Yannick Mahlich

Illuminating dark genes and dark metabolites: calibrated functional association across kingdoms with autoencoders and correlation

VaLPAS pairs a bi-directional autoencoder with correlation for omics guilt-by-association with calibrated confidence; in L. starkeyi its autoencoder linked 176 unidentified metabolites to known-function proteins at ≥50% confidence.

Integrated ex vivo screening and transcriptomic profiling to prioritize drug combinations for rare cancers

The paper develops EXACT, a framework combining ex vivo drug screening with transcriptomic analysis to identify effective drug combinations for rare cancers, finding a MEK and HDAC inhibitor combination shows enhanced activity.

spammR: an R package designed for analysis and integration of spatial multi-omic measurements

spammR is an R package for analyzing and integrating spatial multi-omic data, focusing on mass-spectrometry datasets and enabling cross-type integration within tissue samples.

Learning from the unknown: exploring the range of bacterial functionality

This paper introduces a novel method to explore bacterial functional repertoires without reference databases, showing it outperforms existing approaches in taxonomic assignment and captures environment-driven diversity.

An exhaustive analysis of single amino acid variants in helical transmembrane proteins

The paper analyzes the impact of common and rare single amino acid variants in helical transmembrane proteins, finding common variants have stronger effects and are enriched in membrane helices, while 7TM proteins are depleted of SAVs.

fusionDB: assessing microbial diversity and environmental preferences via functional similarity networks

fusionDB links microbial functions to environmental metadata through functional similarity networks, enabling comparisons and identification of horizontal gene transfer events.