Constantin Ahlmann-Eltze
@const-ae.bsky.social
Postdoc at UCL with James Reading. Previously at EMBL working with Wolfgang Huber. Biostats, R, cancer immunology
Reposted by Constantin Ahlmann-Eltze
🚀 Excited to share our new preprint: msBayesImpute - A Versatile Framework for Addressing Missing Values in Biomedical Mass Spectrometry Proteomics Data
👉 Improves imputation accuracy, normalization, and differential expression detection
📝https://www.biorxiv.org/content/10.1101/2025.10.02.679746v1
👉 Improves imputation accuracy, normalization, and differential expression detection
📝https://www.biorxiv.org/content/10.1101/2025.10.02.679746v1
October 7, 2025 at 8:47 AM
🚀 Excited to share our new preprint: msBayesImpute - A Versatile Framework for Addressing Missing Values in Biomedical Mass Spectrometry Proteomics Data
👉 Improves imputation accuracy, normalization, and differential expression detection
📝https://www.biorxiv.org/content/10.1101/2025.10.02.679746v1
👉 Improves imputation accuracy, normalization, and differential expression detection
📝https://www.biorxiv.org/content/10.1101/2025.10.02.679746v1
Reposted by Constantin Ahlmann-Eltze
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 Constantin Ahlmann-Eltze
We're excited to share that our preprint on anndataR, a new package bringing Python's AnnData to R, is now available on bioRxiv 🎉
🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com
🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com
August 25, 2025 at 3:24 PM
We're excited to share that our preprint on anndataR, a new package bringing Python's AnnData to R, is now available on bioRxiv 🎉
🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com
🔗 Read the paper: www.biorxiv.org/content/10.1...
💻 Check the package in action: anndatar.data-intuitive.com
Reposted by Constantin Ahlmann-Eltze
Now on CRAN, ggdiagram is a #ggplot2 extension that draws diagrams programmatically in #Rstats. Allows for precise control in how objects, labels, and equations are placed in relation to each other.
wjschne.github.io/ggdiagram/ar...
wjschne.github.io/ggdiagram/ar...
August 20, 2025 at 10:43 AM
Now on CRAN, ggdiagram is a #ggplot2 extension that draws diagrams programmatically in #Rstats. Allows for precise control in how objects, labels, and equations are placed in relation to each other.
wjschne.github.io/ggdiagram/ar...
wjschne.github.io/ggdiagram/ar...
Reposted by Constantin Ahlmann-Eltze
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
August 4, 2025 at 1:52 PM
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
Reposted by Constantin Ahlmann-Eltze
🚨 PhD Position available in our lab 🚨 exploring the power of blood immune multi-omics to detect lung cancer years prior to clinical diagnosis in a unique cohort of >10,000 CT screened individuals.
✅ Wet & dry lab
✅ September 2025 enrolment
✅ UK tuition fees only
www.ucl.ac.uk/medical-scie...
✅ Wet & dry lab
✅ September 2025 enrolment
✅ UK tuition fees only
www.ucl.ac.uk/medical-scie...
Pre-Cancer Immunology
The Pre-Cancer Immunology Lab (James Reading Lab) is mapping pre-invasive T cell dynamics during carcinogenesis to detect and intercept cancer development.
www.ucl.ac.uk
August 5, 2025 at 5:57 PM
🚨 PhD Position available in our lab 🚨 exploring the power of blood immune multi-omics to detect lung cancer years prior to clinical diagnosis in a unique cohort of >10,000 CT screened individuals.
✅ Wet & dry lab
✅ September 2025 enrolment
✅ UK tuition fees only
www.ucl.ac.uk/medical-scie...
✅ Wet & dry lab
✅ September 2025 enrolment
✅ UK tuition fees only
www.ucl.ac.uk/medical-scie...
Reposted by Constantin Ahlmann-Eltze
I wrote about AI foundation models for biology last year: www.nytimes.com/2024/03/10/s... Benchmarking tests since then aren't finding that they're better than simpler models of how genes and cells work.
August 4, 2025 at 4:45 PM
I wrote about AI foundation models for biology last year: www.nytimes.com/2024/03/10/s... Benchmarking tests since then aren't finding that they're better than simpler models of how genes and cells work.
Reposted by Constantin Ahlmann-Eltze
An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Deep-learning-based gene perturbation effect prediction does not yet outperform simple linear baselines - Nature Methods
The analysis presented in this Brief Communication shows that, despite their complexity, current deep learning models do not outperform linear baselines in predicting gene perturbation effects, thus e...
www.nature.com
August 4, 2025 at 4:07 PM
An analysis shows that current deep learning models do not beat linear baselines in predicting gene perturbation effects, thus emphasizing the importance of further method development and evaluation. @const-ae.bsky.social @wkhuber.bsky.social @s-anders.bsky.social
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
August 4, 2025 at 1:52 PM
Our paper benchmarking foundation models for perturbation effect prediction is finally published 🎉🥳🎉
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
www.nature.com/articles/s41...
We show that none of the available* models outperform simple linear baselines. Since the original preprint, we added more methods, metrics, and prettier figures!
🧵
Reposted by Constantin Ahlmann-Eltze
In October 2024, I twote that "something is deeply wrong" with what we now call virtual cell models. A lot has happened since then. How am I updating? New blog post: ekernf01.github.io/virtual-cell...
A recap of virtual cell releases circa June 2025
In October 2024, I twote that “something is deeply wrong” with what we now call virtual cell models. A lot has happened since then: modelers are advancing new architectures and mining new sources of i...
ekernf01.github.io
July 27, 2025 at 11:48 PM
In October 2024, I twote that "something is deeply wrong" with what we now call virtual cell models. A lot has happened since then. How am I updating? New blog post: ekernf01.github.io/virtual-cell...
Reposted by Constantin Ahlmann-Eltze
Going from methods dev to full on cancer bio has been tough. All the more excited to see this out at last—
www.biorxiv.org/content/10.1...
@pascual-reguant.bsky.social
@brukerspatial.bsky.social
@hoheyn.bsky.social
www.biorxiv.org/content/10.1...
@pascual-reguant.bsky.social
@brukerspatial.bsky.social
@hoheyn.bsky.social
Tracing colorectal malignancy transformation from cell to tissue scale
The transformation of normal intestinal epithelium into colorectal cancer (CRC) involves coordinated changes across molecular, cellular, and architectural scales; yet, how these layers integrate remai...
www.biorxiv.org
June 27, 2025 at 6:33 PM
Going from methods dev to full on cancer bio has been tough. All the more excited to see this out at last—
www.biorxiv.org/content/10.1...
@pascual-reguant.bsky.social
@brukerspatial.bsky.social
@hoheyn.bsky.social
www.biorxiv.org/content/10.1...
@pascual-reguant.bsky.social
@brukerspatial.bsky.social
@hoheyn.bsky.social
Reposted by Constantin Ahlmann-Eltze
With {tidylog}, you see friendly messages like:
summarise: now 3 rows and 3 columns, ungrouped
filter: removed 2 rows (67%), one row remaining
✨ It’s like having a gentle co-pilot, helping you track what each step is doing — super useful for debugging and learning!
summarise: now 3 rows and 3 columns, ungrouped
filter: removed 2 rows (67%), one row remaining
✨ It’s like having a gentle co-pilot, helping you track what each step is doing — super useful for debugging and learning!
May 8, 2025 at 1:28 PM
With {tidylog}, you see friendly messages like:
summarise: now 3 rows and 3 columns, ungrouped
filter: removed 2 rows (67%), one row remaining
✨ It’s like having a gentle co-pilot, helping you track what each step is doing — super useful for debugging and learning!
summarise: now 3 rows and 3 columns, ungrouped
filter: removed 2 rows (67%), one row remaining
✨ It’s like having a gentle co-pilot, helping you track what each step is doing — super useful for debugging and learning!
Reposted by Constantin Ahlmann-Eltze
New preprint out!
We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data.
Built on xarray and dask, with seamless integration into the scverse ecosystem.
www.biorxiv.org/content/10.1...
We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data.
Built on xarray and dask, with seamless integration into the scverse ecosystem.
www.biorxiv.org/content/10.1...
May 5, 2025 at 11:30 AM
New preprint out!
We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data.
Built on xarray and dask, with seamless integration into the scverse ecosystem.
www.biorxiv.org/content/10.1...
We introduce 𝐬𝐩𝐚𝐭𝐢𝐚𝐥𝐩𝐫𝐨𝐭𝐞𝐨𝐦𝐢𝐜𝐬, a Python package for end-to-end processing and analysis of highly multiplexed immunofluorescence imaging data.
Built on xarray and dask, with seamless integration into the scverse ecosystem.
www.biorxiv.org/content/10.1...
Reposted by Constantin Ahlmann-Eltze
(2/3)
Constantin Ahlmann-Eltze showcased impressive work on assembling an atlas of T cells in precancerous samples. They developed the R packages treelabel and Shinytreelabel, which showed GITR+ Tregs are enriched in several precancerous samples, suggesting avenues for future treatments
Constantin Ahlmann-Eltze showcased impressive work on assembling an atlas of T cells in precancerous samples. They developed the R packages treelabel and Shinytreelabel, which showed GITR+ Tregs are enriched in several precancerous samples, suggesting avenues for future treatments
April 10, 2025 at 11:43 AM
(2/3)
Constantin Ahlmann-Eltze showcased impressive work on assembling an atlas of T cells in precancerous samples. They developed the R packages treelabel and Shinytreelabel, which showed GITR+ Tregs are enriched in several precancerous samples, suggesting avenues for future treatments
Constantin Ahlmann-Eltze showcased impressive work on assembling an atlas of T cells in precancerous samples. They developed the R packages treelabel and Shinytreelabel, which showed GITR+ Tregs are enriched in several precancerous samples, suggesting avenues for future treatments
Reposted by Constantin Ahlmann-Eltze
🦎 Differential expression analysis relies on cluster identities, unless you perform a regression along continuous representation in latent space. LEMUR from @const-ae.bsky.social & @wkhuber.bsky.social does that neatly for scRNA-seq data!
🔗 doi.org/10.1038/s415... 🧪 @naturegenet.bsky.social
🔗 doi.org/10.1038/s415... 🧪 @naturegenet.bsky.social
Analysis of multi-condition single-cell data with latent embedding multivariate regression
Nature Genetics - Latent embedding multivariate regression models multi-condition single-cell RNA-seq using a continuous latent space, enabling data integration, per-cell gene expression prediction...
doi.org
March 19, 2025 at 7:44 AM
🦎 Differential expression analysis relies on cluster identities, unless you perform a regression along continuous representation in latent space. LEMUR from @const-ae.bsky.social & @wkhuber.bsky.social does that neatly for scRNA-seq data!
🔗 doi.org/10.1038/s415... 🧪 @naturegenet.bsky.social
🔗 doi.org/10.1038/s415... 🧪 @naturegenet.bsky.social
Reposted by Constantin Ahlmann-Eltze
We are recruiting a PhD student in Computational Biology to work on omics data and spatial integration in cellular immunotherapy of cancer. Joint project with the group of Florian Büttner. @loewe-fci.bsky.social
agimkeller.github.io/recruit.html
agimkeller.github.io/recruit.html
Open positions - AG Imkeller
agimkeller.github.io
March 11, 2025 at 8:59 AM
We are recruiting a PhD student in Computational Biology to work on omics data and spatial integration in cellular immunotherapy of cancer. Joint project with the group of Florian Büttner. @loewe-fci.bsky.social
agimkeller.github.io/recruit.html
agimkeller.github.io/recruit.html
Reposted by Constantin Ahlmann-Eltze
Blog post by @const-ae.bsky.social with a simple explanation of the manifold regression algorithm & code that underlies our paper “Analysis of multi-condition single-cell data with latent embedding multivariate regression” (doi.org/10.1002/eji....).
const-ae.name/post/2025-01...
const-ae.name/post/2025-01...
LEMUR simplified | const-ae
A simplified implementation of the LEMUR algorithm.
const-ae.name
March 4, 2025 at 6:27 PM
Blog post by @const-ae.bsky.social with a simple explanation of the manifold regression algorithm & code that underlies our paper “Analysis of multi-condition single-cell data with latent embedding multivariate regression” (doi.org/10.1002/eji....).
const-ae.name/post/2025-01...
const-ae.name/post/2025-01...
Reposted by Constantin Ahlmann-Eltze
Abstract submissions are now open for the European Bioconductor Conference (EuroBioC2025), 17-19 September 2025 in Barcelona.
This event will bring together the Bioconductor community in Europe to advance bioinformatics, data science, and open-source software.
eurobioc2025.bioconductor.org
This event will bring together the Bioconductor community in Europe to advance bioinformatics, data science, and open-source software.
eurobioc2025.bioconductor.org
February 28, 2025 at 3:07 PM
Abstract submissions are now open for the European Bioconductor Conference (EuroBioC2025), 17-19 September 2025 in Barcelona.
This event will bring together the Bioconductor community in Europe to advance bioinformatics, data science, and open-source software.
eurobioc2025.bioconductor.org
This event will bring together the Bioconductor community in Europe to advance bioinformatics, data science, and open-source software.
eurobioc2025.bioconductor.org
Is there some clever syntax to control when a quasi-quotation is evaluated so that the wrap_in_tibble function works? 🧐
(Context in stackoverflow.com/questions/79...)
#Rstats #rlang
(Context in stackoverflow.com/questions/79...)
#Rstats #rlang
![wrap_in_df <- function(...){
dots <- rlang::enquos(...)
eval_in_mtcars(data.frame(!!! dots))
}
wrap_in_tibble <- function(...){
dots <- rlang::enquos(...)
eval_in_mtcars(tibble::tibble(!!! dots))
}
eval_in_mtcars <- function(expr){
quo <- rlang::enquo(expr)
rlang::eval_tidy(quo, data = mtcars[1:3,])
}
wrap_in_df(mpg * 2, cyl + 3)
#> X.mpg...2 X.cyl...3
#> 1 42.0 9
#> 2 42.0 9
#> 3 45.6 7
wrap_in_tibble(mpg * 2, cyl + 3)
#> Error: object 'mpg' not found](https://cdn.bsky.app/img/feed_thumbnail/plain/did:plc:pa4xdweapw6gnh42xqptt6vb/bafkreihxqsxhceomx7l4lv6g5zk5ocw4vy7mlpyxf7fg5qssa5gnvjbe4q@jpeg)
February 19, 2025 at 9:17 AM
Is there some clever syntax to control when a quasi-quotation is evaluated so that the wrap_in_tibble function works? 🧐
(Context in stackoverflow.com/questions/79...)
#Rstats #rlang
(Context in stackoverflow.com/questions/79...)
#Rstats #rlang
Reposted by Constantin Ahlmann-Eltze
Thrilled to share that our work from Trumpp Lab @hi-stem @dkfz.bsky.social is out in Nature.
We provide the first single-cell data on neurons infiltrating pancreatic tumors, offering new insights into cancer therapy. #cancerneuroscience @cn-hd.bsky.social
www.nature.com/articles/s41...
We provide the first single-cell data on neurons infiltrating pancreatic tumors, offering new insights into cancer therapy. #cancerneuroscience @cn-hd.bsky.social
www.nature.com/articles/s41...
February 18, 2025 at 9:37 AM
Thrilled to share that our work from Trumpp Lab @hi-stem @dkfz.bsky.social is out in Nature.
We provide the first single-cell data on neurons infiltrating pancreatic tumors, offering new insights into cancer therapy. #cancerneuroscience @cn-hd.bsky.social
www.nature.com/articles/s41...
We provide the first single-cell data on neurons infiltrating pancreatic tumors, offering new insights into cancer therapy. #cancerneuroscience @cn-hd.bsky.social
www.nature.com/articles/s41...
I just uploaded the first version of {{exactplot}} to github.com/const-ae/exa... 🎉
It produces figures with consistent font size, Latex labels, and millimeter-perfect layouting. It's an alternative to patchwork with less elegant syntax but much more flexibility.
#rstats
It produces figures with consistent font size, Latex labels, and millimeter-perfect layouting. It's an alternative to patchwork with less elegant syntax but much more flexibility.
#rstats
February 12, 2025 at 11:40 AM
I just uploaded the first version of {{exactplot}} to github.com/const-ae/exa... 🎉
It produces figures with consistent font size, Latex labels, and millimeter-perfect layouting. It's an alternative to patchwork with less elegant syntax but much more flexibility.
#rstats
It produces figures with consistent font size, Latex labels, and millimeter-perfect layouting. It's an alternative to patchwork with less elegant syntax but much more flexibility.
#rstats
Reposted by Constantin Ahlmann-Eltze
@epigenci.bsky.social makes a pretty convincing case for pseudobulk (as opposed to GLMMs) in multi-sample single cell studies here: doi.org/10.1093/bioi... . #bioinformatics
Pseudobulk with proper offsets has the same statistical properties as generalized linear mixed models in single-cell case-control studies
AbstractMotivation. Generalized linear mixed models (GLMMs), such as the negative-binomial or Poisson linear mixed model, are widely applied to single-cell
doi.org
January 31, 2025 at 10:55 PM
@epigenci.bsky.social makes a pretty convincing case for pseudobulk (as opposed to GLMMs) in multi-sample single cell studies here: doi.org/10.1093/bioi... . #bioinformatics
Reposted by Constantin Ahlmann-Eltze
We have additional available spots. Please consider joining! It will be a blast.
I am Stoked about our upcoming @scverse.bsky.social
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
and @owkin.bsky.social hackathon, focused on spatial omics data analysis.
📅 March 17-19, 2025
📍 Owkin office, Paris
Apply now: docs.google.com/forms/d/e/1F...
Scverse x Owkin Hackathon in Paris
We're pleased to announce the next Scverse Hackathon will take place in the Owkin offices in Paris from 17/03/2025 9am to 19/03/2025 1:30pm.
This hackathon is a joint initiative between the scverse c...
docs.google.com
January 30, 2025 at 4:24 PM
We have additional available spots. Please consider joining! It will be a blast.
Reposted by Constantin Ahlmann-Eltze
CSAMA 2025 Biological Data Science Summer School
in Brixen, South Tyrol, 7-11 July
We cover (sc)-RNA-seq and spatial omics data analysis, underlying (bio)statistical topics, multi-omics, ... All hands-on using R/Bioconductor tools.
csama2025.bioconductor.eu
Registration opens on 1 Feb
in Brixen, South Tyrol, 7-11 July
We cover (sc)-RNA-seq and spatial omics data analysis, underlying (bio)statistical topics, multi-omics, ... All hands-on using R/Bioconductor tools.
csama2025.bioconductor.eu
Registration opens on 1 Feb
January 27, 2025 at 4:06 PM
CSAMA 2025 Biological Data Science Summer School
in Brixen, South Tyrol, 7-11 July
We cover (sc)-RNA-seq and spatial omics data analysis, underlying (bio)statistical topics, multi-omics, ... All hands-on using R/Bioconductor tools.
csama2025.bioconductor.eu
Registration opens on 1 Feb
in Brixen, South Tyrol, 7-11 July
We cover (sc)-RNA-seq and spatial omics data analysis, underlying (bio)statistical topics, multi-omics, ... All hands-on using R/Bioconductor tools.
csama2025.bioconductor.eu
Registration opens on 1 Feb
Reposted by Constantin Ahlmann-Eltze
My first post here on BlueSky to share our recent work with Claudia Feng and @leopoldparts.bsky.social - a large-scale single cell CRISPR screen to chart out gene regulation and the role of genomic background in iPSCs. Check out the data here: www.sanger.ac.uk/tool/crispri...
Does my mutation have the same impact as yours? Population genetics 🤠 🥸 🤓 🤡 meets single cell CRISPRi ⚡ ! www.biorxiv.org/content/10.1... Led by Claudia Feng, Oliver Stegle, Britta Velten, @sangerinstitute.bsky.social .
LinkedIn
This link will take you to a page that’s not on LinkedIn
lnkd.in
January 14, 2025 at 12:42 PM
My first post here on BlueSky to share our recent work with Claudia Feng and @leopoldparts.bsky.social - a large-scale single cell CRISPR screen to chart out gene regulation and the role of genomic background in iPSCs. Check out the data here: www.sanger.ac.uk/tool/crispri...