Julien Roux

IMO it’s weird and probably irresponsible to teach bioinformatics without some nod to the group dynamics that shaped (otherwise inexplicable) things like the GFF file format or the Gene Ontology. Not to mention why tools back then had names like BLAST and FASTA,but now are named after cuddly animals

and if we imagine that the increase in the number of projects submitted may also be due to the use of AI, we will end up with an AI evaluating an AI 🫣

Amos Bairoch, Swiss pioneer of bioinformatics, passes away We are deeply saddened to announce the passing of our co-founder and Group Leader Amos Bairoch. Emeritus professor at the University of Geneva, he shaped the development of bioinformatics over more th...

We are deeply saddened to share the passing of Amos Bairoch, pioneer of bioinformatics and co-founder of SIB. His lifelong commitment for high-quality, open data transformed global research. We honour his legacy by continuing to build the future of bioinformatics.

Amos Bairoch, Swiss pioneer of bioinformatics, passes away We are deeply saddened to announce the passing of our co-founder and Group Leader Amos Bairoch. Emeritus professor at the University of Geneva, he shaped the development of bioinformatics over more th...

A #Bioinformatics giant passes away. Very sad to hear this news today. Sad for Switzerland, and for the whole world. Amos Bairoch was a part of the Bioinformatics community for many decades. He will be missed. #Database #Biocuration #SwissProt #Prosite #Cellosaurus |
www.sib.swiss/news/amos-ba...

Comparative analysis of commercial Imaging-based #SpatialTranscriptomics methods

Xenium
CosMx 1k
MERSCOPE

Tissue Microarray
17 tumor+16 normal tissue

Transcript count
vs Reference RNAseq
Segmentation accuracy
Cell type annotation

#NatComms 2025
www.nature.com/articles/s41...

Sabine Himmelsbach

The Faculty of Science awarded Sabine Himmelsbach an honorary doctorate for her outstanding communication of scientific topics through art. As Director of the House of Electronic Arts in Basel, she promotes dialogue between art, technology and society.

Janet Hering

The Faculty of Medicine awarded @janethering.bsky.social an honorary doctorate for her pioneering research on the relationship between the environment and health. Her great commitment to equal opportunities has empowered women to advance in traditionally male-dominated fields of science.

Orchestrating Spatial Transcriptomics Analysis with Bioconductor
(including interoperability with Python)

Paper: www.biorxiv.org/content/10.1...
Book: bioconductor.org/books/OSTA/

#Rstats

We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor”!

Not sure why @lpachter.bsky.social did not post this here. But it is brilliant. Single cell genomics finally makes it to the clinic.

Spatial omics images? bsky.app/profile/lape...

steven spielberg is sitting in a chair with his hands folded ALT: steven spielberg is sitting in a chair with his hands folded

Today's pro-tip for effective research seminars: Invest your efforts in clear and accessible visuals! Figures from papers often have too high complexity for seminars - a bit like a book needs to be streamlined when making a movie out of it. 😅📚🎬

Unbelievable! How can this crap still be published?

James Watson, dead at 97, was a scientific legend and a pariah among his peers James Watson, the co-discoverer of the structure of DNA who died Thursday at 97, was a scientific legend and a pariah among his peers.

I like this obit better...

One of the curiosities of genomics history is that James Watson was vehemently against cDNA sequencing (for ESTs), and fought with Craig Venter & Bernadine Healy who championed it. Tl;dr Watson ended up resigning from the HGP, Venter plowed ahead... and we now have #scRNAseq.

#ECCB2026 European Conference on Computational Biology, Geneva🇨🇭:

Call for tutorials & workshops.

⬇️⬇️⬇️

Editorial_Board Editorial Team Editor-in-Chief Xun Xu, PhD; BGI Research, Shenzhen, China Executive Editor Hongling Zhou; GigaScience Press, BGI Shenzhen, China Edito

About half the GigaScience editorial board (incl me) just resigned (academic.oup.com/gigascience/... is not yet updated). I resigned because it is very unclear what is happening and why - see @scedmunds.bsky.social blog post gigasciencejournal.com/blog/and-its..., for eg

If a function isn't implemented yet, DON'T put examples in the docs 😅 Nothing more frustrating than copying code from official documentation. Example: dds.lfcShrink Clearly mark what's ready vs what's not. Your users will thank you 🙏 inmoose.readthedocs.io/en/stable/de...

Two panel comic: Left: a mostly completed puzzle with a regular-looking piece missing labeled "My Story So Far" Right: a blobby and irregular shape, with an arrow pointing at the missing piece (it obviously does not fit) labeled "My Latest Experiment"

Sigh. We're gonna need a bigger story...

Fig. 1. Dynamic sex variability - An integrative, multidimensional framework. A framework that centers sex variability will enable the study of sex across multiple levels of biological analysis (colored boxes). A) Visual schematic representing the degree of sex variability (y-axis) across biological scale (x-axis) and time (z-axis), with example sex variables of interest (not all possible covariates and functional relationships are presented). In this example, to decipher mechanisms linking gonadal hormones to receptive reproductive behavior in adult rodents (lordosis), the functional relationships (black subset of possible gray relationships) between select variables (bold words) need to be identified. At each level of analysis, numerous variables differ across sex to contribute to reproductive behavior through these functional interactions. Importantly, the degree of variability across sex categories is dynamic and is affected by developmental stage, experience, and environment.

Fig. 2. Approaches for the statistical analysis of sex-associated traits. Flow chart of example approaches for analyzing datasets with sex-associated variables. These analyses answer questions about whether and how sex-associated variables explain variation in dependent variables of interest, how independent variables of interest explain variation in dependent sex-associated variables, and how sex-associated variables (within and/or across levels of analysis) relate to one another. The examples match those in the text where possible, but the approaches are widely applicable and flexible. The choice(s) of analyses should follow directly from the research question(s), and it is likely that multiple approaches will be used in the analysis of an integrative dataset.

Fig. 3. Questions for evaluating frameworks and approaches which study sex variability and diversity. Here, we present a set of questions to ask when critically evaluating work (whether it is your own or others) that addresses sex diversity and variability. Note that these questions reflect the integration of the conceptual framework, experimental approaches, and analysis and interpretation, as each of these aspects informs the other.

The sex binary is dead!
Long live sex diversity & variability!

Sex is one of the greatest sources of variation seen in life. How do we advance the scientific study of sex across the animal kingdom? Read our latest article in Hormones & Behavior to find out!

🧪 🧠 #neuroskyence

Meet the team of EU-SABV!
This is a group of researchers with a special interest of including sex as a biological variable into their work.
For the next 4 years, this team will work to enhance current SABV policy in preclinical research!
#SABV
@costprogramme.bsky.social
@jaricivana.bsky.social

📣 Last day to register to our course!
It's happening next Monday, all-day (CEST), and it's online so you can attend from anywhere

How thoughtful experimental design can empower biologists in the omics era - Nature Communications Here, the authors discuss principles of experimental design that are relevant for all biology research, along with special considerations for projects using -omics approaches, highlighting common expe...

Fantastic review on the importance of rigorous experimental design. Amen. 😊

"'To consult the statistician after an experiment is finished is often merely to ask him to conduct a post mortem examination. He can perhaps say what the experiment died of.' – Ronald A. Fisher"

@manuelkleiner.bsky.social

How thoughtful experimental design can empower biologists in the omics era - Nature Communications Here, the authors discuss principles of experimental design that are relevant for all biology research, along with special considerations for projects using -omics approaches, highlighting common expe...

Great publication from Maggie Wagner (KU) and Manuel Kleiner (NCS) on how to design microbiome (+ other Omic) projects with downstream statistics in mind!

A must read for trainees!
www.nature.com/articles/s41...

The article has also a table with more in depth resources on various aspects of experimental design for more advance design needs.

How thoughtful experimental design can empower biologists in the omics era - Nature Communications Here, the authors discuss principles of experimental design that are relevant for all biology research, along with special considerations for projects using -omics approaches, highlighting common expe...

I am really excited to see this article on basic experimental design principles published. Definitely will be mandatory reading for incoming graduate students in my lab. Maggie Wagner who led this article did an amazing job with the illustrations of basic principles www.nature.com/articles/s41...

For example many people would think that you need to double the number of animals if you plan an experiment including both sexes and want to keep statistical power... Which is actually not true

Yes, we will discuss experimental design and power issues. Even for bioinformaticians, it's important to be able to weigh in on a discussion about study design!

One challenge is to analyze the data rigorously, for example extract significant interactions between sex and other factors of interest. Another is to then interpret the results (e.g., no significance doesn't always mean there is no effect, maybe the experiment is underpowered...)

Correction: our course will now be taught online!