Network-based strategies in metabolomics data analysis and interpretation: from molecular networking to biological interpretation
Introduction Metabolomics has become a crucial part of systems biology; however, data
analysis is still often undertaken in a reductionist way focusing on changes in individual …
analysis is still often undertaken in a reductionist way focusing on changes in individual …
Inferring biological networks by sparse identification of nonlinear dynamics
Inferring the structure and dynamics of network models is critical to understanding the
functionality and control of complex systems, such as metabolic and regulatory biological …
functionality and control of complex systems, such as metabolic and regulatory biological …
Inverse data-driven modeling and multiomics analysis reveals phgdh as a metabolic checkpoint of macrophage polarization and proliferation
JL Wilson, T Nägele, M Linke, F Demel, SD Fritsch… - Cell reports, 2020 - cell.com
Mechanistic or mammalian target of rapamycin complex 1 (mTORC1) is an important
regulator of effector functions, proliferation, and cellular metabolism in macrophages. The …
regulator of effector functions, proliferation, and cellular metabolism in macrophages. The …
Metabolic network discovery by top-down and bottom-up approaches and paths for reconciliation
T Çakır, MJ Khatibipour - Frontiers in Bioengineering and …, 2014 - frontiersin.org
The primary focus in the network-centric analysis of cellular metabolism by systems biology
approaches is to identify the active metabolic network for the condition of interest. Two major …
approaches is to identify the active metabolic network for the condition of interest. Two major …
Self-organizing networks in complex infrastructure projects
S Pryke, S Badi, H Almadhoob… - Project …, 2018 - journals.sagepub.com
While significant importance is given to establishing formal organizational and contractual
hierarchies, existing project management techniques neglect the management of self …
hierarchies, existing project management techniques neglect the management of self …
System level analysis of cacao seed ripening reveals a sequential interplay of primary and secondary metabolism leading to polyphenol accumulation and …
Theobroma cacao and its popular product, chocolate, are attracting attention due to potential
health benefits including antioxidative effects by polyphenols, anti‐depressant effects by …
health benefits including antioxidative effects by polyphenols, anti‐depressant effects by …
COVRECON: automated integration of genome-and metabolome-scale network reconstruction and data-driven inverse modeling of metabolic interaction networks
J Li, S Waldherr, W Weckwerth - Bioinformatics, 2023 - academic.oup.com
Motivation One central goal of systems biology is to infer biochemical regulations from large-
scale OMICS data. Many aspects of cellular physiology and organismal phenotypes can be …
scale OMICS data. Many aspects of cellular physiology and organismal phenotypes can be …
Toward a unification of system-theoretical principles in biology and ecology—the stochastic lyapunov matrix equation and its inverse application
W Weckwerth - Frontiers in Applied Mathematics and Statistics, 2019 - frontiersin.org
System theory has its roots in mathematical formalisms developed by mathematicians and
physicists, such as Leibniz, Euler, and Newton, and applied by congenial chemists and …
physicists, such as Leibniz, Euler, and Newton, and applied by congenial chemists and …
Exploration and exploitation of the yeast volatilome
B E. Ebert, C Halbfeld, L M. Blank - Current Metabolomics, 2017 - benthamdirect.com
Background: Volatile organic compounds (VOCs) are small molecular mass substances,
which exhibit high-vapor pressures, low boiling points, and lipophilic character. VOCs are …
which exhibit high-vapor pressures, low boiling points, and lipophilic character. VOCs are …
JacLy: a Jacobian-based method for the inference of metabolic interactions from the covariance of steady-state metabolome data
MJ Khatibipour, F Kurtoğlu, T Çakır - PeerJ, 2018 - peerj.com
Reverse engineering metabolome data to infer metabolic interactions is a challenging
research topic. Here we introduce JacLy, a Jacobian-based method to infer metabolic …
research topic. Here we introduce JacLy, a Jacobian-based method to infer metabolic …