Damian Szklarczyk

SPACE: STRING proteins as complementary embeddings

The paper develops cross-species protein embeddings using network data and shows they improve subcellular localization and function prediction when combined with sequence embeddings.

PaxDB 5.0: curated protein quantification data suggests adaptive proteome changes

PaxDB 5.0 provides updated protein abundance data across species, highlighting expanded coverage and comparative analysis with existing resources.

Clade-wise alignment integration improves co-evolutionary signals for protein-protein interaction prediction

The paper improves protein-protein interaction prediction by integrating clade-wise alignments, enhancing co-evolutionary signals and reducing false positives for genome-wide scans.

CanIsoNet: A Database to Study the Functional Impact of Isoform Switching Events in Diseases

CanIsoNet is a database that integrates isoform expression data with interaction networks and ClinVar annotations to predict the pathogenic impact of isoform switching events in diseases.

GUNC: Detection of Chimerism and Contamination in Prokaryotic Genomes

GUNC detects and quantifies chimerism in prokaryotic genomes by analyzing contig lineage homogeneity, improving genome quality.

Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies

The paper improves the inference of orthologous group hierarchies by combining tree reconciliation with subsampling, showing comparable or better performance than previous methods.

Viruses.STRING: A virus-host protein-protein interaction database

The paper introduces Viruses.STRING, a database of virus-host protein-protein interactions combining experimental and text-mining evidence.

Analysis of the human kinome and phosphatome reveals diseased signaling networks induced by overexpression

The paper analyzes the human kinome and phosphatome to identify signaling networks altered by protein overexpression, revealing novel relationships and mechanisms of cancer progression.

Fast genome-wide functional annotation through orthology assignment by eggNOG-mapper

The paper introduces eggNOG-mapper, a tool for fast genome-wide functional annotation through orthology assignment, showing improved accuracy and efficiency compared to BLAST and InterProScan.