Sign in

christofseiler.bsky.social

@christofseiler.bsky.social
253 followers 1.4K following 2 posts

Applying statistics to biomedicine. ORCID: orcid.org/0000-0001-8802-3642

PostsRepliesMedia
Reposted by @christofseiler.bsky.social
arxiv math.ST @arxiv-math-st.bsky.social · 15/07/2026
Edgar Dobriban The Benjamini--Hochberg Procedure Can Fail to Control the FDR for Correlated Two-Sided Gaussian Tests arxiv.org/abs/2607.12208
021
Reposted by @christofseiler.bsky.social
František Bartoš @fbartos.bsky.social · 02/06/2026
Check out the great program of the *1st Interdisciplinary Symposium on Meta Science for Methods Research* organized 31 August and 1 September in Zürich! Ton of cool speakers and meta-methodological reseach! crsuzh.pages.uzh.ch/msmr/program/ (registration still open)
crsuzh.pages.uzh.ch
index – MSMR 2026
02013
Reposted by @christofseiler.bsky.social
Tim Morris @timpmorris.bsky.social · 02/06/2026
The program is up for the first 1st Interdisciplinary Symposium on Meta Science for Methods Research and it promises to be a BANGER! crsuzh.pages.uzh.ch/msmr/program/
crsuzh.pages.uzh.ch
index – MSMR 2026
2136
Reposted by @christofseiler.bsky.social
Mark Robinson @markrobinsonca.bsky.social · 27/04/2026
Still ~3 days left to submit an abstract to MSMR (Meta Science for Methods Research) 2026 in Zurich .. scicomm.xyz/@SamuelPawel... crsuzh.pages.uzh.ch/msmr/ Come join us and discuss how quantitative/computational methods are developed, evaluated (benchmarked!) ..
scicomm.xyz
Samuel Pawel (@SamuelPawel@scicomm.xyz)
Registration and abstract submission now open: 1st Interdisciplinary Symposium on Meta Science for Methods Research (MSMR 2026) How can we improve research on research methods? This symposium will br...
062
Reposted by @christofseiler.bsky.social
Will Macnair @willmacnair.bsky.social · 13/03/2026
scprocess is the result of an *unbelievable* amount of hard work by Maruša Koderman, PhD at University of Zürich co-supervised by me and @markrobinsonca.bsky.social. Maruša did so much: ideas, writing so much code, testing and debugging, writing all of the docs, tolerating me changing my mind... 🙈
132
Reposted by @christofseiler.bsky.social
Helena Lucia Crowell @helucro.bsky.social · 02/02/2026
Registration now open for CSAMA! 📜 csama2026.bioconductor.eu Highly recommend for learning data science with a scenery, plus a fantastic crowd of students and faculty alike! 📸 from the traditional mid-week hike during last year’s edition.
065
christofseiler.bsky.social @christofseiler.bsky.social · 14/01/2026
Save the date: April 9 from 4pm to 6pm CET. Our department is hosting an online seminar with @noeliaferruz.bsky.social @sdomcke.bsky.social @const-ae.bsky.social who will talk about models for protein design, large-scale perturbation screens, and benchmarking of perturbation prediction models.
063
Reposted by @christofseiler.bsky.social
Wolfgang Huber @wkhuber.bsky.social · 22/12/2025
Announcing the Ascona Workshop "Statistical and AI methods for multi-modal multi-scale modeling of biological systems" on 28 June - 3 July 2026 in Ascona, CH www.huber.embl.de/group/events... Reserve the dates!
View from Monte Verità onto Ascona and Lago Maggiore
1228
Reposted by @christofseiler.bsky.social
Egon Willigh☮gen 🟥 @egonw.mastodon.social.ap.brid.gy · 18/12/2025
former BiGCaT colleague Serena Bonaretti has written the #openaccess book about #python: "Learn Python with Jupyter", now available from various stores and online at www.learnpythonwithjupyter.com
Screenshot from the website with the two "Get the book" options, with the cover for both (the same, orange with white letters, and color stripes) and the author name, one to buy a physical copy and one to download the free ebook, with the option to by Serena a coffee.
054
Reposted by @christofseiler.bsky.social
Bioconductor @bioconductor.bsky.social · 29/10/2025
🧬 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
01211
Reposted by @christofseiler.bsky.social
Elisabeth Bik @elisabethbik.bsky.social · 04/06/2025
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 😀
Susan Holmes in an orange and pink dress, laughing.
0263
Reposted by @christofseiler.bsky.social
Elisabeth Bik @elisabethbik.bsky.social · 04/06/2025
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/
The speaker with a thank you slide to Susan
271
Reposted by @christofseiler.bsky.social
Elisabeth Bik @elisabethbik.bsky.social · 04/06/2025
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.
The speaker in front of her title slide.
131
Reposted by @christofseiler.bsky.social
Elisabeth Bik @elisabethbik.bsky.social · 03/06/2025
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.
181
Reposted by @christofseiler.bsky.social
Elisabeth Bik @elisabethbik.bsky.social · 03/06/2025
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.
The speaker with her title slide
161
Reposted by @christofseiler.bsky.social
Elisabeth Bik @elisabethbik.bsky.social · 03/06/2025
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.
151
Reposted by @christofseiler.bsky.social
Elisabeth Bik @elisabethbik.bsky.social · 03/06/2025
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.
The speaker showing a slide with a photo of people, including Susan, at a conference. In Switzerland.
181
Reposted by @christofseiler.bsky.social
Elisabeth Bik @elisabethbik.bsky.social · 03/06/2025
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
Screen of speaker saying “Sorry that I can’t be there”
2143
Reposted by @christofseiler.bsky.social
Elisabeth Bik @elisabethbik.bsky.social · 03/06/2025
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.
The speaker with his title slide
1123
Reposted by @christofseiler.bsky.social
Elisabeth Bik @elisabethbik.bsky.social · 03/06/2025
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.
The speaker and his title slide.
2182
Reposted by @christofseiler.bsky.social
Elisabeth Bik @elisabethbik.bsky.social · 03/06/2025
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...
eventcreate.com
Bridging Biology and Statistics: Insights and Innovations for Modern Biology | June 03, 2025
Join us on June 03
722131
Reposted by @christofseiler.bsky.social
Helena Lucia Crowell @helucro.bsky.social · 19/05/2025
EuroBioC goes south! The most south since… ever? Come join us in Barcelona 🇪🇸 for great science, community, and scholarly chats by the sea 🌊
072
Reposted by @christofseiler.bsky.social
Mark Robinson @markrobinsonca.bsky.social · 29/04/2025
Heads-up that Genome Biology is starting a new benchmark collection ("Benchmarks v2.0"): www.biomedcentral.com/collections/...
biomedcentral.com
Call for papers - Benchmarks v2.0
21010
Reposted by @christofseiler.bsky.social
Bioconductor @bioconductor.bsky.social · 20/02/2025
📣 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 buff.ly/3EN9w6P #EuroBioC2025 #Bioinformatics #RStats #DataScience
buff.ly
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…
01817
christofseiler.bsky.social @christofseiler.bsky.social · 19/03/2025
🌟 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
Flyer of the event.
011
Reposted by @christofseiler.bsky.social
Santiago Carmona 🧬 🖥️ 🧑🏾‍🔬 @carmonation.bsky.social · 18/03/2025
Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data | bioRxiv www.biorxiv.org/content/10.1...
biorxiv.org
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 ...
071
Reposted by @christofseiler.bsky.social
Mark Robinson @markrobinsonca.bsky.social · 05/03/2025
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
Ascona 2025 - Schedule
Tentative Conference Schedule
053
Reposted by @christofseiler.bsky.social
Sam Power @spmontecarlo.bsky.social · 05/02/2025
Lovely little pedagogical note; well worth a look. arxiv.org/abs/2502.02305 'Information-Theoretic Proofs for Diffusion Sampling' - Galen Reeves, Henry D. Pfister
1235
Reposted by @christofseiler.bsky.social
Constantin Ahlmann-Eltze @const-ae.bsky.social · 06/01/2025
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...
const-ae.name
LEMUR simplified | const-ae
A simplified implementation of the LEMUR algorithm.
0191
Reposted by @christofseiler.bsky.social
Constantin Ahlmann-Eltze @const-ae.bsky.social · 03/01/2025
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⬇️
Overview of the LEMUR steps: (1) subspace alignment, (2) differential expression, (3) DE neighborhoods, (4) pseudobulking.
815435
Reposted by @christofseiler.bsky.social
Wolfgang Huber @wkhuber.bsky.social · 03/01/2025
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
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 ...
724793
Reposted by @christofseiler.bsky.social
Lisa Sikkema @lisasikkema.bsky.social · 13/12/2024
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.
15017
Reposted by @christofseiler.bsky.social
Davis McCarthy @davisjmcc.bsky.social · 10/12/2024
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... 🧪🧬💻
biorxiv.org
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...
24724
Reposted by @christofseiler.bsky.social
Bart Deplancke @bartdeplancke.bsky.social · 08/12/2024
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...
biorxiv.org
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...
05324
Reposted by @christofseiler.bsky.social
Anne Carpenter @drannecarpenter.bsky.social · 04/12/2024
Now on biorxiv! The JUMP-Cell Painting Consortium’s paper: “Morphological map of under- and over-expression of genes in human cells” This is the genetic perturbation portion of the JUMP’s dataset; our chemical perturbation paper will come in a few months www.biorxiv.org/content/10.1...
biorxiv.org
Morphological map of under- and over-expression of genes in human cells
Cell Painting images offer valuable insights into the state of a cell and enable many biological applications, but publicly available arrayed datasets only include hundreds of genes perturbed. The JUM...
17121
Reposted by @christofseiler.bsky.social
Samuel Gunz @samuelgunz.bsky.social · 04/12/2024
Interested in spatial statistics for spatial omics data? Check out our new resource: pasta. We show how different technologies lead to different data modalities give and overview of point-pattern and lattice-based spatial analysis. Feedback welcome! arxiv.org/abs/2412.01561
arxiv.org
pasta: Pattern Analysis for Spatial Omics Data
Spatial omics assays allow for the molecular characterisation of cells in their spatial context. Notably, the two main technological streams, imaging-based and high-throughput sequencing-based, can gi...
1207
Reposted by @christofseiler.bsky.social
Tomàs Montserrat Ayuso @tmontsay.bsky.social · 03/12/2024
Not checking nuclear markers like MALAT1 or intronic reads in your scRNA-seq data?🚨 We show their power to flag low-quality cells—even in top public datasets. It’s time to prioritize better QC for cleaner, more reliable genomics research! Read more: bmcgenomics.biomedcentral.com/articles/10.... 1/8
bmcgenomics.biomedcentral.com
High content of nuclei-free low-quality cells in reference single-cell atlases: a call for more stringent quality control using nuclear fraction - BMC Genomics
The advent of droplet-based single-cell RNA-sequencing (scRNA-seq) has dramatically increased data throughput, enabling the release of a diverse array of tissue cell atlases to the public. However, we...
4244126
Reposted by @christofseiler.bsky.social
Will Macnair @willmacnair.bsky.social · 04/12/2024
Idea: - Get challenging samples, best would be human disease (e.g. cancer, neurodegeneration) - Do single nuclei experiment with SmartSeq - Image each well, and annotate the images with "intact", "lysed", etc (maybe you annotate a subset, then train a classifier) - Link QC metrics to labels - Profit
151
Reposted by @christofseiler.bsky.social
Helena Lucia Crowell @helucro.bsky.social · 04/12/2024
A little piece that's been in the works with former MSc, now PhD student, Jiayi Wang & @markrobinsonca.bsky.social in the multi-sample/-condition/-subpopulation theme: ...
1137
Reposted by @christofseiler.bsky.social
bioRxivpreprint @biorxivpreprint.bsky.social · 06/10/2023
spillR: Spillover Compensation in Mass Cytometry Data www.biorxiv.org/content/10.1101/202…
biorxiv.org
spillR: Spillover Compensation in Mass Cytometry Data https://www.biorxiv.org/content/10.1101/2023.10.04.560870v1
Channel interference in mass cytometry can cause spillover and may result in miscounting of protein
011
Reposted by @christofseiler.bsky.social
arxiv math.ST @arxiv-math-st.bsky.social · 19/11/2024
Anastasios N. Angelopoulos, Rina Foygel Barber, Stephen Bates Theoretical Foundations of Conformal Prediction arxiv.org/abs/2411.11824
052