Purpose

Alkan Lab for Bioinformatics and Computational Genomics started at the Bilkent University Department of Computer Engineering in January 2012. We are primarily an algorithms and heterogenous computing group, and we develop combinatorial algorithms to analyze genomic sequence data focusing on algorithms for pangenomics, de novo genome assembly, and discovery of structural variation. We also work on hardware/software co-design and heterogeneous computing to accelerate computational workloads using processing-in-memory, GPU, NPU, and FPGA.

Our collaborators

We engage in collaborative projects from across the globe. Here are some of the folks we collaborate with:

• S. Cenk Şahinalp, Cancer Data Science Laboratory, National Cancer Institute, Bethesda, MD, United States
• Evan E. Eichler, Eichler Lab, University of Washington, Seattle, WA, United States
• Fereydoun Hormozdiari, UC Davis Computational Genomics, UC Davis, Davis, CA, United States
• Iman Hajirasouliha, IH Computational Genomics Lab, Weill Cornell Medicine, New York, NY, United States
• Faraz Hach, Hach Lab, University of British Columbia, Vancouver, BC, Canada
• Ömer Gökçümen, Buffalo Evolutionary and Anthropological Genomics Laboratory (BEAGL), University at Buffalo, Buffalo, NY, United States
• Faraz Hach, Hach Lab, University of British Columbia, Vancouver, BC, Canada
• Ibrahim Numanagic, University of Victoria, Victoria, BC, Canada
• Onur Mutlu, SAFARI Group, ETH Zürich, Switzerland
• Mehmet Somel, Middle East Technical University, Ankara, Turkey
• Ercüment Çiçek, Bilkent University, Ankara, Turkey
• Tuğkan Batu, Department of Mathematics, London School of Economics and Political Science, London, United Kingdom
• Mohammed Alser, Georgia State University, Atlanta, GA, United States
• Can Fırtına, STORM Research Group (http://storm.cs.umd.edu/), University of Maryland, College Park, MD, United States

Website

The Alkan Lab website was heavily inspired by the site for Trevor Bedford’s lab. Trevor put together a site that showcases his lab’s science to the world, as they produce it, in real time.

You can see the source code for the Bedford lab site. It is pfreely available on GitHub. All code is placed under the MIT license. The Bedford lab also provides some documentation about how they link each project’s GitHub repository into the main site.

Source code

All source code that’s necessary to construct the site is freely available on GitHub. All code is placed under the MIT license. You’re welcome to borrow / repurpose code to build your own site, but I would very much appreciate attribution and a link back to bedford.io from your about page.