Postdoctoral Fellow
A postdoctoral position is available immediately for multiple projects that involve combinatorial optimization, sequence analysis algorithms, and graph theory. The main project will involve discovery and characterization of genomic variation using high throughput sequence data, however there may be other projects that might need minor contributions. Successful applicant will also have a chance to contribute to many international consortiums including the 1000 Genomes Project and will be involved in other international collaborations.Requirements:
- Ph.D. degree in computer science, computer engineering, electrical engineering, or mathematics with strong background in combinatorial algorithm design. Ph.D. candidates who expect to graduate soon are welcome to apply.
- Experience in bioinformatics research is strongly preferred.
- Strong skills in high level programming languages, Linux operating systems and shell scripting. Proficiency in C/C++ is a must.
- Our
group has several large-scale collaborative efforts, and interested
candidates must be able to work closely with international teams of
scientists with broad areas of expertise.
Graduate Students
Self motivated, hard working graduate students (both M.Sc. and Ph.D.) are wanted for multiple projects that involve combinatorial optimization, sequence analysis algorithms, graph theory, and field programmable gate array designs. Successful applicants will also have a chance to contribute to many international consortiums such as the 1000 Genomes Project and the Genome 10K, and will involve in other international collaborations. Current projects are:- Discovery and characterization of genomic variation using high throughput sequencing
(HTS) data. This project is funded by a European Union Marie Curie
Actions Career Integration Grant, and one graduate student will be fully supported. Ph.D. student applications only.
- Algorithms and hardware designs for
ultra-fast mapping of HTS reads to reference genome assemblies. This
research will involve algorithm development for GPGPU clusters and hardware designs for field programmable
gate arrays (FPGA). This project is funded by the U.S. National
Institutes of Health in collaboration with Onur Mutlu
at the Carnegie Mellon University. Full support for two graduate
students is available.
- Genomic repeat discovery, classification and annotation. This
research will involve development of algorithms based on graph theory
and sequence analysis to discover genomic repeats from HTS data.
- Distributed
algorithms for genome assembly. A typical raw dataset to build de novo
genome sequence assemblies is composed of billions of short sequence
reads. This project aims to build a distributed genome assembler based on Pregel
or other similar distributed graph processing framework.
Requirements:
- B.Sc. or M.Sc. degree in computer science, computer engineering, electrical engineering, or mathematics.
- Expertise in data structures and combinatorial algorithms (dynamic programming, greedy algorithms, approximation algorithms, graph theory).
- Strong skills in high level programming languages. Proficiency in C is a must, Java programming experience is a plus.
- Minimum requirements for application to graduate level study at
the Bilkent University must be fulfilled. For the summary of
requirements, click here.
Undergraduate volunteers with good programming skills (C/C++/Java) are also welcome to contact me for implementation based short projects. For sample projects, click here.