SBML Level 3: an extensible format for the exchange and reuse of biological models
Abstract Systems biology has experienced dramatic growth in the number, size, and
complexity of computational models. To reproduce simulation results and reuse models …
complexity of computational models. To reproduce simulation results and reuse models …
Hepatectomy-induced alterations in hepatic perfusion and function-toward multi-scale computational modeling for a better prediction of post-hepatectomy liver function
Liver resection causes marked perfusion alterations in the liver remnant both on the organ
scale (vascular anatomy) and on the microscale (sinusoidal blood flow on tissue level) …
scale (vascular anatomy) and on the microscale (sinusoidal blood flow on tissue level) …
Addressing barriers in comprehensiveness, accessibility, reusability, interoperability and reproducibility of computational models in systems biology
Computational models are often employed in systems biology to study the dynamic
behaviours of complex systems. With the rise in the number of computational models, finding …
behaviours of complex systems. With the rise in the number of computational models, finding …
Making PBPK models more reproducible in practice
E Domínguez-Romero, S Mazurenko… - Briefings in …, 2024 - academic.oup.com
Abstract Systems biology aims to understand living organisms through mathematically
modeling their behaviors at different organizational levels, ranging from molecules to …
modeling their behaviors at different organizational levels, ranging from molecules to …
High-Quality Genome-Scale Reconstruction of Corynebacterium glutamicum ATCC 13032
M Feierabend, A Renz, E Zelle, K Nöh… - Frontiers in …, 2021 - frontiersin.org
Corynebacterium glutamicum belongs to the microbes of enormous biotechnological
relevance. In particular, its strain ATCC 13032 is a widely used producer of L-amino acids at …
relevance. In particular, its strain ATCC 13032 is a widely used producer of L-amino acids at …
The first 10 years of the international coordination network for standards in systems and synthetic biology (COMBINE)
This paper presents a report on outcomes of the 10th Computational Modeling in Biology
Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The …
Network (COMBINE) meeting that was held in Heidelberg, Germany, in July of 2019. The …
Consistency, inconsistency, and ambiguity of metabolite names in biochemical databases used for genome-scale metabolic modelling
Genome-scale metabolic models (GEMs) are manually curated repositories describing the
metabolic capabilities of an organism. GEMs have been successfully used in different …
metabolic capabilities of an organism. GEMs have been successfully used in different …
Exploring the metabolic profile of A. baumannii for antimicrobial development using genome-scale modeling
N Leonidou, Y **a, L Friedrich, MS Schütz… - PLoS …, 2024 - journals.plos.org
With the emergence of multidrug-resistant bacteria, the World Health Organization published
a catalog of microorganisms urgently needing new antibiotics, with the carbapenem …
a catalog of microorganisms urgently needing new antibiotics, with the carbapenem …
A pathway model of glucose-stimulated insulin secretion in the pancreatic β-cell
The pancreas plays a critical role in maintaining glucose homeostasis through the secretion
of hormones from the islets of Langerhans. Glucose-stimulated insulin secretion (GSIS) by …
of hormones from the islets of Langerhans. Glucose-stimulated insulin secretion (GSIS) by …
Specifications of standards in systems and synthetic biology: status, developments, and tools in 2024
The “COmputational Modeling in BIology NEtwork”(COMBINE) initiative aims to harmonise
the development of diverse community standards for computational models in biology [1, 2] …
the development of diverse community standards for computational models in biology [1, 2] …