Network pharmacology approach for medicinal plants: review and assessment

F Noor, M Tahir ul Qamar, UA Ashfaq, A Albutti… - Pharmaceuticals, 2022 - mdpi.com
Natural products have played a critical role in medicine due to their ability to bind and
modulate cellular targets involved in disease. Medicinal plants hold a variety of bioactive …

Biological network analysis with deep learning

G Muzio, L O'Bray, K Borgwardt - Briefings in bioinformatics, 2021 - academic.oup.com
Recent advancements in experimental high-throughput technologies have expanded the
availability and quantity of molecular data in biology. Given the importance of interactions in …

A guide to conquer the biological network era using graph theory

M Koutrouli, E Karatzas, D Paez-Espino… - … in bioengineering and …, 2020 - frontiersin.org
Networks are one of the most common ways to represent biological systems as complex sets
of binary interactions or relations between different bioentities. In this article, we discuss the …

Gene essentiality and synthetic lethality in haploid human cells

VA Blomen, P Májek, LT Jae, JW Bigenzahn… - Science, 2015 - science.org
Although the genes essential for life have been identified in less complex model organisms,
their elucidation in human cells has been hindered by technical barriers. We used extensive …

Identification of cancer driver genes based on nucleotide context

F Dietlein, D Weghorn, A Taylor-Weiner, A Richters… - Nature …, 2020 - nature.com
Cancer genomes contain large numbers of somatic mutations but few of these mutations
drive tumor development. Current approaches either identify driver genes on the basis of …

Integrated intra‐and intercellular signaling knowledge for multicellular omics analysis

D Türei, A Valdeolivas, L Gul… - Molecular systems …, 2021 - embopress.org
Molecular knowledge of biological processes is a cornerstone in omics data analysis.
Applied to single‐cell data, such analyses provide mechanistic insights into individual cells …

Protein interaction networks revealed by proteome coevolution

Q Cong, I Anishchenko, S Ovchinnikov, D Baker - Science, 2019 - science.org
Residue-residue coevolution has been observed across a number of protein-protein
interfaces, but the extent of residue coevolution between protein families on the whole …

[HTML][HTML] Systematic evaluation of molecular networks for discovery of disease genes

JK Huang, DE Carlin, MK Yu, W Zhang, JF Kreisberg… - Cell systems, 2018 - cell.com
Gene networks are rapidly growing in size and number, raising the question of which
networks are most appropriate for particular applications. Here, we evaluate 21 human …

Complex networks: Structure and dynamics

S Boccaletti, V Latora, Y Moreno, M Chavez… - Physics reports, 2006 - Elsevier
Coupled biological and chemical systems, neural networks, social interacting species, the
Internet and the World Wide Web, are only a few examples of systems composed by a large …

Uncovering the overlapping community structure of complex networks in nature and society

G Palla, I Derényi, I Farkas, T Vicsek - nature, 2005 - nature.com
Many complex systems in nature and society can be described in terms of networks
capturing the intricate web of connections among the units they are made of 1, 2, 3, 4. A key …