Aki Samuli Havulinna

Pulmonary primary oxysterol and bile acid synthesis as a predictor of outcomesin pulmonary arterial hypertension

The paper identifies pulmonary primary oxysterol and bile acid synthesis as a prognostic biomarker for pulmonary arterial hypertension, outperforming current clinical risk scores.

KANN: estimation of genetic ancestry profiles by nearest neighbor regression

KANN estimates genetic ancestry profiles using k-nearest neighbor regression on principal components, showing strong agreement with haplotype-based methods in large-scale genomic data.

Orchestrating Microbiome Analysis with Bioconductor

The paper introduces an open-source ecosystem for microbiome data science using Bioconductor, supporting modular workflows for analyzing complex, multi-modal datasets.

Microbiome variations in osteoarthritis reflect aging and metabolic factors, not the disease

This study analyzes microbiome data from multiple OA cohorts and finds no significant differences between OA patients and controls, attributing microbiome changes to age and BMI instead of OA.

Integration of polygenic and gut metagenomic risk prediction for common diseases

This study integrates polygenic risk scores and gut metagenomic data to improve prediction of common diseases, showing enhanced predictive performance over conventional risk factors.

Pregnancy-Associated Bleeding and Genetics: Five Sequence Variants in the Myometrium and Progesterone Signaling Pathway are associated with postpartum hemorrhage

The paper identifies five genetic loci associated with postpartum hemorrhage through a meta-analysis and links them to progesterone receptor binding sites and related traits.

A FinnGen pilot clinical recall study for Alzheimer's disease

The paper demonstrates the feasibility of conducting clinical recall studies from the FinnGen biobank to collect customized clinical data from participants with Alzheimer's disease or mild cognitive disorder.

Implicating genes, pleiotropy and sexual dimorphism at blood lipid loci through multi-ancestry meta-analysis

This study identifies 118 candidate causal genes and 21 novel lipid loci on the X chromosome through a multi-ancestry meta-analysis of blood lipid levels, revealing sex-biased effects and pleiotropy with cardiovascular and hormonal traits.

Greengenes2 enables a shared data universe for microbiome studies

Greengenes2 aligns 16S rRNA and shotgun metagenomic data using a whole-genome phylogeny, showing agreement in principal coordinates, taxonomy, and phenotype effect size.

Gene-Gene Interaction Detection with Deep Learning

This paper introduces a deep learning method to detect gene-gene interactions by considering all SNPs and complex interactions, outperforming existing methods and identifying novel interactions in a cholesterol study.

Genetic risk factors have a substantial impact on healthy life years

This study estimates the impact of genetic risk factors on disease burden using disability-adjusted life years (DALYs) and finds that both common and rare variants significantly contribute to healthy life years lost.

A multi-layer functional genomic analysis to understand noncoding genetic variation in lipids

This paper integrates GWAS data with functional genomic datasets to identify regulatory mechanisms and causal genes underlying lipid-related traits.

Early prediction of liver disease using conventional risk factors and gut microbiome-augmented gradient boosting

This study uses gut microbiome data and machine learning to improve liver disease risk prediction, showing that combining microbiome features with conventional risk factors enhances model performance.

Combined effects of host genetics and diet on human gut microbiota and incident disease in a single population cohort

In 5,959 Finns with genotypes and stool metagenomes, GWAS found 583 independent SNP-taxon associations; dairy intake modified LCT effects on Bifidobacterium, and ABO-linked Faecalicatena lactaris tracked secretor status.

Improving Neural Networks for Genotype-Phenotype Prediction Using Published Summary Statistics

This paper introduces a regularization method called main effect prior (MEP) to improve genotype-phenotype prediction using GWAS summary statistics, showing improved performance on small datasets.

Mono- and bi-allelic effects of coding variants on disease in 176,899 Finns

The paper analyzes homozygous and heterozygous effects of coding variants on disease in 176,899 Finns using EHR data, finding novel associations and challenging traditional dominant/recessive classifications.

Mitochondrial genome copy number measured by DNA sequencing in human blood is strongly associated with metabolic traits via cell-type composition differences

ANGPTL8 protein-truncating variant and the risk of coronary disease, type 2 diabetes and adverse effects

The paper identifies protein-truncating variants in ANGPTL8, ANGPTL4, and LIPG associated with lipid levels and cardiometabolic disease risk, and reports their associations with type 2 diabetes, coronary artery disease, and other adverse effects.

OGUs enable effective, phylogeny-aware analysis of even shallow metagenome community structures

This paper introduces OGUs, a metagenome analysis method that uses sequence alignment hits to reference genomes for community analysis, showing better performance in predicting biological traits than taxonomic or 16S rRNA methods.

Association of Structural Variation with Cardiometabolic Traits in Finns

This study identifies 31 genome-wide significant associations between structural variations and cardiometabolic traits in Finns, including two novel loci with strong phenotypic effects.

Genetic analysis of obstructive sleep apnoea discovers a strong association with cardiometabolic health

This study identifies five genetic loci associated with obstructive sleep apnoea and finds a causal link between BMI and OSA through polygenic risk scores and Mendelian randomization.

Genome-wide Screen of Otosclerosis in Population Biobanks: 18 Loci and Shared Heritability with Skeletal Structure

This study identifies 15 new risk loci for otosclerosis and replicates known associations, highlighting shared genetic links with skeletal structure and bone-related disorders.

An efficient and accurate frailty model approach for genome-wide survival association analysis controlling for population structure and relatedness in large-scale biobanks

The paper introduces a frailty model for genome-wide survival analysis in large biobanks, handling population structure and relatedness, and demonstrates its performance on real-world datasets.

Genome-wide association and Mendelian randomization analysis prioritizes bioactive metabolites with putative causal effects on common diseases

This study identifies 118 genetic loci associated with 2,319 metabolite features and finds 46 causal effects of metabolites on common diseases using genome-wide association and Mendelian randomization.

Rare protein-altering variants in ANGPTL7 lower intraocular pressure and protect against glaucoma

The paper identifies rare protein-altering variants in ANGPTL7 that lower intraocular pressure and reduce glaucoma risk by analyzing genotyping data from UK Biobank and FinnGen.

A missense variant in Mitochondrial Amidoxime Reducing Component 1 gene and protection against liver disease

The paper identifies a missense variant in the MARC1 gene associated with protection against cirrhosis and lower liver enzyme and cholesterol levels.

Multivariate genome-wide association analysis of a cytokine network reveals variants with widespread immune, haematological and cardiometabolic pleiotropy

This study identifies genetic variants with pleiotropic effects on cytokines and related traits using a multivariate genome-wide association analysis.

Polygenic and clinical risk scores and their impact on age at onset of cardiometabolic diseases and common cancers

The paper evaluates polygenic risk scores and clinical risk factors for predicting early-onset cardiometabolic diseases and cancers, showing comparable performance to clinical scores.

Elevated alpha-1 antitrypsin is a major component of GlycA-associated risk for future morbidity and mortality

The paper identifies alpha-1 antitrypsin as a key contributor to GlycA's predictive power for disease risk and mortality across multiple conditions.

Genetic predisposition to myeloproliferative neoplasms implicates hematopoietic stem cell biology

This study identifies 14 genome-wide significant loci and a polygenic signature for myeloproliferative neoplasms, implicating hematopoietic stem cell function and self-renewal in disease risk.