From 'differential expression'to 'differential networking'–identification of dysfunctional regulatory networks in diseases

A de la Fuente - Trends in genetics, 2010 - cell.com
Understanding diseases requires identifying the differences between healthy and affected
tissues. Gene expression data have revolutionized the study of diseases by making it …

[HTML][HTML] Big data: historic advances and emerging trends in biomedical research

CJ Cremin, S Dash, X Huang - Current Research in Biotechnology, 2022 - Elsevier
Big data is transforming biomedical research by integrating massive amounts of data from
laboratory experiments, clinical investigations, healthcare records, and the internet of things …

Gene co-expression analysis for functional classification and gene–disease predictions

S Van Dam, U Vosa, A van der Graaf… - Briefings in …, 2018 - academic.oup.com
Gene co-expression networks can be used to associate genes of unknown function with
biological processes, to prioritize candidate disease genes or to discern transcriptional …

Two-sample covariance matrix testing and support recovery in high-dimensional and sparse settings

T Cai, W Liu, Y **a - Journal of the American Statistical Association, 2013 - Taylor & Francis
In the high-dimensional setting, this article considers three interrelated problems:(a) testing
the equality of two covariance matrices and;(b) recovering the support of; and (c) testing the …

Circulating brain-derived neurotrophic factor and indices of metabolic and cardiovascular health: data from the Baltimore Longitudinal Study of Aging

E Golden, A Emiliano, S Maudsley, BG Windham… - PloS one, 2010 - journals.plos.org
Background Besides its well-established role in nerve cell survival and adaptive plasticity,
brain-derived neurotrophic factor (BDNF) is also involved in energy homeostasis and …

A differential wiring analysis of expression data correctly identifies the gene containing the causal mutation

NJ Hudson, A Reverter… - PLoS computational …, 2009 - journals.plos.org
Transcription factor (TF) regulation is often post-translational. TF modifications such as
reversible phosphorylation and missense mutations, which can act independent of TF …

[BOG][B] Batch effects and noise in microarray experiments: sources and solutions

A Scherer - 2009 - Wiley Online Library
High-content, high-density long or short oligonucleotide microarrays for simultaneous
measurement of redundancy of RNA species are nowadays widely used for hypothesis …

Integrating gene expression and protein-protein interaction network to prioritize cancer-associated genes

C Wu, J Zhu, X Zhang - BMC bioinformatics, 2012 - Springer
Background To understand the roles they play in complex diseases, genes need to be
investigated in the networks they are involved in. Integration of gene expression and …

Differential co-expression-based detection of conditional relationships in transcriptional data: comparative analysis and application to breast cancer

DD Bhuva, J Cursons, GK Smyth, MJ Davis - Genome biology, 2019 - Springer
Background Elucidation of regulatory networks, including identification of regulatory
mechanisms specific to a given biological context, is a key aim in systems biology. This has …

VI-VS: calibrated identification of feature dependencies in single-cell multiomics

P Boyeau, S Bates, C Ergen, MI Jordan, N Yosef - Genome Biology, 2024 - Springer
Unveiling functional relationships between various molecular cell phenotypes from data
using machine learning models is a key promise of multiomics. Existing methods either use …