Ralph Schlapbach

qg: Configuration-Driven, Multi-Vendor Acquisition Queue Generation with Reproducible Run-Order and QC Control for Mass Spectrometry

qg generates reproducible, configuration-driven acquisition queues for mass spectrometry with QC control and vendor-specific file output.

A combination of phenotypic responses and genetic adaptations enables Staphylococcus aureus to withstand inhibitory molecules secreted by Pseudomonas aeruginosa

This paper shows that Staphylococcus aureus uses both genetic and phenotypic changes to resist inhibitory molecules from Pseudomonas aeruginosa.

prolfquapp - A User-Friendly Command-Line Tool Simplifying Differential Expression Analysis in Quantitative Proteomics

prolfquapp simplifies differential expression analysis in quantitative proteomics by providing a command-line tool with dynamic HTML reports and integration with existing analysis tools.

Onco-fetal protein Nogo-A restricts human and mouse glioma vascularization and growth via VEGF-Notch-hippo-metabolic signaling

This study identifies Nogo-A as an onco-fetal protein that inhibits glioma vascularization and growth through VEGF-Notch-Hippo-metabolic signaling in human and mouse models.

Multiomic ALS signatures highlight sex differences and molecular subclusters and identify the MAPK pathway as therapeutic target

The paper performs a multiomic analysis of ALS patients and mouse models to identify sex differences, molecular subclusters, and the MAPK pathway as a therapeutic target.

prolfqua: A Comprehensive R-package for Proteomics Differential Expression Analysis

prolfqua provides an R package for proteomics differential expression analysis with quality control, normalization, and statistical modeling, showing sensitive and specific results.

The haplotype-resolved chromosome pairs and transcriptome of a heterozygous diploid African cassava cultivar

This study presents haplotype-resolved chromosome pairs and transcriptome of a diploid African cassava cultivar using HiFi sequencing and Hi-C, revealing structural variations and allele-specific expression patterns.

Molecular atlas of the human brain vasculature at the single-cell level

The paper constructs a molecular atlas of the human brain vasculature using single-cell RNA sequencing, revealing molecular heterogeneity and disease-related alterations in vascular cells.

Nucleolin is expressed in human fetal brain development and reactivated in human glial brain tumors regulating angiogenesis and vascular metabolism

This study identifies Nucleolin as a factor reactivated in gliomas that promotes angiogenesis and endothelial metabolism by regulating glycolysis through p53-TIGAR-HK2.

HiDRA-seq: High-Throughput SARS-CoV-2 Detection by RNA Barcoding and Amplicon Sequencing

HiDRA-seq enables high-throughput, low-cost SARS-CoV-2 testing using barcoded cDNA and NGS, allowing thousands of samples to be sequenced per run.

Long fragments achieve lower base quality in Illumina paired-end sequencing

The paper shows that longer DNA fragments in Illumina paired-end sequencing lead to lower base quality and higher error rates in the second read.

Pushing the limits of de novo genome assembly for complex prokaryotic genomes harboring very long, near identical repeats

The paper demonstrates that complex prokaryotic genomes with long, near-identical repeats require very long reads and specialized assemblers for accurate de novo assembly.

rawDiag - an R package supporting rational LC-MS method optimization for bottom-up proteomics

rawDiag is an R package that provides diagnostic plots for optimizing LC-MS methods in proteomics.