Attila Kertész‐Farkas

Label-free quantification in the Crux toolkit

The paper introduces a label-free quantification feature in the Crux toolkit, demonstrating improved efficiency and accuracy compared to existing methods.

Fast and memory efficient searching of large-scale mass spectrometry data using Tide

The paper improves the Tide search engine to handle large-scale mass spectrometry data efficiently, achieving faster speeds and lower memory usage than previous versions.

Efficient indexing of peptides for database search using Tide

The paper improves the peptide indexing component of the Tide search engine, reducing resource usage and enabling larger databases, while exploring the impact of digestion parameters and PTMs on statistical power.

The Crux toolkit for analysis of bottom-up tandem mass spectrometry proteomics data

The paper summarizes recent developments in the Crux toolkit for analyzing bottom-up proteomics data, including speedups, new features, and tools.

Test-time augmentation for deep learning-based cell segmentation on microscopy images

This paper applies test-time augmentation to improve cell segmentation accuracy in microscopy images using U-Net and Mask R-CNN models, achieving a better score in the DSB 2018 competition.

Tailor: non-parametric and rapid score calibration method for database search-based peptide identification in shotgun proteomics

Tailor is a non-parametric PSM score calibration method that improves peptide identification in shotgun proteomics by using empirical null distributions, achieving faster performance and better results than existing methods.