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Bilkent CompGen @BilkentCompGen

Alkan Lab for Bioinformatics and Computational Genomics at @CS_Bilkent

Joined June 2013
  • Tweets 313
  • Following 223
  • Followers 605
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Bilkent CompGen@BilkentCompGen
2 Oct 2025
The @BilkentCompGen Group, September 2025.
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Bilkent CompGen retweeted
Cenk Sahinalp & Team@cenksahinalp
Apr 24
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…

LCPan: efficient variation graph construction using locally consistent parsing

Genome Biology - Efficient and consistent string processing is critical in the exponentially growing genomic data era. Locally Consistent Parsing (LCP) addresses this need by partitioning an input...

link.springer.com
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New paper alert!
BioPIM Project@ProjectBioPIM
Feb 11
We’re excited to share our new position paper from the BioPIM Consortium: "Processing-in-memory for genomics workloads", published online in IEEE Micro, and will be a part of the upcoming Special Issue on Data-Centric Computing. Thread below 🧵👇
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Ricardo@rica01234
26 Aug 2025
Replying to @BilkentCompGen
@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)
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Bilkent CompGen retweeted
Ricardo@rica01234
26 Aug 2025
Replying to @BilkentCompGen
@BilkentCompGen M.S.THESIS PRESENTATION Efficient variation graph construction using Locally Consistent Parsing Akmuhammet Ashyralyyev (Supervisor: Assoc.Prof.Can Alkan)

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Can Alkan@calkan_cs
23 Jul 2025
Congratulations to my former MSc student and forever collaborator @FirtinaC for joining @umdcs as Assistant Professor.
UMD Department of Computer Science
@umdcs
23 Jul 2025
📢 @umdcs is welcoming 8 new faculty in 2025–26 with expertise in AI policy, robotics, bioinformatics, vision, language models, simulation & sound design. They’ll strengthen research & teaching across computing. Read more: go.umd.edu/New-Faculty7-2025
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BioPIM Project@ProjectBioPIM
3 Jun 2025
Our consortium-wide position paper is now available as a preprint @arxiv arxiv.org/abs/2506.00597 @SAFARI_ETH_CMU @UPMEM @IBMResearch @RayanChikhi @institutpasteur @BarIlanU @CNRS

Processing-in-memory for genomics workloads

Low-cost, high-throughput DNA and RNA sequencing (HTS) data is the backbone of the life sciences. Genome sequencing is now becoming a part of Predictive, Preventive, Personalized, and...

arxiv.org
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. @BilkentCompGen alumnus @mealser is now an Assistant Professor at the @GeorgiaStateU, and he is hiring. Spread the news!
Mohammed Alser@mealser
22 Nov 2024
📢 I am hiring 2 researchers and 3 PhD students 🧑‍🎓👩‍🎓 @GeorgiaStateU 🇺🇸🇪🇸 Simple Application: CV & Tell us why you are the best candidate 🤩💪 Share & Apply ➡️: alserlab.github.io #Bioinformatics #omics #microbiome #computationalbiology #postdoc #PhD #Research #recomb
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And the Best Poster Award goes to @zulal_b!! #genomeinformatics24
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We are at the beautiful @wellcometrust @sangerinstitute @emblebi campus! We presented our work in hardware/algorithm co-design to accelerate bioinformatics workloads at the #genomeinformatics24 workshop. Big thanks to @eventsWCS for a well-organized meeting.
BioPIM Project@ProjectBioPIM
15 Nov 2024
Last day of #genomeinformatics24! We have presented our work in @ProjectBioPIM with talks from @calkan_cs and @camiladuitama1 and a poster by @zulal_b, increasing the awareness of hardware acceleration in the community.
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@zulal_b also received a Travel Award for her work.
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BioPIM Project@ProjectBioPIM
13 Nov 2024
We are at the Genome Informatics 2024 meeting with two talks and a poster. @calkan_cs @zulal_b @camiladuitama1 @RayanChikhi in attendance.
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BioPIM Project@ProjectBioPIM
4 Nov 2024
We held our third plenary meeting for the BioPIM Project in beautiful Zurich, marking the close of our second review period. Since our last meeting in May, we have published three additional papers, with several more submitted and available as preprints.
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The @BilkentCompGen Group, October 2024.
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AirLift algorithm by #JeremieKim, @FirtinaC @banu_cavlak @damlasenolcali @mealser @NHajinazar @calkan_cs @_onurmutlu_ / @SAFARI_ETH_CMU is now published in IEEE Transactions on Computational Biology and Bioinformatics: ieeexplore.ieee.org/document…
Bilkent CompGen@BilkentCompGen
19 Dec 2019
New preprint in collab with @SAFARI_ETH_CMU "AirLift: A Fast and Comprehensive Technique for Translating Alignments between Reference Genomes", by #JeremieKim @FirtinaC @damlasenolcali @mealser @NHajinazar arxiv.org/abs/1912.08735
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AirLift aims to quickly remap a read set previously mapped to a reference genome to another reference genome version and provides 27.2x speed up compared to full remap from scratch.
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BioPIM Project@ProjectBioPIM
27 Aug 2024
The Genome Informatics 2024 Meeting will be hosted on the Wellcome Genome Campus @eventsWCS in Hinxton, UK, November 13-15, 2024. @calkan_cs will give an invited talk to feature hardware acceleration of bioinformatics workloads and the BioPIM Project.
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We are glad to attend the @UCLA_CGSI in Los Angeles. In the first two weeks Klea and Ricardo presented their work. One more week to go, but we are already looking forward to joining CGSI 2025!
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We are at the @UCLA_CGSI. Can presented @ProjectBioPIM, and Klea presented her project. We also met the leaders in bioinformatics, and one of our alumni, @mealser.
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Bilkent CompGen retweeted
BioPIM Project@ProjectBioPIM
17 Jul 2024
We presented the BioPIM Project at the @UCLA_CGSI 2024.
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