BioPIM Project Positions
Alkan Lab for Bioinformatics and Computational Genomics at Bilkent University, Turkey, is looking for outstanding, self-motivated graduate students (both M.Sc. and Ph.D.) and postdoctoral fellows to join our project as early as May 1, 2022., which is recently funded by the Horizon Europe program. Our project, “Processing-in-memory architectures and programming libraries for bioinformatics algorithms (BioPIM)”, aims to accelerate bioinformatics analyses using modern processing-in-memory (PIM) hardware technologies. Together with our partners from ETH Zurich, IBM, Institut Pasteur, UPMEM, CNRS, and TECHNION, we will focus on co-designing algorithms and data structures commonly used in bioinformatics together with emerging PIM hardware technologies to obtain the highest benefit in terms of cost, energy efficiency, and time savings in genome sequence analysis.
Specific topics within this project will involve rigorous profiling, benchmarking, and workload analysis of existing bioinformatics tools to better optimize hardware/software mapping; developing and optimizing data structures and bioinformatics algorithms to work more efficiently on various types of PIM devices; hardware/software co-design for PIM; and PIM-friendly application programming interface (API) design.
More details can be found on our project page, http://www.biopim.eu
- B.Sc. degree (for M.Sc. students); or M.Sc. degree (for Ph.D. students), or Ph.D. degree (for postdoctoral fellows) in computer science, computer engineering, or electrical engineering.
- Expertise in developing efficient data structures and combinatorial algorithms (dynamic programming, greedy algorithms, approximation algorithms, graph theory) is a must.
- Strong skills in C/C++ is a must.
- Basic understanding of biology/genetics/genomics is a plus.
- Proficiency in hardware description languages (Verilog, VHDL) is a plus.
- Requirements for application to graduate level study at Bilkent University must be fulfilled.
Successful candidates will receive a full tuition waiver (for M.Sc. and Ph.D. students), competitive monthly stipend, health insurance, free accommodation, and transportation. Full-time positions only.
Interested applicants should email their CV and transcripts (graduate student applications) to biopim [at] bilkent [dot] edu [dot] tr
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 involve in other international collaborations. Some possible projects are:
- Discovery and characterization of genomic variation using high throughput sequencing (HTS) data.
- 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).
More details can be found in our Research page.
- B.Sc. or M.Sc. degree in computer science, computer engineering, or electrical engineering.
- 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/C++ is a must, Rust and Java programming experience is a plus.
- Minimum requirements for application to graduate level study at the Bilkent University must be fulfilled.
- Basic understanding of biology/genetics/genomics is preferred, but **not required//. Contact me if you are interested in bioinformatics, computational biology, and genomics.
Undergraduate volunteers with good programming skills (C/C++/Java/Rust) are also welcome to contact me for implementation based short projects.