Grants

Current

• Horizon Europe EIC Pathfinder 101047160, 2022-2026
• Title: Processing-in-memory architectures and programming libraries for bioinformatics algorithms (BioPIM)
• Coordinator: Can Alkan
• Team Leaders: Onur Mutlu (ETH Zürich), Rayan Chikhi (Institut Pasteur), Dominique Lavenier (CNRS), Abu Sebastian (IBM Zürich), Ran Ginosar (Technion), Yann Falevoz (UPMEM), Leonid Yavits (Bar-Ilan).
• Goal: Leveraging the emerging processing-in-memory (PIM) technologies to enable powerful edge computing.

• NVIDIA Applied Research Accelerator Program, 2023-2025
• Title: Fast pathogen screening using DNA sequencing in disaster-stricken areas
• PI: Can Alkan
• Goal: Sequencing-based identification of pathogens quickly using the portable Jetson Nano kits.

Past

• Afyon Health Sciences University Scientific Research Project (20-TEMATIK-004), 2021-2022
• Title: Developing rapid diagnostic kit for sepsis (Sepsi-Fast)
• PI: Nurullah Okumuş
• Co-PI: Can Alkan, Urartu Şeker, Serdar Ceylaner
• Goal: Determining antibiotic resistance and susceptibility in newborn sepsis cases

• European Molecular Biology Organization Installation Grant (IG-2521), 2013-2019
• Title: 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
  
• PI: Can Alkan
• Goal: Analysis of biological sequences generated with the next-gen sequencing platforms.

• Scientific and Technical Research Council of Turkey (TÜBİTAK-1001-115E596), 2016-2019
• Title: BacGenTrack – An integrated system for Bacterial Genome Tracking using high throughput sequencing technology: from identification to visualization
• PI: Can Alkan and Joao Andre Carriço
• Goal: Developing new algorithms for the field of molecular epidemiology.
  

• Scientific and Technical Research Council of Turkey (TÜBİTAK-1001-215E172), 2016-2018

• Title: Algorithms for structural variation discovery using hybrid sequencing technologies and library preparation protocols.
• PI: Can Alkan
• Goal: Discovery and characterization of structural variants using multiple sequencing platforms, linked-reads, and read clouds

• The Science Academy, Turkey, Young Investigator Award (BAGEP), 2013-2014
• PI: Can Alkan

• United States of America National Institutes of Health (R01 HG006004), 2011-2015
  
• Title: Novel algorithms and hardware designs for ultra-fast next-gen sequence analysis
• PI: Onur Mutlu
• Co-PI: Can Alkan
• Goal: Developing specialized hardware architectures to accelerate mapping reads generated with the high throughput sequencing platforms.

• European Union Marie Curie Actions Career Integration Grant (PCIG10-GA-2011-303772), 2012-2016
• Title: Integrated approaches for genomic variation discovery using high throughput sequencing
  
• PI: Can Alkan
• Goal: Developing novel combinatorial algorithms to comprehensively and quickly discover genomic variation.

• Scientific and Technical Research Council of Turkey (TÜBİTAK-1001-112E135), 2012-2015
• Title: Development and application of novel genome assembly algorithms that use multiple data sources
• PI: Can Alkan
• Goal: Developing assembly algorithms to more reliably construct de novo genome assemblies using data from multiple sources.