iiinova — where your digital self keeps evolving

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Deutsches Krebsforschungszentrum (DKFZ) @dkfz.bsky.social · 17/09/2026

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 Winter Selection is open now 👉 apply t1p.de/hl56b

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Nils Homer @nilshomer.com · 28/06/2026

🚀 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/

bwa-mem3.readthedocs.io

Home - bwa-mem3

Accelerated short-read alignment, derived from bwa-mem2

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Physics of Life Dresden @poldresden.bsky.social · 24/06/2026

🏆 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

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Daniel Lipka @dblipka.bsky.social · 29/05/2026

🧵 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 👇

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EACR - European Association for Cancer Research @helloeacr.bsky.social · 13/05/2026

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.

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Matthia Karreman @matthiakarreman.bsky.social · 13/05/2026

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... 🧵👇

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NCT Heidelberg @nct-heidelberg.bsky.social · 10/04/2026

🧬 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)

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Cihan Erkut @cihanerkut.bsky.social · 09/04/2026

Maybe off topic but are remote R sessions stable for you? We have 2 dedicated servers with 256 cores & 1 TB RAM each, and there are user-level resource limits, but R sessions become unresponsive even when they are idle with no reason. Some days it's completely unusable. Any thoughts? @posit.co

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Deutsches Krebsforschungszentrum (DKFZ) @dkfz.bsky.social · 27/03/2026

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

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Xuebing Wu @xuebingwu.bsky.social · 31/01/2026

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

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Hasindu Gamaarachchi @hasindu2008.bsky.social · 04/12/2025

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’.

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EMBL @embl.org · 27/11/2025

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-...

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Lars Velten @larsplus.bsky.social · 20/11/2025

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...

Yes, this is where you would work (the round building, not the boat)

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Deutsches Krebsforschungszentrum (DKFZ) @dkfz.bsky.social · 05/11/2025

🚀 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

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Cihan Erkut @cihanerkut.bsky.social · 20/10/2025

It's probably possible. I would try. Some workflows such as nf-core/rnaseq may require TBs of space just for the intermediate files, which one can remove safely once the workflow succeeds. If they have limited storage, they can run the samples 1-by-1 and clean them up every time. Just an idea.

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Cihan Erkut @cihanerkut.bsky.social · 20/10/2025

Depends on the processor, memory, storage and the pipeline. In theory possible but in practice may take a few days even it works. Do you have the reference FASTA and GTF only or the whole index (for STAR for example)?

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Max Planck Institute for the Science of Light (MPL) @mpi-scienceoflight.bsky.social · 08/10/2025

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

Professor Jochen Guck, Director at the Max Planck Institute for the Science of Light (MPL), He headed the division “Cell Physics” at MPL and the Max-Planck-Zentrum für Physik und Medizin (MPZPM).

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Cihan Erkut @cihanerkut.bsky.social · 04/09/2025

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.

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Cancer Core Europe @cancercoreeurope.bsky.social · 18/08/2025

📢 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

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TanentzapfLab @tanentzapflab.bsky.social · 13/08/2025

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.

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Robert Reich @rbreich.bsky.social · 08/07/2025

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.

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Cihan Erkut @cihanerkut.bsky.social · 19/06/2025

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.

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Cihan Erkut @cihanerkut.bsky.social · 18/06/2025

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.

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Cihan Erkut @cihanerkut.bsky.social · 17/06/2025

This was one of the most inspiring talks I've ever heard in my life! #eacr2025

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Johanna Joyce @johannajoyce.bsky.social · 16/06/2025

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

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Cihan Erkut @cihanerkut.bsky.social · 28/05/2025

Sounds very interesting to me 😂

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ETEP Isolde @etep-isolde.bsky.social · 22/04/2025

„Kinder, die lernen, ihre eigenen Gefühle zu verstehen, können auch die Gefühle anderer besser wahrnehmen.“ Lisa Feldman Barrett #blueLZ

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Janelle Shane @janelleshane.com · 13/04/2025

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.

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Wissenschaftsrat @wissenschaftsrat.de · 09/04/2025

The German Science and Humanities Council and the German Rectors' Conference criticise attacks on academic freedom and declares its solidarity with US institutions and scientists. An attack on science anywhere is an attack on science everywhere. #AcademicFreedom #HandsOff

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Stefan Fröhling @stefanfrohling.bsky.social · 19/03/2025

Are you interested in groundbreaking research in the field of personalized cancer therapies? If so, please join us at DKFZ for an exciting and inspiring afternoon and hear from key opinion leaders and rising stars about what is on the horizon.

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NCT Heidelberg @nct-heidelberg.bsky.social · 19/03/2025

** Meyenburg-Preis an Michel Sadelain ** 🏆Verleihung im Rahmen des Cancer Research Award Symposiums der Meyenburg-Stiftung 📅 2. April 2025 am Deutschen Krebsforschungszentrum in Heidelberg Programm und Anmeldung unter www.nct-heidelberg.de/das-nct/news... @dkfz.bsky.social

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micamer.bsky.social @micamer.bsky.social · 11/03/2025

We would love feedback on a new NCBI-BLAST service we are launching today: sky-blast.com Under the hood it's the same BLAST executable and databases provided by NCBI, with a replica of the NIH's interface - providing an alternative to the US gov service that's less congested, faster & more reliable

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Richard Sever @richardsever.bsky.social · 11/03/2025

Big news: we are setting up a new non-profit organization to run bioRxiv and medRxiv. It's called openRxiv [no it's not a new preprint server; it's dedicated organization to oversee the servers] openrxiv.org 1/n

openrxiv.org

Homepage - openRxiv

openRxiv is an independent non-profit, the new organizational home for bioRxiv and medRxiv, enabling researchers to instantly share groundbreaking findings with the global scientific community.

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The German Human Genome-Phenome Archive @ghga.bsky.social · 26/02/2025

New release headed by GHGA Member Kübra Narcı! This pipeline is designed to assess and validate the accuracy of variant calling methods in genomic research.

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Wolfgang Huber @wkhuber.bsky.social · 15/02/2025

Heidelberg 2025-02-15

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Winkler Laboratory @winklerlab.bsky.social · 12/02/2025

#aufstehenfuerdemokratie Um 11:55 Uhr versammelte sich eine große Gruppe von Wissenschaftlern & Unterstützern, um ein Statement für faktenbasierte Entscheidungen und Demokratie abzugeben: Geht wahlen-mit Verstand! Inspirierende Worte von Prof. E. Winkler und Prof. S. Pfister - Danke an Alle!

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Nadia Davidson @nadia-davidson.bsky.social · 10/02/2025

Our new paper examining how to analyse longread RNA-seq with no reference genome. We compare approaches for assembly and downstream analysis, from transcript accuracy to differential expression. Lead by @alexyfyf.bsky.social. Thnx to all contributors incl. @qgouil.bsky.social for the pea data!

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Cihan Erkut @cihanerkut.bsky.social · 22/01/2025

genetic background, age, sex, nutrition, etc. I strongly advice my colleagues not to use DESeq to analyze patient cohorts. I just wanted to sharey thoughts.

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Cihan Erkut @cihanerkut.bsky.social · 22/01/2025

Additionally, there is the latent variable issue. Tumor samples are rarely 100% pure. Even if there is no contaminating normal tissue, the tumor microenvironment (immune cells, etc.) differ between tumors of the same type. Then, of course, there are so many other factors such as treatment regime,

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Cihan Erkut @cihanerkut.bsky.social · 22/01/2025

There, replicates of the same experiment group can be truly biological replicates, if the experiment is designed properly. For human samples in TCGA cohorts, that's never the case. Ever sample is individual. So DESeq fails to model the dispersion to start with, regardless of sample size.

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Cihan Erkut @cihanerkut.bsky.social · 22/01/2025

I agree. And there is more. I think the true strength of DESeq isn't using negative binomial per se but estimating dispersion accurately despite small sample size. An underlying assumption is that most genes in two sample groups are expressed at the same level, which is true for cell lines, etc.

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