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 …

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 …

Open graph benchmark: Datasets for machine learning on graphs

W Hu, M Fey, M Zitnik, Y Dong, H Ren… - Advances in neural …, 2020 - proceedings.neurips.cc
Abstract We present the Open Graph Benchmark (OGB), a diverse set of challenging and
realistic benchmark datasets to facilitate scalable, robust, and reproducible graph machine …

[图书][B] Biocultural creatures: Toward a new theory of the human

S Frost - 2016 - books.google.com
In Biocultural Creatures, Samantha Frost brings feminist and political theory together with
findings in the life sciences to recuperate the category of the human for politics. Challenging …

Integrative approaches for finding modular structure in biological networks

K Mitra, AR Carvunis, SK Ramesh, T Ideker - Nature Reviews Genetics, 2013 - nature.com
A central goal of systems biology is to elucidate the structural and functional architecture of
the cell. To this end, large and complex networks of molecular interactions are being rapidly …

Panorama of ancient metazoan macromolecular complexes

C Wan, B Borgeson, S Phanse, F Tu, K Drew, G Clark… - Nature, 2015 - nature.com
Macromolecular complexes are essential to conserved biological processes, but their
prevalence across animals is unclear. By combining extensive biochemical fractionation …

BioGRID: a general repository for interaction datasets

C Stark, BJ Breitkreutz, T Reguly, L Boucher… - Nucleic acids …, 2006 - academic.oup.com
Access to unified datasets of protein and genetic interactions is critical for interrogation of
gene/protein function and analysis of global network properties. BioGRID is a freely …

Associating genes and protein complexes with disease via network propagation

O Vanunu, O Magger, E Ruppin, T Shlomi… - PLoS computational …, 2010 - journals.plos.org
A fundamental challenge in human health is the identification of disease-causing genes.
Recently, several studies have tackled this challenge via a network-based approach …

Integration of biological networks and gene expression data using Cytoscape

MS Cline, M Smoot, E Cerami, A Kuchinsky… - Nature protocols, 2007 - nature.com
Cytoscape is a free software package for visualizing, modeling and analyzing molecular and
genetic interaction networks. This protocol explains how to use Cytoscape to analyze the …

[HTML][HTML] A protein complex network of Drosophila melanogaster

KG Guruharsha, JF Rual, B Zhai, J Mintseris, P Vaidya… - Cell, 2011 - cell.com
Determining the composition of protein complexes is an essential step toward
understanding the cell as an integrated system. Using coaffinity purification coupled to mass …