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
Cihangir YANDIM
Visiting Researcher
cihangir.yandim@ibg.edu.tr
Fatih MAMAK
Undergraduate Student
fatih.mamak@ibg.edu.tr
Necati Kaan KUTLU
PhD Student
necatikaan.kutlu@ibg.edu.tr
Elif YILDIZ
MSc Student
elif.yildiz@ibg.edu.tr
Ahenk ER UĞURCAN
PhD Student
ahenk.er@ibg.edu.tr
Necla KOÇHAN
Post-Doc Researcher
necla.kochan@ibg.edu.tr
Hüseyin GÜNER
Researcher
huseyin.guner@ibg.edu.tr
Leman BİNOKAY
Researcher
leman.binokay@ibg.edu.tr
Leman BİNOKAY
PhD Student
leman.binokay@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
Leman BİNOKAY
MSc Student
leman.binokay@ibg.edu.tr
Necla KOÇHAN
Post-Doc Researcher
necla.kochan@ibg.edu.tr
Necati Kaan KUTLU
PhD Student
necatikaan.kutlu@ibg.edu.tr
Uğur DURA
Undergraduate Student
ugur.dura@ibg.edu.tr
Uğur ÇABUK
MSc Student
ugur.cabuk@msfr.ibg.edu.tr
Nurten Ezgi DOĞUDAN
Undergraduate Student
ezgi.dogudan@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
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
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
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