Cihan Erkut
@cihanerkut.bsky.social
Computational Biologist | Integrative Genomics of Rare Cancers | Nanopore Sequencing | Division of Applied Functional Genomics | German Cancer Research Center (DKFZ) | National Center for Tumor Diseases (NCT) Heidelberg
🚀 new bwa-mem3 is out. Why use it? - 🏛️keep using a bwa-mem variant (avoid revalidation/reprocessing) - 🚅 1.7x faster/20% less memory than bwa-mem2 - 🧬native methylation support (asymmetric scoring) - ✅ matches bwa-mem2 output - 👊opt-in knobs to go even 2x faster bwa-mem3.readthedocs.io/en/latest/
Home - bwa-mem3
Accelerated short-read alignment, derived from bwa-mem2
bwa-mem3.readthedocs.io
🏆 Introducing the inaugural Suzanne Eaton Awards for Physics of Life! We're thrilled to announce the 2026 recipients: L. Mahadevan @harvard.edu and Anna Erzberger @embl.org. 👨🔬Both scientists will give award lectures on 20. November, more info to follow ➡️Read our announcement here: tud.link/cjm8t2
🧵 NEW PAPER in @bloodjournal.bsky.social! Why do IDH1 mutations almost exclusively drive myeloid #leukemia, while IDH2 mutations occur in both myeloid AND lymphoid cancers? 🤔 #AML #Epigenetics Despite sharing the same biochemical mechanism, they are NOT equivalent. Here's what we found 👇
We’ve welcomed participants from 33 countries at the EACR's Cancer Genomics, Multiomics and Computational Biology conference in Essen this week! 🤩 This afternoon's poster session has sparked many interesting conversations between researchers.
What if brain metastatic cells do not act alone, but form #networks to help them grow? In our new #preprint, we show that #brainmetastases form malignant, gap-junction mediated #networks that drive cell cycle progression & neural features through Ca²⁺ signaling. www.biorxiv.org/content/10.6... 🧵👇
🧬 Der desmoplastische klein- und rundzellige Tumor ist selten, aggressiv und schwer zu behandeln. Forschende am NCT Heidelberg und am @dkfz.bsky.social haben 30 Tumoren umfassend analysiert und für fast alle Betroffenen potenzielle personalisierte Therapieoptionen abgeleitet. (1/2)
Dreaming of a career in cancer research? Join the International PhD Program at DKFZ - Germany’s largest biomedical research center. Explore #cancerresearch including #cancerbiology, #bioinformatics, #epidemiology & #medicalphysics. The Summer Selection is open now 👉 apply here: t1p.de/hl56b
Does the noncoding genome actually carry more genetic information than coding seqs? Motivated by this question we mutated every bp in the 10kb MYC locus. Results are even more exciting: Decoding the MYC locus reveals a druggable ultraconserved RNA element www.biorxiv.org/content/10.6...
biorxiv.org
We mourn the passing of Peer Bork, EMBO Member since 2000: https://www.embl.org/news/embl-announcements/in-remembrance-of-peer-bork/
In remembrance of Peer Bork | EMBL
EMBL and its community are deeply saddened by the death of Peer Bork, the organisation’s Interim Director General.
embl.org
Cornetto v0.2.0 is now released for using programmable selective nanopore sequencing for genome assembly. GitHub: github.com/hasindu2008/... Paper: nature.com/articles/s41... Datasets: hasindu2008.github.io/cornetto/doc... ... and a banner made by Ira Deveson referring to ‘no boring bits’.
Hasindu Gamaarachchi@hasindu2008.bsky.social · 8mo agoOur cornetto work is now published at www.nature.com/articles/s41... It can do near-T2T assembly using @nanoporetech.com adaptive sampling - with less 💸 - reference agnostic, so works for non-humans - not just blood, even saliva Just presented at #abacbs2025 yesterday.
Now free to read in Genetics (@genetics-gsa.bsky.social): "Preventing evolutionary rescue in cancer using two-strike therapy" #mathonco study by @srishtipatil.bsky.social, @armaanahmed.bsky.social, Yannick Viossat and me, determining the optimal time to switch treatments. doi.org/10.1093/gene...
Preventing evolutionary rescue in cancer using two-strike therapy
Abstract. First-line cancer treatment frequently fails due to initially rare therapeutic resistance. An important clinical question is then how to schedule
doi.org
Anthony A. Hyman will become EMBL’s next Director General. He joins EMBL from @mpi-cbg.de in Dresden. He is also Professor of Molecular Biology @tudresden.bsky.social, and was a group leader at EMBL Heidelberg from 1993 to 1999. www.embl.org/news/people-...
We are looking for a postdoc to join our team! If you're interested in translating a cutting edge genomics technology (www.nature.com/articles/s41...) to real-life applications in hematology, this is for you. We offer a unique working environment ON THE BEACH: recruitment.crg.eu/content/jobs...
🚀 Thinking about your next big career step in science? The Int'l PhD Program at DKFZ could be a perfect fit for you. 🌍 Work in an international environment, with 500+ doctoral researchers 🔬 Do cutting-edge cancer research Curious? Join our online info session on 20 Nov. Register here: t1p.de/ws7q3
With deep sadness, we share that Prof. Jochen Guck, Director at the Max Planck Institute for the Science of Light passed away on October 3. His visionary work bridged physics and medicine. We have lost a brilliant scientist and dear friend. mpl.mpg.de/news/article... @fau.de 📸 Stephan Spangenberg
It has been an honor for me to have worked in this fantastic project with great scientists and brilliant students for the last few years.
Deutsches Krebsforschungszentrum (DKFZ)@dkfz.bsky.social · 11mo agoChordomas are rare bone tumors for which there are currently no effective drugs. A research team from the DKFZ and @nct-heidelberg.bsky.social managed to block the central driver of tumor development and in the result slowed the growth of chordoma cells. #CancerResearch t1p.de/h9izi
📢 Registration now open for HARPOON Conference, Nov 27–28 2025 in Heidelberg! Precision oncology, multi-omics, & translational research. indico.dkfz.de/event/1230/ @nct-heidelberg.bsky.social @dkfz.bsky.social @vhio.bsky.social @ki.se @crukcamcentre.bsky.social @nkinl.bsky.social @gustaveroussy.fr
The goal of a PhD is not to learn some facts or read a few papers or learn a bunch of techniques. The goal of a PhD is to learn independence, problem solving, how to finish things you start, resilience, & gain the ability to adapt & think creatively. Learning these things is hard.
Your Prime Day reminder that half of Amazon warehouse workers struggle with food & housing costs. A third have had to rely on government assistance like SNAP — which is about to get cut. If Bezos can spend $50M on a wedding, Amazon can afford to treat its workers with dignity.
After so many inspiring talks and thought-provoking conversations, it's now time to go home. Many thanks to the organizers of #EACR2025 for this extraordinary event. Hope to meet everyone again next year in Budapest.
If you are at the #EACR2025 today and interested in integrative genomics of rare cancers, feel free to visit me by the poster P-006 in Pavilion 1 during the poster session.
This was one of the most inspiring talks I've ever heard in my life! #eacr2025
Luisa Ferreira@luisa86ferreira.bsky.social · last yr.Jan H. Hoeijmakers shared mindblowing insights on how caloric restriction impact on DNA damage response, cancer, and ageing! Also unexpected effects of carbohydrate and fat vs protein intake. (Less) food for thought —literally! #EACR2025
Incredible opening keynote by Charlie Swanton - spanning tumour initiation, aging, environmental exposure and much more 👏👏 #EACR2025 @charlesswanton.bsky.social @crick.ac.uk @helloeacr.bsky.social
„Kinder, die lernen, ihre eigenen Gefühle zu verstehen, können auch die Gefühle anderer besser wahrnehmen.“ Lisa Feldman Barrett #blueLZ
1. LLM-generated code tries to run code from online software packages. Which is normal but 2. The packages don’t exist. Which would normally cause an error but 3. Nefarious people have made malware under the package names that LLMs make up most often. So 4. Now the LLM code points to malware.
David D. Levine@daviddlevine.com · last yr.LLMs hallucinating nonexistent software packages with plausible names leads to a new malware vulnerability: "slopsquatting."
