Development and application of computational methods to analyze next
generation sequence data to characterize both normal and disease
causing variation, and build de
novo genome assemblies
- European Molecular Biology Organization Installlation Grant
- PI: Can Alkan
- Students: Can Fırtına, Halil İbrahim Özercan, Ezgi Ebren, Zülal
Bingöl, Balanur İçen
- Total €250,000 for five years.
- This is an EMBO Installation Grant that is given to young
researchers to install their independent laboratories. The funds
of this project will be used in various projects within the Lab
for Bioinformatics and Computational Genomics that involves
development of computational methods to utilize high throughput
sequencing (HTS) for different applications.
My main research focus is the analysis of biological sequences generated
with the next-gen sequencing platforms, and my plans for independent
research are twofold: computational algorithm development, and
application of methods to sequencing data to analyze genomic variation
in both normal and diseased individuals. My long term goal is to
accurately and comprehensively predict genomic variation from next
generation datasets routinely.
- Early postzygotic mutations
contribute to de novo variation in a healthy monozygotic twin
pair. Gülşah M Dal, Bekir Ergüner, Mahmut S
Sağıroğlu, Bayram Yüksel, Onur Emre Onat, Can
Alkan, Tayfun Özçelik. J Med Genet,
genome sequencing of Turkish genomes reveals functional private
alleles and impact of genetic interactions with Europe, Asia and
Africa. Can Alkan,
Pınar Kavak, Mehmet Somel, Omer Gokcumen, Serkan Uğurlu, Ceren
Saygı, Elif Dal,
Kuyaş Buğra, Tunga Güngör, S Cenk Sahinalp, Nesrin Özören and
Cemalettin Bekpen. BMC Genomics, 15(1):963, doi:10.1186/1471-2164-15-963,
and genotyping of novel sequence insertions in many sequenced
Kavak, Yen-Yi Lin, Ibrahim Numanagić, Hossein Asghari,
Tunga Güngör, Can Alkan*,
Faraz Hach*. Bioinformatics, Jul 15; 33 (14): i161-i169,
the potential of blockchain technologies in genomics.
Halil Ibrahim Ozercan, Atalay Mert
Ileri, Erman Ayday, Can
Alkan. Genome Research, 28(9):
sequencing technology and tools for genome assembly:
computational analysis of the current state, bottlenecks and
future directions. Damla
Senol Cali, Jeremie S. Kim, Saugata Ghose, Can
Alkan*, Onur Mutlu*. Briefings in
Bioinformatics, [epub Apr 2; doi: 10.1093/bib/bby017], 2018.
characterization of segmental duplications in genome assemblies.
Ibrahim Numanagić, Alim S.
Gökkaya, Lillian Zhang, Bonnie Berger, Can
Hach*. Bioinformatics, Sep 1; 34(17):i706-714, 2018.