Networks and hierarchies: Approaching complexity in evolutionary theory

I Tëmkin, N Eldredge - Macroevolution: Explanation, interpretation and …, 2015 - Springer
This expansion of the hierarchy theory of evolution provides a new perspective in which
biological phenomena are conceptualized. In this work, we (1) attempt to revise the ontology …

Detection of driver metabolites in the human liver metabolic network using structural controllability analysis

X Liu, L Pan - BMC systems biology, 2014 - Springer
Background Abnormal states in human liver metabolism are major causes of human liver
diseases ranging from hepatitis to hepatic tumor. The accumulation in relevant data makes it …

Self-organization and information processing: from basic enzymatic activities to complex adaptive cellular behavior

IM De la Fuente, L Martínez, J Carrasco-Pujante… - Frontiers in …, 2021 - frontiersin.org
One of the main aims of current biology is to understand the origin of the molecular
organization that underlies the complex dynamic architecture of cellular life. Here, we …

An integrative machine learning strategy for improved prediction of essential genes in Escherichia coli metabolism using flux-coupled features

S Nandi, A Subramanian, RR Sarkar - Molecular BioSystems, 2017 - pubs.rsc.org
Prediction of essential genes helps to identify a minimal set of genes that are absolutely
required for the appropriate functioning and survival of a cell. The available machine …

The integrated analysis of metabolic and protein interaction networks reveals novel molecular organizing principles

P Durek, D Walther - BMC systems biology, 2008 - Springer
Background The study of biological interaction networks is a central theme of systems
biology. Here, we investigate the relationships between two distinct types of interaction …

Topological and system-level protein interaction network (PIN) analyses to deduce molecular mechanism of curcumin

A Dhasmana, S Uniyal, Anukriti, VK Kashyap… - Scientific reports, 2020 - nature.com
Curcumin is an important bioactive component of turmeric and also one of the important
natural products, which has been investigated extensively. The precise mode of action of …

The density and length of root hairs are enhanced in response to cadmium and arsenic by modulating gene expressions involved in fate determination and …

R Bahmani, DG Kim, JA Kim, S Hwang - Frontiers in Plant Science, 2016 - frontiersin.org
Root hairs are tubular outgrowths that originate from epidermal cells. Exposure of
Arabidopsis to cadmium (Cd) and arsenic [arsenite, As (III)] increases root hair density and …

Chaperones as integrators of cellular networks: changes of cellular integrity in stress and diseases

R Palotai, MS Szalay, P Csermely - IUBMB life, 2008 - Wiley Online Library
The complex integrity of the cells and its sudden, but often predictable changes can be
described and understood by the topology and dynamism of cellular networks. All these …

[HTML][HTML] Prediction of the anti-inflammatory mechanisms of curcumin by module-based protein interaction network analysis

Y Gan, S Zheng, JPA Baak, S Zhao, Y Zheng… - … Pharmaceutica Sinica B, 2015 - Elsevier
Curcumin, the medically active component from Curcuma longa (Turmeric), is widely used to
treat inflammatory diseases. Protein interaction network (PIN) analysis was used to predict …

The importance of eco-evolutionary potential in the Anthropocene

ZT Wood, EP Palkovacs, BJ Olsen, MT Kinnison - BioScience, 2021 - academic.oup.com
Humans are dominant global drivers of ecological and evolutionary change, rearranging
ecosystems and natural selection. In the present article, we show increasing evidence that …