Antti Honkela

This paper develops a censoring-aware Gaussian process framework to model metatranscriptomic data from broiler meat spoilage, linking functional dynamics to spoilage phases and predicting spoilage rates.

The paper benchmarks generative models for synthetic bulk RNA-seq data, finding trade-offs between utility, biological preservation, and privacy risks across different methods.

This paper introduces a Bayesian model-based clustering method for gene expression time series with multiple replicates, showing improved purity and gene enrichment in synthetic and real data.

The paper introduces a pipeline for genomic epidemiology using mixed samples, showing comparable results to colony picks in a nosocomial setting.

The paper introduces mSWEEP, a method for high-resolution bacterial lineage quantification from plate sweeps, showing improved accuracy in detecting and estimating abundances of bacterial lineages.

This paper introduces SEER, a statistical method to identify sequence elements associated with bacterial phenotypes, demonstrating its application in discovering antibiotic resistance and invasiveness factors in Streptococcus species.