Cihan Erkut

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’.

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

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...

YouTube video by Essentia Foundation Denis Noble: "Neo-Darwinism Is Dead" | We Need A Biology Beyond Genes

youtu.be/NAPhBt8VJCM

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-...

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

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

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.

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)?

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).

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.

📢 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

That's cool!!!

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

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

Sounds very interesting to me 😂

„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.

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

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.

** 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

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

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

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.

Heidelberg 2025-02-15

#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!

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!