Demo Data from EDBT 2026 / reviewers in the wild / expert
Mert Pekey
dblp:356/0132
· DBLP profile ↗
1ranked-venue papers
0as first author
1since 2021 · last 2025
0009-0003-9157-5212ORCID · reported
Domains — the database's venue-derived domains; a paper can count in several
Applied, interdisciplinary, general and emerging computing · 1 · 1 since 2021
Expertise — from the expertise taxonomy: the topics of the expert's papers under the CCF categories. A weight counts papers with recency: 1 for a paper about the topic, 0.3 when the topic is its context, halved every five years.
| Interdisciplinary, comprehensive, and emerging computing
1 paper |
Bioinformatics and computational biology · 100% |
Topics — the 2 heaviest of 3, each with the papers that count most for it
| Topic | Weight | Papers | Last | Evidence papers |
|---|---|---|---|---|
Bioinformatics and computational biology › proteomics
phosphoproteomics |
0.9 | 1 | 2025 | DARKIN: a zero-shot benchmark for phosphosite-dark kinase association using protein language models · Bioinform. 2025 |
Bioinformatics and computational biology
proteomics |
0.9 | 1 | 2025 | DARKIN: a zero-shot benchmark for phosphosite-dark kinase association using protein language models · Bioinform. 2025 |
Methods — techniques the papers use, named apart from their topics
protein language model · 0.9bilinear classifier · 0.9KNN classifier · 0.9
| Year | Publication | Venue | Position |
|---|---|---|---|
| 2025 | DARKIN: a zero-shot benchmark for phosphosite-dark kinase association using protein language modelsabstractMOTIVATION: Protein language models (pLMs) have emerged as powerful tools for capturing the intricate information encoded in protein sequences, facilitating various downstream protein prediction tasks. With numerous pLMs available, there is a critical need for diverse benchmarks to systematically evaluate their performance across biologically relevant tasks. Here, we introduce DARKIN, a zero-shot classification benchmark designed to assign phosphosites to understudied kinases, termed dark kinases. Kinases, which catalyze phosphorylation, are central to cellular signaling pathways. While phosphoproteomics enables the large-scale identification of phosphosites, determining the cognate kinase responsible for the phosphorylation event remains an experimental challenge. RESULTS: In DARKIN, we prepared training, validation, and test folds that respect the zero-shot nature of this classification problem, incorporating stratification based on kinase groups and sequence similarity. We evaluated multiple pLMs using two zero-shot classifiers: a novel, training-free k-NN-based method, and a bilinear classifier. Our findings indicate that ESM, ProtT5-XL, and SaProt exhibit superior performance on this task. DARKIN provides a challenging benchmark for assessing pLM efficacy and fosters deeper exploration of under-characterized (dark) kinases by offering a biologically relevant test bed. AVAILABILITY AND IMPLEMENTATION: The DARKIN benchmark data and the scripts for generating additional splits are publicly available at: https://github.com/tastanlab/darkin. Emine Ayse Sunar, Zeynep Isik, Mert Pekey, Ramazan Gokberk Cinbis, Öznur Tastan |
Bioinform. | 3 |