Benjamin Ostendorf
@ostendorflab.org
Physician scientist @ChariteBerlin.
Interested in tumor immunology, systems biology, and cancer biology.
Lab website: www.ostendorflab.org
Interested in tumor immunology, systems biology, and cancer biology.
Lab website: www.ostendorflab.org
Pinned
Benjamin Ostendorf
@ostendorflab.org
· May 19
BEscreen: a versatile toolkit to design base editing libraries
academic.oup.com
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.
Reposted by Benjamin Ostendorf
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! 👇
October 3, 2025 at 9:10 AM
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! 👇
Reposted by Benjamin Ostendorf
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/...
You got it:
currentprotocols.onlinelibrary.wiley.com/doi/10.1002/...
currentprotocols.onlinelibrary.wiley.com
September 19, 2025 at 2:39 PM
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/...
You got it:
currentprotocols.onlinelibrary.wiley.com/doi/10.1002/...
Reposted by Benjamin Ostendorf
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...
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 ...
www.biorxiv.org
September 7, 2025 at 5:02 PM
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...
What a great thread on budgeting for an academic lab!!
🧵How to write and manage your first research budgets
The point of funding is to convert it into quality research. A well-spent research budget should fund the idea it was raised on, plus revision experiments, plus preliminary data for the next grant. So you need to spend, while avoiding waste.
The point of funding is to convert it into quality research. A well-spent research budget should fund the idea it was raised on, plus revision experiments, plus preliminary data for the next grant. So you need to spend, while avoiding waste.
September 3, 2025 at 7:24 PM
What a great thread on budgeting for an academic lab!!
Reposted by Benjamin Ostendorf
🧨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!
Highly accurate sequencing OR high throughput? We refuse to choose.
Introducing ppmSeq, a method built to deliver both. Our latest from the @landau.bsky.social lab with Ultima Genomics
👀👀👀
See ⬇️ for a primer on the next frontier of genomics
www.biorxiv.org/content/10.1...
Introducing ppmSeq, a method built to deliver both. Our latest from the @landau.bsky.social lab with Ultima Genomics
👀👀👀
See ⬇️ for a primer on the next frontier of genomics
www.biorxiv.org/content/10.1...
Paired plus-minus sequencing is an ultra-high throughput and accurate method for dual strand sequencing of DNA molecules
Distinguishing real biological variation in the form of single-nucleotide variants (SNVs) from errors is a major challenge for genome sequencing technologies. This is particularly true in settings whe...
www.biorxiv.org
August 14, 2025 at 6:11 PM
🧨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!
Reposted by Benjamin Ostendorf
Karolinska is looking for 20 (!!) assistant professors and offering 6 year appointments with ~1M USD startup packages.
ki.se/en/about-ki/...
ki.se/en/about-ki/...
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...
ki.se
June 25, 2025 at 2:56 PM
Karolinska is looking for 20 (!!) assistant professors and offering 6 year appointments with ~1M USD startup packages.
ki.se/en/about-ki/...
ki.se/en/about-ki/...
Reposted by Benjamin Ostendorf
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/...
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.
www.science.org
July 22, 2025 at 7:55 PM
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/...
Reposted by Benjamin Ostendorf
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.
Visit our website ys2c.org for further information.
June 7, 2025 at 11:43 AM
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.
Visit our website ys2c.org for further information.
Reposted by Benjamin Ostendorf
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/job/673667/j...
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.
jobs.sciencecareers.org
June 2, 2025 at 9:29 AM
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/job/673667/j...
Reposted by Benjamin Ostendorf
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:
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
May 30, 2025 at 9:05 AM
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:
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:
Reposted by Benjamin Ostendorf
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...
Using functional genomics, we map the genetic determinants cancer cell sensitivity to tumour-reactive T cells:
www.biorxiv.org/content/10.1...
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...
www.biorxiv.org
April 22, 2025 at 7:56 AM
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...
Using functional genomics, we map the genetic determinants cancer cell sensitivity to tumour-reactive T cells:
www.biorxiv.org/content/10.1...
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.
BEscreen: a versatile toolkit to design base editing libraries
academic.oup.com
May 19, 2025 at 7:21 PM
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.
Reposted by Benjamin Ostendorf
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.
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.
February 7, 2025 at 8:16 AM
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.
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.
Reposted by Benjamin Ostendorf
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?
December 31, 2024 at 1:12 PM
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?
Reposted by Benjamin Ostendorf
Americans are now one-third less likely to die from cancer at the same ages as Americans in 1990
December 9, 2024 at 4:36 PM
Americans are now one-third less likely to die from cancer at the same ages as Americans in 1990
Reposted by Benjamin Ostendorf
Look who‘s here
December 6, 2024 at 9:01 PM
Look who‘s here
Reposted by Benjamin Ostendorf
Wishing the Elsevier editors who desk-accepted this all the best for their next career moves.
doi.org/10.1016/j.ij...
doi.org/10.1016/j.ij...
November 22, 2024 at 2:49 PM
Wishing the Elsevier editors who desk-accepted this all the best for their next career moves.
doi.org/10.1016/j.ij...
doi.org/10.1016/j.ij...
Reposted by Benjamin Ostendorf
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
November 20, 2024 at 10:46 AM
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
Reposted by Benjamin Ostendorf
🚨 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...
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...
November 18, 2024 at 9:18 AM
🚨 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...
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...
Reposted by Benjamin Ostendorf
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
Those new to bluesky will likely want to know about these Feeds. Just find em and pin em
November 15, 2024 at 2:06 AM
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
Reposted by Benjamin Ostendorf
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...
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...
November 17, 2024 at 7:41 PM
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...
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...
Reposted by Benjamin Ostendorf
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.
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.
November 15, 2024 at 10:27 AM
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.
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.
another great cancer biology starter pack!
Here's some new additions to this #Cancer #Research 🧪🔬⚕️🩺 starter pack!
@marinelab.bsky.social
@leilaakkari.bsky.social
@carolynbertozzi.bsky.social
@lydiafinley.bsky.social
@ibcradiation.bsky.social
and many more..
I also included some starting #PIs - welcome to you all & do give them a follow!
@marinelab.bsky.social
@leilaakkari.bsky.social
@carolynbertozzi.bsky.social
@lydiafinley.bsky.social
@ibcradiation.bsky.social
and many more..
I also included some starting #PIs - welcome to you all & do give them a follow!
Inspired by the other amazing starter packs - here's one for cancer researchers!
I tried to make this broad - from immunology to genomics to cell biology and so much more..
This list also includes organizations & institutes supporting cancer researchers 🧪🔬⚕️🩺
Hope its useful!
go.bsky.app/FEoaJMc
I tried to make this broad - from immunology to genomics to cell biology and so much more..
This list also includes organizations & institutes supporting cancer researchers 🧪🔬⚕️🩺
Hope its useful!
go.bsky.app/FEoaJMc
November 15, 2024 at 7:22 PM
another great cancer biology starter pack!
Reposted by Benjamin Ostendorf
November 15, 2024 at 7:44 AM