Boolean modeling: a logic‐based dynamic approach for understanding signaling and regulatory networks and for making useful predictions

R Albert, J Thakar - Wiley Interdisciplinary Reviews: Systems …, 2014 - Wiley Online Library
The biomolecules inside or near cells form a complex interacting system. Cellular
phenotypes and behaviors arise from the totality of interactions among the components of …

Modeling approaches for qualitative and semi-quantitative analysis of cellular signaling networks

R Samaga, S Klamt - Cell communication and signaling, 2013 - Springer
A central goal of systems biology is the construction of predictive models of bio-molecular
networks. Cellular networks of moderate size have been modeled successfully in a …

Hypergraphs and cellular networks

S Klamt, UU Haus, F Theis - PLoS computational biology, 2009 - journals.plos.org
Background The understanding of biological networks is a fundamental issue in
computational biology. When analyzing topological properties of networks, one often tends …

Boolean modeling of biological regulatory networks: a methodology tutorial

A Saadatpour, R Albert - Methods, 2013 - Elsevier
Given the complexity and interactive nature of biological systems, constructing informative
and coherent network models of these systems and subsequently developing efficient …

Engineering a universal and efficient platform for terpenoid synthesis in yeast

Y Ma, Y Zu, S Huang… - Proceedings of the …, 2023 - National Acad Sciences
Engineering microbes for the production of valuable natural products is often hindered by
the regulation of native competing metabolic networks in host. This is particularly evident in …

Construction of a controllable β‐carotene biosynthetic pathway by decentralized assembly strategy in Saccharomyces cerevisiae

W Xie, M Liu, X Lv, W Lu, J Gu… - Biotechnology and …, 2014 - Wiley Online Library
Saccharomyces cerevisiae is an important platform organism for the synthesis of a great
number of natural products. However, the assembly of controllable and genetically stable …

Systems-biology approaches for predicting genomic evolution

B Papp, RA Notebaart, C Pál - Nature Reviews Genetics, 2011 - nature.com
Is evolution predictable at the molecular level? The ambitious goal to answer this question
requires an understanding of the mutational effects that govern the complex relationship …

D-Xylose Sensing in Saccharomyces cerevisiae: Insights from D-Glucose Signaling and Native D-Xylose Utilizers

DP Brink, C Borgström, VC Persson… - International journal of …, 2021 - mdpi.com
Extension of the substrate range is among one of the metabolic engineering goals for
microorganisms used in biotechnological processes because it enables the use of a wide …

Towards genome-scale signalling-network reconstructions

DR Hyduke, BØ Palsson - Nature Reviews Genetics, 2010 - nature.com
Biological signalling networks allow living organisms to issue an integrated response to
current conditions and make limited predictions about future environmental changes. Small …

Molecular communication: crosstalk between the Snf1 and other signaling pathways

S Shashkova, N Welkenhuysen… - FEMS yeast …, 2015 - academic.oup.com
The yeast Saccharomyces cerevisiae employs different conserved signaling pathways to
adapt to altered availability of nutrient and energy sources. Crosstalk between the pathways …