[HTML][HTML] Leveraging network structure in nonlinear control
Over the last twenty years, dynamic modeling of biomolecular networks has exploded in
popularity. Many of the classical tools for understanding dynamical systems are unwieldy in …
popularity. Many of the classical tools for understanding dynamical systems are unwieldy in …
pystablemotifs: Python library for attractor identification and control in Boolean networks
Abstract Summary pystablemotifs is a Python 3 library for analyzing Boolean networks. Its
non-heuristic and exhaustive attractor identification algorithm was previously presented in …
non-heuristic and exhaustive attractor identification algorithm was previously presented in …
[HTML][HTML] Network analysis reveals that the tumor suppressor lncRNA GAS5 acts as a double-edged sword in response to DNA damage in gastric cancer
The lncRNA GAS5 acts as a tumor suppressor and is downregulated in gastric cancer (GC).
In contrast, E2F1, an important transcription factor and tumor promoter, directly inhibits miR …
In contrast, E2F1, an important transcription factor and tumor promoter, directly inhibits miR …
Models of cell processes are far from the edge of chaos
Complex living systems are thought to exist at the “edge of chaos” separating the ordered
dynamics of robust function from the disordered dynamics of rapid environmental …
dynamics of robust function from the disordered dynamics of rapid environmental …
[HTML][HTML] Quadra-stable dynamics of p53 and PTEN in the DNA damage response
Cell fate determination is a complex process that is frequently described as cells traveling on
rugged pathways, beginning with DNA damage response (DDR). Tumor protein p53 (p53) …
rugged pathways, beginning with DNA damage response (DDR). Tumor protein p53 (p53) …
Computing attractors of large-scale asynchronous Boolean networks using minimal trap spaces
VG Trinh, K Hiraishi, B Benhamou - Proceedings of the 13th ACM …, 2022 - dl.acm.org
Boolean Networks (BNs) play a crucial role in modeling, analyzing, and controlling
biological systems. One of the most important problems on BNs is to compute all the …
biological systems. One of the most important problems on BNs is to compute all the …
[HTML][HTML] Leveraging quantum computing for dynamic analyses of logical networks in systems biology
The dynamics of cellular mechanisms can be investigated through the analysis of networks.
One of the simplest but most popular modeling strategies involves logic-based models …
One of the simplest but most popular modeling strategies involves logic-based models …
[HTML][HTML] Effective connectivity and bias entropy improve prediction of dynamical regime in automata networks
Biomolecular network dynamics are thought to operate near the critical boundary between
ordered and disordered regimes, where large perturbations to a small set of elements …
ordered and disordered regimes, where large perturbations to a small set of elements …
[HTML][HTML] Predicting cascading extinctions and efficient restoration strategies in plant–pollinator networks via generalized positive feedback loops
The extinction of a species in a plant–pollinator mutualistic community can cause cascading
effects and lead to major biodiversity loss. The ecologically important task of predicting the …
effects and lead to major biodiversity loss. The ecologically important task of predicting the …
Temporary and permanent control of partially specified Boolean networks
Boolean networks (BNs) are a well-accepted modelling formalism in computational systems
biology. Nevertheless, modellers often cannot identify only a single BN that matches the …
biology. Nevertheless, modellers often cannot identify only a single BN that matches the …