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.
Interested applicants should email their CV and transcripts (graduate student applications) to biopim [at] bilkent [dot] edu [dot] tr