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 …

What is principal component analysis?

M Ringnér - Nature biotechnology, 2008 - nature.com
What is principal component analysis? | Nature Biotechnology Skip to main content Thank
you for visiting nature.com. You are using a browser version with limited support for CSS. To …

Dietary methionine influences therapy in mouse cancer models and alters human metabolism

X Gao, SM Sanderson, Z Dai, MA Reid, DE Cooper… - Nature, 2019 - nature.com
Nutrition exerts considerable effects on health, and dietary interventions are commonly used
to treat diseases of metabolic aetiology. Although cancer has a substantial metabolic …

Capturing heterogeneity in gene expression studies by surrogate variable analysis

JT Leek, JD Storey - PLoS genetics, 2007 - journals.plos.org
It has unambiguously been shown that genetic, environmental, demographic, and technical
factors may have substantial effects on gene expression levels. In addition to the measured …

Singular value decomposition and principal component analysis

ME Wall, A Rechtsteiner, LM Rocha - A practical approach to microarray …, 2003 - Springer
One of the challenges of bioinformatics is to develop effective ways to analyze global gene
expression data. A rigorous approach to gene expression analysis must involve an up-front …

Integrative clustering of multiple genomic data types using a joint latent variable model with application to breast and lung cancer subtype analysis

R Shen, AB Olshen, M Ladanyi - Bioinformatics, 2009 - academic.oup.com
Motivation: The molecular complexity of a tumor manifests itself at the genomic, epigenomic,
transcriptomic and proteomic levels. Genomic profiling at these multiple levels should allow …

CUR matrix decompositions for improved data analysis

MW Mahoney, P Drineas - Proceedings of the National …, 2009 - National Acad Sciences
Principal components analysis and, more generally, the Singular Value Decomposition are
fundamental data analysis tools that express a data matrix in terms of a sequence of …

Geometric interpretation of gene coexpression network analysis

S Horvath, J Dong - PLoS computational biology, 2008 - journals.plos.org
The merging of network theory and microarray data analysis techniques has spawned a new
field: gene coexpression network analysis. While network methods are increasingly used in …

Principal component analysis for clustering gene expression data

KY Yeung, WL Ruzzo - Bioinformatics, 2001 - academic.oup.com
Motivation: There is a great need to develop analytical methodology to analyze and to
exploit the information contained in gene expression data. Because of the large number of …

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 …