Serhan Yılmaz

Exploring Temporal and Sex-Linked Dysregulation in Alzheimer's Disease Phospho-Proteome

This study analyzes phosphoproteome dysregulation in 5XFAD mice, identifying sex-specific and temporal patterns, novel biomarkers, and a key kinase pathway involved in Alzheimer's disease progression.

Making Proteomics Accessible: RokaiXplorer for interactive analysis of phospho-proteomic data

RokaiXplorer provides an intuitive web tool for phospho-proteomic data analysis and visualization, offering multiple functionalities and interactive features for researchers without specialized training.

Are under-studied proteins under-represented? How to fairly evaluate link prediction algorithms in network biology

The paper evaluates link prediction algorithms in network biology and proposes methods to reduce bias toward well-studied proteins.

Prediction of Kinase-Substrate Associations Using The Functional Landscape of Kinases and Phosphorylation Sites

The paper develops NetKSA, a network-based machine learning framework to predict kinase-substrate associations, outperforming existing methods and enabling annotation of phosphosites targeted by less-studied kinases.

Uncovering complementary sets of variants for predicting quantitative phenotypes

This paper introduces Macarons, a fast algorithm for selecting complementary genetic variants to predict quantitative phenotypes, achieving similar or better performance than existing methods with significantly reduced runtime.

Constructing Functional Networks of Phosphorylation Sites Using Co-Phosphorylation

The paper investigates co-phosphorylation across diseases, showing functionally related sites exhibit significant co-phosphorylation and can predict pathway or kinase associations.

Robust Inference of Kinase Activity using Functional Networks

This paper introduces RoKAI, a network-based framework that improves kinase activity inference by integrating functional information, showing enhanced accuracy and robustness in identifying dysregulated kinases in diseases.

SPADIS: An Algorithm for Selecting Predictive and Diverse SNPs in GWAS

SPADIS selects diverse SNPs for GWAS to improve predictive performance by prioritizing remote SNPs in SNP-SNP networks, outperforming SConES in regression and gene identification.