Modeling and simulation of genetic regulatory systems: a literature review

H De Jong - Journal of computational biology, 2002 - liebertpub.com
In order to understand the functioning of organisms on the molecular level, we need to know
which genes are expressed, when and where in the organism, and to which extent. The …

Bistability, bifurcations, and Waddington's epigenetic landscape

JE Ferrell - Current biology, 2012 - cell.com
Waddington's epigenetic landscape is probably the most famous and most powerful
metaphor in developmental biology. Cells, represented by balls, roll downhill through a …

Detection of multistability, bifurcations, and hysteresis in a large class of biological positive-feedback systems

D Angeli, JE Ferrell Jr… - Proceedings of the …, 2004 - National Acad Sciences
It is becoming increasingly clear that bistability (or, more generally, multistability) is an
important recurring theme in cell signaling. Bistability may be of particular relevance to …

Interaction between emotional state and learning underlies mood instability

E Eldar, Y Niv - Nature communications, 2015 - nature.com
Intuitively, good and bad outcomes affect our emotional state, but whether the emotional
state feeds back onto the perception of outcomes remains unknown. Here, we use …

Dynamical behaviour of biological regulatory networks—I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state

R Thomas, D Thieffry, M Kaufman - Bulletin of mathematical biology, 1995 - Springer
In the field of biological regulation, models dictated by expreimental work are usually
complex networks comprising intertwined feedback loops. In this paper the biological roles …

Alzheimer's disease-associated (hydroxy) methylomic changes in the brain and blood

R Lardenoije, JAY Roubroeks, E Pishva, M Leber… - Clinical …, 2019 - Springer
Abstract Background Late-onset Alzheimer's disease (AD) is a complex multifactorial
affliction, the pathogenesis of which is thought to involve gene-environment interactions that …

The hive bee to forager transition in honeybee colonies: the double repressor hypothesis

GV Amdam, SW Omholt - Journal of theoretical biology, 2003 - Elsevier
In summer, the honeybee (Apis mellifera) worker population consists of two temporal castes,
a hive bee group performing a multitude of tasks including nursing inside the nest, and a …

Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior

R Thomas, M Kaufman - Chaos: An Interdisciplinary Journal of …, 2001 - pubs.aip.org
A biological introduction serves to remind us that differentiation is an epigenetic process,
that multistationarity can account for epigenetic differences, including those involved in cell …

Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis.

L Mendoza, D Thieffry… - Bioinformatics (Oxford …, 1999 - academic.oup.com
MOTIVATION: A large number of molecular mechanisms at the basis of gene regulation
have been described during the last few decades. It is now becoming possible to address …

Positive and negative circuits in dynamical systems

JL Gouzé - Journal of Biological Systems, 1998 - World Scientific
We state precisely and demonstrate two conjectures of R. Thomas following which (a) the
existence of a positive circuit in the oriented interaction graph of a differential system is a …