Bilkent CompGen

Alkan Lab for Bioinformatics and Computational Genomics at @CS_Bilkent

[Bilkent CompGen @BilkentCompGen]

The @BilkentCompGen Group, September 2025.

[Cenk Sahinalp & Team @cenksahinalp]

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: https://t.co/0a0vQKCjyd

[Bilkent CompGen @BilkentCompGen]

New paper alert!

[BioPIM Project @ProjectBioPIM]

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 🧵👇

[Ricardo @rica01234]

@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: https://t.co/mlNicmsUml.Can Alkan)

[Ricardo @rica01234]

@BilkentCompGen
M.S.THESIS PRESENTATION
Efficient variation graph construction using Locally Consistent Parsing
Akmuhammet Ashyralyyev
(Supervisor: https://t.co/mlNicmsUml.Can Alkan)

[Can Alkan @calkan_cs]

Congratulations to my former MSc student and forever collaborator @FirtinaC for joining @umdcs as Assistant Professor.

[BioPIM Project @ProjectBioPIM]

Our consortium-wide position paper is now available as a preprint @arxiv https://t.co/6c74aD9rZc @SAFARI_ETH_CMU @UPMEM @IBMResearch @RayanChikhi @institutpasteur @BarIlanU @CNRS

[Bilkent CompGen @BilkentCompGen]

. @BilkentCompGen alumnus @mealser is now an Assistant Professor at the @GeorgiaStateU, and he is hiring. Spread the news!

[Mohammed Alser @mealser]

📢 I am hiring 2 researchers and 3 PhD students 🧑‍🎓👩‍🎓 @GeorgiaStateU 🇺🇸🇪🇸

Simple Application: CV & Tell us why you are the best candidate 🤩💪

Share & Apply ➡️: https://t.co/2FgVWTQKrj

#Bioinformatics #omics #microbiome #computationalbiology #postdoc #PhD #Research #recomb

[Bilkent CompGen @BilkentCompGen]

And the Best Poster Award goes to @zulal_b!! #genomeinformatics24

[Bilkent CompGen @BilkentCompGen]

@zulal_b also received a Travel Award for her work.

[Bilkent CompGen @BilkentCompGen]

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]

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.

[BioPIM Project @ProjectBioPIM]

We are at the Genome Informatics 2024 meeting with two talks and a poster. @calkan_cs @zulal_b @camiladuitama1 @RayanChikhi in attendance.

[BioPIM Project @ProjectBioPIM]

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.

[Bilkent CompGen @BilkentCompGen]

The @BilkentCompGen Group, October 2024.

[Bilkent CompGen @BilkentCompGen]

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.

[Bilkent CompGen @BilkentCompGen]

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: https://t.co/LCJrOrt1pI

[Bilkent CompGen @BilkentCompGen]

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 https://t.co/gcWzkzuOuz

[BioPIM Project @ProjectBioPIM]

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.

[Bilkent CompGen @BilkentCompGen]

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!

[Bilkent CompGen @BilkentCompGen]

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.

[BioPIM Project @ProjectBioPIM]

We presented the BioPIM Project at the @UCLA_CGSI 2024.