Vital nodes identification in complex networks

L Lü, D Chen, XL Ren, QM Zhang, YC Zhang, T Zhou - Physics reports, 2016 - Elsevier
Real networks exhibit heterogeneous nature with nodes playing far different roles in
structure and function. To identify vital nodes is thus very significant, allowing us to control …

[HTML][HTML] Recent advances in clustering methods for protein interaction networks

J Wang, M Li, Y Deng, Y Pan - BMC genomics, 2010 - Springer
The increasing availability of large-scale protein-protein interaction data has made it
possible to understand the basic components and organization of cell machinery from the …

PageRank beyond the web

DF Gleich - siam REVIEW, 2015 - SIAM
Google's PageRank method was developed to evaluate the importance of web-pages via
their link structure. The mathematics of PageRank, however, are entirely general and apply …

Multilinear pagerank

DF Gleich, LH Lim, Y Yu - SIAM Journal on Matrix Analysis and Applications, 2015 - SIAM
In this paper, we first extend the celebrated PageRank modification to a higher-order Markov
chain. Although this system has attractive theoretical properties, it is computationally …

AptRank: an adaptive PageRank model for protein function prediction on bi-relational graphs

B Jiang, K Kloster, DF Gleich, M Gribskov - Bioinformatics, 2017 - academic.oup.com
Motivation: Diffusion-based network models are widely used for protein function prediction
using protein network data and have been shown to outperform neighborhood-based and …

[HTML][HTML] Improving protein function prediction using domain and protein complexes in PPI networks

W Peng, J Wang, J Cai, L Chen, M Li, FX Wu - BMC systems biology, 2014 - Springer
Background Characterization of unknown proteins through computational approaches is
one of the most challenging problems in silico biology, which has attracted world-wide …

[HTML][HTML] A new extrapolation method for PageRank computations

X Tan - Journal of Computational and Applied Mathematics, 2017 - Elsevier
The PageRank algorithm is widely considered these years because of its great significance
in search engine technology and other scientific domains. Though the power method is the …

MetaboRank: network-based recommendation system to interpret and enrich metabolomics results

C Frainay, S Aros, M Chazalviel, T Garcia… - …, 2019 - academic.oup.com
Motivation Metabolomics has shown great potential to improve the understanding of
complex diseases, potentially leading to therapeutic target identification. However, no single …

Tracking the random surfer: empirically measured teleportation parameters in PageRank

DF Gleich, PG Constantine, AD Flaxman… - Proceedings of the 19th …, 2010 - dl.acm.org
PageRank computes the importance of each node in a directed graph under a random
surfer model governed by a teleportation parameter. Commonly denoted alpha, this …

Random alpha pagerank

PG Constantine, DF Gleich - Internet Mathematics, 2009 - Taylor & Francis
We suggest a revision to the PageRank random surfer model that considers the influence of
a population of random surfers on the PageRank vector. In the revised model, each member …