Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems

S Ghosh, MG Baltussen, NM Ivanov, R Haije… - Chemical …, 2024 - ACS Publications
The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in
the emergence and sustenance of life. Constructing such networks in vitro enables stepwise …

[HTML][HTML] Single-cell multi-omics and lineage tracing to dissect cell fate decision-making

L Haghverdi, LS Ludwig - Stem Cell Reports, 2023 - cell.com
The concept of cell fate relates to the future identity of a cell, and its daughters, which is
obtained via cell differentiation and division. Understanding, predicting, and manipulating …

Systems biology informed deep learning for inferring parameters and hidden dynamics

A Yazdani, L Lu, M Raissi… - PLoS computational …, 2020 - journals.plos.org
Mathematical models of biological reactions at the system-level lead to a set of ordinary
differential equations with many unknown parameters that need to be inferred using …

Deciphering microbial interactions in synthetic human gut microbiome communities

OS Venturelli, AV Carr, G Fisher, RH Hsu… - Molecular systems …, 2018 - embopress.org
The ecological forces that govern the assembly and stability of the human gut microbiota
remain unresolved. We developed a generalizable model‐guided framework to predict …

Modelingtoolkit: A composable graph transformation system for equation-based modeling

Y Ma, S Gowda, R Anantharaman, C Laughman… - arXiv preprint arXiv …, 2021 - arxiv.org
Getting good performance out of numerical equation solvers requires that the user has
provided stable and efficient functions representing their model. However, users should not …

Building kinetic models for metabolic engineering

CJ Foster, L Wang, HV Dinh, PF Suthers… - Current Opinion in …, 2021 - Elsevier
Highlights•Kinetic models integrate heterogeneous data to give metabolic engineering
insights.•Need accurate catalytic and allostery kinetic parameters for quality kinetic …

[HTML][HTML] Parameter identifiability analysis: Mitigating the non-uniqueness issue in the inverse identification of an anisotropic yield function

Y Zhang, A Van Bael, A Andrade-Campos… - International Journal of …, 2022 - Elsevier
A large number of conventional mechanical tests are required to calibrate advanced
anisotropic yield functions. A well-designed non-conventional mechanical test generating …

A microfluidic optimal experimental design platform for forward design of cell-free genetic networks

B van Sluijs, RJM Maas, AJ van der Linden… - Nature …, 2022 - nature.com
Cell-free protein synthesis has been widely used as a “breadboard” for design of synthetic
genetic networks. However, due to a severe lack of modularity, forward engineering of …

[HTML][HTML] Digitally enabled approaches for the scale up of mammalian cell bioreactors

MK Alavijeh, I Baker, YY Lee, SL Gras - Digital Chemical Engineering, 2022 - Elsevier
With recent advances in digitisation and big data analytics, more pharmaceutical firms are
adopting digital tools to achieve modernisation. The biological phenomena within …

Comprehensive review of models and methods for inferences in bio-chemical reaction networks

P Loskot, K Atitey, L Mihaylova - Frontiers in genetics, 2019 - frontiersin.org
The key processes in biological and chemical systems are described by networks of
chemical reactions. From molecular biology to biotechnology applications, computational …