Johannes Rainer

Beyond the classical plasma secretome: genetic architecture and disease associations of the expanded human plasma proteome in 13,445 Europeans

This study expands the human plasma proteome analysis using an enhanced SomaScan platform, identifying new genetic associations and disease mechanisms beyond the classical secretome.

Haplomics: A Snakemake pipeline for haplotype-based association analysis in multi-omics studies

Haplomics is a Snakemake pipeline for haplotype-based association analysis in GWAS loci, identifying significant associations in a multi-omics study.

Phenotypic spectrum of FAM47E-SHROOM3 haplotype composition in a general population sample

The paper identifies haplotypes at the FAM47E-SHROOM3 locus associated with kidney function, electrolyte, and hematological traits in a population sample.

MsQuality - an interoperable open-source packagefor the calculation of standardized quality metricsof mass spectrometry data

MsQuality calculates 40 standardized quality metrics for mass spectrometry data using the mzQC vocabulary to improve data quality assessment and comparability across datasets.

A Universal Language for Finding Mass Spectrometry Data Patterns

MassQL, an open-source query language, lets users search raw mass spectrometry data from any vendor for isotope, fragmentation and neutral-loss patterns, from one file to entire public repositories.

Ion Identity Molecular Networking in the GNPS Environment

The paper introduces Ion Identity Molecular Networking to connect ion species of the same molecule, improving network connectivity and annotation.

MSnbase, efficient and elegant R-based processing and visualisation of raw mass spectrometry data

The paper introduces version 2 of the MSnbase R/Bioconductor package, enhancing its ability to handle large mass spectrometry datasets efficiently.

Feature-based Molecular Networking in the GNPS Analysis Environment

The paper introduces FBMN, a method for improving molecular networking by enhancing quantitative analysis and isomer distinction using feature detection and alignment tools in the GNPS platform.