the relationship between sequences and secondary structures or shapes , exhibits robust statistical properties which are casted into three notions: (1) the notion...
Chance and Necessity in Evolution: Lessons from RNA (1998)
Schuster, Peter, Fontana, Walter
The relationship between sequences and secondary structures or shapes in RNA exhibits robust statistical properties summarized by three notions: (1) the notion of a typical shape (that among all...
Shaping space: The possible and the attainable in RNA genotype-phenotype mapping (1998)
Walter Fontana, Peter Schuster
Understanding which phenotypes are accessible from which genotypes is fundamental for understanding the evolutionary process. This notion of accessibility can be used to define a relation of nearness...
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures (1998)
Stefan Wuchty, Walter Fontana, Ivo L. Hofacker, Peter Schuster
An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm is particularly fast in the...
Shaping Space: The Possible and the Attainable in RNA Genotype-Phenotype Mapping (1998)
Walter Fontana And, Walter Fontana, Peter Schuster
Understanding which phenotypes are accessible from which genotypes is fundamental for understanding the evolutionary process. This notion of accessibility can be used to define a relation of nearness...
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures (1998)
Stefan Wuchty, Walter Fontana, Ivo L. Hofacker, Peter Schuster
this paper we describe a fairly simple algorithm which generates all suboptimal folds of a sequence within a desired energy range from the mfe. The idea underlying the algorithm is straightforward,...
Shaping Space: The Possible and the Attainable in RNA Genotype-Phenotype Mapping (1998)
Walter Fontana, Peter Schuster
Understanding which phenotypes are accessible from which genotypes is fundamental for understanding the evolutionary process. This notion of accessibility can be used to define a relation of nearness...
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures (1998)
Stefan Wuchty, Walter Fontana, Ivo L. Hofacker, Peter Schuster
this paper we describe a fairly simple algorithm which generates all suboptimal folds of a sequence within a desired energy range from the mfe. The idea underlying the algorithm is straightforward,...
Shaping Space: The Possible and the Attainable in RNA Genotype-Phenotype Mapping (1998)
Walter Fontana, Peter Schuster, J. Theor Biol, In Press
Understanding which phenotypes are accessible from which genotypes is fundamental for understanding the evolutionary process. This notion of accessibility can be used to define a relation of nearness...
Shaping Space: The Possible and the Attainable in RNA Genotype-Phenotype Mapping (1998)
Walter Fontana, Peter Schuster, J. Theor Biol, In Press
Understanding which phenotypes are accessible from which genotypes is fundamental for understanding the evolutionary process. This notion of accessibility can be used to define a relation of nearness...
Shaping Space: The Possible and the Attainable in RNA Genotype-Phenotype Mapping (1998)
Walter Fontana, Peter Schuster
Understanding which phenotypes are accessible from which genotypes is fundamental for understanding the evolutionary process. This notion of accessibility can be used to define a relation of nearness...
Walter Fontana, Peter Schuster
Understanding which phenotypes are accessible from which genotypes is fundamental for understanding the evolutionary process. This notion of acessibility can be used to define a relation of nearness...
David Lane, Franco Malerba, Robert Maxfield, Michael Cohen, Jim Dickey, Stuart Dreyfus, ...
In this essay, we argue that rational choice (RC) provides an inadequate foundation for a theory of economic action. After defining RC sufficiently broadly to encompass much of the bounded...
Smoothness Within Ruggedness: The Role of Neutrality in Adaptation (1996)
Martijn Huynen, Peter Stadler, Walter Fontana
RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure. On such networks evolving populations split into subpopulations which...
1996, at the University of Chicago on the occasion of the Dean's Symposium 1996 (Division of the Social Siences) "The Dynamic Emergence of Individuals and Cognition". This is joint...
Smoothness Within Ruggedness: The Role of Neutrality in Adaptation (1996)
Martijn Huynen, Peter F. Stadler, Walter Fontana
RNA secondary structure folding algorithms predict the existence of connected networks of RNA sequences with identical structure. On such networks evolving populations split into subpopulations which...
Beyond Digital Naturalism (1994)
Walter Fontana, Gunter Wagner, Leo W. Buss
The success of Artificial Life depends on whether it will help solving the conceptual problems of biology. Biology may be viewed as the science of the transformation of organizations. And, yet,...
Fast Folding and Comparison of RNA Secondary Structures (The Vienna RNA Package) (1994)
Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. Sebastian Bonhoeffer, Manfred Tacker, Peter Schuster
Computer codes for computation and comparison of RNA secondary structures, the Vienna RNA package, are presented, that are based on dynamic programming algorithms and aim at predictions of structures...
Beyond Digital Naturalism (1994)
Walter Fontana, Gunter Wagner, Leo W. Buss
The success of Artificial Life depends on whether it will help solving the conceptual problems of biology. Biology may be viewed as the science of the transformation of organizations. And, yet,...
Random Catalytic Reaction Networks (1993)
Peter F. Stadler, Walter Fontana, John H. Miller
We study networks that are a generalization of replicator (or Lotka-Volterra) equations. They model the dynamics of a population of object types whose binary interactions determine the specific type...
What Would Be Conserved If "The Tape Were Played Twice"? (1993)
We develop an abstract chemistry, implemented in a -calculus based modelling platform, and argue that the following features are generic to this particular abstraction of chemistry, hence would be...
Statistics of RNA Melting Kinetics (1993)
Manfred Tacker, Walter Fontana, Peter F. Stadler, Peter Schuster
We present and study the behavior of a simple kinetic model for the melting of RNA secondary structures, given that those structures are known. The model is then used as a map that assigns structure...
RNA Folding and Combinatory Landscapes (1993)
Walter Fontana, Peter F. Stadler, Thomas Griesmacher, Ivo L. Hofacker, Manfred Tacker, ...
In this paper we view the folding of polynucleotide (RNA) sequences as a map that assigns to each sequence a minimum free energy pattern of base pairings, known as secondary structure. Considering...
Random Catalytic Reaction Networks (1993)
Peter Stadler, Walter Fontana, John H. Miller
We study networks that are a generalization of replicator (or Lotka-Volterra) equations. They model the dynamics of a population of object types whose binary interactions determine the specific type...
Perspective: Evolution And Detection Of Genetic Robustness (1972)
J. Arjan, G. M. Visser, Joachim Hermisson, Günter P. Wagner, Lauren Ancel Meyers, ...
Robustness is the invariance of phenotypes in the face of perturbation. The robustness of phenotypes appears at various levels of biological organization, including gene expression, protein folding,...
The Topology of the Possible: Formal Spaces Underlying Patterns of Evolutionary Change
Peter F. Stadler, GŸnter P. Wagner, Walter Fontana
The current implementation of the Neo-Darwinian model of evolution typically assumes that the set of possible phenotypes is organized into a highly symmetric and regular space equipped with a notion...
RNA Folding at Elementary Step Resolution
Christoph Flamm, Walter Fontana, Ivo L. Hofacker, Peter Schuster
We study the stochastic folding kinetics of RNA sequences into secondary structures with a new algorithm based on the formation, dissociation, and the shifting of individual base pairs. We discuss...
Plasticity, Evolvability and Modularity in RNA
Lauren W. Ancel, Walter Fontana
RNA folding from sequences into secondary structures is a simple yet powerful, biophysically grounded model of a genotype-phenotype map in which concepts like plasticity, evolvability, epistasis and...
Chance and Necessity in Evolution: Lessons from RNA
Peter Schuster, Walter Fontana
The RNA folding map, understood as the relationship between sequences and secondary structures or shapes, exhibits robust statistical properties summarized by three notions: (1) the notion of a...
Complete Suboptimal Folding of RNA and the Stability of Secondary Structures
Stefan Wuchty, Walter Fontana, Ivo L. Hofacker, Peter Schuster
An algorithm is presented for generating rigorously all suboptimal secondary structures between the minimum free energy and an arbitrary upper limit. The algorithm performs particularly well in the...
Shaping Space: The Possible and the Attainable in RNA Genotype-Phenotype Mapping
Walter Fontana, Peter Schuster
Understanding which phenotypes are accessible from which genotypes is fundamental for understanding the evolutionary process. This notion of accessibility can be used to define a relation of nearness...
The stochastic behavior of a molecular switching circuit with feedback
Krishnamurthy, Supriya, Smith, Eric, Krakauer, David, Fontana, Walter
Sizing Up Allometric Scaling Theory
Savage, Van M., Deeds, Eric J., Fontana, Walter
Metabolic rate, heart rate, lifespan, and many other physiological properties vary with body mass in systematic and interrelated ways. Present empirical data suggest that these scaling relationships...
Continuity in Evolution: On the Nature of Transition
Walter Fontana, Peter Schuster
To distinguish continuous from discontinuous evolutionary change, a relation of nearness between phenotypes is needed. Such a relation is based on the probability of one phenotype being accessible...
Evolutionary Dynamics of RNA and the Neutral Theory
Martijn Huynen, Peter Stadler, Walter Fontana
Understanding the relationship between genotype and phenotype is essential for understanding evolutionary dynamics. RNA is an extremely simple yet highly instructive case: both genotype (sequence)...
What Would Be Conserved If ``The Tape Were Played Twice''?
We develop an abstract chemistry, implemented in a $\lambda$-calculus based modelling platform, and argue that the following features are generic to this particular abstraction of chemistry, hence...
Walter Fontana, G\"unter Wagner, Leo W. Buss
The success of Artificial Life depends on whether it will help solving the conceptual problems of biology. Biology may be viewed as the science of the transformation of organizations. And, yet,...
The Arrival of the Fittest: Toward a Theory of Biological Organization
The formal structure of evolutionary theory is based upon the dynamics of alleles, individuals and populations. As such, the theory must assume the prior existence of these entities. This existence...
From Sequences to Shapes and Back: A Case Study in RNA Secondary Structures
Peter Schuster, Walter Fontana, Peter F. Stadler, Ivo L. Hofacker
RNA folding is viewed as a map assigning secondary structures to sequences. At fixed chain length the number of sequences exceeds by far the number of structures. Frequencies of structures are highly...
Fast Folding and Comparison of RNA Secondary Structures
Ivo L. Hofacker, Walter Fontana, Peter F. Stadler, L. Sebastian Bonhoeffer, Manfred Tacker, Peter Schuster
Computer codes for computation and comparison of RNA secondary structures, the {\tt Vienna RNA package}, are presented, that are based on dynamic programming algorithms and aim at predictions of...
Statistics of RNA Melting Kinectics
Manfred Tacker, Walter Fontana, Peter F. Stadler, Peter Schuster
We present and study the behavior of a simple kinetic model for the melting of RNA secondary structures, given that those structures are known. The model is then used as a map that assigns structure...
Internal coarse-graining of molecular systems
Feret, Jérôme, Danos, Vincent, Krivine, Jean, Harmer, Russ, Fontana, Walter
Modelers of molecular signaling networks must cope with the combinatorial explosion of protein states generated by posttranslational modifications and complex formation. Rule-based models provide a...