Decoding disease: from genomes to networks to phenotypes

AK Wong, RSG Sealfon, CL Theesfeld… - Nature Reviews …, 2021 - nature.com
Interpreting the effects of genetic variants is key to understanding individual susceptibility to
disease and designing personalized therapeutic approaches. Modern experimental …

Network medicine in the age of biomedical big data

AR Sonawane, ST Weiss, K Glass, A Sharma - Frontiers in Genetics, 2019 - frontiersin.org
Network medicine is an emerging area of research dealing with molecular and genetic
interactions, network biomarkers of disease, and therapeutic target discovery. Large-scale …

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 …

Evaluation of GRCh38 and de novo haploid genome assemblies demonstrates the enduring quality of the reference assembly

VA Schneider, T Graves-Lindsay, K Howe… - Genome …, 2017 - genome.cshlp.org
The human reference genome assembly plays a central role in nearly all aspects of today's
basic and clinical research. GRCh38 is the first coordinate-changing assembly update since …

A novel approach to high-quality postmortem tissue procurement: the GTEx project

LJ Carithers, K Ardlie, M Barcus… - Biopreservation and …, 2015 - liebertpub.com
The Genotype-Tissue Expression (GTEx) project, sponsored by the NIH Common Fund, was
established to study the correlation between human genetic variation and tissue-specific …

Understanding tissue-specific gene regulation

AR Sonawane, J Platig, M Fagny, CY Chen… - Cell reports, 2017 - cell.com
Although all human tissues carry out common processes, tissues are distinguished by gene
expression patterns, implying that distinct regulatory programs control tissue specificity. In …

Tissue-specific regulatory circuits reveal variable modular perturbations across complex diseases

D Marbach, D Lamparter, G Quon, M Kellis, Z Kutalik… - Nature …, 2016 - nature.com
Mapping perturbed molecular circuits that underlie complex diseases remains a great
challenge. We developed a comprehensive resource of 394 cell type–and tissue-specific …

Transfer learning for high-dimensional linear regression: Prediction, estimation and minimax optimality

S Li, TT Cai, H Li - Journal of the Royal Statistical Society Series …, 2022 - academic.oup.com
This paper considers estimation and prediction of a high-dimensional linear regression in
the setting of transfer learning where, in addition to observations from the target model …

Network analysis reveals rare disease signatures across multiple levels of biological organization

P Buphamalai, T Kokotovic, V Nagy… - Nature communications, 2021 - nature.com
Rare genetic diseases are typically caused by a single gene defect. Despite this clear
causal relationship between genotype and phenotype, identifying the pathobiological …

Mechanisms of tissue and cell-type specificity in heritable traits and diseases

I Hekselman, E Yeger-Lotem - Nature Reviews Genetics, 2020 - nature.com
Hundreds of heritable traits and diseases that are caused by germline aberrations in
ubiquitously expressed genes manifest in a remarkably limited number of cell types and …