PANTHER: Making genome‐scale phylogenetics accessible to all
PD Thomas, D Ebert, A Muruganujan… - Protein …, 2022 - Wiley Online Library
Phylogenetics is a powerful tool for analyzing protein sequences, by inferring their
evolutionary relationships to other proteins. However, phylogenetics analyses can be …
evolutionary relationships to other proteins. However, phylogenetics analyses can be …
MetaNetX/MNXref: unified namespace for metabolites and biochemical reactions in the context of metabolic models
MetaNetX/MNXref is a reconciliation of metabolites and biochemical reactions providing
cross-links between major public biochemistry and Genome-Scale Metabolic Network …
cross-links between major public biochemistry and Genome-Scale Metabolic Network …
Gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models
Genome-scale metabolic models of microorganisms are powerful frameworks to predict
phenotypes from an organism's genotype. While manual reconstructions are laborious …
phenotypes from an organism's genotype. While manual reconstructions are laborious …
COVID19 Disease Map, a computational knowledge repository of virus–host interaction mechanisms
We need to effectively combine the knowledge from surging literature with complex datasets
to propose mechanistic models of SARS‐CoV‐2 infection, improving data interpretation and …
to propose mechanistic models of SARS‐CoV‐2 infection, improving data interpretation and …
Modernizing the NEURON simulator for sustainability, portability, and performance
The need for reproducible, credible, multiscale biological modeling has led to the
development of standardized simulation platforms, such as the widely-used NEURON …
development of standardized simulation platforms, such as the widely-used NEURON …
[HTML][HTML] Advances in flux balance analysis by integrating machine learning and mechanism-based models
The availability of multi-omics data sets and genome-scale metabolic models for various
organisms provide a platform for modeling and analyzing genotype-to-phenotype …
organisms provide a platform for modeling and analyzing genotype-to-phenotype …
[HTML][HTML] Systems biology at the giga-scale: Large multiscale models of complex, heterogeneous multicellular systems
Agent-based modelling has proven its usefulness in several biomedical projects by
explaining and uncovering mechanisms in diseases. Nevertheless, the scenarios addressed …
explaining and uncovering mechanisms in diseases. Nevertheless, the scenarios addressed …
libRoadRunner 2.0: a high performance SBML simulation and analysis library
Motivation This article presents libRoadRunner 2.0, an extensible, high-performance, cross-
platform, open-source software library for the simulation and analysis of models expressed …
platform, open-source software library for the simulation and analysis of models expressed …
Hepatectomy-induced alterations in hepatic perfusion and function-toward multi-scale computational modeling for a better prediction of post-hepatectomy liver function
B Christ, M Collatz, U Dahmen, KH Herrmann… - Frontiers in …, 2021 - frontiersin.org
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) …