Tom Altenburg

usiGrabber: Automating the curation of proteomics spectra data at scale, making large datasets ready for use in machine learning systems

usiGrabber automates proteomics data curation from repositories, enabling large-scale dataset creation for machine learning, achieving comparable performance to manual curation.

Foundation Model Enables Interpretable Open and Error-Tolerant Searching for Mass Spectrometry-Based Proteomics

The paper introduces yHydra, a foundation model for mass spectrometry-based proteomics that enables open and error-tolerant peptide and protein identification with improved performance.

Benchmarking Next-Generation Sequencing Platforms: A Comprehensive Comparison Of Single-Cell RNA-Seq from Ultima UG 100 vs. Illumina NovaSeq X Plus

This study compares the performance of Ultima UG 100 and Illumina NovaSeq X Plus platforms for single-cell RNA sequencing, finding comparable results in cell type identification and gene expression.

AHLF: ad hoc learning of peptide fragmentation from mass spectra enables an interpretable detection of phosphorylated and cross-linked peptides

AHLF is a deep learning model trained on mass spectra to detect phosphorylated and cross-linked peptides with improved performance and interpretability.

CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance

CovRadar provides a platform for tracking and filtering SARS-CoV-2 mutations in the spike gene, enabling users to analyze and visualize mutational changes and spatio-temporal distributions.

Osmolyte homeostasis controls single-cell growth rate and maximum cell size of Saccharomyces cerevisiae

The paper develops a single-cell growth model for yeast that links osmolyte dynamics to growth rate and cell size, showing osmolyte uptake primarily governs these traits.

Probability-based detection of phosphoproteomic uncertainty reveals rare signaling events driven by oncogenic kinase gene fusion

The paper introduces a Bayesian method to estimate protein concentrations and phosphorylation site occupancy ratios from mass spectrometry data, applied to study PRKAR1A-RET gene fusion effects.