Someone call the visualization police 🚨
November 29, 2025 at 6:17 AM
Someone call the visualization police 🚨
My university teaches stats but not logic and honestly they could do with some jaynes
One way I am quite philosophically conservative is I do basically think that knowledge of logic (like the traditional discipline including in its modern mathematical format) makes one better at following and reconstructing ordinary language arguments, and thus should be mandatory for grad students.
November 27, 2025 at 6:30 AM
My university teaches stats but not logic and honestly they could do with some jaynes
I learned about Nyguist-Shannon ~1year ago and now firmly believe everyone designing time series experiments should know this. I hardly see it being discussed in transcriptomics…
1/2
New open access paper in which we apply the Nyquist-Shannon thereom from signal processing to 2 EMA datasets to figure out the optimal sampling frequency for EMA assessments.
🧪 #psychscisky #statssky
www.cambridge.org/core/journal...
New open access paper in which we apply the Nyquist-Shannon thereom from signal processing to 2 EMA datasets to figure out the optimal sampling frequency for EMA assessments.
🧪 #psychscisky #statssky
www.cambridge.org/core/journal...
Optimizing the frequency of ecological momentary assessments using signal processing | Psychological Medicine | Cambridge Core
Optimizing the frequency of ecological momentary assessments using signal processing - Volume 55
www.cambridge.org
November 27, 2025 at 6:20 AM
I learned about Nyguist-Shannon ~1year ago and now firmly believe everyone designing time series experiments should know this. I hardly see it being discussed in transcriptomics…
Reposted by Rens Holmer
The kinds of databases:
• Fancy files
• 1970s stays winning
• This would be so cool if it worked at scale
• Oh, that's why google has a monopoly on search
• Fancy files
• 1970s stays winning
• This would be so cool if it worked at scale
• Oh, that's why google has a monopoly on search
November 27, 2025 at 12:26 AM
The kinds of databases:
• Fancy files
• 1970s stays winning
• This would be so cool if it worked at scale
• Oh, that's why google has a monopoly on search
• Fancy files
• 1970s stays winning
• This would be so cool if it worked at scale
• Oh, that's why google has a monopoly on search
Reposted by Rens Holmer
We (Nordborg & Weigel labs) need input on the next generation of genome browsers & data download modes for the #Arabidopsis #1001GenomesPlus project. We have now a curated collection of over 500 long read genomes.
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Next generation of 1001 Genomes Plus browser and data download
Please indicate all features you would like to see in a browser that displays features of completely sequenced Arabidopsis thaliana genomes
docs.google.com
November 24, 2025 at 2:49 PM
We (Nordborg & Weigel labs) need input on the next generation of genome browsers & data download modes for the #Arabidopsis #1001GenomesPlus project. We have now a curated collection of over 500 long read genomes.
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Please help us by filling out this questionnaire: docs.google.com/forms/d/e/1F...
Reposted by Rens Holmer
Live your life in a way that quotations like these don't show up in your obituary.
November 10, 2025 at 5:54 PM
Live your life in a way that quotations like these don't show up in your obituary.
If ever you needed evidence of dot com 2.0
Scientists just called out Ursula von der Leyen for claiming that AI will match human reasoning by 2026. Her "evidence" consisted, it turns out, of CEO statements from OpenAI, Anthropic and Nvidia. Not research. Marketing materials. 🧵
#AI #PublicServices #TechHype #Politics #NHS #EUPolitics
#AI #PublicServices #TechHype #Politics #NHS #EUPolitics
November 10, 2025 at 5:56 PM
If ever you needed evidence of dot com 2.0
Students should absolutely have a say in evaluating their education, but standardized forms measure overall satisfaction/mood and are not a good indicator of quality
In this commentary, I argue that student-based teaching evaluations are problematic bc
✳️ systematic biases (e.g., racism, sexism)
✳️ poor construct validity
✳️ undermine standards and learning
We should evaluate teaching as seriously as we do research. Or don't do teaching evaluations.
✳️ systematic biases (e.g., racism, sexism)
✳️ poor construct validity
✳️ undermine standards and learning
We should evaluate teaching as seriously as we do research. Or don't do teaching evaluations.
It is time to abandon student evaluations of teaching
Comment by Gordon Hodson (@gordonhodsonphd.bsky.social)
Web: go.nature.com/4jfAzXo
PDF: rdcu.be/ef9y5
Comment by Gordon Hodson (@gordonhodsonphd.bsky.social)
Web: go.nature.com/4jfAzXo
PDF: rdcu.be/ef9y5
November 2, 2025 at 8:44 AM
Students should absolutely have a say in evaluating their education, but standardized forms measure overall satisfaction/mood and are not a good indicator of quality
Reposted by Rens Holmer
In this commentary, I argue that student-based teaching evaluations are problematic bc
✳️ systematic biases (e.g., racism, sexism)
✳️ poor construct validity
✳️ undermine standards and learning
We should evaluate teaching as seriously as we do research. Or don't do teaching evaluations.
✳️ systematic biases (e.g., racism, sexism)
✳️ poor construct validity
✳️ undermine standards and learning
We should evaluate teaching as seriously as we do research. Or don't do teaching evaluations.
It is time to abandon student evaluations of teaching
Comment by Gordon Hodson (@gordonhodsonphd.bsky.social)
Web: go.nature.com/4jfAzXo
PDF: rdcu.be/ef9y5
Comment by Gordon Hodson (@gordonhodsonphd.bsky.social)
Web: go.nature.com/4jfAzXo
PDF: rdcu.be/ef9y5
April 2, 2025 at 4:30 PM
In this commentary, I argue that student-based teaching evaluations are problematic bc
✳️ systematic biases (e.g., racism, sexism)
✳️ poor construct validity
✳️ undermine standards and learning
We should evaluate teaching as seriously as we do research. Or don't do teaching evaluations.
✳️ systematic biases (e.g., racism, sexism)
✳️ poor construct validity
✳️ undermine standards and learning
We should evaluate teaching as seriously as we do research. Or don't do teaching evaluations.
Reposted by Rens Holmer
Hot off the press! Our paper, “Global comparative structural analysis of responses to protein phosphorylation”, is now out in Nature Communications!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Global comparative structural analysis of responses to protein phosphorylation - Nature Communications
Phosphorylation is central to protein regulation, yet its structural mechanisms remain poorly understood. Here, the authors conduct a global, systematic analysis of phosphorylated versus non-phosphory...
www.nature.com
October 27, 2025 at 10:29 AM
Hot off the press! Our paper, “Global comparative structural analysis of responses to protein phosphorylation”, is now out in Nature Communications!
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Rens Holmer
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com
📄 www.nature.com/articles/s41...
💿 mmseqs.com
GPU-accelerated homology search with MMseqs2 - Nature Methods
Graphics processing unit-accelerated MMseqs2 offers tremendous speedups for homology retrieval from metagenomic databases, query-centered multiple sequence alignment generation for structure predictio...
www.nature.com
September 21, 2025 at 8:06 AM
MMseqs2-GPU sets new standards in single query search speed, allows near instant search of big databases, scales to multiple GPUs and is fast beyond VRAM. It enables ColabFold MSA generation in seconds and sub-second Foldseek search against AFDB50. 1/n
📄 www.nature.com/articles/s41...
💿 mmseqs.com
📄 www.nature.com/articles/s41...
💿 mmseqs.com
A double edged sword: not patenting IP saves universities money, and open source is always a win
"Do Universities Investing In Technology Transfer Via Patenting Lose Money?"
This study reaches a conclusion I've believed to be true since seeing how tech transfer offices work. The paper calls for closing tech transfer offices and instead open sourcing all innovations.
ttb.sk/clanky/do-un...
This study reaches a conclusion I've believed to be true since seeing how tech transfer offices work. The paper calls for closing tech transfer offices and instead open sourcing all innovations.
ttb.sk/clanky/do-un...
September 15, 2025 at 10:22 AM
A double edged sword: not patenting IP saves universities money, and open source is always a win
Reposted by Rens Holmer
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
September 15, 2025 at 8:40 AM
Heads up: ignore samtools dot org, similarly minimap2 dot com and likely others. It's owned by a known phishing site and while the binaries they offer look valid currently (but note they may be serving us different binaries to others), that could change.
Ie: it's not us (Samtools team)! Be warned
Ie: it's not us (Samtools team)! Be warned
Reposted by Rens Holmer
It seems trendy lately to have visualizations of 3D proteins structures generated by AI. These show very ugly artifacts, akin to AI pictures of humans with the wrong number of fingers. It is really not hard to make a visualization of a random protein structure using free software! #AI-slop
September 12, 2025 at 1:18 PM
It seems trendy lately to have visualizations of 3D proteins structures generated by AI. These show very ugly artifacts, akin to AI pictures of humans with the wrong number of fingers. It is really not hard to make a visualization of a random protein structure using free software! #AI-slop
Reposted by Rens Holmer
We are looking for a 3-year postdoc to work with Daniel Probst, Justin van der Hooft and myself on an exciting project involving federated learning and integrative omics for discovery of new antibiotics from natural products.
Apply here: www.wur.nl/en/vacancy/p...
Please share!
Apply here: www.wur.nl/en/vacancy/p...
Please share!
www.wur.nl
September 8, 2025 at 9:07 AM
We are looking for a 3-year postdoc to work with Daniel Probst, Justin van der Hooft and myself on an exciting project involving federated learning and integrative omics for discovery of new antibiotics from natural products.
Apply here: www.wur.nl/en/vacancy/p...
Please share!
Apply here: www.wur.nl/en/vacancy/p...
Please share!
Reposted by Rens Holmer
We're looking for a postdoc who wants to tackle multi-modal federated learning applied to drug discovery.
There will be:
- A great team
- Loads of data
- An interesting and important application
- A beautiful, modern campus
...
There will be:
- A great team
- Loads of data
- An interesting and important application
- A beautiful, modern campus
...
We are looking for a 3-year postdoc to work with Daniel Probst, Justin van der Hooft and myself on an exciting project involving federated learning and integrative omics for discovery of new antibiotics from natural products.
Apply here: www.wur.nl/en/vacancy/p...
Please share!
Apply here: www.wur.nl/en/vacancy/p...
Please share!
www.wur.nl
September 8, 2025 at 9:47 AM
We're looking for a postdoc who wants to tackle multi-modal federated learning applied to drug discovery.
There will be:
- A great team
- Loads of data
- An interesting and important application
- A beautiful, modern campus
...
There will be:
- A great team
- Loads of data
- An interesting and important application
- A beautiful, modern campus
...
New RL target just dropped 🙃
Designing LLM-Resistant Programming Assignments: Insights and Strategies for CS Educators dl.acm.org/doi/10.1145/... 🧬🖥️🧪
August 25, 2025 at 4:41 PM
New RL target just dropped 🙃
Reposted by Rens Holmer
Grrrr. We don't call protein phosphorylation or acteylation epiproteomics. So let's not call RNA modification epitranscriptomics. In fact, realisitically, epigenetics has so many definitions, some of them non-overlapping, that this whole epi-XXXX (genetics/genomics whatever) is just not helping us.
August 21, 2025 at 7:36 AM
Grrrr. We don't call protein phosphorylation or acteylation epiproteomics. So let's not call RNA modification epitranscriptomics. In fact, realisitically, epigenetics has so many definitions, some of them non-overlapping, that this whole epi-XXXX (genetics/genomics whatever) is just not helping us.
Reposted by Rens Holmer
learning from a chatbot is definitely possible (i am using it for learning) but it requires approaching it with an adversarial mindset and only works in fields where you can verify the result
You don’t “learn” from a chatbot. You consume. There’s a difference.
They’re spewing slop and people are gobbling it up (and eroding their intelligence in the process).
Misinformation is everywhere. Please don’t rely on a chatbot for anything important.
They can’t replace real human connection
They’re spewing slop and people are gobbling it up (and eroding their intelligence in the process).
Misinformation is everywhere. Please don’t rely on a chatbot for anything important.
They can’t replace real human connection
August 16, 2025 at 4:47 PM
learning from a chatbot is definitely possible (i am using it for learning) but it requires approaching it with an adversarial mindset and only works in fields where you can verify the result
We heard you like neural networks, so we put a neural network inside your neural network
August 2, 2025 at 7:46 AM
We heard you like neural networks, so we put a neural network inside your neural network
Reposted by Rens Holmer
Longdust, a new tool to identify highly repetitive STRs, VNTRs, satellite DNA and other low-complexity regions (LCRs). Similar to SDUST but for long regions.
github.com/lh3/longdust
github.com/lh3/longdust
GitHub - lh3/longdust: Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome
Identify long STRs, VNTRs, satellite DNA and other low-complexity regions in a genome - lh3/longdust
github.com
July 31, 2025 at 7:59 PM
Longdust, a new tool to identify highly repetitive STRs, VNTRs, satellite DNA and other low-complexity regions (LCRs). Similar to SDUST but for long regions.
github.com/lh3/longdust
github.com/lh3/longdust
Reposted by Rens Holmer
Sassy is out now!
Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!
Available now wherever you get your code
With @rickbitloo.bsky.social
curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...
Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!
Available now wherever you get your code
With @rickbitloo.bsky.social
curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...
July 18, 2025 at 8:20 PM
Sassy is out now!
Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!
Available now wherever you get your code
With @rickbitloo.bsky.social
curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...
Ever need to search for approximate matches of short DNA strings?
Sassy is the tool to use!
Available now wherever you get your code
With @rickbitloo.bsky.social
curiouscoding.nl/papers/sassy...
github.com/ragnarGrootK...
Reposted by Rens Holmer
Please share: I'm still looking for a postdoc in computational genomics to join my team in Oxford. If you want to help develop better ways to detect AML from epigenetic profiles in blood, then get in touch!
Great team and environment, 3-year secured funding, ideal for transition to independence.
Great team and environment, 3-year secured funding, ideal for transition to independence.
Job Details
cutt.cx
June 18, 2025 at 9:40 PM
Please share: I'm still looking for a postdoc in computational genomics to join my team in Oxford. If you want to help develop better ways to detect AML from epigenetic profiles in blood, then get in touch!
Great team and environment, 3-year secured funding, ideal for transition to independence.
Great team and environment, 3-year secured funding, ideal for transition to independence.
Reposted by Rens Holmer
PhD programmes need to prepare students for careers outside universities and stop talking about “Plan B”…
www.nature.com/articles/d41...
www.nature.com/articles/d41...
How many PhDs does the world need? Doctoral graduates vastly outnumber jobs in academia
PhD programmes need to better prepare students for careers outside universities, researchers warn.
www.nature.com
June 23, 2025 at 7:54 AM
PhD programmes need to prepare students for careers outside universities and stop talking about “Plan B”…
www.nature.com/articles/d41...
www.nature.com/articles/d41...