10 Search Results for "Gilbert, David Roger"

Document
DOI: 10.4230/LIPIcs.WABI.2025.20
A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences

Authors: Haonan Wu, Antonio Blanca, and Paul Medvedev

Published in: LIPIcs, Volume 344, 25th International Conference on Algorithms for Bioinformatics (WABI 2025)

Abstract
K-mer-based analysis of genomic data is ubiquitous, but the presence of repetitive k-mers continues to pose problems for the accuracy of many methods. For example, the Mash tool (Ondov et al. 2016) can accurately estimate the substitution rate between two low-repetitive sequences from their k-mer sketches; however, it is inaccurate on repetitive sequences such as the centromere of a human chromosome. Follow-up work by Blanca et al. (2021) has attempted to model how mutations affect k-mer sets based on strong assumptions that the sequence is non-repetitive and that mutations do not create spurious k-mer matches. However, the theoretical foundations for extending an estimator like Mash to work in the presence of repeat sequences have been lacking. In this work, we relax the non-repetitive assumption and propose a novel estimator for the mutation rate. We derive theoretical bounds on our estimator’s bias. Our experiments show that it remains accurate for repetitive genomic sequences, such as the alpha satellite higher order repeats in centromeres. We demonstrate our estimator’s robustness across diverse datasets and various ranges of the substitution rate and k-mer size. Finally, we show how sketching can be used to avoid dealing with large k-mer sets while retaining accuracy. Our software is available at https://github.com/medvedevgroup/Repeat-Aware_Substitution_Rate_Estimator.
Cite as

Haonan Wu, Antonio Blanca, and Paul Medvedev. A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences. In 25th International Conference on Algorithms for Bioinformatics (WABI 2025). Leibniz International Proceedings in Informatics (LIPIcs), Volume 344, pp. 20:1-20:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{wu_et_al:LIPIcs.WABI.2025.20,
  author =	{Wu, Haonan and Blanca, Antonio and Medvedev, Paul},
  title =	{{A k-mer-Based Estimator of the Substitution Rate Between Repetitive Sequences}},
  booktitle =	{25th International Conference on Algorithms for Bioinformatics (WABI 2025)},
  pages =	{20:1--20:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-386-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{344},
  editor =	{Brejov\'{a}, Bro\v{n}a and Patro, Rob},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.WABI.2025.20},
  URN =		{urn:nbn:de:0030-drops-239465},
  doi =		{10.4230/LIPIcs.WABI.2025.20},
  annote =	{Keywords: k-mers, sketching, mutation rates}
}
Document
DOI: 10.4230/LIPIcs.OPODIS.2024.36
Distributed Branching Random Walks and Their Applications

Authors: Vijeth Aradhya, Seth Gilbert, and Thorsten Götte

Published in: LIPIcs, Volume 324, 28th International Conference on Principles of Distributed Systems (OPODIS 2024)

Abstract
In recent years, the explosion of big data and analytics has necessitated distributed storage and processing with several compute nodes (e.g., multiple datacenters). These nodes collaboratively perform parallel computation, where the data is typically partitioned across these nodes to ensure scalability, redundancy and load-balancing. But the nodes may not always be co-located; in many cases, they are part of a larger communication network. Since those nodes only need to communicate among themselves, a key challenge is to design efficient routes catered to that subnetwork. In this work, we initiate the study of distributed sampling and routing problems for subnetworks in any well-connected network. Given any network G = (V, E) with mixing time τ_mix, consider the canonical problem of permutation routing [Ghaffari, Kuhn and Su, PODC 2017] that aims to minimize both congestion and dilation of the routes, where the demands (i.e., set of source-terminal pairs) are such that each node sends or receives number of messages proportional to its degree. We show that the permutation routing problem, when demands are restricted to any subset S ⊆ V (i.e., subnetwork), can be solved in exp(O(√(log|S|))) ⋅ Õ(τ_mix) rounds (where Õ(⋅) hides polylogarithmic factors of |V|). This means that the running time depends subpolynomially on the subnetwork size (i.e., not on the entire network size). The ability to solve permutation routing efficiently immediately implies that a large class of parallel algorithms can be simulated efficiently on the subnetwork. As a prerequisite to constructing efficient routes, we design and analyze distributed branching random walks that distribute tokens started by the nodes in the subnetwork. At a high-level, these algorithms operate by always moving each token according to a (lazy) simple random walk, but also branching a token into multiple tokens at some specified intervals; ultimately, if a node starts a branching walk, with its id in a token, then by the end of execution, several tokens with its id would be randomly distributed among the nodes. As these random walks can be started by many nodes, a crucial challenge is to ensure low-congestion, which is a primary focus of this paper.
Cite as

Vijeth Aradhya, Seth Gilbert, and Thorsten Götte. Distributed Branching Random Walks and Their Applications. In 28th International Conference on Principles of Distributed Systems (OPODIS 2024). Leibniz International Proceedings in Informatics (LIPIcs), Volume 324, pp. 36:1-36:20, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2025)

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@InProceedings{aradhya_et_al:LIPIcs.OPODIS.2024.36,
  author =	{Aradhya, Vijeth and Gilbert, Seth and G\"{o}tte, Thorsten},
  title =	{{Distributed Branching Random Walks and Their Applications}},
  booktitle =	{28th International Conference on Principles of Distributed Systems (OPODIS 2024)},
  pages =	{36:1--36:20},
  series =	{Leibniz International Proceedings in Informatics (LIPIcs)},
  ISBN =	{978-3-95977-360-7},
  ISSN =	{1868-8969},
  year =	{2025},
  volume =	{324},
  editor =	{Bonomi, Silvia and Galletta, Letterio and Rivi\`{e}re, Etienne and Schiavoni, Valerio},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/LIPIcs.OPODIS.2024.36},
  URN =		{urn:nbn:de:0030-drops-225723},
  doi =		{10.4230/LIPIcs.OPODIS.2024.36},
  annote =	{Keywords: Distributed Graph Algorithms, Random Walks, Permutation Routing}
}
Document
DOI: 10.4230/DagSemProc.09091.1
09091 Abstracts Collection – Formal Methods in Molecular Biology

Authors: Rainer Breitling, David Roger Gilbert, Monika Heiner, and Corrado Priami

Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)

Abstract
From 23. February to 27. February 2009, the Dagstuhl Seminar 09091 ``Formal Methods in Molecular Biology '' was held in Schloss Dagstuhl~--~Leibniz Center for Informatics. During the seminar, several participants presented their current research, and ongoing work and open problems were discussed. Abstracts of the presentations given during the seminar as well as abstracts of seminar results and ideas are put together in this paper. The first section describes the seminar topics and goals in general. Links to extended abstracts or full papers are provided, if available.
Cite as

Rainer Breitling, David Roger Gilbert, Monika Heiner, and Corrado Priami. 09091 Abstracts Collection – Formal Methods in Molecular Biology. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-24, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{breitling_et_al:DagSemProc.09091.1,
  author =	{Breitling, Rainer and Gilbert, David Roger and Heiner, Monika and Priami, Corrado},
  title =	{{09091 Abstracts Collection – Formal Methods in Molecular Biology }},
  booktitle =	{Formal Methods in Molecular Biology},
  pages =	{1--24},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9091},
  editor =	{Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.1},
  URN =		{urn:nbn:de:0030-drops-19972},
  doi =		{10.4230/DagSemProc.09091.1},
  annote =	{Keywords: Formal models, systems biology, biological processes}
}
Document
DOI: 10.4230/DagSemProc.09091.2
09091 Executive Summary – Formal Methods in Molecular Biology

Authors: Rainer Breitling, David Roger Gilbert, Monika Heiner, and Corrado Priami

Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)

Abstract
Formal logical models play an increasing role in the newly emerging field of Systems Biology. Compared to the classical, well-established approach of modeling biological processes using continuous and stochastic differential equations, formal logical models offer a number of important advantages. Many different formal modeling paradigms have been applied to molecular biology, each with its own community, formalisms and tools. In this seminar we brought together modelers from various backgrounds to stimulate closer interaction within the field and to create a common platform for discussion. A central feature of the seminar was a modeling competition (with a highly collaborative flavor) of various modeling paradigms.
Cite as

Rainer Breitling, David Roger Gilbert, Monika Heiner, and Corrado Priami. 09091 Executive Summary – Formal Methods in Molecular Biology. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{breitling_et_al:DagSemProc.09091.2,
  author =	{Breitling, Rainer and Gilbert, David Roger and Heiner, Monika and Priami, Corrado},
  title =	{{09091 Executive Summary – Formal Methods in Molecular Biology}},
  booktitle =	{Formal Methods in Molecular Biology},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9091},
  editor =	{Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.2},
  URN =		{urn:nbn:de:0030-drops-19964},
  doi =		{10.4230/DagSemProc.09091.2},
  annote =	{Keywords: Formal models, systems biology, biological processes.}
}
Document
DOI: 10.4230/DagSemProc.09091.3
Analyzing various models of Circadian Clock and Cell Cycle coupling

Authors: Attila Csikász-Nagy, Adrien Faure, Roberto Larcher, Paola Lecca, Ivan Mura, Ferenc Jordan, Alida Palmisano, Alessandro Romanel, Sean Sedwards, Heike Siebert, Sylvain Soliman, Denis Thieffry, Judit Zámborszky, Tommaso Mazza, and Paolo Ballarini

Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)

Abstract
The daily rhythm can influence the proliferation rate of many cell types. In the mammalian system the transcription of the cell cycle regulatory protein Wee1 is controlled by the circadian clock. Zamborszky et al. (2007) present a computational model coupling the cell cycle and circadian rhythm, showing that this coupling can lead to multimodal cell cycle time distributions. Biological data points to additional couplings, including a link back from the cell cycle to the circadian clock. Proper modelling of this coupling requires a more detailed description of both parts of the model. Hence, we aim at further extending and analysing earlier models using a combination of modelling techniques and computer software, including CoSBI lab, BIOCHAM, and GINsim.
Cite as

Attila Csikász-Nagy, Adrien Faure, Roberto Larcher, Paola Lecca, Ivan Mura, Ferenc Jordan, Alida Palmisano, Alessandro Romanel, Sean Sedwards, Heike Siebert, Sylvain Soliman, Denis Thieffry, Judit Zámborszky, Tommaso Mazza, and Paolo Ballarini. Analyzing various models of Circadian Clock and Cell Cycle coupling. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-6, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{csikasznagy_et_al:DagSemProc.09091.3,
  author =	{Csik\'{a}sz-Nagy, Attila and Faure, Adrien and Larcher, Roberto and Lecca, Paola and Mura, Ivan and Jordan, Ferenc and Palmisano, Alida and Romanel, Alessandro and Sedwards, Sean and Siebert, Heike and Soliman, Sylvain and Thieffry, Denis and Z\'{a}mborszky, Judit and Mazza, Tommaso and Ballarini, Paolo},
  title =	{{Analyzing various models of Circadian Clock and Cell Cycle coupling}},
  booktitle =	{Formal Methods in Molecular Biology},
  pages =	{1--6},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9091},
  editor =	{Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.3},
  URN =		{urn:nbn:de:0030-drops-19944},
  doi =		{10.4230/DagSemProc.09091.3},
  annote =	{Keywords: Cell cycle, circadian clock, computational modelling}
}
Document
DOI: 10.4230/DagSemProc.09091.4
BioModel Engineering: Its role in Systems Biology and Synthetic Biology

Authors: David Roger Gilbert, Rainer Breitling, and Monika Heiner

Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)

Abstract
BioModel Engineering takes place at the interface of computing science, mathematics, engineering and biology, and provides a systematic approach for designing, constructing and analyzing computational models of biological systems. Some of its central concepts are inspired by efficient software engineering strategies. BioModel Engineering does not aim at engineering biological systems per se, but rather aims at describing their structure and behavior, in particular at the level of intracellular molecular processes, using computational tools and techniques in a principled way. The two major application areas of BioModel Engineering are systems biology and synthetic biology. In the former, the aim is the design and construction of models of existing biological systems, which explain observed properties and predict the response to experimental interventions; in the latter, BioModel Engineering is used as part of a general strategy for designing and constructing synthetic biological systems with novel functionalities. The overall steps in building computational models in a BioModel Engineering framework are: Problem Identification, Model Construction, Static and Dynamic Analysis, Simulation, and Model management and development. A major theme in BioModel Engineering is that of constructing a (qualitative) model means (1) finding the structure, (2) obtaining an initial state and (3) parameter fitting. In an approach that we have taken, the structure is obtained by piecewise construction of models from modular parts, the initial state which describes concentrations of species or numbers of molecules is obtained by analysis of the structure, and parameter fitting comprises determining the rate parameters of the kinetic equations by reference to trusted data. Model checking can play a key role in BioModel Engineering – for example in recent work we have shown how parameter estimation can be achieved by characterising the desired behaviour of a model with a temporal logic property and altering the model to make it conform to the property as determined through model checking.
Cite as

David Roger Gilbert, Rainer Breitling, and Monika Heiner. BioModel Engineering: Its role in Systems Biology and Synthetic Biology. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-2, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{gilbert_et_al:DagSemProc.09091.4,
  author =	{Gilbert, David Roger and Breitling, Rainer and Heiner, Monika},
  title =	{{BioModel Engineering: Its role in Systems Biology and Synthetic Biology}},
  booktitle =	{Formal Methods in Molecular Biology},
  pages =	{1--2},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9091},
  editor =	{Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.4},
  URN =		{urn:nbn:de:0030-drops-19929},
  doi =		{10.4230/DagSemProc.09091.4},
  annote =	{Keywords: Biochemical systems, models, design, construction, systems biology, synthetic biology, model checking.}
}
Document
DOI: 10.4230/DagSemProc.09091.5
Modelling and analysis of the NF-$kappa$B pathway in Bio-PEPA

Authors: Federica Ciocchetta, Andrea Degasperi, John Heath, and Jane Hillston

Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)

Abstract
In this work we present a Bio-PEPA model describing the Nuclear Factor $kappa$B (NF-$kappa$B) signalling pathway. In particular our model focuses on the dynamic response of NF-$kappa$B to an external stimulus. Each biochemical species in the pathway is represented by a specific Bio-PEPA component and the external stimulus is abstracted by Bio-PEPA events. The Bio-PEPA model is a formal intermediate representation of the pathway on which various kinds of analysis can be performed. Both stochastic and deterministic simulations are carried out to validate our model against the experimental data in the literature and to verify some properties, such as the impact of the stimulus duration and of the NF-$kappa$B initial amount on the behaviour of some species. Finally, sensitivity analysis is considered to investigate the most influential parameters of the model.
Cite as

Federica Ciocchetta, Andrea Degasperi, John Heath, and Jane Hillston. Modelling and analysis of the NF-$kappa$B pathway in Bio-PEPA. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-18, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{ciocchetta_et_al:DagSemProc.09091.5,
  author =	{Ciocchetta, Federica and Degasperi, Andrea and Heath, John and Hillston, Jane},
  title =	{{Modelling and analysis of the NF-\$kappa\$B pathway in Bio-PEPA}},
  booktitle =	{Formal Methods in Molecular Biology},
  pages =	{1--18},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9091},
  editor =	{Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.5},
  URN =		{urn:nbn:de:0030-drops-19911},
  doi =		{10.4230/DagSemProc.09091.5},
  annote =	{Keywords: Process algebras, NF-\$kappa\$B pathway, modelling, analysis}
}
Document
DOI: 10.4230/DagSemProc.09091.6
Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon

Authors: Céline Kuttler, Cédric Lhoussaine, and Mirabelle Nebut

Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)

Abstract
Transcriptional attenuation at E.coli's tryptophan operon is a prime example of RNA-mediated gene regulation. In this paper, we present a discrete stochastic model for this phenomenon based on chemical reactions. Our model is compact and intelligible, due to n-ary reactions (which preclude object-centric approaches) and to rule schemas that define finite sets of chemical reactions. Stochastic simulations with our model confirm results that were previously obtained by master equations or differential equations. In addition, our approach permits to reflect mutation experiments by simple model modifications, and to re-use model components for transcriptional attenuation in other genes and organisms.
Cite as

Céline Kuttler, Cédric Lhoussaine, and Mirabelle Nebut. Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-22, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{kuttler_et_al:DagSemProc.09091.6,
  author =	{Kuttler, C\'{e}line and Lhoussaine, C\'{e}dric and Nebut, Mirabelle},
  title =	{{Rule-based Modeling of Transcriptional Attenuation at the Tryptophan Operon}},
  booktitle =	{Formal Methods in Molecular Biology},
  pages =	{1--22},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9091},
  editor =	{Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.6},
  URN =		{urn:nbn:de:0030-drops-19938},
  doi =		{10.4230/DagSemProc.09091.6},
  annote =	{Keywords: Systems biology, rule-based modeling languages, stochastic simulation, kappa.}
}
Document
DOI: 10.4230/DagSemProc.09091.7
Stochastic modelling of cellular growth and division by means of the pi@ calculus

Authors: Cristian Versari

Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)

Abstract
The application of Concurrency Theory to Systems Biology is in its earliest stage of progress. The metaphor of cells as computing systems by Regev and Shapiro opened the employment of concurrent languages for the modelling of biological systems. Their peculiar characteristics led to the design of many bio-inspired formalisms which achieve higher faithfulness and specificity. In this paper we discuss the application to the biological modelling of pi@, a core calculus for the representation of biological systems. The pi@ language represents a keystone in this respect, thanks to its expressiveness capabilities which allow the modelling of a wide variety of phenomena (e.g. simple chemical reactions, but also formation of molecular or protein complexes, organisation of complex system in dynamical compartment hierarchies) despite of its simplicity and conservativeness. Here we analyse a biological case study involving cellular growth and division, modelled in the stochastic variant of pi@: the case study is formalised and stochastically simulated according to a multi-compartment extension of Gillespie's stochastic simulation algorithm. The results underline the usefulness of the modelling approach adopted in pi@ for the correct handling of systems with variable volume.
Cite as

Cristian Versari. Stochastic modelling of cellular growth and division by means of the pi@ calculus. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-15, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{versari:DagSemProc.09091.7,
  author =	{Versari, Cristian},
  title =	{{Stochastic modelling of cellular growth and division by means of the pi@ calculus}},
  booktitle =	{Formal Methods in Molecular Biology},
  pages =	{1--15},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9091},
  editor =	{Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.7},
  URN =		{urn:nbn:de:0030-drops-19907},
  doi =		{10.4230/DagSemProc.09091.7},
  annote =	{Keywords: Process algebra, pi-calculus, simulation, stochastic}
}
Document
DOI: 10.4230/DagSemProc.09091.8
Symbolic Steady States and Dynamically Essential Subnetworks of Discrete Regulatory Networks

Authors: Heike Siebert

Published in: Dagstuhl Seminar Proceedings, Volume 9091, Formal Methods in Molecular Biology (2009)

Abstract
Analyzing complex networks is a difficult task, regardless of the chosen modeling framework. For a discrete regulatory network, even if the number of components is in some sense manageable, we have to deal with the problem of analyzing the dynamics in an exponentially large state space. A well known idea to approach this difficulty is to identify smaller building blocks of the system the study of which in isolation still renders information on the dynamics of the whole network. In this talk, we introduce the notion of symbolic steady state which allows us to identify such building blocks. We state explicit rules how to derive attractors of the network from subnetwork attractors valid for synchronous as well as asynchronous dynamics. Illustrating those rules, we derive general conditions for circuits embedded in the network to transfer their behavioral characteristics pertaining number and size of attractors observed in isolation to the complex network.
Cite as

Heike Siebert. Symbolic Steady States and Dynamically Essential Subnetworks of Discrete Regulatory Networks. In Formal Methods in Molecular Biology. Dagstuhl Seminar Proceedings, Volume 9091, pp. 1-3, Schloss Dagstuhl – Leibniz-Zentrum für Informatik (2009)

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@InProceedings{siebert:DagSemProc.09091.8,
  author =	{Siebert, Heike},
  title =	{{Symbolic Steady  States and Dynamically Essential Subnetworks of Discrete Regulatory Networks}},
  booktitle =	{Formal Methods in Molecular Biology},
  pages =	{1--3},
  series =	{Dagstuhl Seminar Proceedings (DagSemProc)},
  ISSN =	{1862-4405},
  year =	{2009},
  volume =	{9091},
  editor =	{Rainer Breitling and David Roger Gilbert and Monika Heiner and Corrado Priami},
  publisher =	{Schloss Dagstuhl -- Leibniz-Zentrum f{\"u}r Informatik},
  address =	{Dagstuhl, Germany},
  URL =		{https://drops.dagstuhl.de/entities/document/10.4230/DagSemProc.09091.8},
  URN =		{urn:nbn:de:0030-drops-19957},
  doi =		{10.4230/DagSemProc.09091.8},
  annote =	{Keywords: Discrete networks, logical analysis, symbolic steady states}
}
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