IBG-BIP on 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.

Group Members

IBG-BIP on Bioinformatics Platform

Group Leader

GÖKHAN KARAKÜLAH
gokhan.karakulah@ibg.edu.tr
+90 232 299 41 00 (5051)
+9 02322994155

UĞUR SEZERMAN Research Group Member  ugur.sezerman@ibg.edu.tr


ALIRIZA 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


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


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


NECATI KAAN KUTLU Ph.D. Student  necatikaan.kutlu@msfr.ibg.edu.tr


TEMMUZ ATA TÜRK KARAKUM Graduate Student  temmuz.karakum@msfr.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.

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.

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.

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

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.

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.

Total: 7

Contact

IBG-BIP on Bioinformatics Platform

Group Leader

GÖKHAN KARAKÜLAH
gokhan.karakulah@ibg.edu.tr
+90 232 299 41 00 (5051)
+9 02322994155