Transcriptional Dynamics of the Embryonic Stem Cell Switch (2008)
Vijay Chickarmane, Carl Troein, Ulrike A. Nuber, Herbert M. Sauro, Carsten Peterson
Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the...
Is Transcriptional Regulation of Metabolic Pathways an Optimal Strategy for Fitness? (2008)
Carl Troein, Dag Ahrén, Morten Krogh, Carsten Peterson
Background. Transcriptional regulation of the genes in metabolic pathways is a highly successful strategy, which is virtually universal in microorganisms. The lac operon of E. coli is but one example...
Gene Regulatory Networks: Dynamics and Stability (2007)
Life as we know it is based on cells that use proteins and RNA to carry out metabolism, self-replication, and other essential tasks. The genes that code for these molecules are encoded in DNA, and...
Transcriptional Dynamics of the Embryonic Stem Cell Switch (2006)
Vijay Chickarmane, Carl Troein, Ulrike A. Nuber, Herbert M. Sauro, Carsten Peterson
Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the...
Transcriptional Dynamics of the Embryonic Stem Cell Switch (2006)
Vijay Chickarmane, Carl Troein, Ulrike Nuber, Herbert M Sauro, Carsten Peterson
Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the...
Signal transduction pathway profiling of individual tumor samples (2005)
Breslin, Thomas, Krogh, Morten, Peterson, Carsten, Troein, Carl
Abstract Background Signal transduction pathways convey information from the outside of the cell to transcription factors, which in turn regulate gene expression. Our objective is to analyze tumor...
Random maps and attractors in random Boolean networks (2005)
Samuelsson, Björn, Troein, Carl
Despite their apparent simplicity, random Boolean networks display a rich variety of dynamical behaviors. Much work has been focused on the properties and abundance of attractors. The topologies of...
Thomas Breslin, Morten Krogh, Carsten Peterson, Carl Troein, Carl Troein
Background: Signal transduction pathways convey information from the outside of the cell to transcription factors, which in turn regulate gene expression. Our objective is to analyze tumor gene...
Counting attractors in synchronously updated random Boolean networks (2004)
Samuelsson, Björn, Troein, Carl
Despite their apparent simplicity, random Boolean networks display a rich variety of dynamical behaviors. Much work has been focused on the properties and abundance of attractors. We here derive an...
Genetic networks with canalyzing Boolean rules are always stable (2004)
Kauffman, Stuart, Peterson, Carsten, Samuelsson, Björn, Troein, Carl
We determine stability and attractor properties of random Boolean genetic network models with canalyzing rules for a variety of architectures. For all power law, exponential, and flat in-degree...
Random Boolean Network Models and the Yeast Transcriptional Network (2004)
Kauffman, Stuart, Peterson, Carsten, Samuelsson, Björn, Troein, Carl
The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable...
Saal, Lao H, Troein, Carl, Vallon-Christersson, Johan, Gruvberger, Sofia, Borg, Åke, Peterson, Carsten
Abstract The microarray technique requires the organization and analysis of vast amounts of data. These data include information about the samples hybridized, the hybridization images and their...
Enumerating Designing Sequences in the HP Model (2002)
The hydrophobic/polar HP model on the square lattice has been widely used to investigate basics of protein folding. In the cases where all designing sequences (sequences with unique ground states)...
Lao H Saal, Carl Troein, Johan Vallon-christersson, Sofia Gruvberger, Åke Borg, Carsten Peterson
(Print ISSN 1465-6906; Online ISSN 1465-6914) The microarray technique requires the organization and analysis of vast amounts of data. These data include information about the samples hybridized, the...
Enumerating designing sequences in the HP model (2002)
Submitted to J. Chem. Phys. The hydrophobic/polar HP model on the square lattice has been widely used to investigate basics of protein folding. In the cases where all designing sequences were...
Saal, Lao H, Troein, Carl, Vallon-Christersson, Johan, Gruvberger, Sofia, Borg, Åke, Peterson, Carsten
The microarray technique requires the organization and analysis of vast amounts of data. These data include information about the samples hybridized, the hybridization images and their extracted data...
Random Boolean network models and the yeast transcriptional network
Kauffman, Stuart, Peterson, Carsten, Samuelsson, Björn, Troein, Carl
The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable...
Genetic networks with canalyzing Boolean rules are always stable
Kauffman, Stuart, Peterson, Carsten, Samuelsson, Björn, Troein, Carl
We determine stability and attractor properties of random Boolean genetic network models with canalyzing rules for a variety of architectures. For all power law, exponential, and flat in-degree...
Signal transduction pathway profiling of individual tumor samples
Breslin, Thomas, Krogh, Morten, Peterson, Carsten, Troein, Carl
Transcriptional Dynamics of the Embryonic Stem Cell Switch
Chickarmane, Vijay, Troein, Carl, Nuber, Ulrike A, Sauro, Herbert M, Peterson, Carsten
Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the...
Saal, Lao H, Troein, Carl, Vallon-Christersson, Johan, Gruvberger, Sofia, Borg, Åke, Peterson, Carsten
The microarray technique requires the organization and analysis of vast amounts of data. These data include information about the samples hybridized, the hybridization images and their extracted data...
Random Boolean network models and the yeast transcriptional network
Kauffman, Stuart, Peterson, Carsten, Samuelsson, Björn, Troein, Carl
The recently measured yeast transcriptional network is analyzed in terms of simplified Boolean network models, with the aim of determining feasible rule structures, given the requirement of stable...
Genetic networks with canalyzing Boolean rules are always stable
Kauffman, Stuart, Peterson, Carsten, Samuelsson, Björn, Troein, Carl
We determine stability and attractor properties of random Boolean genetic network models with canalyzing rules for a variety of architectures. For all power law, exponential, and flat in-degree...
Signal transduction pathway profiling of individual tumor samples
Breslin, Thomas, Krogh, Morten, Peterson, Carsten, Troein, Carl
Transcriptional Dynamics of the Embryonic Stem Cell Switch
Chickarmane, Vijay, Troein, Carl, Nuber, Ulrike A, Sauro, Herbert M, Peterson, Carsten
Recent ChIP experiments of human and mouse embryonic stem cells have elucidated the architecture of the transcriptional regulatory circuitry responsible for cell determination, which involves the...