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 (IG-2521), 2013-2016
  
• 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.
  

Abstract

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.

Dissemination

• 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, 51(7):455-459, 2014.
• Whole 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, 2014.
• Discovery and genotyping of novel sequence insertions in many sequenced individuals. Pınar Kavak, Yen-Yi Lin, Ibrahim Numanagić, Hossein Asghari, Tunga Güngör, Can Alkan*, Faraz Hach*. Bioinformatics, Jul 15; 33 (14): i161-i169, 2017.
• Realizing the potential of blockchain technologies in genomics. Halil Ibrahim Ozercan, Atalay Mert Ileri, Erman Ayday, Can Alkan. Genome Research, 28(9): 1255-1263, 2018.
• Nanopore 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.
• Fast characterization of segmental duplications in genome assemblies. Ibrahim Numanagić, Alim S. Gökkaya, Lillian Zhang, Bonnie Berger, Can Alkan*, Faraz Hach*. Bioinformatics, Sep 1; 34(17):i706-714, 2018.