Edgar Dobriban The Benjamini--Hochberg Procedure Can Fail to Control the FDR for Correlated Two-Sided Gaussian Tests https://arxiv.org/abs/2607.12208

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)

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/

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!) ..

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... 🙈

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.

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.

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!

former BiGCaT colleague Serena Bonaretti has written the #openaccess book about #python: "Learn Python with Jupyter", now available from various stores and online at https://www.learnpythonwithjupyter.com/

🧬 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

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 😀

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/

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.

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.

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.

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.

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.

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

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.

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.

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...

EuroBioC goes south! The most south since… ever? Come join us in Barcelona 🇪🇸 for great science, community, and scholarly chats by the sea 🌊

Bioconductor@bioconductor.bsky.social · last yr.

📣 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

Heads-up that Genome Biology is starting a new benchmark collection ("Benchmarks v2.0"): www.biomedcentral.com/collections/...

📣 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

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

🌟 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

Comparison and evaluation of methods to infer gene regulatory networks from multimodal single-cell data | bioRxiv 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 ...

biorxiv.org

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.

Ascona 2025 - Schedule

Tentative Conference Schedule

sites.google.com

Mark Robinson@markrobinsonca.bsky.social · 2y ago

so one last call .. abstracts due today (6pm, time zone of your choice 😀) .. Ascona, Switzerland in March 2025 .. conference about all things benchmarking: sites.google.com/view/ascona2... Abstract submission link: t.co/zGGZ9Xd60E

Lovely little pedagogical note; well worth a look. arxiv.org/abs/2502.02305 'Information-Theoretic Proofs for Diffusion Sampling' - Galen Reeves, Henry D. Pfister

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...

LEMUR simplified | const-ae

A simplified implementation of the LEMUR algorithm.

const-ae.name

Constantin Ahlmann-Eltze@const-ae.bsky.social · 2y ago

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⬇️

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⬇️