SEÇİLİ YAYINLAR

Yayınların tam listesine  Akademik Kadro sayfasında yer alan öğretim üyeleri bilgilerinden ulaşabilirsiniz.

Prof. Dr. Erdem Karabulut

• A Methodological Research on Radiogenomics: Combining Radiomics and Genomics for Classification, M KAŞIKCI, E Coşgun, E Karabulut, Journal of Biostatistics 16 (1), 2024
• Biomarker detection using corrected degree of domesticity in hybrid social network feature selection for improving classifier performance, HY Zengin, E Karabulut, BMC bioinformatics 24 (1), 407, 2023
• voomSOM: voom-based Self-Organizing Maps for Clustering RNASequencing Data, A Cephe, N Koçhan, GE Zararsız, V Eldem, E Coşgun, E Karabulut, ..., Current Bioinformatics 18 (2), 154-169, 2023

Doç. Dr. Ceren Sucularlı

• Murray K, Oldfield L, Stefanova I, Gentiluomo M, Aretini P, O'Sullivan R, Greenhalf W, Paiella S, Aoki MN, Pastore A, Birch-Ford J, Rao BH, Uysal-Onganer P, Walsh CM, Hanna GB, Narang J, Sharma P, Campa D, Rizzato C, Turtoi A, Sever EA, Felici A, Sucularli C, Peduzzi G, Öz E, Sezerman OU, Van der Meer R, Thompson N, Costello E.Biomarkers, omics and artificial intelligence for early detection of pancreatic cancer. Semin Cancer Biol. Jun;111:76-88. 2025
• Parveen M, Karaosmanoglu B, Sucularli C, Uner A, Taskiran EZ, Esendagli G.Acquired immune resistance is associated with interferon signature and modulation of KLF6/c-MYB transcription factors in myeloid leukemia. Eur J Immunol. May;54(5):e2350717. 2024
• Sucularli C, Şimay Demir YD, Özdemir A, Ark M. Temporal regulation of gene expression and pathways in chemotherapy-induced senescence in HeLa cervical cancer cell line. Biosystems. Mar;237:105140. 2024
• Durmaz CD, Karabulut HG, Saka MC, Sucularlı C, Gümüş Akay G, Atbaşoğlu C, Ilgın Ruhi H. Genetic Analysis of RASD1 as a Candidate Gene for Schizophrenia. Balkan Med J. Nov 7;39(6):422-428. 2022
• Sucularli C. Identification of BRIP1, NSMCE2, ANAPC7, RAD18 and TTL from chromosome segregation gene set associated with hepatocellular carcinoma. Cancer Genet. Nov;268-269:28-36. 2022
• Karaaslan C, Karaguzel D, Sarac BE, Sucularli C, Bilgic HA, Kalayci O. The Expression Profile of Protease Inhibitors in the Airway Epithelial Cells after Allergen (Der p 1) Stimulation. Int Arch Allergy Immunol. 183(1):25-33. 2022

Dr. Öğretim Üyesi İdil Yet 

• Xiaopu Zhang, Idil Yet, Sergio Villicaña, Juan Castillo-Fernandez, Massimo Mangino, Jouke Jan Hottenga, Pei-Chien Tsai, Josine L Min, Mario Falchi, Andrew Wong, Dorret I Boomsma, Ken K Ong, Jenny van Dongen, Jordana T Bell,Genetic impacts on within-pair DNA methylation variance in monozygotic twins capture gene-environment interactions and cell-type effects, Genome Biology, 2025
• Bihter Muratoğlu, Cansu Özdemir, Cemil Can Eylem, Tuba Reçber, Emirhan Nemutlu, İdil Yet, Duygu Uçkan-Çetinkaya, Circadian rhythm and aryl hydrocarbon receptor crosstalk in bone marrow adipose tissue and implications in leukemia, Scientific Reports, 2025
• Ceyhun Kayıhan, Efe Dallı, Şeküre Çulha Erdal, İdil Yet, Nuran Cicek, Yasemin Ekmekçi,Transcriptional profiling and proteomic validation revealed higher boron tolerance in Arabidopsis thaliana exposed to salt pre-treatment,South African Journal of Botany,2025
• Serhat Aladağ, Ilayda Demirdiş, Burcu Gökçal Kapucu, Bilge Başak Fidan, Batuhan Erhan Aktaş, Merve Gizer, Ozan Kaplan, Idil Yet, Melis Şardan Ekiz, Petek Korkusuz, Mustafa Çelebier, Ömür Çelikbıçak, Ali Tuncel, Feza Korkusuz,Synovial Joint Fluid Omics Researches in Osteoarthritis: An Affinity Chromatography-Based Perspective,Nano-Biomaterials in Tissue Repair and Regeneration: Surgical Aspect for Hard Tissues,2025/4/21,47-78
• İ Yet, Comparative Metabolomics Analysis, Elsevier, 528-535, 2025
• İ Yet - Acta Medica, 2024, Identification of bio-markers for insulin resistance and sensitivity through multi-omics analysis

• A comparative urinary proteomic and metabolomic analysis between renal aa amyloidosis and membranous nephropathy with clinicopathologic correlations, DA Ozbek, SC Koc, NE Özkan, SE Kablan, I Yet, M Uner, N Ozlu, ..., Journal of Proteomics 293, 105064, 2024
• Comparing the melissopalynological and next generation sequencing (NGS) methods for the determining of botanical origin of honey, A Özkök, HA Bilgic, C Kosukcu, G Arık, D Canlı, I Yet, C Karaaslan, Food Control 148, 109630, 4, 2023
• Plasma proteomic analysis reveals the potential role of Lectin and Alternative Complement pathways in IgA Vasculitis Pathogenesis, S Demir, I Yet, M Sardan Ekiz, E Sag, Y Bilginer, O Celikbicak, I Lay, ..., Diagnostics 13 (10), 1729, 3, 2023
• Multiomics Integration at Single-Cell Resolution Using Bayesian Networks: A Case Study in Hepatocellular Carcinoma, M Jihad, İ Yet, Omics: a journal of integrative biology 27 (1), 24-33, 1, 2023

Dr. Öğretim Üyesi Gülşah Merve Kılınç

• Comprehensive αβ T‐Cell Receptor Repertoire Analysis Reveals a Unique CD8+ TCR Landscape in DOCK8‐Deficient Patients

C Bozkurt, G Cildir, U Aba, RK Erdogan, NI Warnock, CH Kok, AP Sefer, ...

Allergy,2025

• Evaluation of genotype imputation using Glimpse tools on low coverage ancient DNA

H Çubukcu, GM Kılınç

Mammalian Genome, 1-13,2024

• Bioinformatics Approaches for Detecting Selection

GM Kılınç, Elsevier, 2024

• Spatial and temporal heterogeneity in human mobility patterns in Holocene Southwest Asia and the East Mediterranean, D Koptekin, E Yüncü, R Rodríguez-Varela, NE Altınışık, N Psonis, ..., Current Biology 33 (1), 41-57. e15       15, 2023
• The genetic history of Scandinavia from the Roman Iron Age to the present, Cell 186 (1), 32-46. e19, 12, 2023

Prof. Dr. Tunca Doğan

• Target-specific de novo design of drug candidate molecules with graph-transformer-based generative adversarial networks

A Ünlü, E Çevrim, MG Yiğit, A Sarıgün, H Çelikbilek, O Bayram, ...

Nature Machine Intelligence, 1-17,2025

• Mpox: disease manifestations and therapeutic development

Y Wang, X Wang, T Doğan, NA Sam-Agudu, JA Al-Tawfiq, Q Pan

Journal of Virology, e00152-25,2025

• A Benchmarking Platform for Assessing Protein Language Models on Function-related Prediction Tasks

E Çevrim, MG Yiğit, E Ulusoy, A Yılmaz, T Doğan

Protein Function Prediction: Methods and Protocols, 241-268,2025

• ChemPile: A 250GB Diverse and Curated Dataset for Chemical Foundation Models

A Mirza, N Alampara, M Ríos-García, M Abdelalim, J Butler, B Connolly, ...

arXiv preprint arXiv:2505.12534,2025

• ProtHGT: Heterogeneous Graph Transformers for Automated Protein Function Prediction Using Biological Knowledge Graphs and Language Models

E Ulusoy, T Doğan

bioRxiv, 2025.04. 19.649272,2025

• Protein language models for predicting drug–target interactions: Novel approaches, emerging methods, and future directions

A Ünlü, E Ulusoy, MG Yiğit, M Darcan, T Doğan

Current Opinion in Structural Biology 91, 103017,2025

• Molecular Contrastive Learning with Graph Attention Network (MoCL-GAT) for Enhanced Molecular Representation

A Dalkiran, AS Rifaioglu, R Cetin-Atalay, AC Acar, T Dogan, VM Atalay

bioRxiv, 2025.09. 17.676724,2025

• OmniPath: integrated knowledgebase for multi-omics analysis

D Turei, J Schaul, N Palacio-Escat, B Bohar, Y Bai, F Ceccarelli, E Cevrim, ...

bioRxiv, 2025.09. 11.675512

2025

• Multi-modal Representation Learning Enables Accurate Protein Function Prediction in Low-Data Setting

S Ünsal, S Özdemir, B Kasap, ME Kalaycı, K Turhan, T Doğan, AC Acar

arXiv preprint arXiv:2412.08649,2024

• Design, synthesis, and evaluation of novel Indole‐Based small molecules as sirtuin inhibitors with anticancer activities

B Binarci, EK Kilic, T Dogan, R Cetin Atalay, DC Kahraman, ...

Drug Development Research 85 (7), e70008,2024

• Mutual annotation‐based prediction of protein domain functions with Domain2GO, E Ulusoy, T Doğan, Protein Science 33 (6), e4988, 2024
• An integrative framework for clinical diagnosis and knowledge discovery from exome sequencing data, M Shojaei, N Mohammadvand, T Doğan, C Alkan, RÇ Atalay, AC Acar, Computers in Biology and Medicine 169, 107810, 2024
• ASCARIS: Positional feature annotation and protein structure-based representation of single amino acid variations, F Cankara, T Doğan, Computational and Structural Biotechnology Journal 21, 4743-4758, 2023
• Democratizing knowledge representation with BioCypher, S Lobentanzer, P Aloy, J Baumbach, B Bohar, VJ Carey, P Charoentong, K Danhauser, T Doğan ..., Nature Biotechnology, 1-4 21, 2023
• UniProt: the Universal Protein knowledgebase in 2023, Nucleic Acids Research 51 (D1), D523-D531, 1716,2023

Dr. Öğretim Üyesi Arda Çetinkaya

• Extreme Phenotypic Variation in Siblings with Identical Homozygous Mutations Causing ADA2 Deficiency: A Case Series, Aksu, MD (Aksu, Muhammed D.) ; Özen, S (Ozen, Seza) ; Aksu, T (Aksu, Tekin) ; Gürel, A (Gurel, Ayse) ; Çetinkaya, A (Cetinkaya, Arda) ; Ünal, S (Unal, Sule),
  TURKISH JOURNAL OF HEMATOLOGY ,42, 2025
• Alu-Mediated Deletion of FANCA in Turkish Families With Fanconi Anemia: Evidence of a Founder Effect, Durmaz, CD (Durmaz, Ceren Damla) ; Gümrük, F (Gumruk, Fatma) ; Celkan, T (Celkan, Tiraje) ; Unal, S (Unal, Sule) ; Çetinkaya, A (Cetinkaya, Arda), AMERICAN JOURNAL OF MEDICAL GENETICS PART A, 197,4,2025
• Decreased calcium permeability caused by biallelic TRPV5 mutation leads to autosomal recessive renal calcium-wasting hypercalciuria, N Guleray Lafci, M van Goor, S Cetinkaya, J van der Wijst, M Acun, ..., European Journal of Human Genetics, 1-9, 1, 2024