Recent advances in 2D and 3D in vitro systems using primary hepatocytes, alternative hepatocyte sources and non-parenchymal liver cells and their use in …

P Godoy, NJ Hewitt, U Albrecht, ME Andersen… - Archives of …, 2013 - Springer
This review encompasses the most important advances in liver functions and hepatotoxicity
and analyzes which mechanisms can be studied in vitro. In a complex architecture of nested …

Structure and dynamics of molecular networks: a novel paradigm of drug discovery: a comprehensive review

P Csermely, T Korcsmáros, HJM Kiss, G London… - Pharmacology & …, 2013 - Elsevier
Despite considerable progress in genome-and proteome-based high-throughput screening
methods and in rational drug design, the increase in approved drugs in the past decade did …

The why, how, and when of representations for complex systems

L Torres, AS Blevins, D Bassett, T Eliassi-Rad - SIAM Review, 2021 - SIAM
Complex systems, composed at the most basic level of units and their interactions, describe
phenomena in a wide variety of domains, from neuroscience to computer science and …

[图书][B] Analysis of biological networks

BH Junker, F Schreiber - 2008 - Wiley Online Library
Analysis of biological networks ANALYSIS OF BIOLOGICAL NETWORKS Page 2
ANALYSIS OF BIOLOGICAL NETWORKS EDITED BY BJO RN H. JUNKER and FALK …

Structural and functional analysis of cellular networks with CellNetAnalyzer

S Klamt, J Saez-Rodriguez, ED Gilles - BMC systems biology, 2007 - Springer
Background Mathematical modelling of cellular networks is an integral part of Systems
Biology and requires appropriate software tools. An important class of methods in Systems …

Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome

MH Mirhakkak, X Chen, Y Ni, T Heinekamp… - Nature …, 2023 - nature.com
Aspergillus fumigatus, an opportunistic human pathogen, frequently infects the lungs of
people with cystic fibrosis and is one of the most common causes of infectious-disease …

Modular epistasis in yeast metabolism

D Segre, A DeLuna, GM Church, R Kishony - Nature genetics, 2005 - nature.com
Epistatic interactions, manifested in the effects of mutations on the phenotypes caused by
other mutations, may help uncover the functional organization of complex biological …

A methodology for the structural and functional analysis of signaling and regulatory networks

S Klamt, J Saez-Rodriguez, JA Lindquist, L Simeoni… - BMC …, 2006 - Springer
Background Structural analysis of cellular interaction networks contributes to a deeper
understanding of network-wide interdependencies, causal relationships, and basic …

Genome-scale models of bacterial metabolism: reconstruction and applications

M Durot, PY Bourguignon… - FEMS microbiology …, 2008 - academic.oup.com
Genome-scale metabolic models bridge the gap between genome-derived biochemical
information and metabolic phenotypes in a principled manner, providing a solid …

Subgraph centrality and clustering in complex hyper-networks

E Estrada, JA Rodríguez-Velázquez - Physica A: Statistical Mechanics and …, 2006 - Elsevier
The representation of complex systems as networks is inappropriate for the study of certain
problems. We show several examples of social, biological, ecological and technological …