Reconstructing organisms in silico: genome-scale models and their emerging applications

X Fang, CJ Lloyd, BO Palsson - Nature Reviews Microbiology, 2020 - nature.com
Escherichia coli is considered to be the best-known microorganism given the large number
of published studies detailing its genes, its genome and the biochemical functions of its …

Network medicine: a network-based approach to human disease

AL Barabási, N Gulbahce, J Loscalzo - Nature reviews genetics, 2011 - nature.com
Given the functional interdependencies between the molecular components in a human cell,
a disease is rarely a consequence of an abnormality in a single gene, but reflects the …

Controllability of complex networks

YY Liu, JJ Slotine, AL Barabási - nature, 2011 - nature.com
The ultimate proof of our understanding of natural or technological systems is reflected in
our ability to control them. Although control theory offers mathematical tools for steering …

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 …

Network pharmacology: the next paradigm in drug discovery

AL Hopkins - Nature chemical biology, 2008 - nature.com
The dominant paradigm in drug discovery is the concept of designing maximally selective
ligands to act on individual drug targets. However, many effective drugs act via modulation …

Data based identification and prediction of nonlinear and complex dynamical systems

WX Wang, YC Lai, C Grebogi - Physics Reports, 2016 - Elsevier
The problem of reconstructing nonlinear and complex dynamical systems from measured
data or time series is central to many scientific disciplines including physical, biological …

Analyzing and modeling real-world phenomena with complex networks: a survey of applications

LF Costa, ON Oliveira Jr, G Travieso… - Advances in …, 2011 - Taylor & Francis
The success of new scientific areas can be assessed by their potential in contributing to new
theoretical approaches and in applications to real-world problems. Complex networks have …

[HTML][HTML] Realistic control of network dynamics

SP Cornelius, WL Kath, AE Motter - Nature communications, 2013 - nature.com
The control of complex networks is of paramount importance in areas as diverse as
ecosystem management, emergency response and cell reprogramming. A fundamental …

Basic and applied uses of genome‐scale metabolic network reconstructions of Escherichia coli

D McCloskey, BØ Palsson, AM Feist - Molecular systems biology, 2013 - embopress.org
The genome‐scale model (GEM) of metabolism in the bacterium Escherichia coli K‐12 has
been in development for over a decade and is now in wide use. GEM‐enabled studies of E …

Emergent cooperation in microbial metabolism

EH Wintermute, PA Silver - Molecular systems biology, 2010 - embopress.org
Mixed microbial communities exhibit emergent biochemical properties not found in clonal
monocultures. We report a new type of synthetic genetic interaction, synthetic mutualism in …