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Benjamin Ostendorf

@ostendorflab.org
3.4K followers 915 following 35 posts

Physician scientist @ChariteBerlin. Interested in tumor immunology, systems biology, and cancer biology. Lab website: www.ostendorflab.org

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Reposted by Benjamin Ostendorf
Dani León-Periñán @danilexn.bsky.social · 26/08/2026
Malva out in Nature! 🚀 RNA sequences make cells different from each other. Single-cell data captures much of this, but most stays in the dark because we reduce it to gene counts. We introduce Malva to make the world's single-cell data searchable. What took days is now one query in seconds.
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Christian Zierhut @zierlab.bsky.social · 21/08/2026
Supremely excited to share our new paper in @natcellbio.nature.com With an updated genetic cGAMP reporter, we reveal that cGAS activation by DNA damage is a rare event, and that cGAS enrichment on intracellular structures cannot be taken as evidence of activation. www.nature.com/articles/s41...
nature.com
A versatile cGAMP reporter reveals principles of cGAS activation by DNA damage and chromosome instability - Nature Cell Biology
Lebrec et al. present a FRET-based cGAS reporter and show that cGAS activation by genotoxic stress is rare and uncoupled from micronuclei. The study implicates R-loop structures and subtypes of chroma...
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Reposted by Benjamin Ostendorf
Miguel Reina-Campos @reinacampos.bsky.social · 03/08/2026
FITdb, a one-stop shop for immune functional genomics so you can query, browse, and analyze your favorite genes and pathways across multiple contexts in mouse and human immune cells. #immunefunction visit fitdb.lji.org
biorxiv.org
FITdb, an Integrated Functional Immunogenomics and Transcriptomics Database
Genetic screens in immune cells enable the systematic interrogation of gene function at scale, uncovering key regulators of cell functions such as tumor cell killing and persistence. However, existing...
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Reposted by Benjamin Ostendorf
European Commission @ec.europa.eu · 01/08/2026
Japan has now joined Horizon Europe. Japan’s researchers can now partner with teams across the EU. Together, we will advance global research in health, digital technologies, and climate neutrality ↓ link.europa.eu/YP7MtB
Visual featuring Mount Fuji framed by pink cherry blossoms. At the centre are the overlapping flags of the European Union and Japan, with the text "EU-JAPAN HORIZON EUROPE" overlaid below.
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Aydan Bulut-Karslioglu @bulutkarslioglu.bsky.social · 26/06/2026
I have been thinking since yesterday about why I find the 1% thing so, so disturbing. It's a visceral reaction of 'just no', which goes beyond the general yuck towards the enshittification of/via AI. I have finally put my finger on it: it is the feeling you get when
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Reposted by Benjamin Ostendorf
Richard Sever @richardsever.bsky.social · 26/06/2026
“the academic community is enormously heterogeneous and it’s almost impossible to keep everyone happy” Never a truer word said in this analysis of downstream consequences of openness by @jacoates.bsky.social ripplingideas.org/2026/06/26/t...
ripplingideas.org
The 1% club and the rocky road ahead for bioRxiv
The recent launch of qed’s “top 1%” preprint ranking has sparked controversy, with concerns about its arbitrary nature, potential harm to authors, and low-quality inclusions. Whil…
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NEJM.org @nejm.org · 31/05/2026
Among patients with previously treated metastatic pancreatic ductal adenocarcinoma, the RAS(ON) inhibitor daraxonrasib led to significantly longer overall survival and progression-free survival than chemotherapy. Full phase 3 RASolute 302 trial results: nej.md/4nWaxvM #ASCO26
Graph from a study published in the New England Journal of Medicine on daraxonrasib versus chemotherapy for metastatic pancreatic cancer. The x-axis represents months, and the y-axis shows the percentage of patients alive. Two lines indicate survival rates: daraxonrasib (blue) and chemotherapy (gray). The bottom section lists patients at risk over time. Title and journal logo are included.
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Benjamin Ostendorf @ostendorflab.org · 30/04/2026
Regarding ELNs, after all these years I still wish Findingsapp by @cparnot.bsky.social got resurrected. Benchling is fine, but Findings was such a joy to work with. Maybe in the age of LLMs it would be feasible to do that, add an optional web interface and collaboration features
community.findingsapp.com
Findings has been discontinued and will no longer be developed 😥
Dear Findings user, We have some sad news to share with you today. More than 10 years ago we set out to make the lab notebook app we would have loved to have when we were still in the lab. The result ...
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Reposted by Benjamin Ostendorf
Our World in Data @ourworldindata.org · 11/03/2026
The number of cancer deaths worldwide has more than doubled since the 1980s. Does that mean we're losing the fight against cancer? Not necessarily, because it depends on how you measure it. On this chart, you can see three ways to look at the same data. 🧵
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The Rockefeller University @rockefeller.edu · 05/03/2026
A new tool from Rockefeller's @danmucida.bsky.social and @czbiohub.bsky.social allows scientists to closely follow newly activated T cells as they travel and change during an infection—it may inform future therapies for infection, cancer, and autoimmunity. 🔗: bit.ly/3NjZEWD
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Journal of Experimental Medicine @jem.org · 10/02/2026
@ostendorflab.org, @immushuang.bsky.social, @sohailtavazoie.bsky.social et al. show that activation of LXRs elicits a T cell "pre-effector" state that enhances priming and promotes anti-tumor immunity. rupress.org/jem/article/... #TumorImmunology
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Benjamin Ostendorf @ostendorflab.org · 10/02/2026
Delighted to share our new paper on LXR agonism pre-conditioning T cells to more readily adopt effector states, out in @jem.org today. This was a long project started in @sohailtavazoie.bsky.social's lab and completed across the atlantic here in Berlin at Charité.
doi.org
Liver-X-receptor agonism enhances T cell priming and activation to promote anti-tumor immunity
Ostendorf et al. show that activation of liver-X-receptors preconditions T cells to render them more receptive to adopting effector states upon activation.
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Claudi Giesecke-Thiel @missesthiel.bsky.social · 10/02/2026
📣 We’re hiring! Pls share! Join my lab to study human antigen-specific B cells across vaccination & infection backgrounds & explore their plasticity. Passionate about B cells, cutting-edge immunology, molecular biology & bioinformatics? 📄Details & apply: karriere.charite.de/stellenangeb... ⏳ Feb 28
karriere.charite.de
Wissenschaftliche Mitarbeiterin/ Wissenschaftlicher Mitarbeiter (d/w/m) /DoktorandIn
Teilzeit | 28.02.2026 | Campus Virchow-Klinikum, Wedding
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Mark Riedl @markriedl.bsky.social · 31/01/2026
“We found that using AI assistance led to a statistically significant decrease in mastery.” Props to Anthropic for studying the effects of their creation and reporting results that are not probably what they wished for www.anthropic.com/research/AI-...
anthropic.com
How AI assistance impacts the formation of coding skills
Anthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems.
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Benjamin Ostendorf @ostendorflab.org · 31/01/2026
A fascinating finding on the therapeutic potential of targeting non-coding regions of MYC!
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Saloni @scientificdiscovery.dev · 28/12/2025
New post! There was a lot of innovation in medicine and biomedical research this year, and I've tried to summarize the biggest ones in this blogpost. Medical breakthroughs in 2025. Plus a serious note at the end. www.scientificdiscovery.dev/p/medical-br...
scientificdiscovery.dev
Medical breakthroughs in 2025
... and a happy new year.
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Benjamin Ostendorf @ostendorflab.org · 19/11/2025
Completely agree! Now I mainly wish for Prism and Flowjo replacements...
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Oded Rechavi @odedrechavi.bsky.social · 03/10/2025
Friday Papers Club! 🍿In light of Pubmed going down, the collapse of social media, and my recent success at getting recommendations for interesting papers from those still around, I am starting a new tradition! - Recommend a good scientific manuscript! 👇
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Adrian Liston @labliston.bsky.social · 19/09/2025
For our #flowcytometry peeps, would you like to have a single fix/perm protocol that is optimised for everything? One that preserves fluorophores while allowing simultaneous TF and cytokine staining? How about 100-fold cheaper? You got it: currentprotocols.onlinelibrary.wiley.com/doi/10.1002/...
currentprotocols.onlinelibrary.wiley.com
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John Doench @johndoench.bsky.social · 07/09/2025
Doomscrolling pause to chat CRISPR libraries! Preprint describes our new, data-driven approach to combine on-target and off-target predictions much more intelligently for *selecting* guides, which we use to develop our newest Cas9 knockout library, Jacquere. Thread: www.biorxiv.org/content/10.1...
biorxiv.org
Balancing off-target and on-target considerations for optimized Cas9 CRISPR knockout library design
The continued development of high-dimensional CRISPR screen readouts, such as single-cell RNA sequencing and high-content imaging, necessitates compact libraries to enable functional interrogation at ...
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Benjamin Ostendorf @ostendorflab.org · 03/09/2025
What a great thread on budgeting for an academic lab!!
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Dan Landau @landau.bsky.social · 14/08/2025
🧨Exciting new pre-print 🧨 Introducing ppmSeq - cost effective, scalable dual-strand 🧬🧬 sequencing. Scalability & ultra-low error in one! A game changer for somatic genome discovery science and cfDNA clinical apps. Check out thread for deets!
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Mathew Kiang @mathewkiang.com · 25/06/2025
Karolinska is looking for 20 (!!) assistant professors and offering 6 year appointments with ~1M USD startup packages. ki.se/en/about-ki/...
ki.se
Call for 20 Assistant Professor positions
Karolinska Institutet is a world-leading medical university with a long and proud history of ground-breaking research. We are now recruiting outstanding early-career researchers with particularly exce...
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Elizabeth McKenna @elizsmckenna.bsky.social · 22/07/2025
It's my first #newPI roll call on BlueSky! Calling all new #cancer PIs who just started or who are about to start their labs! Please say hi and what you work on so I can follow you if I don't already! 😃
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Nils Blüthgen @molsysbio.bsky.social · 22/07/2025
Different modes of resistance to RAS inhibitors unveiled by dual Erk reporters that monitor erk activity in the nucleus and the cytoplasm. Cool new paper led by Markus Morkel and Oleksandra Aust www.science.org/doi/10.1126/...
science.org
Reporter-based screening identifies RAS-RAF mutations as drivers of resistance to active-state RAS inhibitors in colorectal cancer
A cell-sorting approach reveals distinct modes of cancer resistance to active-state RAS inhibitors.
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Steffen E. Fuchs @steffenfuchs.bsky.social · 07/06/2025
We're very happy to invite you to the 𝟑𝐫𝐝 𝐘𝐨𝐮𝐧𝐠 𝐒𝐜𝐢𝐞𝐧𝐭𝐢𝐬𝐭 𝐂𝐚𝐧𝐜𝐞𝐫 𝐂𝐨𝐧𝐠𝐫𝐞𝐬𝐬 𝐚𝐭 𝐭𝐡𝐞 𝐅𝐫𝐞𝐧𝐜𝐡 𝐄𝐦𝐛𝐚𝐬𝐬𝐲 𝐢𝐧 𝐁𝐞𝐫𝐥𝐢𝐧 𝐨𝐧 𝐎𝐜𝐭𝐨𝐛𝐞𝐫 𝟗 &𝟏𝟎. Visit our website ys2c.org for further information.
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Dominic Grün @dominicgrun.bsky.social · 02/06/2025
We have an attractive opening for a tenure-track professorship in Single-Cell Systems Biology. Excellent package and infrastructure at @uni-wuerzburg.de Institute of Systems Immunology. Great place to live and work in the heart of the franconian wine region! jobs.sciencecareers.org/job/673667/j...
jobs.sciencecareers.org
junior professorship position (f/m/d) in Single-Cell Systems Biology - Würzburg (Stadt), Bayern (DE) job with Julius-Maximilians-University Würzburg - Faculty of Medicine | 673667
The Julius-Maximilians-University Würzburg, Faculty of Medicine is offering one junior professorship position (f/m/d) in Single-Cell Systems Biology.
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NEJM.org @nejm.org · 30/05/2025
Presented at #ASCO25: The addition of encorafenib and cetuximab to mFOLFOX6 chemotherapy improved outcomes in the primary treatment of metastatic BRAF V600E–mutated colorectal cancer. Full BREAKWATER phase 3 trial results:
nej.md
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Matt Coelho @mattcoelho.bsky.social · 22/04/2025
Excited to announce our preprint today @biorxivpreprint.bsky.social Using functional genomics, we map the genetic determinants cancer cell sensitivity to tumour-reactive T cells: www.biorxiv.org/content/10.1...
biorxiv.org
CRISPR screens in the context of immune selection identify CHD1 and MAP3K7 as mediators of cancer immunotherapy resistance
Cancer immunotherapy is only effective in a subset of patients, highlighting the need for effective biomarkers and combination therapies. Here we systematically identify genetic determinants of cancer...
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Benjamin Ostendorf @ostendorflab.org · 19/05/2025
Very happy that the first paper that started in our lab came out in @narjournal.bsky.social today ⭐🎊: BEscreen is a computational tool to design base editor sgRNA libraries for a broad range of use cases. It also allows for conveniently designing positive and negative controls and much more.
academic.oup.com
BEscreen: a versatile toolkit to design base editing libraries
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European Research Council (ERC) @erc.europa.eu · 07/02/2025
Hello, Bluesky! ☀️ We fund frontier research in Europe—bold ideas, unexpected discoveries and science that shapes the future. So it’s only fitting we’ve landed here. Sorry for being late. Follow us for updates on ERC funding, research policy, and our grantees' discoveries.
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Gaetano Gargiulo @ggargiul.bsky.social · 31/12/2024
End-of-the-year preprint & first 🧵 where the sky is blue! Ever wondered how a cancer driven by a single mutant oncogene becomes molecularly & cellularly heterogeneous? Why metastases share drivers w/primary tumors but are more aggressive?
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Our World in Data @ourworldindata.org · 09/12/2024
Americans are now one-third less likely to die from cancer at the same ages as Americans in 1990
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Leif Erik Sander 🇪🇺🇺🇦 @sanderlab.bsky.social · 06/12/2024
Look who‘s here
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Thorn-Seshold Lab @thornsesholdlab.bsky.social · 22/11/2024
Wishing the Elsevier editors who desk-accepted this all the best for their next career moves. doi.org/10.1016/j.ij...
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Anna Obenauf @obenaufa.bsky.social · 20/11/2024
Pls share 🌟Join the IMP as a Group Leader We are 👀 for a colleague, ready to lead a groundbreaking research program. Enjoy generous funding, outstanding facilities & a vibrant scientific community in one of the world's most livable cities @impvienna.bsky.social 👉https://tinyurl.com/impgl2025
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Christian Gaebler @cgaebler.bsky.social · 18/11/2024
🚨 One week left to apply! 🚨 Don’t miss the chance to join the Gaebler & Ibrahim Labs for a cutting-edge postdoc position at the intersection of viral immunology, virology & gene regulation. 👉Apply here charite.hrpuls.de/de/job-offer...
charite.hrpuls.de
Postdoctoral Scientist (d/f/m) in Life Sciences/Genetics
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Jon Coutts @joncoutts.bsky.social · 15/11/2024
These are such good feeds. Time to scroll? Stay on Following. Just catching up? Go Mutuals or Only Posts. Wondering if you missed someone? Go Quiet Posters
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Razvan Borza @rborza.bsky.social · 17/11/2024
Cancer Immunology: bsky.app/starter-pack... A repertoire of immunologists II: bsky.app/starter-pack... Immunometabolism: bsky.app/starter-pack... Immunoengineering: bsky.app/starter-pack... A repertoire of immunologists: bsky.app/starter-pack...
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Will Macnair @willmacnair.bsky.social · 15/11/2024
Restarting a previous discussion on here: How convinced are #SingleCell people by cell-cell communication methods? I'm still at "not very" 😅 I see them used everywhere, but I don't know of any really good way to validate them... More importantly, I don't know of any *non-simulated* training data.
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Benjamin Ostendorf @ostendorflab.org · 15/11/2024
another great cancer biology starter pack!
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Satpal (Sati) Jhujh @drjhujh.bsky.social · 15/11/2024
go.bsky.app/KxWyLE4 Trying to put together a starter pack for journals!
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AndreaVentura @andreaventura.bsky.social · 14/11/2024
First post here. Our lab at MSKCC studies how #cancer form. Hoping for a vibrant and safe place to talk #science, connect with fellow #scientists, and inform the public about science and rationality. Interested in #genome_editing, #ecDNAs, #non-coding RNAs, and #cancer_biology
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Magdalena Skipper @magdalenaskipper.bsky.social · 10/11/2024
This week in Nature - four papers probe the relationship between ecDNA & cancer * an atlas of ecDNA in cancer * ecDNA inheritance in cancer during cell division * a potential way to leverage ecDNA for treatment * ecDNA role in tumour evolution & therapy resistance www.nature.com/nature/volum...
nature.com
Nature - Outside influence
The cover shows circular extrachromosomal DNA (ecDNA) sitting next to a chromosome. ecDNA has a significant effect on the outcome of cancer treatment —...
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John Doench @johndoench.bsky.social · 13/11/2024
Here's another recent paper from the group describing the Fragmid resource, thread below. Paper is now published at Cell Genomics, and the kit is now available @addgene.bsky.social www.cell.com/cell-genomic... www.addgene.org/kits/doench-...
cell.com
Modular vector assembly enables rapid assessment of emerging CRISPR technologies
McGee et al. develop Fragmid, a modular toolkit and online portal for the creation of CRISPR vectors compatible with many delivery approaches, enzymes, and mechanisms. They also develop a set of posit...
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dan @danabra.mov · 08/11/2024
my main “bluesky tip” is simply — like and follow posts and people you enjoy seeing in your feed, and “show less” what you don’t enjoy. “training” Discover algorithm takes annoyingly long for now — but it does get more specific with time, and the team will be making it more responsive. data helps.
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Andreas Horn @andreashorn.org · 11/11/2024
Dear everyone, I am closing down my twitter handle today and will be here full time from now on. Also migrated @leaddbs.bsky.social @netstim.bsky.social, @stimbrains.bsky.social and @braincircuits.bsky.social Let's build a better world together!
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Piotr Jung-Sillah @jung-sillah.bsky.social · 09/11/2024
go.bsky.app/7xTwrrn
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Daniel MacArthur @dgmacarthur.bsky.social · 04/11/2024
Really excited to have this out: a cell type-specific map of the impact of an understudied class of genetic variation (tandem repeats) on gene expression, at serious scale: nearly 1800 people with both WGS and blood scRNA-seq. So much signal!
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Beth Cimini 🔬💻📊 @bethcimini.bsky.social · 08/11/2024
Another starter pack of fine fine folks - New PIs! We're all figuring it out together! Please do (self-)nominate go.bsky.app/KJXNgfZ
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