Karakulah Lab. on Computational Sequence Analysis

OVERVIEW

NGS has opened opportunities and challenges of “big data science” to biologists and clinicians for genome-wide evaluation of genetic variations, expression of distinct RNA species, and epigenetic changes associated with development, aging, and disease. The rapid evolution of NGS and associated methodologies presents significant challenges in acquisition, management, and analysis of large data sets and for extracting biologically or clinically relevant information. Current computational methods are not able to harness the full potential of large genomic and epigenomic datasets being generated by innovations in NGS technology. Thus, a greater focus is needed on developing novel tools for computational and systems level analysis.    

RESEARCH INTERESTS

Currently, I have been focused on:

(i) Analysis, mining and modeling of NGS data to extract its biological relevance and place it into the context of our understanding,

(ii) Developing bioinformatics analysis pipelines to integrate diverse biological data sets at different resolutions, including genome, transcriptome and epigenome levels to address biological questions,

(iii) Building online bioinformatics databases and analysis tools for scientific community.

Selected Publications

Suner A, Carr BI, Akkiz H, Karakülah G, Üsküdar O, Yalçın K, Kuran S, Tokat Y, Yilmaz S, Özakyol A, Tokmak S, Ballı T, Yücesoy M, Bahçeci Hİ, Ülkü A, Akçam T, Polat KY, Ekinci N, Şimşek H, Örmeci N, Sonsuz A, Demir M, Kılıç M, Uygun A, Demir A, Delik A, Arslan B, Doran F, Altıntaş E, Temel T, Bektaş A. C-Reactive Protein and Platelet-Lymphocyte Ratio as Potential Tumor Markers in Low-Alpha-Fetoprotein Hepatocellular Carcinoma. Oncology. 2019 ; 96 (1): 25-32. doi:10.1159/000492473.

Karakülah G, Pavlopoulou A. In silico Phylogenetic Analysis of hAT Transposable Elements in Plants. Genes. 2018 Jun ; 9 (6): 284. doi:10.3390/genes9060284.

Aslı Suner, Hikmet Akkiz, Oguz Uskudar, 26 other authors. Inflammatory markers C-reactive protein and PLR in relation to HCC characteristics. Journal of Translational Science. 2018 ; 5 (3): 1-6. doi:10.15761/JTS.1000260.

Karakülah G. RTFAdb: A database of computationally predicted associations between retrotransposons and transcription factors in the human and mouse genomes. Genomics. 2018 Sep ; 110 (5): 257-262. doi:10.1016/j.ygeno.2017.11.002.

Karakülah G. Discovery and Annotation of Plant Endogenous Target Mimicry Sequences from Public Transcriptome Libraries: A Case Study of Prunus persica. Journal of Integrative Bioinformatics. 2017 Jun ; 14 (4): . doi:10.1515/jib-2017-0009.

Karakülah G. Investigation of Tissue Expression Patterns and Putative Functions of Human Long Non-Coding RNAs with Affinity Propagation Algorithm. Iğdır Üniversitesi Fen Bilimleri Enstitüsü Dergisi. 2017 ; 7 (2): 249-257. doi:10.21597/jist.2017.138.

Gümürdü A., Yildiz R., Eren E., Karakülah G., Ünver T., Genç Ş. & Park Y. MicroRNA exocytosis by large dense-core vesicle fusion. Scientific Reports. 2017 Mar ; 7 45661. doi:0.1038/srep45661.

Karakülah G, Suner A. PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants. Genomics. 2017 Oct ; 109 (5-6): 336-340. doi:10.1016/j.ygeno.2017.05.008.

Zelinger L, Karakülah G, Chaitankar V, Kim JW, Yang HJ, Brooks MJ, Swaroop A. Regulation of Noncoding Transcriptome in Developing Photoreceptors by Rod Differentiation Factor NRL. Investigative ophthalmology & visual science. 2017 Sep ; 58 (11): 4422-4435. doi:10.1167/iovs.17-21805.

Contact

Karakulah Lab. on Computational Sequence Analysis

Assoc.Prof. Gokhan KARAKULAH
gokhan.karakulah@ibg.edu.tr
+90 232 299 41 00 (5051)
+90 232 299 41 55