Evert Bosdriesz
@evertbosdriesz.bsky.social
assistant professor @VU Amsterdam | physicist turned computational biology | cancer biology | single cell | signal transduction
https://evertbosdriesz.github.io
https://evertbosdriesz.github.io
Pinned
Cell-state specific drug-responses are associated with differences in signaling network wiring
Intracellular signaling pathways form networks through which information is transmitted, often in the form of kinase-mediated phosphorylation events, to interpret extracellular signals and elicit appr...
www.biorxiv.org
Why do cells respond differently to the same perturbations, even if they are isogenic? Turns out that cell-state affects information flow through the intracellular signaling networks, which can affect the treatment response. New preprint with the lab of Klaas Mulder www.biorxiv.org/content/10.1...
Reposted by Evert Bosdriesz
There was never any point to having reference letters. That's why we've all started using AI to do this nonesense task.
References should only be used for short-listed candidates for important positions/awards, and ideally, be done via a call to get the most honest opinion possible.
References should only be used for short-listed candidates for important positions/awards, and ideally, be done via a call to get the most honest opinion possible.
From my discussions with other faculty, the use of generative AI I hear about the most is writing reference letters.
What's the point of having reference letters anymore if everyone is just having them written by machine?
What's the point of having reference letters anymore if everyone is just having them written by machine?
November 14, 2025 at 7:10 PM
There was never any point to having reference letters. That's why we've all started using AI to do this nonesense task.
References should only be used for short-listed candidates for important positions/awards, and ideally, be done via a call to get the most honest opinion possible.
References should only be used for short-listed candidates for important positions/awards, and ideally, be done via a call to get the most honest opinion possible.
Reposted by Evert Bosdriesz
Beyond excited to share my first work with Omer's group at Sanger!
With amazing co-authors Alexander & Fani we are passionate about neurodevelopmental genetics and this work really showed us the power of uncovering new genetics with spatial transcriptomics!
🧵👇 Background / motivation / key results
With amazing co-authors Alexander & Fani we are passionate about neurodevelopmental genetics and this work really showed us the power of uncovering new genetics with spatial transcriptomics!
🧵👇 Background / motivation / key results
Which human brain circuits are implicated in neurodevelopmental conditions? We bridged human genetics, spatial transcriptomics and neurodevelopment to discover the convergence of autism-associated genes in the developing human thalamus! www.biorxiv.org/content/10.1...
November 11, 2025 at 9:00 PM
Beyond excited to share my first work with Omer's group at Sanger!
With amazing co-authors Alexander & Fani we are passionate about neurodevelopmental genetics and this work really showed us the power of uncovering new genetics with spatial transcriptomics!
🧵👇 Background / motivation / key results
With amazing co-authors Alexander & Fani we are passionate about neurodevelopmental genetics and this work really showed us the power of uncovering new genetics with spatial transcriptomics!
🧵👇 Background / motivation / key results
Reposted by Evert Bosdriesz
We're going to see a lot of bullshit in the coming days and weeks about "causes of autism", and most will be based on flawed, over-interpreted observational studies (1/n)
September 7, 2025 at 10:57 AM
We're going to see a lot of bullshit in the coming days and weeks about "causes of autism", and most will be based on flawed, over-interpreted observational studies (1/n)
Reposted by Evert Bosdriesz
Dear universities,
I am begging you to stop requiring letters of recommendation for master's programmes. You and I both know you don't read them, so stop asking for them.
Instead, have applicants list a name and get in touch if it's a borderline case.
Signed,
Everyone.
I am begging you to stop requiring letters of recommendation for master's programmes. You and I both know you don't read them, so stop asking for them.
Instead, have applicants list a name and get in touch if it's a borderline case.
Signed,
Everyone.
July 28, 2025 at 6:28 PM
Dear universities,
I am begging you to stop requiring letters of recommendation for master's programmes. You and I both know you don't read them, so stop asking for them.
Instead, have applicants list a name and get in touch if it's a borderline case.
Signed,
Everyone.
I am begging you to stop requiring letters of recommendation for master's programmes. You and I both know you don't read them, so stop asking for them.
Instead, have applicants list a name and get in touch if it's a borderline case.
Signed,
Everyone.
Reposted by Evert Bosdriesz
This Nakba Remembrance Day, instead of silencing voices in support of Palestinian human rights, the EU and all states must act and stop the genocide.
May 15, 2025 at 1:17 PM
This Nakba Remembrance Day, instead of silencing voices in support of Palestinian human rights, the EU and all states must act and stop the genocide.
Reposted by Evert Bosdriesz
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...
I'm so excited about this!
www.biorxiv.org/content/10.1...
Bonsai: Tree representations for distortion-free visualization and exploratory analysis of single-cell omics data
Single-cell omics methods promise to revolutionize our understanding of gene regulatory processes during cell differentiation, but analysis of such data continues to pose a major challenge. Apart from...
www.biorxiv.org
May 9, 2025 at 10:49 AM
Here it is! Bonsai. Now there is really no more excuse for using t-SNE/UMAP. Bonsai not only makes cool pictures of your data. It actually rigorously preserves its structure. No tunable parameters. Incredible work by @dhdegroot.bsky.social.
I'm so excited about this!
www.biorxiv.org/content/10.1...
I'm so excited about this!
www.biorxiv.org/content/10.1...
Wow! What an elegant/simple growth optimizing mechanism.
The most profound insights are often also the most simple:
growth-rate, by setting the dilution rate of intra-cellular molecules, controls the sensitivity of gene regulatory circuits. In retrospect it seems crazy that this effect seems to have been overlooked so far.
www.science.org/doi/10.1126/...
growth-rate, by setting the dilution rate of intra-cellular molecules, controls the sensitivity of gene regulatory circuits. In retrospect it seems crazy that this effect seems to have been overlooked so far.
www.science.org/doi/10.1126/...
Growth rate controls the sensitivity of gene regulatory circuits
Through the simple effect of dilution rate, regulatory circuits systematically change their sensitivity with growth rate.
www.science.org
May 1, 2025 at 3:22 PM
Wow! What an elegant/simple growth optimizing mechanism.
Reposted by Evert Bosdriesz
Heard from a former (undergrad) student who just defended her PhD. Students: tell your old profs about your successes and achievements. It's not bragging, and we love to hear about it. It's one of the best parts of being an educator.
#academicsky
#academicsky
April 26, 2025 at 12:36 PM
Heard from a former (undergrad) student who just defended her PhD. Students: tell your old profs about your successes and achievements. It's not bragging, and we love to hear about it. It's one of the best parts of being an educator.
#academicsky
#academicsky
Reposted by Evert Bosdriesz
A large study in Sweden found levels of autism *symptoms* were constant over time, even as autism *diagnoses* increased (implying broadening diagnostic criteria rather than real underlying increase) www.bmj.com/content/350/...
Autism phenotype versus registered diagnosis in Swedish children: prevalence trends over 10 years in general population samples
Objective To compare the annual prevalence of the autism symptom phenotype and of registered diagnoses for autism spectrum disorder during a 10 year period in children.
Design Population based study....
www.bmj.com
April 11, 2025 at 1:14 PM
A large study in Sweden found levels of autism *symptoms* were constant over time, even as autism *diagnoses* increased (implying broadening diagnostic criteria rather than real underlying increase) www.bmj.com/content/350/...
Reposted by Evert Bosdriesz
"Your job is to have ideas and spread them so that they impact other people’s work. Writing is your job. Nothing else. Therefore, everything else that you do is subservient to the activity of writing. Let this revolution take place in your mind."
www.nature.com/articles/s41...
www.nature.com/articles/s41...
An open letter to graduate students and other procrastinators: it’s time to write - Nature Biotechnology
Nature Biotechnology - An open letter to graduate students and other procrastinators: it’s time to write
www.nature.com
March 20, 2025 at 2:51 AM
"Your job is to have ideas and spread them so that they impact other people’s work. Writing is your job. Nothing else. Therefore, everything else that you do is subservient to the activity of writing. Let this revolution take place in your mind."
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Evert Bosdriesz
How do embryos ensure precise tissue patterning? It’s all about timing cell divisions! Our new preprint reveals how cell proliferation syncs with signaling oscillations to regulate precision of somite formation and growth. Check the full story: www.biorxiv.org/content/10.1...
March 11, 2025 at 12:29 PM
How do embryos ensure precise tissue patterning? It’s all about timing cell divisions! Our new preprint reveals how cell proliferation syncs with signaling oscillations to regulate precision of somite formation and growth. Check the full story: www.biorxiv.org/content/10.1...
Reposted by Evert Bosdriesz
Europe as “a haven” for US researcher - The EU’s research funding bodies are thinking of ways to welcome US scientists and European ex-patriots who might be looking for a more sympathetic place to work now that Donald Trump is in the White House
#AcademicSky 🧪
sciencebusiness.net/internationa...
#AcademicSky 🧪
sciencebusiness.net/internationa...
Europe could be a ‘haven’ for US researchers, says ERC president
The EU’s research funding bodies are thinking of ways to welcome US scientists and European ex-patriots who might be looking for a more sympathetic place to work now that Donald Trump is in the White ...
sciencebusiness.net
February 28, 2025 at 4:01 PM
Europe as “a haven” for US researcher - The EU’s research funding bodies are thinking of ways to welcome US scientists and European ex-patriots who might be looking for a more sympathetic place to work now that Donald Trump is in the White House
#AcademicSky 🧪
sciencebusiness.net/internationa...
#AcademicSky 🧪
sciencebusiness.net/internationa...
Reposted by Evert Bosdriesz
Decoupling.
🇺🇲 Google ---> 🇪🇺 Ecosia
🇺🇲 Chrome ---> 🇪🇺 Vivaldi
🇺🇲 Translate ---> 🇪🇺 DeepL
🇺🇲 Gmail ---> 🇪🇺 Mailfence
🇺🇲 Maps ---> 🇪🇺 Here WeGo
🇺🇲 ChatGPT ---> 🇪🇺 Le Chat
🇺🇲 Chrome ---> 🇪🇺 Vivaldi
🇺🇲 Translate ---> 🇪🇺 DeepL
🇺🇲 Gmail ---> 🇪🇺 Mailfence
🇺🇲 Maps ---> 🇪🇺 Here WeGo
🇺🇲 ChatGPT ---> 🇪🇺 Le Chat
March 1, 2025 at 8:11 AM
Decoupling.
Reposted by Evert Bosdriesz
The analogy of omics data normalization and cooking:
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.
February 27, 2025 at 8:01 AM
The analogy of omics data normalization and cooking:
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.
some processing is usually necessary, overcooking makes it bland, highly over-processed foods are unhealthy, and the quality of the ingredients matters.
Reposted by Evert Bosdriesz
Sad to know about the passing of Béla Novák. This review from Tyson, Chen and Novak was such a revelation for me as an introduction to control theory in biological systems. A classic that will remain relevant for many years to come. www.sciencedirect.com/science/arti...
February 25, 2025 at 6:30 PM
Sad to know about the passing of Béla Novák. This review from Tyson, Chen and Novak was such a revelation for me as an introduction to control theory in biological systems. A classic that will remain relevant for many years to come. www.sciencedirect.com/science/arti...
Reposted by Evert Bosdriesz
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
February 8, 2025 at 9:21 PM
It’s been a tough few weeks. My 10yo daughter was diagnosed with a very rare, aggressive cancer called interdigitating dendritic cell sarcoma (IDCS). I’m reaching out to identify clinicians/patients who have encountered pediatric IDCS or other (non-LCH) dendritic or histiocytic sarcomas cases.
Reposted by Evert Bosdriesz
Happy to share this concise review and outlook for single-cell sequencing methods to unravel cell biology of the nucleus! Big shoutout to my friend and former colleague Peter Zeller for sharing the work!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Shining a light on cell biology of the nucleus with single-cell sequencing
From the preservation of genomic integrity to the regulation of RNA translation, nearly all cellular processes are regulated in a cell context-depende…
www.sciencedirect.com
February 4, 2025 at 7:27 AM
Happy to share this concise review and outlook for single-cell sequencing methods to unravel cell biology of the nucleus! Big shoutout to my friend and former colleague Peter Zeller for sharing the work!
www.sciencedirect.com/science/arti...
www.sciencedirect.com/science/arti...
Reposted by Evert Bosdriesz
Our paper on Stopless-ORF Circular RNAs (socRNAs) is now out in Cell. By high-res tracking and comparing translation by either single or multiple ribosomes, we find that ribosomes cooperate to overcome pausing to ensure fast and efficient translation
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Long-term imaging of individual ribosomes reveals ribosome cooperativity in mRNA translation
Ribosomes cooperate through transient collisions to ensure efficient translation.
www.cell.com
February 3, 2025 at 7:38 AM
Our paper on Stopless-ORF Circular RNAs (socRNAs) is now out in Cell. By high-res tracking and comparing translation by either single or multiple ribosomes, we find that ribosomes cooperate to overcome pausing to ensure fast and efficient translation
www.cell.com/cell/fulltex...
www.cell.com/cell/fulltex...
Reposted by Evert Bosdriesz
Why do cells respond differently to the same perturbations, even if they are isogenic? Turns out that cell-state affects information flow through the intracellular signaling networks, which can affect the treatment response. New preprint with the lab of Klaas Mulder www.biorxiv.org/content/10.1...
Cell-state specific drug-responses are associated with differences in signaling network wiring
Intracellular signaling pathways form networks through which information is transmitted, often in the form of kinase-mediated phosphorylation events, to interpret extracellular signals and elicit appr...
www.biorxiv.org
January 31, 2025 at 4:12 PM
Why do cells respond differently to the same perturbations, even if they are isogenic? Turns out that cell-state affects information flow through the intracellular signaling networks, which can affect the treatment response. New preprint with the lab of Klaas Mulder www.biorxiv.org/content/10.1...
Why do cells respond differently to the same perturbations, even if they are isogenic? Turns out that cell-state affects information flow through the intracellular signaling networks, which can affect the treatment response. New preprint with the lab of Klaas Mulder www.biorxiv.org/content/10.1...
Cell-state specific drug-responses are associated with differences in signaling network wiring
Intracellular signaling pathways form networks through which information is transmitted, often in the form of kinase-mediated phosphorylation events, to interpret extracellular signals and elicit appr...
www.biorxiv.org
January 31, 2025 at 4:12 PM
Why do cells respond differently to the same perturbations, even if they are isogenic? Turns out that cell-state affects information flow through the intracellular signaling networks, which can affect the treatment response. New preprint with the lab of Klaas Mulder www.biorxiv.org/content/10.1...
Reposted by Evert Bosdriesz
The FT reports OpenAI suspects DeepSeek of "a potential breach of intellectual property." As a columnist for NYT, which is suing OpenAI for copyright infringement, and the author of nine books OpenAI apparently used to train its model, I couldn't possibly comment. www.ft.com/content/a0df...
OpenAI says it has evidence China’s DeepSeek used its model to train competitor
White House AI tsar David Sacks raises possibility of alleged intellectual property theft
www.ft.com
January 29, 2025 at 2:06 PM
The FT reports OpenAI suspects DeepSeek of "a potential breach of intellectual property." As a columnist for NYT, which is suing OpenAI for copyright infringement, and the author of nine books OpenAI apparently used to train its model, I couldn't possibly comment. www.ft.com/content/a0df...
Reposted by Evert Bosdriesz
Cell-state specific drug-responses are associated with differences in signaling network wiring. https://www.biorxiv.org/content/10.1101/2025.01.27.635060v1
January 28, 2025 at 6:07 PM
Cell-state specific drug-responses are associated with differences in signaling network wiring. https://www.biorxiv.org/content/10.1101/2025.01.27.635060v1
Reposted by Evert Bosdriesz
How long does an mRNA stay in the nucleus? How long does it stay in the cytoplasm? In an amazing collaboration with @landthalerm.bsky.social, we used metabolic labeling, cell fractionation and mathematical modeling to quantify mRNA flow through the cell. Finally out in MSB: doi.org/10.1038/s443...
November 21, 2024 at 2:56 PM
How long does an mRNA stay in the nucleus? How long does it stay in the cytoplasm? In an amazing collaboration with @landthalerm.bsky.social, we used metabolic labeling, cell fractionation and mathematical modeling to quantify mRNA flow through the cell. Finally out in MSB: doi.org/10.1038/s443...
Reposted by Evert Bosdriesz
Interesting thread from Carl on reproducibility strategies. His point that the issues in oncology =/ those in psychology etc echo my own conclusions from talking to people in the field
Otherwise we risk crushing ourselves under the weight of yet more self-imposed bureaucracy.
Core CoS strategies may get at why papers fail replicate in social psych, but oncologists I spent many days talking to think cancer biology papers fail to replicate for a very different set of reasons.
Core CoS strategies may get at why papers fail replicate in social psych, but oncologists I spent many days talking to think cancer biology papers fail to replicate for a very different set of reasons.
September 26, 2024 at 10:28 AM
Interesting thread from Carl on reproducibility strategies. His point that the issues in oncology =/ those in psychology etc echo my own conclusions from talking to people in the field
Reposted by Evert Bosdriesz
There's a lot of excitement about foundation models and their ability to learn biology 🧬💻
But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress.
www.biorxiv.org/content/10.1...
But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress.
www.biorxiv.org/content/10.1...
September 20, 2024 at 9:39 AM
There's a lot of excitement about foundation models and their ability to learn biology 🧬💻
But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress.
www.biorxiv.org/content/10.1...
But current tools for perturbation prediction perform worse than simple linear models! We need more careful benchmarking to make progress.
www.biorxiv.org/content/10.1...