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Reposted by Cihan Erkut

Max Planck Institute for the Science of Light (MPL) @mpi-scienceoflight.bsky.social · 2d

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 · Sep 4

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 · Sep 4

Chordomas 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

Rare bone tumors: Tailor-made mini-proteins switch off tumor drivers

Chordomas are rare bone tumors for which there are currently no effective drugs. A research team from the German Cancer Research Center (DKFZ) and the National Center for Tumor Diseases (NCT) Heidelbe...

t1p.de

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Reposted by Cihan Erkut

Cancer Core Europe @cancercoreeurope.bsky.social · Aug 18

📢 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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Cihan Erkut @cihanerkut.bsky.social · Aug 13

That's cool!!!

Posit @posit.co · Aug 13

Announcing Positron's dedicated console for interactive coding!

Run single lines of #RStats or #Python code, switch languages & versions on the fly, and quickly scan outputs.

Learn more about Positron’s dedicated console: positron.posit.co

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TanentzapfLab @tanentzapflab.bsky.social · Aug 13

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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Reposted by Cihan Erkut

Robert Reich @rbreich.bsky.social · Jul 8

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 · Jun 19

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 · Jun 18

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 · Jun 17

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

#eacr2025

Luisa Ferreira @luisa86ferreira.bsky.social · Jun 16

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

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Johanna Joyce @johannajoyce.bsky.social · Jun 16

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 · May 28

Sounds very interesting to me 😂

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Reposted by Cihan Erkut

ETEP Isolde @etep-isolde.bsky.social · Apr 22

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

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Reposted by Cihan Erkut

Janelle Shane @janelleshane.com · Apr 12

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 · Apr 12

LLMs hallucinating nonexistent software packages with plausible names leads to a new malware vulnerability: "slopsquatting."

LLMs can't stop making up software dependencies and sabotaging everything

: Hallucinated package names fuel 'slopsquatting'

www.theregister.com

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Wissenschaftsrat @wissenschaftsrat.de · Apr 9

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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Reposted by Cihan Erkut

Stefan Fröhling @stefanfrohling.bsky.social · Mar 19

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.

NCT Heidelberg @nct-heidelberg.bsky.social · Mar 19

** 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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Reposted by Cihan Erkut

NCT Heidelberg @nct-heidelberg.bsky.social · Mar 19

** 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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Reposted by Cihan Erkut

micamer.bsky.social @micamer.bsky.social · Mar 11

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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Reposted by Cihan Erkut

Richard Sever @richardsever.bsky.social · Mar 11

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

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.

openrxiv.org

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Reposted by Cihan Erkut

The German Human Genome-Phenome Archive @ghga.bsky.social · Feb 26

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.

nf-core @nf-co.re · Feb 24

Pipeline release! nf-core/variantbenchmarking v1.0.0 - Innocent Pamuk

Please see the changelog: github.com/nf-core/vari...

Release 1.0.0 Innocent Pamuk · nf-core/variantbenchmarking

First release! by @kubranarci What's Changed pin nf-validation version by @nvnieuwk in #6 wittyer added by @kubranarci in #24 sv + small analysis implemented by @kubranarci in #30 sv benchmark par...

github.com

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Wolfgang Huber @wkhuber.bsky.social · Feb 15

Heidelberg 2025-02-15

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Winkler Laboratory @winklerlab.bsky.social · Feb 12

#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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Reposted by Cihan Erkut

Nadia Davidson @nadia-davidson.bsky.social · Feb 10

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 · Jan 22

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 · Jan 22

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 · Jan 22

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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