Alkan Lab for Bioinformatics and Computational Genomics at @CS_Bilkent
Ankara, Turkey
Joined June 2013
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Several changes in our group in the 2026-2027 Academic Year. Most recently, Zülal has finished her Ph.D., and new members have joined our group. Here is the @BilkentCompGen, October 2026.
Our new paper, "De Bruijn graphs for pangenomics: in-depth performance benchmarking of de Bruijn graph-based tools for read mapping," is now published in Briefings in Bioinformatics.
doi.org/10.1093/bib/bbag440
... memory usage, memory bus utilization, and execution speed. Through our rigorous analysis, we aim to provide insights for hardware acceleration of pangenomics workloads, such as domain-specific accelerators and processing-in-memory architectures.
This work was completed within the @ProjectBioPIM, in collaboration with our partners at @SAFARI_ETH_CMU, namely Konstantina Koliogeorgi, @FirtinaC, and @_onurmutlu_
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We also met with our alumnus Mohammed Alser, and three of his brilliant students, Adrian Tkachenko, Sepehr Salem, and Mohammed Nayeem Uddin. It was also great to reconnect with many of our friends and to sow the seeds of several collaborative projects.
Another one of our alumni, Damla Senol Cali, visited us from San Diego. Thanks to Eleazar Eskin, Stacey Beggs, and Kevin Kim for organizing yet another great meeting. One more @UCLA_CGSI in the books, already looking forward to the next!
We attended the @UCLA_CGSI Computational Genomics Summer Institute 2026 hosted by UCLA.
@calkan_cs gave two talks: a tutorial on accelerating bioinformatics workloads, and a research paper presentation on string processing using locally consistent parsing.
Our new paper, "PG2: algorithms and a web-based tool for effective layout and visual analysis of pangenome graphs," in collaboration with the Bilkent i-Vis Research Lab, is officially out in BMC Bioinformatics.
Led by Ugur Dogrusoz, and completed by a brilliant undergraduate student (at the time), Görkem Kadir Solun (now pursuing M.Sc. at ETH Zurich), and contributed to by my PhD student Zülal Bingöl ...
... PG2 provides the algorithms and an intuitive web-based interface for the seamless and scalable visual analysis of pangenome graphs.
Read the paper here: link.springer.com/article/10…
And test it out at: pg2.cs.bilkent.edu.tr/
A few weeks ago, we attended the RECOMB 2026 Conference and its associated Satellite Conferences RECOMB-Seq and RECOMB-Arch in Thessaloniki, Greece. Arda İçöz and Tuna Okçu presented their works in person, and Berkan Şahin presented his work remotely.
Bilkent CompGen retweeted
Our collaborative project with Can Alkan lab for implementing the full version of locally consistent parsing (LCP) as an alternative to all kmer based sequence analysis methods is now out in Genome Biology: link.springer.com/article/10…
Bilkent CompGen retweeted
@BilkentCompGen
DATE: August 27, Wednesday @ 14:00 Place: EA 409
M.S.THESIS PRESENTATION
Using Bloom filters to quickly and efficiently characterize genomic repeats and segmental duplications
Klea Zambaku
Master Student
(Supervisor: Assoc.Prof.Can Alkan)
Bilkent CompGen retweeted
@BilkentCompGen
M.S.THESIS PRESENTATION
Efficient variation graph construction using Locally Consistent Parsing
Akmuhammet Ashyralyyev
(Supervisor: Assoc.Prof.Can Alkan)