Transfer learning enables predictions in network biology

CV Theodoris, L Xiao, A Chopra, MD Chaffin… - Nature, 2023 - nature.com
Mapping gene networks requires large amounts of transcriptomic data to learn the connections
between genes, which impedes discoveries in settings with limited data, including rare …

Multi-ethnic genome-wide association study for atrial fibrillation

C Roselli, MD Chaffin, LC Weng, S Aeschbacher… - Nature …, 2018 - nature.com
Atrial fibrillation (AF) affects more than 33 million individuals worldwide 1 and has a complex
heritability 2 . We conducted the largest meta-analysis of genome-wide association studies (…

[HTML][HTML] Genome-wide association and Mendelian randomisation analysis provide insights into the pathogenesis of heart failure

…, ÅK Hedman, JB Wilk, MP Morley, MD Chaffin… - Nature …, 2020 - nature.com
Heart failure (HF) is a leading cause of morbidity and mortality worldwide. A small proportion
of HF cases are attributable to monogenic cardiomyopathies and existing genome-wide …

A genome-wide cross-trait analysis from UK Biobank highlights the shared genetic architecture of asthma and allergic diseases

Z Zhu, PH Lee, MD Chaffin, W Chung, PR Loh, Q Lu… - Nature …, 2018 - nature.com
Clinical and epidemiological data suggest that asthma and allergic diseases are associated
and may share a common genetic etiology. We analyzed genome-wide SNP data for …

Deep learning enables genetic analysis of the human thoracic aorta

JP Pirruccello, MD Chaffin, EL Chou, SJ Fleming… - Nature …, 2022 - nature.com
Enlargement or aneurysm of the aorta predisposes to dissection, an important cause of
sudden death. We trained a deep learning model to evaluate the dimensions of the ascending …

Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender

SJ Fleming, MD Chaffin, A Arduini, AD Akkad… - Nature …, 2023 - nature.com
Droplet-based single-cell assays, including single-cell RNA sequencing (scRNA-seq),
single-nucleus RNA sequencing (snRNA-seq) and cellular indexing of transcriptomes and …

Genetic analysis of right heart structure and function in 40,000 people

…, M Nekoui, SF Friedman, MDR Klarqvist, MD Chaffin… - Nature …, 2022 - nature.com
Congenital heart diseases often involve maldevelopment of the evolutionarily recent right
heart chamber. To gain insight into right heart structure and function, we fine-tuned deep …

[HTML][HTML] Multi-ancestry GWAS of the electrocardiographic PR interval identifies 202 loci underlying cardiac conduction

…, NR Tucker, SH Choi, MD Chaffin… - Nature …, 2020 - nature.com
The electrocardiographic PR interval reflects atrioventricular conduction, and is associated
with conduction abnormalities, pacemaker implantation, atrial fibrillation (AF), and …

[HTML][HTML] Genomic and metabolic diversity of Marine Group I Thaumarchaeota in the mesopelagic of two subtropical gyres

BK Swan, MD Chaffin, M Martinez-Garcia… - PloS one, 2014 - journals.plos.org
Marine Group I (MGI) Thaumarchaeota are one of the most abundant and cosmopolitan
chemoautotrophs within the global dark ocean. To date, no representatives of this archaeal …

[PDF][PDF] Rare coding variants in 35 genes associate with circulating lipid levels—A multi-ancestry analysis of 170,000 exomes

G Hindy, P Dornbos, MD Chaffin, DJ Liu… - The American Journal of …, 2022 - cell.com
Large-scale gene sequencing studies for complex traits have the potential to identify causal
genes with therapeutic implications. We performed gene-based association testing of blood …