IBG-BIP Bioinformatics Platform


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.

You can contact us directly for the services you request from IBG-BIP Platform.


IBG-BIP Bioinformatics Platform

Platform Director

+90 232 299 41 00 (5051)
+9 0 232 299 41 55

Necla KOÇHAN Post-Doc Researcher  necla.kochan@ibg.edu.tr

Leman BİNOKAY Researcher  leman.binokay@ibg.edu.tr

Leman BİNOKAY PhD Student  leman.binokay@ibg.edu.tr

Hüseyin GÜNER Researcher  huseyin.guner@ibg.edu.tr

Ahenk ER UĞURCAN PhD Student  ahenk.er@ibg.edu.tr

Cihangir YANDIM Visiting Researcher  cihangir.yandim@ibg.edu.tr

Fatih MAMAK Undergraduate Student  fatih.mamak@ibg.edu.tr

Elif YILDIZ MSc Student  elif.yildiz@ibg.edu.tr

Fatih MAMAK Undergraduate Student  fatih.mamak@ibg.edu.tr

Necati Kaan KUTLU PhD Student  necatikaan.kutlu@ibg.edu.tr

Başak KESKİNOĞLU Researcher  basak.keskinoglu@ibg.edu.tr

Doğa ESKİER R&D PhD Student  doga.eskier@ibg.edu.tr

Tutku YARAŞ Collaborative Research and Customized Services Researcher  tutku.yaras@ibg.edu.tr

Former Personnel

Alirıza ARIBAŞ R&D Personnel  aliriza.aribas@ibg.edu.tr

Necla KOÇHAN Post-Doc Researcher  necla.kochan@ibg.edu.tr

Nurten Ezgi DOĞUDAN Undergraduate Student  ezgi.dogudan@msfr.ibg.edu.tr

Leman BİNOKAY MSc Student  leman.binokay@ibg.edu.tr

Necati Kaan KUTLU PhD Student  necatikaan.kutlu@ibg.edu.tr

Uğur ÇABUK MSc Student  ugur.cabuk@msfr.ibg.edu.tr

Uğur DURA Undergraduate Student  ugur.dura@ibg.edu.tr

Uğur SEZERMAN R&D Research Group Member  ugur.sezerman@ibg.edu.tr

Nazmiye ARSLAN R&D R&D Personnel  nazmiye.arslan@ibg.edu.tr

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

Temmuz Ata Türk KARAKUM R&D MSc Student  temmuz.karakum@msfr.ibg.edu.tr

Işık Barış FİDANER High Performance Computing (HPC) R&D Personnel  baris.fidaner@ibg.edu.tr
+90 232 299 41 00 (5251)
0 (232) 299 41 75

Ahmet BURSALI Collaborative Research and Customized Services R&D Personnel  ahmet.bursali@ibg.edu.tr

Selected Publications

Yandim, Cihangir; Karakulah, Gokhan. Expression dynamics of repetitive DNA in early human embryonic development. BMC GENOMICS. 2019 May ; 20 . doi:10.1186/s12864-019-5803-1. Download

Yandım C, Karakülah G. Dysregulated expression of repetitive DNA in ER+/HER2- breast cancer.. Cancer Genetics. 2019 November ; 239 : 36-45. doi:10.1016/j.cancergen.2019.09.002. Download

Karakülah G, Arslan N, Yandım C, Suner A. TEffectR: an R package for studying the potential effects of transposable elements on gene expression with linear regression model.. PeerJ. 2019 December ; 7 : e8192. doi:10.7717/peerj.8192. Download

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. Download

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

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. Download

Karakulah, Gokhan; Kurtoglu, Kuaybe Yucebilgili; Unver, Turgay. PeTMbase: A Database of Plant Endogenous Target Mimics (eTMs). PLOS ONE. 2016 December ; 11 (12) . doi:10.1371/journal.pone.0167698. Download

Total : 7

Selected Book Chapters

In Silico Identification of Stress-Associated Transposable Elements in Arabidopsis thaliana Using Public Transcriptome Data (2021). Methods in Molecular Biology - Springer. Humana, New York, NY.

Total : 1


IBG-BIP Bioinformatics Platform

Platform Director

+90 232 299 41 00 (5051)
+9 0 232 299 41 55