Temet nosce.

Is computer science dead? No, just evolving.

ExactCN: Predicting Exact Copy Numbers on Whole Exome Sequencing Data https://t.co/ecS4TgiBSb

CHALLENGER: Detecting Copy Number Variants in Challenging Regions Using Whole Genome Sequencing Data https://t.co/FqgLdIqEJz

Very happy to announce that our study on designing RNA to bind and target proteins is now published @PLOSCompBiol. RNAtranslator is a generative language model that formulates protein-conditional RNA design as a sequence-to-sequence natural language translation problem for the

#RECOMB2026 will be in Thessaloniki, Greece on May 26-29, 2026. Satellites on May 24-25. Save the date! Το συνέδριο #RECOMB2026 θα πραγματοποιηθεί στη Θεσσαλονίκη, στις 26-29 Μαΐου 2026. Οι δορυφορικές εκδηλώσεις θα διεξαχθούν στις 24-25 Μαΐου 2026. Σημειώστε την ημερομηνία!

It is a wrap. #ISMBECCB2025 was a nice mix of jetlag, catching up with friends, observing the state-of-the-art and presenting. It is time to go back home after a loong journey (Izmir - Ayvalık - Los Angeles - London - Liverpool). See ya, mate!

Finally, we have a poster presentation (C-335) on DeepSynba; our deep learning model to predict dose-response profiles in synergistic drug combination detection led by our recent PhD graduate @hllibrhmkuru and @HaotingZhang1. It will be in Session C: July 23, 2025 at 10:00-11:20

I will give a talk on RNAtranslator; our recent language model to design protein-binding RNA for virtually any protein. The talk will take place in the iRNA session on July 24 at 12:00 in room 02N. This is the result of a great effort of my current/former students

We are headed to #ISMBECCB2025 Conference organized in Liverpool, UK! We have two oral and one poster presentation this year. @m_alperyilmaz from our group will present our proceedings paper on detecting copy number variations on ancient DNA 🗿🧬samples in the HitSeq session on

🛫 @UCLA_CGSI is in the books. The best meeting ever.

'About your cat, Mr. Schrödinger — I have good news and bad news.' (Benjamin Schwartz, New Yorker)

Team Bilkent @UCLA_CGSI

Enjoying the ocean view @UCLA_CGSI 2025 with @AhmetArdaCeylan from our group 📸

📢📢Our study on designing novel 5’ UTRs to that yield higher expression levels and mean ribosome load for the target genes is now published in @BioinfoAdv. This was a study with graduates from my group @sinabr01, @furkozden; and a collaboration with @uosseker and his student

UTRGAN: Learning to Generate 5’ UTR Sequences for Optimized Translation Efficiency and Gene Expression. #5UTRs #TranslationalControl #TranslationOptimization #GeneExpression #Genomics #Bioinformatics @BioinfoAdv https://t.co/1FNnxEHLv2

We also thank our collaborators Haoting Zhang, Carl Henrik Ek, Magnus Rattray & @marta_milo; the jury members Arzucan Ozturk, @tuncadogan, Selim Aksoy & @calkan_cs for their contributions to this thesis.

🎓 Yesterday, @hllibrhmkuru successfully defended his Ph.D. thesis. Co-advised with @TastanOznur, he worked on deep learning-based techniques for drug synergy prediction. We were very lucky to have him and wish him the best in the next chapter of his career.

Yann LeCun is not so optimistic about LLMs. 😟 "We are not going to get to human level AI by just scaling up MLMs. This is just not going to happen. There's no way. Okay, absolutely no way. And whatever you can hear from some of my uh more adventurous colleagues, it's not going

See our new paper with @muhayyileli and Kousar Saleem about a new vulnerability of the genomic data sharing beacon protocol in Bioinformatics👇