Danielle
@daniposthu.bsky.social
Scientist. Mother. Captain's wife. Loves numbers.
https://cncr.nl/ctg/
https://cncr.nl/ctg/
Out today from CTGlab as part of the EU funded REALMENT consortium, hear hear👇 #PRS #machinelearning #prediction #genetic
When do machine learning models actually outperform standard polygenic scores? 🤔
In our new preprint, we benchmark how non-additive genetic effects (i.e, dominance deviations) shape polygenic prediction across simulated and UK Biobank traits.
👉 www.medrxiv.org/content/10.1...
🧵 1/6
In our new preprint, we benchmark how non-additive genetic effects (i.e, dominance deviations) shape polygenic prediction across simulated and UK Biobank traits.
👉 www.medrxiv.org/content/10.1...
🧵 1/6
Benchmarking non-additive genetic effects on polygenic prediction and machine learning-based approaches
Polygenic scores (PGSs) are widely used to translate genome-wide association study (GWAS) findings into tools for genetic risk prediction. Most current approaches assume additive effects, yet the cont...
www.medrxiv.org
October 14, 2025 at 11:45 AM
Out today from CTGlab as part of the EU funded REALMENT consortium, hear hear👇 #PRS #machinelearning #prediction #genetic
Proud that the third GWAS for Alzheimer's dementia from the PGC-ALZ working group was just posted online! Huge amounts of work, and what a great collaboration! Check out our exciting findings below 👇 @pgcgenetics.bsky.social #ctglab #alzheimer #dementia #GWAS
🚨 The preprint for our GWAS of Alzheimer’s disease (AD) is out
Preprint: medrxiv.org/content/10.1...
🧵
Preprint: medrxiv.org/content/10.1...
🧵
Genomic analyses reveal new insights into Alzheimer's disease
Alzheimer's disease (AD) is the most common cause of dementia, with global case numbers projected to reach 153 million in 2050. AD is highly heritable, with twin-based heritability estimates of 60-80%...
medrxiv.org
October 14, 2025 at 7:24 AM
Proud that the third GWAS for Alzheimer's dementia from the PGC-ALZ working group was just posted online! Huge amounts of work, and what a great collaboration! Check out our exciting findings below 👇 @pgcgenetics.bsky.social #ctglab #alzheimer #dementia #GWAS
Reposted by Danielle
If you are preparing your bachelor statistics course and would like to add optional material for students to better understand statistics on a conceptual level (see topics in the screenshot) my free textbook provides a state of the art overview. lakens.github.io/statistical_...
August 25, 2025 at 4:54 AM
If you are preparing your bachelor statistics course and would like to add optional material for students to better understand statistics on a conceptual level (see topics in the screenshot) my free textbook provides a state of the art overview. lakens.github.io/statistical_...
Check out the latest from @euffelmann.bsky.social #cgtlab!
📣 New paper published in @natcomms.nature.com, where we explored sex differences in local genetic correlations, local heritabilities, and magnitude of effect sizes in quantitative traits.
link: rdcu.be/ezuZd
1/7
link: rdcu.be/ezuZd
1/7
Local genetic sex differences in quantitative traits
Nature Communications - Analysing 157 traits, this study finds widespread local genetic sex differences masked at the genome-wide level. Using LAVA, it tests for sex-specific heritability, genetic...
rdcu.be
August 23, 2025 at 3:43 PM
Check out the latest from @euffelmann.bsky.social #cgtlab!
Reposted by Danielle
#ctglab is hiring! We have #vacancies! 2 PhD & 2 postdoc positions, in #statistical #genetics and/or #bioinformatics - if you like GWAS, method development and linking with biology - check these out 👇
werkenbij.vu.nl/vacatures/tw...
werkenbij.vu.nl/vacatures/po...
werkenbij.vu.nl/vacatures/po...
werkenbij.vu.nl/vacatures/tw...
werkenbij.vu.nl/vacatures/po...
werkenbij.vu.nl/vacatures/po...
May 24, 2025 at 3:02 PM
#ctglab is hiring! We have #vacancies! 2 PhD & 2 postdoc positions, in #statistical #genetics and/or #bioinformatics - if you like GWAS, method development and linking with biology - check these out 👇
werkenbij.vu.nl/vacatures/tw...
werkenbij.vu.nl/vacatures/po...
werkenbij.vu.nl/vacatures/po...
werkenbij.vu.nl/vacatures/tw...
werkenbij.vu.nl/vacatures/po...
werkenbij.vu.nl/vacatures/po...
#ctglab is hiring! We have #vacancies! 2 PhD & 2 postdoc positions, in #statistical #genetics and/or #bioinformatics - if you like GWAS, method development and linking with biology - check these out 👇
werkenbij.vu.nl/vacatures/tw...
werkenbij.vu.nl/vacatures/po...
werkenbij.vu.nl/vacatures/po...
werkenbij.vu.nl/vacatures/tw...
werkenbij.vu.nl/vacatures/po...
werkenbij.vu.nl/vacatures/po...
May 24, 2025 at 3:02 PM
#ctglab is hiring! We have #vacancies! 2 PhD & 2 postdoc positions, in #statistical #genetics and/or #bioinformatics - if you like GWAS, method development and linking with biology - check these out 👇
werkenbij.vu.nl/vacatures/tw...
werkenbij.vu.nl/vacatures/po...
werkenbij.vu.nl/vacatures/po...
werkenbij.vu.nl/vacatures/tw...
werkenbij.vu.nl/vacatures/po...
werkenbij.vu.nl/vacatures/po...
Reposted by Danielle
Current integrative prioritization methods use either functional data (L2G, cS2G) or network convergence of GWAS signal (PoPS).
FLAMES combines both, by combining XGBoost predictions using functional evidence in the GWAS locus with PoPS predictions.
FLAMES combines both, by combining XGBoost predictions using functional evidence in the GWAS locus with PoPS predictions.
February 11, 2025 at 9:58 AM
Current integrative prioritization methods use either functional data (L2G, cS2G) or network convergence of GWAS signal (PoPS).
FLAMES combines both, by combining XGBoost predictions using functional evidence in the GWAS locus with PoPS predictions.
FLAMES combines both, by combining XGBoost predictions using functional evidence in the GWAS locus with PoPS predictions.
Just out from #ctglab by @mjschipper.bsky.social
- our new tool FLAMES 🔥🔥, to identify the most likely causal genes in GWAS loci, using machine learning techniques, thoroughly benchmarked and freely available
Paper: rdcu.be/d9iQP
Code: github.com/Marijn-Schip...
- our new tool FLAMES 🔥🔥, to identify the most likely causal genes in GWAS loci, using machine learning techniques, thoroughly benchmarked and freely available
Paper: rdcu.be/d9iQP
Code: github.com/Marijn-Schip...
Prioritizing effector genes at trait-associated loci using multimodal evidence
Nature Genetics - FLAMES is a machine learning approach combining variant fine-mapping, SNP-to-gene annotations and convergence-based gene prioritization scores to identify candidate effector genes...
rdcu.be
February 11, 2025 at 8:42 AM
Just out from #ctglab by @mjschipper.bsky.social
- our new tool FLAMES 🔥🔥, to identify the most likely causal genes in GWAS loci, using machine learning techniques, thoroughly benchmarked and freely available
Paper: rdcu.be/d9iQP
Code: github.com/Marijn-Schip...
- our new tool FLAMES 🔥🔥, to identify the most likely causal genes in GWAS loci, using machine learning techniques, thoroughly benchmarked and freely available
Paper: rdcu.be/d9iQP
Code: github.com/Marijn-Schip...
Reposted by Danielle
🚨 This will become a curated list of awesome tools for complex trait genetics, **add yours**! it may become a review in which case those who contribute are invited as co-authors.
GitHub - MichelNivard/awesome-complex-trait-genetics: A list of awesome tools for complex trait genetics.
A list of awesome tools for complex trait genetics. - MichelNivard/awesome-complex-trait-genetics
github.com
November 28, 2024 at 9:21 AM
🚨 This will become a curated list of awesome tools for complex trait genetics, **add yours**! it may become a review in which case those who contribute are invited as co-authors.
Reposted by Danielle
I've set 2 personal goals.
One is to identify the causal gene for every lead snp in the @gwascatalog.bsky.social
The other is to assign a GWAS trait to every human gene.
Unfortunately the gwas catalog is growing exponentially and I'm not.
I'm at 103,605 "solved" loci out of 563,097 lead snps
One is to identify the causal gene for every lead snp in the @gwascatalog.bsky.social
The other is to assign a GWAS trait to every human gene.
Unfortunately the gwas catalog is growing exponentially and I'm not.
I'm at 103,605 "solved" loci out of 563,097 lead snps
November 24, 2024 at 8:07 PM
I've set 2 personal goals.
One is to identify the causal gene for every lead snp in the @gwascatalog.bsky.social
The other is to assign a GWAS trait to every human gene.
Unfortunately the gwas catalog is growing exponentially and I'm not.
I'm at 103,605 "solved" loci out of 563,097 lead snps
One is to identify the causal gene for every lead snp in the @gwascatalog.bsky.social
The other is to assign a GWAS trait to every human gene.
Unfortunately the gwas catalog is growing exponentially and I'm not.
I'm at 103,605 "solved" loci out of 563,097 lead snps
Reposted by Danielle
The bacteria in your gut depend on where you are in the social network around you.
The microbes within us treat our social networks as the extended environment in which they thrive. They can spread from person to person.
New #HNL work out today in @natureportfolio.bsky.social . 1/
The microbes within us treat our social networks as the extended environment in which they thrive. They can spread from person to person.
New #HNL work out today in @natureportfolio.bsky.social . 1/
November 21, 2024 at 3:45 PM
The bacteria in your gut depend on where you are in the social network around you.
The microbes within us treat our social networks as the extended environment in which they thrive. They can spread from person to person.
New #HNL work out today in @natureportfolio.bsky.social . 1/
The microbes within us treat our social networks as the extended environment in which they thrive. They can spread from person to person.
New #HNL work out today in @natureportfolio.bsky.social . 1/
So sorry to miss #wcpg2025 #stuckwithgrantwriting BUT #ctglab is well represented, please look out for Marijn Schipper, Emil Uffelmann, Nathan Bell, Bernardo Maciel, Cato Romero, Jeanne Savage & Zeli Chen - they will be presenting the latest outcomes from our lab this week!
October 15, 2024 at 7:22 AM
So sorry to miss #wcpg2025 #stuckwithgrantwriting BUT #ctglab is well represented, please look out for Marijn Schipper, Emil Uffelmann, Nathan Bell, Bernardo Maciel, Cato Romero, Jeanne Savage & Zeli Chen - they will be presenting the latest outcomes from our lab this week!
Reposted by Danielle
#EEGManyLabs will replicate 20 of the highest impact findings in the field in at least three labs each. All studies will be planned and published as Registered Reports.
Paper: d1wqtxts1xzle7.cloudfront.net/95338626/1_s...
Paper: d1wqtxts1xzle7.cloudfront.net/95338626/1_s...
October 21, 2023 at 4:44 PM
#EEGManyLabs will replicate 20 of the highest impact findings in the field in at least three labs each. All studies will be planned and published as Registered Reports.
Paper: d1wqtxts1xzle7.cloudfront.net/95338626/1_s...
Paper: d1wqtxts1xzle7.cloudfront.net/95338626/1_s...
Reposted by Danielle
A 2023 Nature survey of 1,600 researchers found that more than 25% use AI to help them write manuscripts and that more than 15% use the technology to help them write grant proposals. 👀
AI and science: what 1,600 researchers think
A Nature survey finds that scientists are concerned, as well as excited, by the increasing use of artificial-intelligence tools in research. A Nature survey finds that scientists are concerned, as wel...
www.nature.com
October 14, 2023 at 4:31 PM
A 2023 Nature survey of 1,600 researchers found that more than 25% use AI to help them write manuscripts and that more than 15% use the technology to help them write grant proposals. 👀
Reposted by Danielle
Now what happens if we estimate direct/indirect heritability (using a within-family method) in the presence of assortative mating and shared environment? Direct estimates are reasonable/deflated, but indirect estimates are HUGELY inflated by AM. Indirect heritability is NOT "genetic nurture".
October 11, 2023 at 11:23 PM
Now what happens if we estimate direct/indirect heritability (using a within-family method) in the presence of assortative mating and shared environment? Direct estimates are reasonable/deflated, but indirect estimates are HUGELY inflated by AM. Indirect heritability is NOT "genetic nurture".
Reposted by Danielle
#rstats
What are your favourite examples when teaching students to think critically about data/figures and interpretations?
For example, Simpson's Paradox and the importance of considering important subpopulations - is brilliantly displayed in the Palmer Penguins dataset.
What are your favourite examples when teaching students to think critically about data/figures and interpretations?
For example, Simpson's Paradox and the importance of considering important subpopulations - is brilliantly displayed in the Palmer Penguins dataset.
October 9, 2023 at 12:34 PM
#rstats
What are your favourite examples when teaching students to think critically about data/figures and interpretations?
For example, Simpson's Paradox and the importance of considering important subpopulations - is brilliantly displayed in the Palmer Penguins dataset.
What are your favourite examples when teaching students to think critically about data/figures and interpretations?
For example, Simpson's Paradox and the importance of considering important subpopulations - is brilliantly displayed in the Palmer Penguins dataset.