Ercument Cicek

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Ercument Cicek

Ercument Cicek

@crashius

Computer Scientist, Computational Biologist, Assoc. Prof. at Bilkent University @BilkentUniv & Adj. Faculty at @CarnegieMellon @CMUCompbio 🦋@crashius

Katılım Temmuz 2011
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Ercument Cicek
Ercument Cicek@crashius·
Temet nosce.
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Ercument Cicek
Ercument Cicek@crashius·
It was great to meet with old and new friends at @dagstuhl where we discussed the future of privacy-preserving solutions for biomedical data sharing. Big shout out to all organizers: @bradmalin, @kantarcioglu, Fruzsina Molnar-Gabor, Fabian Prasser and Daniel Ruckert.
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Brad Malin@bradmalin

Another exhilarating Dagstuhl Seminar (dagstuhl.de/en/seminars/se…) in the books. It was a long week, but very inspiring to see what the future of privacy-aware health data sharing will look like!

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antisense.
antisense.@razoralign·
CHALLENGER: Detecting Copy Number Variants in Challenging Regions Using Whole Genome Sequencing Data biorxiv.org/content/10.110…
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sonradan_gourme
sonradan_gourme@sonradan_gourme·
Dünyanın en eski restoranı nerede? Madrid’de bulunan “Sobrino de Botin” 300 yıldır yani 1725 yılından bu yana açık. Bu özelliği ile Guinness rekorlar kitabı’na da girmiş. Menüsü nerede ise 300 yıldır değişmemiş ve hala 1725’deki aynı taş fırın kullanılıyor. En ünlü yemeği ise Cochinillo Asado. Goya ünlü bir ressam olmadan önce burada bulaşıkçı olarak çalışmış. Ernest Hemingway “Güneş de Doğar” romanında Botin’den bahsediyor. Bu kitap daha çok ünlenmesinde önemli bir rol oynuyor.
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Ercument Cicek
Ercument Cicek@crashius·
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 first time. Aside from enabling the design of RNAs with natural-like properties and high binding affinity, this approach also allows us to target proteins for which no RNA interaction data are available—something that was not previously possible. As an example, we designed an RNA (red) that binds with PRP4K (blue) with high affinity, and the resulting complex is shown below. This is the result of the hard work of our grad students at CICEKLAB: Sobhan Shukueian Tabrizi @sobhanshukueian, Sina Barazandeh @sinabr01 & Helyasadat Hashemi Aghdam @HelyaHashemi. Paper is available here - open access: journals.plos.org/ploscompbiol/a… The code is available at GitHub: github.com/ciceklab/RNAtr…
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RECOMB Conference Series
RECOMB Conference Series@RECOMBconf·
#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!
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Tunca Doğan
Tunca Doğan@tuncadogan·
🚀🚨🧪🤖 A generative AI that can design drug candidate molecules! Thrilled to share our research in Nature Machine Intelligence: DrugGEN, a graph-transformer GAN for target-specific de novo molecular design Paper: nature.com/articles/s4225… @NatMachIntell @Nature ++
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Ercument Cicek
Ercument Cicek@crashius·
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!
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Ercument Cicek
Ercument Cicek@crashius·
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 July 24 at 14:40 in room 01A. Great job by my current/former students Ahmet Arda Ceylan and @gun_kaynar. doi.org/10.1093/bioinf…
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Paul Halpern
Paul Halpern@phalpern·
'About your cat, Mr. Schrödinger — I have good news and bad news.' (Benjamin Schwartz, New Yorker)
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Can Alkan
Can Alkan@calkan_cs·
Team Bilkent @UCLA_CGSI
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Can Alkan
Can Alkan@calkan_cs·
Los Angeles. Who is around?
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Ercument Cicek
Ercument Cicek@crashius·
📢📢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 Ahmet Hincer.
Bioinformatics Advances@BioinfoAdv

🧬 Just out in Bioinformatics Advances: “UTRGAN: Learning to generate 5’ UTR sequences for optimized translation efficiency and gene expression”   Explore the full study: doi.org/10.1093/bioadv… Authors include: @sinabr01, @uosseker, @crashius

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