IBG-BIP

OVERVIEW

The IBG Bioinformatics Platform (IBG-BIP) is a unit established to carry out research and development activities on bioinformatics and computational biology, as well as to support the scientific research conducted at IBG. The unit is composed of four divisions.

1) Research and Development:
The IBG-BIP-RD division works on methods used in bioinformatic computing, software tools and databases. It utilises existing scientific methods and tools, in addition to developing new ones according to scientific requirements. Specifically, the division conducts work specialising on new generation sequencing technologies. The division supervisor is Nazmiye Arslan.

2) Collaborative Research:
The IBG-BIP-CR division initiates and conducts collaborative research with scientists working at IBG. Data from different sources is modelled and subjected to various biostatistical analyses with the ultimate aim of turning the data into scientific knowledge. The division supervisor is Ahmet Bursalı.

3) High-Performance Computing:
The IBG-BIP-HPC division manages the high-performance computing (HPC) unit used for bioinformatic computing at IBG. Resources of the HPC such as storage and processor are provided for users. The division supervisor is Alirıza Arıbaş.

4) Education and Training:
The IBG-BIP-ET division provides training to IBG personnel on access to and usage of bioinformatics resources, as well as conducting scientific studies with graduate students on bioinformatics. The division supervisor is Gökhan Karakülah.

Personnel

Alirıza ARIBAŞ System Manager  aliriza.aribas@ibg.edu.tr


Ahmet BURSALI Bioinformatics Specialist  ahmet.bursali@ibg.edu.tr


Nazmiye ARSLAN Bioinformatics Technician  nazmiye.arslan@ibg.edu.tr


DOĞA ESKİER Ph.D. Student  doga.eskier@msfr.ibg.edu.tr


Hamdiye UZUNER MSc Student  hamdiye.uzuner@msfr.ibg.edu.tr


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 June; 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 September; 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 June; 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 March; 7: 45661. doi:10.1038/srep45661.

Karakülah G, Suner A. PlanTEnrichment: A tool for enrichment analysis of transposable elements in plants. Genomics. 2017 October; 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 September; 58 (11): 4422-4435. doi:10.1167/iovs.17-21805.

Total: 9

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