AGRIS: the Arabidopsis Gene Regulatory Information Server, an update. - Alper Yilmaz 003; Maria Katherine Mejia-Guerra; Kyle Kurz; Xiaoyu Liang; Lonnie R. Welch; Erich Grotewold (Nucleic Acids Res., 2011)

A novel method for splice sites prediction using sequence component and hidden Markov model. - Elham Pashaei; Alper Yilmaz 003; Mustafa Ozen; Nizamettin Aydin (EMBC, 2016)

Prediction of splice site using AdaBoost with a new sequence encoding approach. - Elham Pashaei; Alper Yilmaz 003; Mustafa Ozen; Nizamettin Aydin (SMC, 2016)

A New Network-Based Tool to Analyse Competing Endogenous RNAs. - Selcen Ari Yuka; Alper Yilmaz 003 (ISBRA, 2020)

Robust and rigorous identification of tissue-specific genes by statistically extending tau score. - Hatice Büsra Lüleci; Alper Yilmaz 003 (BioData Min., 2022)

Decoding dynamic miRNA: ceRNA interactions unveils therapeutic insights and targets across predominant cancer landscapes. - Selcen Ari Yuka; Alper Yilmaz 003 (BioData Min., 2024)