Network approaches to systems biology analysis of complex disease: integrative methods for multi-omics data

J Yan, SL Risacher, L Shen… - Briefings in bioinformatics, 2018 - academic.oup.com
In the past decade, significant progress has been made in complex disease research across
multiple omics layers from genome, transcriptome and proteome to metabolome. There is an …

Molecular networks in Network Medicine: Development and applications

EK Silverman, HHHW Schmidt… - … Systems Biology and …, 2020 - Wiley Online Library
Network Medicine applies network science approaches to investigate disease
pathogenesis. Many different analytical methods have been used to infer relevant molecular …

Association analysis identifies 65 new breast cancer risk loci

K Michailidou, S Lindström, J Dennis, J Beesley, S Hui… - Nature, 2017 - nature.com
Breast cancer risk is influenced by rare coding variants in susceptibility genes, such as
BRCA1, and many common, mostly non-coding variants. However, much of the genetic …

The genetic architecture of type 2 diabetes

C Fuchsberger, J Flannick, TM Teslovich, A Mahajan… - Nature, 2016 - nature.com
The genetic architecture of common traits, including the number, frequency, and effect sizes
of inherited variants that contribute to individual risk, has been long debated. Genome-wide …

Identification of ten variants associated with risk of estrogen-receptor-negative breast cancer

RL Milne, KB Kuchenbaecker, K Michailidou… - Nature …, 2017 - nature.com
Most common breast cancer susceptibility variants have been identified through genome-
wide association studies (GWAS) of predominantly estrogen receptor (ER)-positive disease …

Computational network biology: data, models, and applications

C Liu, Y Ma, J Zhao, R Nussinov, YC Zhang, F Cheng… - Physics Reports, 2020 - Elsevier
Biological entities are involved in intricate and complex interactions, in which uncovering the
biological information from the network concepts are of great significance. Benefiting from …

Discovery of new risk loci for IgA nephropathy implicates genes involved in immunity against intestinal pathogens

K Kiryluk, Y Li, F Scolari, S Sanna-Cherchi, M Choi… - Nature …, 2014 - nature.com
We performed a genome-wide association study (GWAS) of IgA nephropathy (IgAN), the
most common form of glomerulonephritis, with discovery and follow-up in 20,612 individuals …

Genetics of COPD

EK Silverman - Annual review of physiology, 2020 - annualreviews.org
Although chronic obstructive pulmonary disease (COPD) risk is strongly influenced by
cigarette smoking, genetic factors are also important determinants of COPD. In addition to …

Leveraging models of cell regulation and GWAS data in integrative network-based association studies

A Califano, AJ Butte, S Friend, T Ideker, E Schadt - Nature genetics, 2012 - nature.com
PERSPECTIVE interplay of signal transduction, transcriptional, post-transcriptional,
metabolic and other regulatory events that determine cell behavior. Even today, entirely new …

Heterogeneous network edge prediction: a data integration approach to prioritize disease-associated genes

DS Himmelstein, SE Baranzini - PLoS computational biology, 2015 - journals.plos.org
The first decade of Genome Wide Association Studies (GWAS) has uncovered a wealth of
disease-associated variants. Two important derivations will be the translation of this …