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
Reposted by Cihan Erkut
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
mpl.mpg.de/news/article...
@fau.de
📸 Stephan Spangenberg
October 8, 2025 at 1:26 PM
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
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.
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
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
September 4, 2025 at 8:05 PM
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.
Reposted by Cihan Erkut
📢 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
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
August 18, 2025 at 7:02 AM
📢 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
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!!!
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
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
August 13, 2025 at 6:09 PM
That's cool!!!
Reposted by Cihan Erkut
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.
August 13, 2025 at 5:28 PM
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.
Reposted by Cihan Erkut
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.
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.
July 8, 2025 at 4:41 PM
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.
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.
June 19, 2025 at 1:11 PM
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.
June 18, 2025 at 11:48 AM
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.
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
#EACR2025
June 17, 2025 at 9:41 AM
Reposted by Cihan Erkut
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
#EACR2025
@charlesswanton.bsky.social
@crick.ac.uk
@helloeacr.bsky.social
June 16, 2025 at 3:47 PM
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
#EACR2025
@charlesswanton.bsky.social
@crick.ac.uk
@helloeacr.bsky.social
Reposted by Cihan Erkut
Reposted by Cihan Erkut
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.
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.
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
April 12, 2025 at 11:43 PM
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.
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.
Reposted by Cihan Erkut
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
April 9, 2025 at 8:33 AM
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
Reposted by Cihan Erkut
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
🏆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
March 19, 2025 at 6:57 PM
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.
Reposted by Cihan Erkut
** 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
🏆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
March 19, 2025 at 5:33 PM
** 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
🏆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
Reposted by Cihan Erkut
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
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
March 11, 2025 at 11:50 PM
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
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
Reposted by Cihan Erkut
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
March 11, 2025 at 1:20 PM
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
Reposted by Cihan Erkut
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.
Pipeline release! nf-core/variantbenchmarking v1.0.0 - Innocent Pamuk
Please see the changelog: github.com/nf-core/vari...
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
February 26, 2025 at 10:08 AM
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.
Reposted by Cihan Erkut
Heidelberg 2025-02-15
February 15, 2025 at 3:26 PM
Heidelberg 2025-02-15
Reposted by Cihan Erkut
#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!
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!
February 12, 2025 at 11:22 AM
#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!
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!
Reposted by Cihan Erkut
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!
February 10, 2025 at 12:39 AM
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!
Reposted by Cihan Erkut
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Analysis of multi-condition single-cell data with latent embedding multivariate regression - Nature Genetics
Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction and clustering-free ...
doi.org
January 3, 2025 at 7:18 PM
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Reposted by Cihan Erkut
HOW COOL IS THIS?! Scientists have discovered a new way to destroy cancer cells. By stimulating aminocyanine molecules with near-infrared light, cancer cells vibrate in sync, enough to break apart their membranes! These “molecular jackhammers” DESTROYED 99% of cancer cells! 🧪🧵⬇️
December 27, 2024 at 5:00 PM
HOW COOL IS THIS?! Scientists have discovered a new way to destroy cancer cells. By stimulating aminocyanine molecules with near-infrared light, cancer cells vibrate in sync, enough to break apart their membranes! These “molecular jackhammers” DESTROYED 99% of cancer cells! 🧪🧵⬇️
Reposted by Cihan Erkut
Excited to announce two DFG-funded PhD positions to study Lipid Droplet Heterogeneity in cancer as part of FOR5815. Join us @dkfz-heidelberg if you are interested in #cancermetabolism and #lipidbiology
jobs.dkfz.de/en/jobs/1673...
jobs.dkfz.de/de/jobs/1673...
jobs.dkfz.de/en/jobs/1673...
jobs.dkfz.de/de/jobs/1673...
PhD Student in Lipid Metabolism in Cancer
jobs.dkfz.de
December 20, 2024 at 10:04 AM
Excited to announce two DFG-funded PhD positions to study Lipid Droplet Heterogeneity in cancer as part of FOR5815. Join us @dkfz-heidelberg if you are interested in #cancermetabolism and #lipidbiology
jobs.dkfz.de/en/jobs/1673...
jobs.dkfz.de/de/jobs/1673...
jobs.dkfz.de/en/jobs/1673...
jobs.dkfz.de/de/jobs/1673...
Reposted by Cihan Erkut
Exciting times ahead! The first joint clinical trial of the National Center for Tumor Diseases #OneNCT will address the unresolved question of whether treatment based on multi-layered molecular profiling can improve outcomes in patients with advanced #RareCancers. nct.dkfz.de/en/nct/news/...
RATIONALE focuses on rare cancers
First multi-site study by the National Center for Tumor Diseases (NCT)
nct.dkfz.de
December 16, 2024 at 6:17 PM
Exciting times ahead! The first joint clinical trial of the National Center for Tumor Diseases #OneNCT will address the unresolved question of whether treatment based on multi-layered molecular profiling can improve outcomes in patients with advanced #RareCancers. nct.dkfz.de/en/nct/news/...