Niina Haiminen

CuNA: Cumulant-based Network Analysis of genotype-phenotype associations in Parkinson's Disease

CuNA identifies genes associated with Parkinson's Disease symptoms by analyzing higher-order relationships between eQTLs and clinical phenotypes.

DNA extraction and host depletion methods significantly impact and potentially bias bacterial detection in a biological fluid

The paper evaluates DNA extraction and host depletion methods in bovine milk to improve bacterial detection for food safety, finding that magnetic-based methods are most effective and some methods introduce microbial detection bias.

Challenges in Benchmarking Metagenomic Profilers

This paper highlights challenges in benchmarking metagenomic profilers due to confusion between sequence abundance and taxonomic abundance.

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.

Functional profiling of COVID-19 respiratory tract microbiomes

The paper analyzes RNA sequencing data from respiratory tract samples to identify functional differences in microbiomes between COVID-19 patients, pneumonia patients, and healthy controls.

EMPress enables tree-guided, interactive, and exploratory analyses of multi-omic datasets

EMPress provides an interactive tool for visualizing phylogenetic trees alongside multi-omic data, enabling exploratory analyses of microbiome and metabolome datasets.

Explainable AI reveals changes in skin microbiome compositionlinked to phenotypic differences

The paper develops an explainable AI approach to predict skin-related phenotypes from leg skin microbiome data and identifies microbial composition changes linked to these traits.

Haplotype assembly of autotetraploid potato using integer linear programming

This paper develops an integer linear programming method for haplotype assembly in autotetraploid potato, showing improved accuracy over existing methods on both simulated and real data.