61 Result(s)

Chapter and Conference Paper

Generating the Logicome of a Biological Network

There has been much progress in recent years towards building larger and larger computational models for biochemical networks, driven by advances both in high throughput data techniques, and in computational m...

Charmi Panchal, Sepinoud Azimi, Ion Petre in Algorithms for Computational Biology (2016)

Chapter and Conference Paper

Target Controllability of Linear Networks

Computational analysis of the structure of intra-cellular molecular interaction networks can suggest novel therapeutic approaches for systemic diseases like cancer. Recent research in the area of network scien...

Eugen Czeizler, Cristian Gratie, Wu Kai Chiu… in Computational Methods in Systems Biology (2016)

Chapter and Conference Paper

An Excursion Through Quantitative Model Refinement

There is growing interest in creating large-scale computational models for biological process. One of the challenges in such a project is to fit and validate larger and larger models, a process that requires m...

Sepinoud Azimi, Eugen Czeizler, Cristian Gratie, Diana Gratie… in Membrane Computing (2015)

Chapter and Conference Paper

Fit-Preserving Data Refinement of Mass-Action Reaction Networks

The systematic development of large biological models can benefit from an iterative approach based on a refinement process that gradually adds more details regarding the reactants and/or reactions of the model...

Cristian Gratie, Ion Petre in Language, Life, Limits (2014)

Chapter and Conference Paper

On the Implementation of Quantitative Model Refinement

The iterative process of adding details to a model while preserving its numerical behavior is called quantitative model refinement, and it has been previously discussed for ODE-based models and for kappa-based mo...

Bogdan Iancu, Diana-Elena Gratie, Sepinoud Azimi… in Algorithms for Computational Biology (2014)

Chapter

ODE Analysis of Biological Systems

This chapter aims to introduce some of the basics of modeling with ODEs in biology. We focus on computational, numerical techniques, rather than on symbolic ones. We restrict our attention to reaction-based mo...

Diana-Elena Gratie, Bogdan Iancu, Ion Petre in Formal Methods for Dynamical Systems (2013)

Article

Preface

Jarkko Kari, Ion Petre in Natural Computing (2012)

Chapter and Conference Paper

Self-assembly Models of Variable Resolution

Model refinement is an important aspect of the model-building process. It can be described as a procedure which, starting from an abstract model of a system, performs a number of refinement steps in result of ...

Andrzej Mizera, Eugen Czeizler, Ion Petre in Transactions on Computational Systems Biol… (2012)

Reference Work Entry In depth

Computational Nature of Gene Assembly in Ciliates

Ciliates are a very diverse and ancient group of unicellular eukaryotic organisms. A feature that is essentially unique to ciliates is the nuclear dualism, meaning that they have two functionally different typ...

Robert Brijder, Mark Daley, Tero Harju, Nataša Jonoska… in Handbook of Natural Computing (2012)

Article

Complexity-preserving simulations among three variants of accepting networks of evolutionary processors

In this paper we consider three variants of accepting networks of evolutionary processors. It is known that two of them are equivalent to Turing machines. We propose here a direct simulation of one device by t...

Paolo Bottoni, Anna Labella, Florin Manea, Victor Mitrana, Ion Petre… in Natural Computing (2011)

Article

A simple mass-action model for the eukaryotic heat shock response and its mathematical validation

The heat shock response is a primordial defense mechanism against cell stress and protein misfolding. It proceeds with the minimum number of mechanisms that any regulatory network must include, a stress-induce...

Ion Petre, Andrzej Mizera, Claire L. Hyder, Annika Meinander… in Natural Computing (2011)

Chapter

A New Mathematical Model for the Heat Shock Response

We present in this paper a novel molecular model for the gene regulatory network responsible for the eukaryotic heat shock response. Our model includes the temperature-induced protein misfolding, the chaperone...

Ion Petre, Andrzej Mizera, Claire L. Hyder, Andrey Mikhailov… in Algorithmic Bioprocesses (2009)

Chapter and Conference Paper

Computational Heuristics for Simplifying a Biological Model

Computational biomodelers adopt either of the following approaches: build rich, as complete as possible models in an effort to obtain very realistic models, or on the contrary, build as simple as possible mode...

Ion Petre, Andrzej Mizera, Ralph-Johan Back in Mathematical Theory and Computational Prac… (2009)

Chapter and Conference Paper

Control Strategies for the Regulation of the Eukaryotic Heat Shock Response

Elevated temperatures cause proteins in living cells to misfold. They start forming larger and larger aggregates that can eventually lead to the cell’s death. The heat shock response is an evolutionary well co...

Elena Czeizler, Eugen Czeizler… in Computational Methods in Systems Biology (2009)

Chapter

Algebraic Systems and Pushdown Automata

We concentrate in this chapter on the core aspects of algebraic series, pushdown automata, and their relation to formal languages. We choose to follow here a presentation of their theory based on the concept o...

Ion Petre, Arto Salomaa in Handbook of Weighted Automata (2009)