@christofseiler.bsky.social
Applying statistics to biomedicine.
ORCID: https://orcid.org/0000-0001-8802-3642
ORCID: https://orcid.org/0000-0001-8802-3642
Reposted
🧬 EuroBioC2026 is coming to Turku, Finland, from June 3–5, 2026!
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
October 29, 2025 at 9:02 AM
🧬 EuroBioC2026 is coming to Turku, Finland, from June 3–5, 2026!
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
Expect 3 exciting days with the Bioconductor community, showcasing the latest advances in Bioconductor software and emerging technologies shaping computational biology.
👉 More details soon at eurobioc2026.bioconductor.org
Reposted
We close the day by many people thanking Susan Holmes for helping them with their data sets, loving the data, losing their fear of statistics, and her great teaching. Susan thanks everyone for them actually listening and doing what she told them to do 😀
June 3, 2025 at 11:54 PM
We close the day by many people thanking Susan Holmes for helping them with their data sets, loving the data, losing their fear of statistics, and her great teaching. Susan thanks everyone for them actually listening and doing what she told them to do 😀
Reposted
Next up: Diana Proctor: Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes. She thanks Susan for surviving her PhD. Susan inspired her own lab principles, like open data and your code is good enough to publish! New work on Candida: pubmed.ncbi.nlm.nih.gov/40011766/
June 3, 2025 at 11:30 PM
Next up: Diana Proctor: Clonal Candida auris and ESKAPE pathogens on the skin of residents of nursing homes. She thanks Susan for surviving her PhD. Susan inspired her own lab principles, like open data and your code is good enough to publish! New work on Candida: pubmed.ncbi.nlm.nih.gov/40011766/
Reposted
Next: Catherine Blish: Mapping cell-cell communication to understand host-pathogen interactions
She met Susan at a women’s faculty network event that she almost did not go to, and now they published over 30 papers together.
Study of the harmony of immune cell communication using Scriabin.
She met Susan at a women’s faculty network event that she almost did not go to, and now they published over 30 papers together.
Study of the harmony of immune cell communication using Scriabin.
June 3, 2025 at 11:00 PM
Next: Catherine Blish: Mapping cell-cell communication to understand host-pathogen interactions
She met Susan at a women’s faculty network event that she almost did not go to, and now they published over 30 papers together.
Study of the harmony of immune cell communication using Scriabin.
She met Susan at a women’s faculty network event that she almost did not go to, and now they published over 30 papers together.
Study of the harmony of immune cell communication using Scriabin.
Reposted
Next: Jess Grembi with ‘Uncovering the latent variable in my statistical trajectory’
Jess was asked to beta-test Susan’s book, which was helpful to both.
Working with a statistician is better than trying to become one.
Thank you, Susan to make statistical methods accessible for biologists.
Jess was asked to beta-test Susan’s book, which was helpful to both.
Working with a statistician is better than trying to become one.
Thank you, Susan to make statistical methods accessible for biologists.
June 3, 2025 at 10:47 PM
Next: Jess Grembi with ‘Uncovering the latent variable in my statistical trajectory’
Jess was asked to beta-test Susan’s book, which was helpful to both.
Working with a statistician is better than trying to become one.
Thank you, Susan to make statistical methods accessible for biologists.
Jess was asked to beta-test Susan’s book, which was helpful to both.
Working with a statistician is better than trying to become one.
Thank you, Susan to make statistical methods accessible for biologists.
Reposted
Next: Julia Fukuyama: The power of multiple views for exploring diversity across phylogenetic scales
There are many ways of measuring distances between communities, taking phylogenetic relations between the species into account.
There are many ways of measuring distances between communities, taking phylogenetic relations between the species into account.
June 3, 2025 at 9:36 PM
Next: Julia Fukuyama: The power of multiple views for exploring diversity across phylogenetic scales
There are many ways of measuring distances between communities, taking phylogenetic relations between the species into account.
There are many ways of measuring distances between communities, taking phylogenetic relations between the species into account.
Reposted
Next: Pratheepa Jeganathan (online): Spatial Statistics Meets Biology: Extending Constrained Clustering with Spatial Pattern Similarity
How can we detect tumor micro-environments? Susan’s book chapter on image analysis has helped us choose appropriate methods.
How can we detect tumor micro-environments? Susan’s book chapter on image analysis has helped us choose appropriate methods.
June 3, 2025 at 9:14 PM
Next: Pratheepa Jeganathan (online): Spatial Statistics Meets Biology: Extending Constrained Clustering with Spatial Pattern Similarity
How can we detect tumor micro-environments? Susan’s book chapter on image analysis has helped us choose appropriate methods.
How can we detect tumor micro-environments? Susan’s book chapter on image analysis has helped us choose appropriate methods.
Reposted
Next: Nikos Ignatiadis How does variance moderation for differential expression work?
How to best analyze small variations in a set of 400k probes (genes) and large numbers of samples measured in two experimental conditions.
How to best analyze small variations in a set of 400k probes (genes) and large numbers of samples measured in two experimental conditions.
June 3, 2025 at 8:59 PM
Next: Nikos Ignatiadis How does variance moderation for differential expression work?
How to best analyze small variations in a set of 400k probes (genes) and large numbers of samples measured in two experimental conditions.
How to best analyze small variations in a set of 400k probes (genes) and large numbers of samples measured in two experimental conditions.
Reposted
After lunch: Wolfgang Huber (online) with: Single cell differential expression without discrete cell types
Can we replace +/- cell type characterization with a continuous parameterization?
Susan and I wrote a book together: www.huber.embl.de/msmb/ Modern Statistics for Modern Biology
Can we replace +/- cell type characterization with a continuous parameterization?
Susan and I wrote a book together: www.huber.embl.de/msmb/ Modern Statistics for Modern Biology
June 3, 2025 at 8:46 PM
After lunch: Wolfgang Huber (online) with: Single cell differential expression without discrete cell types
Can we replace +/- cell type characterization with a continuous parameterization?
Susan and I wrote a book together: www.huber.embl.de/msmb/ Modern Statistics for Modern Biology
Can we replace +/- cell type characterization with a continuous parameterization?
Susan and I wrote a book together: www.huber.embl.de/msmb/ Modern Statistics for Modern Biology
Reposted
Next: Christof Seiler: Prediction Intervals at the Tour de France
Using AI to predict calorie consumption, to plan meals for cyclists. Used variables such as race type, BMI, weather etc.
We also can calculate and correct for spillover in flow cytometry data.
Using AI to predict calorie consumption, to plan meals for cyclists. Used variables such as race type, BMI, weather etc.
We also can calculate and correct for spillover in flow cytometry data.
June 3, 2025 at 6:52 PM
Next: Christof Seiler: Prediction Intervals at the Tour de France
Using AI to predict calorie consumption, to plan meals for cyclists. Used variables such as race type, BMI, weather etc.
We also can calculate and correct for spillover in flow cytometry data.
Using AI to predict calorie consumption, to plan meals for cyclists. Used variables such as race type, BMI, weather etc.
We also can calculate and correct for spillover in flow cytometry data.
Reposted
Next: Joey McMurdie: From R packages to Human Disease Startups: A Journey in Statistical Biology with guidance from Susan Holmes
He shares a timeline of his life with Susan, as his PhD committee, postdoc advisor, advisory board, and co-author. Together, they wrote phyloseq and dada2.
He shares a timeline of his life with Susan, as his PhD committee, postdoc advisor, advisory board, and co-author. Together, they wrote phyloseq and dada2.
June 3, 2025 at 4:42 PM
Next: Joey McMurdie: From R packages to Human Disease Startups: A Journey in Statistical Biology with guidance from Susan Holmes
He shares a timeline of his life with Susan, as his PhD committee, postdoc advisor, advisory board, and co-author. Together, they wrote phyloseq and dada2.
He shares a timeline of his life with Susan, as his PhD committee, postdoc advisor, advisory board, and co-author. Together, they wrote phyloseq and dada2.
Reposted
Today I will be attending a conference at Stanford University, in honor of Susan Holmes, who is retiring. She has been an essential driving force for our microbiome research.
Bridging Biology and Statistics: Insights and Innovations for Modern Biology
www.eventcreate.com/e/stats4mode...
Bridging Biology and Statistics: Insights and Innovations for Modern Biology
www.eventcreate.com/e/stats4mode...
Bridging Biology and Statistics: Insights and Innovations for Modern Biology | June 03, 2025
Join us on June 03
www.eventcreate.com
June 3, 2025 at 3:24 PM
Today I will be attending a conference at Stanford University, in honor of Susan Holmes, who is retiring. She has been an essential driving force for our microbiome research.
Bridging Biology and Statistics: Insights and Innovations for Modern Biology
www.eventcreate.com/e/stats4mode...
Bridging Biology and Statistics: Insights and Innovations for Modern Biology
www.eventcreate.com/e/stats4mode...
Reposted
EuroBioC goes south! The most south since… ever? Come join us in Barcelona 🇪🇸 for great science, community, and scholarly chats by the sea 🌊
📣 EuroBioC2025 Registration is Open! 🎉
📍 Barcelona, 17–19 Sept 2025
Join us for keynotes, talks, workshops & more on open-source bioinformatics & Bioconductor.
🔗 eurobioc2025.bioconductor.org/pages/regist...
#EuroBioC2025 #Bioinformatics
📍 Barcelona, 17–19 Sept 2025
Join us for keynotes, talks, workshops & more on open-source bioinformatics & Bioconductor.
🔗 eurobioc2025.bioconductor.org/pages/regist...
#EuroBioC2025 #Bioinformatics
registration – EuroBioC2025
The budget EuroBioC2025 is conceived to break even after the conference. As a result, the organization of the EuroBioC2025 is unable to offer individual refunds.
eurobioc2025.bioconductor.org
May 19, 2025 at 8:04 AM
EuroBioC goes south! The most south since… ever? Come join us in Barcelona 🇪🇸 for great science, community, and scholarly chats by the sea 🌊
Reposted
Heads-up that Genome Biology is starting a new benchmark collection ("Benchmarks v2.0"):
www.biomedcentral.com/collections/...
www.biomedcentral.com/collections/...
Call for papers - Benchmarks v2.0
www.biomedcentral.com
April 29, 2025 at 7:08 AM
Heads-up that Genome Biology is starting a new benchmark collection ("Benchmarks v2.0"):
www.biomedcentral.com/collections/...
www.biomedcentral.com/collections/...
Reposted
📣 EuroBioC2025: Abstract Submissions Open!
Join us in Barcelona, Spain 🇪🇸, Sep 17-19, 2025, for the European Bioconductor Conference! Submit your abstract for a short talk, workshop, or poster by Apr 24.
➡️ Submit https://buff.ly/3EN9w6P
#EuroBioC2025 #Bioinformatics #RStats #DataScience
Join us in Barcelona, Spain 🇪🇸, Sep 17-19, 2025, for the European Bioconductor Conference! Submit your abstract for a short talk, workshop, or poster by Apr 24.
➡️ Submit https://buff.ly/3EN9w6P
#EuroBioC2025 #Bioinformatics #RStats #DataScience
European Bioconductor Conference 2025
EuroBioC2025 is the European edition of the Bioconductor conference that will take place on September 17th to 19th, 2025, in Barcelona, Spain. EuroBioC2025 will bring together the Bioconductor…
buff.ly
February 20, 2025 at 9:09 AM
📣 EuroBioC2025: Abstract Submissions Open!
Join us in Barcelona, Spain 🇪🇸, Sep 17-19, 2025, for the European Bioconductor Conference! Submit your abstract for a short talk, workshop, or poster by Apr 24.
➡️ Submit https://buff.ly/3EN9w6P
#EuroBioC2025 #Bioinformatics #RStats #DataScience
Join us in Barcelona, Spain 🇪🇸, Sep 17-19, 2025, for the European Bioconductor Conference! Submit your abstract for a short talk, workshop, or poster by Apr 24.
➡️ Submit https://buff.ly/3EN9w6P
#EuroBioC2025 #Bioinformatics #RStats #DataScience
🌟 Upcoming Online Seminar: Immune Dysregulation in Sjögren's Disease 🌟
Our Department of Rheumatology is excited to host this seminar discussing multiomics approaches, spatial techniques, and disease pathology.
📍Zoom: uzh.zoom.us/j/6944721108...
📅 Thursday, June 19, 16.00-17.30 CET
Our Department of Rheumatology is excited to host this seminar discussing multiomics approaches, spatial techniques, and disease pathology.
📍Zoom: uzh.zoom.us/j/6944721108...
📅 Thursday, June 19, 16.00-17.30 CET
March 19, 2025 at 9:42 AM
🌟 Upcoming Online Seminar: Immune Dysregulation in Sjögren's Disease 🌟
Our Department of Rheumatology is excited to host this seminar discussing multiomics approaches, spatial techniques, and disease pathology.
📍Zoom: uzh.zoom.us/j/6944721108...
📅 Thursday, June 19, 16.00-17.30 CET
Our Department of Rheumatology is excited to host this seminar discussing multiomics approaches, spatial techniques, and disease pathology.
📍Zoom: uzh.zoom.us/j/6944721108...
📅 Thursday, June 19, 16.00-17.30 CET
Reposted
Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data | bioRxiv
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data
Cells regulate their functions through gene expression, driven by a complex interplay of transcription factors and other regulatory mechanisms that together can be modeled as gene regulatory networks ...
www.biorxiv.org
March 18, 2025 at 8:51 AM
Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data | bioRxiv
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted
Quick update. We have a pretty exciting lineup of topics/speakers in and around benchmarking that will be presented in Ascona at the end of the month:
sites.google.com/view/ascona2...
There are few registration slots left, so if you are interested to join us, get in touch.
sites.google.com/view/ascona2...
There are few registration slots left, so if you are interested to join us, get in touch.
March 5, 2025 at 1:56 PM
Quick update. We have a pretty exciting lineup of topics/speakers in and around benchmarking that will be presented in Ascona at the end of the month:
sites.google.com/view/ascona2...
There are few registration slots left, so if you are interested to join us, get in touch.
sites.google.com/view/ascona2...
There are few registration slots left, so if you are interested to join us, get in touch.
Reposted
Lovely little pedagogical note; well worth a look.
arxiv.org/abs/2502.02305
'Information-Theoretic Proofs for Diffusion Sampling'
- Galen Reeves, Henry D. Pfister
arxiv.org/abs/2502.02305
'Information-Theoretic Proofs for Diffusion Sampling'
- Galen Reeves, Henry D. Pfister
February 5, 2025 at 9:43 AM
Lovely little pedagogical note; well worth a look.
arxiv.org/abs/2502.02305
'Information-Theoretic Proofs for Diffusion Sampling'
- Galen Reeves, Henry D. Pfister
arxiv.org/abs/2502.02305
'Information-Theoretic Proofs for Diffusion Sampling'
- Galen Reeves, Henry D. Pfister
Reposted
For the Monday morning crowds :)
Also take a look at my blog post where I compress the full lemur package into 100 lines of code and explain the core algorithm.
const-ae.name/post/2025-01...
Also take a look at my blog post where I compress the full lemur package into 100 lines of code and explain the core algorithm.
const-ae.name/post/2025-01...
January 6, 2025 at 11:46 AM
For the Monday morning crowds :)
Also take a look at my blog post where I compress the full lemur package into 100 lines of code and explain the core algorithm.
const-ae.name/post/2025-01...
Also take a look at my blog post where I compress the full lemur package into 100 lines of code and explain the core algorithm.
const-ae.name/post/2025-01...
Reposted
After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳
www.nature.com/articles/s41...
LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.
Some highlights⬇️
www.nature.com/articles/s41...
LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.
Some highlights⬇️
January 3, 2025 at 7:25 PM
After 4y in the making, I am super excited that my main PhD project is published 🎉🥳🎉🎉🥳
www.nature.com/articles/s41...
LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.
Some highlights⬇️
www.nature.com/articles/s41...
LEMUR is a tool to analyze multi-condition single-cell data and model differential expression as a continuous function of the cell-state space.
Some highlights⬇️
Reposted
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
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 and clustering-free ...
doi.org
January 3, 2025 at 7:18 PM
How to do differential expression with scRNAseq data? State of the art is "pseudo-bulk" analysis with RNA-seq methods like edgeR or DESeq2, where "cell type" is encoded as discrete categories. Biologically, discrete categories are not always the most appropriate concept.(1/3)
doi.org/10.1038/s415...
doi.org/10.1038/s415...
Reposted
1/7 Planning to build a single-cell atlas? Or wondering how atlases can be useful to your research? Read our guide on single-cell atlases www.nature.com/articles/s41... published in Nature Methods, by @lisasikkema.bsky.social, @khrovatin.bsky.social, Malte Luecken, @fabiantheis.bsky.social et al.
December 13, 2024 at 10:33 AM
1/7 Planning to build a single-cell atlas? Or wondering how atlases can be useful to your research? Read our guide on single-cell atlases www.nature.com/articles/s41... published in Nature Methods, by @lisasikkema.bsky.social, @khrovatin.bsky.social, Malte Luecken, @fabiantheis.bsky.social et al.
Reposted
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...
🧪🧬💻
Reposted
Major milestone: Tabula Sapiens 2.0 maps tissue composition & TF expression in 175 cell types, identifying 745 ubiquitous & 890 cell type-specific TFs (many still uncharacterized -> #Codebook) w/ roles in tissue homeostasis, stress response & metabolism. #SingleCell www.biorxiv.org/content/10.1...
Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues
The Tabula Sapiens is a reference human cell atlas containing single cell transcriptomic data from more than two dozen organs and tissues. Here we report Tabula Sapiens 2.0 which includes data from ni...
www.biorxiv.org
December 8, 2024 at 8:55 AM
Major milestone: Tabula Sapiens 2.0 maps tissue composition & TF expression in 175 cell types, identifying 745 ubiquitous & 890 cell type-specific TFs (many still uncharacterized -> #Codebook) w/ roles in tissue homeostasis, stress response & metabolism. #SingleCell www.biorxiv.org/content/10.1...