Koen Van den Berge
@koenvdberge.bsky.social
Statistical genomics. Currently working on single-cell data analysis in context of drug development. Previously post-doc at UC Berkeley and Ghent University.
We're looking for a post-doc to support target discovery in lymphoma using single-cell and spatial 'omics modalities.
You will be embedded in our Discovery Statistics organization, and supported by myself and colleagues. Feel free to reach out for any additional information.
tinyurl.com/36uyca7f
You will be embedded in our Discovery Statistics organization, and supported by myself and colleagues. Feel free to reach out for any additional information.
tinyurl.com/36uyca7f
Post Doc PD DD PCCD
At Johnson & Johnson, we believe health is everything. Our strength in healthcare innovation empowers us to build a world where complex diseases are prevented, treated, and cured, where treatments...
tinyurl.com
November 24, 2025 at 8:20 AM
We're looking for a post-doc to support target discovery in lymphoma using single-cell and spatial 'omics modalities.
You will be embedded in our Discovery Statistics organization, and supported by myself and colleagues. Feel free to reach out for any additional information.
tinyurl.com/36uyca7f
You will be embedded in our Discovery Statistics organization, and supported by myself and colleagues. Feel free to reach out for any additional information.
tinyurl.com/36uyca7f
Reposted by Koen Van den Berge
After two weeks, I'm finally done!
In this post, I explain different approaches for solving linear regression in R: directly, using QR, singular value and Cholesky decompositions, and do some benchmarking for comparison with in-built approaches.
thomvolker.github.io/blog/2506_re...
In this post, I explain different approaches for solving linear regression in R: directly, using QR, singular value and Cholesky decompositions, and do some benchmarking for comparison with in-built approaches.
thomvolker.github.io/blog/2506_re...
June 18, 2025 at 2:22 PM
After two weeks, I'm finally done!
In this post, I explain different approaches for solving linear regression in R: directly, using QR, singular value and Cholesky decompositions, and do some benchmarking for comparison with in-built approaches.
thomvolker.github.io/blog/2506_re...
In this post, I explain different approaches for solving linear regression in R: directly, using QR, singular value and Cholesky decompositions, and do some benchmarking for comparison with in-built approaches.
thomvolker.github.io/blog/2506_re...
Reposted by Koen Van den Berge
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...
Reposted by Koen Van den Berge
New preprint from Ajay Nadig @nadigajay.bsky.social in Luke O'Connor's lab, with "a suite of statistical tools for formally modeling distributions of DE effects from RNA-seq experiments, including Perturb-seq"
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Transcriptome-wide characterization of genetic perturbations
Single cell CRISPR screens such as Perturb-seq enable transcriptomic profiling of genetic perturbations at scale. However, the data produced by these screens are often noisy due to cost and technical ...
www.biorxiv.org
April 23, 2025 at 1:22 AM
New preprint from Ajay Nadig @nadigajay.bsky.social in Luke O'Connor's lab, with "a suite of statistical tools for formally modeling distributions of DE effects from RNA-seq experiments, including Perturb-seq"
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Koen Van den Berge
Colossal Bioscience did not revive dire wolves, despite a sensationalist Time Magazine cover story.
Making genetically modified animals that are cosplaying as extinct species is not de-extinction.
Making genetically modified animals that are cosplaying as extinct species is not de-extinction.
Dire wolves were not close relatives of gray wolves. They last shared a common ancestor more than 5 million years ago. What Colossal has done is make something new and slapped a dire wolf sticker on it, as if an organism equals a hypothetical genome.
Dire Wolves Were Not Really Wolves, New Genetic Clues Reveal
The extinct giant canids were a remarkable example of convergent evolution
www.scientificamerican.com
April 7, 2025 at 3:40 PM
Colossal Bioscience did not revive dire wolves, despite a sensationalist Time Magazine cover story.
Making genetically modified animals that are cosplaying as extinct species is not de-extinction.
Making genetically modified animals that are cosplaying as extinct species is not de-extinction.
Reposted by Koen Van den Berge
We've just released radEmu v2.0.0 🥳🦤😻
`remotes::install_github("statdivlab/radEmu")`
A huge thanks to users for sharing their requests and questions, and to the maintenance team (Sarah and @davidandacat.bsky.social ) for their time and commitment!
Release notes: github.com/statdivlab/r...
`remotes::install_github("statdivlab/radEmu")`
A huge thanks to users for sharing their requests and questions, and to the maintenance team (Sarah and @davidandacat.bsky.social ) for their time and commitment!
Release notes: github.com/statdivlab/r...
March 14, 2025 at 10:47 AM
We've just released radEmu v2.0.0 🥳🦤😻
`remotes::install_github("statdivlab/radEmu")`
A huge thanks to users for sharing their requests and questions, and to the maintenance team (Sarah and @davidandacat.bsky.social ) for their time and commitment!
Release notes: github.com/statdivlab/r...
`remotes::install_github("statdivlab/radEmu")`
A huge thanks to users for sharing their requests and questions, and to the maintenance team (Sarah and @davidandacat.bsky.social ) for their time and commitment!
Release notes: github.com/statdivlab/r...
Reposted by Koen Van den Berge
In Science, researchers detail a nanoscale-resolution reconstruction of a millimeter-scale fragment of human cerebral cortex, giving an unprecedented view into the structural organization of brain tissue at the supracellular, cellular, and subcellular levels. scim.ag/3FvpAKy #BrainAwarenessWeek
March 11, 2025 at 2:08 PM
In Science, researchers detail a nanoscale-resolution reconstruction of a millimeter-scale fragment of human cerebral cortex, giving an unprecedented view into the structural organization of brain tissue at the supracellular, cellular, and subcellular levels. scim.ag/3FvpAKy #BrainAwarenessWeek
Reposted by Koen Van den Berge
I am happy to announce our new paper "Univariate-guided sparse regression". It's a new lasso that leverages the signs and magnitude of univariate coefficients .
Sparser and more interpretable than the lasso. We're excited! arxiv.org/abs/2501.18360
R: github.com/trevorhastie...
Sparser and more interpretable than the lasso. We're excited! arxiv.org/abs/2501.18360
R: github.com/trevorhastie...
Univariate-Guided Sparse Regression
In this paper, we introduce ``UniLasso'' -- a novel statistical method for sparse regression. This two-stage approach preserves the signs of the univariate coefficients and leverages their magnitude. ...
arxiv.org
February 24, 2025 at 4:57 AM
I am happy to announce our new paper "Univariate-guided sparse regression". It's a new lasso that leverages the signs and magnitude of univariate coefficients .
Sparser and more interpretable than the lasso. We're excited! arxiv.org/abs/2501.18360
R: github.com/trevorhastie...
Sparser and more interpretable than the lasso. We're excited! arxiv.org/abs/2501.18360
R: github.com/trevorhastie...
Reposted by Koen Van den Berge
This is long overdue, but over the winter break we were finally able to write up our sgdGMF paper:
arxiv.org/abs/2412.20509
We present a stochastic gradient descent method that allows to efficiently and very quickly estimate latent factors for, e.g., dimensionality reduction of single-cell data
arxiv.org/abs/2412.20509
We present a stochastic gradient descent method that allows to efficiently and very quickly estimate latent factors for, e.g., dimensionality reduction of single-cell data
January 21, 2025 at 11:06 AM
This is long overdue, but over the winter break we were finally able to write up our sgdGMF paper:
arxiv.org/abs/2412.20509
We present a stochastic gradient descent method that allows to efficiently and very quickly estimate latent factors for, e.g., dimensionality reduction of single-cell data
arxiv.org/abs/2412.20509
We present a stochastic gradient descent method that allows to efficiently and very quickly estimate latent factors for, e.g., dimensionality reduction of single-cell data
Reposted by Koen Van den Berge
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
www.encodeproject.org/single-cell/...
Single cell – ENCODEHomo sapiens clickable body map
www.encodeproject.org
January 7, 2025 at 9:29 PM
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
www.encodeproject.org/single-cell/...
Reposted by Koen Van den Berge
A few papers I think worth reading. Mostly open access.
Causal inference is hard:
www.nature.com/articles/s41...
Causal inference is hard:
www.nature.com/articles/s41...
Causal inference on human behaviour - Nature Human Behaviour
In this Review, Drew Bailey et al. present an accessible, non-technical overview of key challenges for causal inference in studies of human behaviour as well as methodological solutions to these chall...
www.nature.com
December 17, 2024 at 1:28 AM
A few papers I think worth reading. Mostly open access.
Causal inference is hard:
www.nature.com/articles/s41...
Causal inference is hard:
www.nature.com/articles/s41...
Reposted by Koen Van den Berge
Have you been thinking hard about statistical modelling of scATAC-seq data? (No.)
Luckily for you, @aaronkwc.bsky.social has!
Aaron will help you grok:
What's going on?
What is TF-IDF?
Is there really single-cell level chromatin information?
Check it out 👇
www.biorxiv.org/content/10.1...
🧪🧬💻
Luckily for you, @aaronkwc.bsky.social has!
Aaron will help you grok:
What's going on?
What is TF-IDF?
Is there really single-cell level chromatin information?
Check it out 👇
www.biorxiv.org/content/10.1...
🧪🧬💻
Going beyond cell clustering and feature aggregation: Is there single cell level information in single-cell ATAC-seq data?
Single-cell Assay for Transposase Accessible Chromatin with sequencing (scATAC-seq) has become a widely used method for investigating chromatin accessibility at single-cell resolution. However, the re...
www.biorxiv.org
December 10, 2024 at 6:37 AM
Have you been thinking hard about statistical modelling of scATAC-seq data? (No.)
Luckily for you, @aaronkwc.bsky.social has!
Aaron will help you grok:
What's going on?
What is TF-IDF?
Is there really single-cell level chromatin information?
Check it out 👇
www.biorxiv.org/content/10.1...
🧪🧬💻
Luckily for you, @aaronkwc.bsky.social has!
Aaron will help you grok:
What's going on?
What is TF-IDF?
Is there really single-cell level chromatin information?
Check it out 👇
www.biorxiv.org/content/10.1...
🧪🧬💻