IBG-BIP Bioinformatics Platform

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.

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

Personnel

IBG-BIP Bioinformatics Platform

Platform Director

Gökhan KARAKÜLAH
gokhan.karakulah@ibg.edu.tr
+90 232 299 41 00 (5051)
+9 0 232 299 41 55

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


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


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


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


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


Cihangir YANDIM Visiting Researcher  cihangir.yandim@msfr.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


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


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


Former Personnel

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


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


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


Hamdiye UZUNER R&D MSc Student  hamdiye.uzuner@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

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

Contact

IBG-BIP Bioinformatics Platform

Platform Director

Gökhan KARAKÜLAH
gokhan.karakulah@ibg.edu.tr
+90 232 299 41 00 (5051)
+9 0 232 299 41 55