Reposted by Benjamin OstendorfDani León-Periñán @danilexn.bsky.social · 26/08/2026Malva 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. 1207
Reposted by Benjamin OstendorfChristian Zierhut @zierlab.bsky.social · 21/08/2026Supremely 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.comA versatile cGAMP reporter reveals principles of cGAS activation by DNA damage and chromosome instability - Nature Cell BiologyLebrec 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... 97030
Reposted by Benjamin OstendorfMiguel Reina-Campos @reinacampos.bsky.social · 03/08/2026FITdb, 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.orgbiorxiv.orgFITdb, an Integrated Functional Immunogenomics and Transcriptomics DatabaseGenetic 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... 042
Reposted by Benjamin OstendorfEuropean Commission @ec.europa.eu · 01/08/2026Japan 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 6642158
Reposted by Benjamin OstendorfAydan Bulut-Karslioglu @bulutkarslioglu.bsky.social · 26/06/2026I 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 610931
Reposted by Benjamin OstendorfRichard 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.orgThe 1% club and the rocky road ahead for bioRxivThe 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… 26024
Reposted by Benjamin OstendorfNEJM.org @nejm.org · 31/05/2026Among 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 15030
Benjamin Ostendorf @ostendorflab.org · 30/04/2026Regarding 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 featurescommunity.findingsapp.comFindings 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 ... 010
Reposted by Benjamin OstendorfOur World in Data @ourworldindata.org · 11/03/2026The 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. 🧵 311641
Reposted by Benjamin OstendorfThe Rockefeller University @rockefeller.edu · 05/03/2026A 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 164
Reposted by Benjamin OstendorfJournal 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 042
Benjamin Ostendorf @ostendorflab.org · 10/02/2026Delighted 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.orgLiver-X-receptor agonism enhances T cell priming and activation to promote anti-tumor immunityOstendorf et al. show that activation of liver-X-receptors preconditions T cells to render them more receptive to adopting effector states upon activation. 4124
Reposted by Benjamin OstendorfClaudi 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 28karriere.charite.deWissenschaftliche Mitarbeiterin/ Wissenschaftlicher Mitarbeiter (d/w/m) /DoktorandInTeilzeit | 28.02.2026 | Campus Virchow-Klinikum, Wedding 051
Reposted by Benjamin OstendorfMark 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.comHow AI assistance impacts the formation of coding skillsAnthropic is an AI safety and research company that's working to build reliable, interpretable, and steerable AI systems. 14508183
Benjamin Ostendorf @ostendorflab.org · 31/01/2026A fascinating finding on the therapeutic potential of targeting non-coding regions of MYC! 051
Reposted by Benjamin OstendorfSaloni @scientificdiscovery.dev · 28/12/2025New 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.devMedical breakthroughs in 2025... and a happy new year. 14261113
Benjamin Ostendorf @ostendorflab.org · 19/11/2025Completely agree! Now I mainly wish for Prism and Flowjo replacements... 020
Reposted by Benjamin OstendorfOded Rechavi @odedrechavi.bsky.social · 03/10/2025Friday 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! 👇 157722
Reposted by Benjamin OstendorfAdrian Liston @labliston.bsky.social · 19/09/2025For 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 1015869
Reposted by Benjamin OstendorfJohn Doench @johndoench.bsky.social · 07/09/2025Doomscrolling 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.orgBalancing off-target and on-target considerations for optimized Cas9 CRISPR knockout library designThe 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 ... 27524
Benjamin Ostendorf @ostendorflab.org · 03/09/2025What a great thread on budgeting for an academic lab!! 041
Reposted by Benjamin OstendorfDan 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! 0225
Reposted by Benjamin OstendorfMathew Kiang @mathewkiang.com · 25/06/2025Karolinska is looking for 20 (!!) assistant professors and offering 6 year appointments with ~1M USD startup packages. ki.se/en/about-ki/...ki.seCall for 20 Assistant Professor positionsKarolinska 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... 1278277
Reposted by Benjamin OstendorfElizabeth McKenna @elizsmckenna.bsky.social · 22/07/2025It'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! 😃 02711
Reposted by Benjamin OstendorfNils Blüthgen @molsysbio.bsky.social · 22/07/2025Different 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.orgReporter-based screening identifies RAS-RAF mutations as drivers of resistance to active-state RAS inhibitors in colorectal cancerA cell-sorting approach reveals distinct modes of cancer resistance to active-state RAS inhibitors. 172
Reposted by Benjamin OstendorfSteffen E. Fuchs @steffenfuchs.bsky.social · 07/06/2025We'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. 1169
Reposted by Benjamin OstendorfDominic Grün @dominicgrun.bsky.social · 02/06/2025We 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.orgjunior professorship position (f/m/d) in Single-Cell Systems Biology - Würzburg (Stadt), Bayern (DE) job with Julius-Maximilians-University Würzburg - Faculty of Medicine | 673667The Julius-Maximilians-University Würzburg, Faculty of Medicine is offering one junior professorship position (f/m/d) in Single-Cell Systems Biology. 01015
Reposted by Benjamin OstendorfNEJM.org @nejm.org · 30/05/2025Presented 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 1239
Reposted by Benjamin OstendorfMatt Coelho @mattcoelho.bsky.social · 22/04/2025Excited 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.orgCRISPR screens in the context of immune selection identify CHD1 and MAP3K7 as mediators of cancer immunotherapy resistanceCancer 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... 165
Benjamin Ostendorf @ostendorflab.org · 19/05/2025Very 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.comBEscreen: a versatile toolkit to design base editing libraries 4142
Reposted by Benjamin OstendorfEuropean Research Council (ERC) @erc.europa.eu · 07/02/2025Hello, 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. 411111375
Reposted by Benjamin OstendorfGaetano Gargiulo @ggargiul.bsky.social · 31/12/2024End-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? 3288
Reposted by Benjamin OstendorfOur World in Data @ourworldindata.org · 09/12/2024Americans are now one-third less likely to die from cancer at the same ages as Americans in 1990 414743
Reposted by Benjamin OstendorfLeif Erik Sander 🇪🇺🇺🇦 @sanderlab.bsky.social · 06/12/2024Look who‘s here 1307
Reposted by Benjamin OstendorfThorn-Seshold Lab @thornsesholdlab.bsky.social · 22/11/2024Wishing the Elsevier editors who desk-accepted this all the best for their next career moves. doi.org/10.1016/j.ij... 1021492505
Reposted by Benjamin OstendorfAnna 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 210399
Reposted by Benjamin OstendorfChristian 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.dePostdoctoral Scientist (d/f/m) in Life Sciences/Genetics 11311
Reposted by Benjamin OstendorfJon Coutts @joncoutts.bsky.social · 15/11/2024These 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 22588197
Reposted by Benjamin OstendorfRazvan Borza @rborza.bsky.social · 17/11/2024Cancer 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... 24026
Reposted by Benjamin OstendorfWill Macnair @willmacnair.bsky.social · 15/11/2024Restarting 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. 154918
Reposted by Benjamin OstendorfSatpal (Sati) Jhujh @drjhujh.bsky.social · 15/11/2024go.bsky.app/KxWyLE4 Trying to put together a starter pack for journals! 109437
Reposted by Benjamin OstendorfAndreaVentura @andreaventura.bsky.social · 14/11/2024First 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 191
Reposted by Benjamin OstendorfMagdalena Skipper @magdalenaskipper.bsky.social · 10/11/2024This 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.comNature - Outside influenceThe cover shows circular extrachromosomal DNA (ecDNA) sitting next to a chromosome. ecDNA has a significant effect on the outcome of cancer treatment —... 072
Reposted by Benjamin OstendorfJohn Doench @johndoench.bsky.social · 13/11/2024Here'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.comModular vector assembly enables rapid assessment of emerging CRISPR technologiesMcGee 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... 2144
Reposted by Benjamin Ostendorfdan @danabra.mov · 08/11/2024my 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. 462659343
Reposted by Benjamin OstendorfAndreas Horn @andreashorn.org · 11/11/2024Dear 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! 0145
Reposted by Benjamin OstendorfPiotr Jung-Sillah @jung-sillah.bsky.social · 09/11/2024go.bsky.app/7xTwrrn 13911076
Reposted by Benjamin OstendorfDaniel MacArthur @dgmacarthur.bsky.social · 04/11/2024Really 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! 1143
Reposted by Benjamin OstendorfBeth Cimini 🔬💻📊 @bethcimini.bsky.social · 08/11/2024Another starter pack of fine fine folks - New PIs! We're all figuring it out together! Please do (self-)nominate go.bsky.app/KJXNgfZ 99157111