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Emine Ayse Sunar

dblp:425/7785 · DBLP profile ↗
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1ranked-venue papers
1as first author
1since 2021 · last 2025
—ORCID · none

Domains — the database's venue-derived domains; a paper can count in several

Applied, interdisciplinary, general and emerging computing · 1 · 1 first-author · 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

TopicWeightPapersLastEvidence papers
Bioinformatics and computational biology › proteomics
phosphoproteomics
0.912025
DARKIN: a zero-shot benchmark for phosphosite-dark kinase association using protein language models · Bioinform. 2025
Bioinformatics and computational biology
proteomics
0.912025
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
YearPublicationVenuePosition
2025 DARKIN: a zero-shot benchmark for phosphosite-dark kinase association using protein language models
abstract
MOTIVATION: 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.1