The full list of publications – IYTE NON-CODING RNA LABORATORY

2026

Z.B. Orhan, E.B. Köşlü, B. Akgül, “Beyond the non-coding paradigm: ncRNA-encoded peptides in cellular regulation and clinical implications in cancer,” In preparation.

H. Li, A. Akçaöz-Alasar, Y. Wang, M. Perez-Pepe, B. Han, B. Akgül, D. Klein, C. R. Alarcon, “METTL3 Ser43 phosphorylation controls RNA substrate selection,” Under review.

Z.B. Orhan, E.B. Köşlü, Ş.N. Menemenli, B. Akgül, “Decoding the non-coding genome: Integrative frameworks for identification and validation of ncRNA-encoded peptides,” Under review.

G. Eroğul, E. Alasar, Ş.N. Menemenli, A. Akçaöz-Alasar, B. Akgül, “Unsupervised transcriptomic profiling identifies context-dependent m6A regulatory and apoptotic programs in TNF-a and TRAIL-treated cancer cells,” In revision.

B. Sağlam-Şen, A. Akçaöz-Alasar, A. Batuhan Dondurur, Ekin Yıldız, Dilek Cansu Gürer-Er, B. Akgül, “METTL3 modulates cell viability and motility in HCC1143 and MDA-MB-231 triple-negative breast cancer cells,” In revision.

D.C. Gürer-Er, G. Karakülah, D. Gautheret, B. Akgül, “MOCHI enables systematic identification of candidate independent intronic transcriptional signals from short-read RNA-seq data,” BioRXiv, 2026.

O. Moubset, Z.B. Orhan, E.B. Köşlü, B. Akgül, C. Alix-Panabieres, “Circular RNAs in the breast cancer tumor microenvironment: mechanisms, biomarker potential, and therapeutic perspectives,” Front. Immunol., 2026, In press.

O. Akkuş, Buket Sağlam-Şen, Azime Akçaöz-Alasar, B. Akgül, G. Güler, “Infrared vibrational fingerprinting of nucleic acid methylation with structural validation by circular dichroism,” Spect. Acta Part A: Mol. Biomol. Spect., 2026, In press.

E. B. Köşlü, A.Akçaöz-Alasar, B. Akgül, “Experimental and computational strategies to identify translationally active circular RNAs: From ORF prediction to protein-level validation,” Methods in Mol. Biol., 2026, In press.

A. Akçaöz-Alasar, Y. Wang, H. Li, D. Ostapenko, C.A.R. Parrado, D. Villalobos, W. Li, P.C. Boddu, A.H. Nguyen, H. Li, M. Perez-Pepe, P. Darnat, B. Akgül, M.M. Pillai, Y. Liu, L. Kabeche, C.R. Alarcón , “ METTL3 promotes cell cycle progression via activation of transcriptional elongation,” Molecular Cell, 86, 1-10, 2026. Please click on this link for a highlight of this article in Nat. Rev. Mol. Cell Biol.

N. S. Menemenli and B. Akgül, ” The role of long noncoding RNAs in modulation of stress granules in cancer,” J. Cell. Mol. Med., 30(13), e71261, 2026.

Y. Gazaloğlu, B.S.-Şen, B. Akgül, “m1A and m6A RNA methylations as druggable targets in cancer,” Pharmaceuticals, 19(7), 990, 2026.

Y.C. Çiftçi, İ.E. Vatansever, and B. Akgül, “DRAQ7 overcomes the complications associated with autofluorescence of doxorubicin during flow cytometric analyses,” Biology Methods & Protocols, 11:1, bpag025, 2026.

B. Akgül*, G. Güler*, B. Sağlam, O. Akkuş, A. Akçaöz Alasar, “Linking RNA methylation to structure: A biophysical perspective,” The FEBS Journal, 293, 2799-2810, 2026.

2025

G. Ozduman, A. Javed, A.A.-Alasar, B. Akgül, K.S. Korkmaz, “HN1 functions in protein synthesis regulation via mTOR-RPS6 axis and maintains nucleolar integrity,” Cell Proliferation, 58:e13805.

2024

B. Sağlam*, O. Akkuş*, A. Akçaöz Alasar, Ç. Ceylan, G. Güler, B. Akgül, “Investigation of RNA methylations with biophysical approaches in a cervical cancer cell model”, Cells, 13(22), 1832, 2024.

B. Akgül, A.A.-Alasar, B. Sağlam, “RNA m6A methylation at the juxtaposition of apoptosis and RNA therapeutics,” Trends in Cell Biology, 34(10), 801-804, 2024.

Y.C. Ciftci, Y. Yurtsever, B. Akgül, “Long non-coding RNA-mediated modulation of Endoplasmic Reticulum stress under pathological conditions,” J. Cell. & Mol. Med., 28, e18561, 2024.

Y.C. Ciftci, I.E. Vatansever, B. Akgül, “Unraveling the intriguing interplay: Exploring the role of lncRNAs in caspase-independent cell ceath,” WIREs RNA,15, e1862, 2024.