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julienroux.bsky.social
Julien Roux
@julienroux.bsky.social
1.5K followers 670 following 99 posts
Bioinformatician, Department of Biomedicine @ Uni Basel & Swiss Institute of Bioinformatics Interested in bulk and single-cell omics, data analysis, experimental design, data visualization, R/Bioc, open science, EDI, etc 🧬 🖥️
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · 19d
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
julienroux.bsky.social
Julien Roux @julienroux.bsky.social · 19d
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!
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · 20d
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...)
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · 24d
Correction: our course will now be taught online!
julienroux.bsky.social
Julien Roux @julienroux.bsky.social · 24d
Our course will actually be taught online, to make it easier for people abroad to attend!
julienroux.bsky.social
Julien Roux @julienroux.bsky.social · Sep 8
Registrations now open for our course 𝐁𝐞𝐬𝐭 𝐏𝐫𝐚𝐜𝐭𝐢𝐜𝐞𝐬 𝐟𝐨𝐫 𝐈𝐧𝐯𝐞𝐬𝐭𝐢𝐠𝐚𝐭𝐢𝐧𝐠 𝐆𝐞𝐧𝐞 𝐄𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐃𝐢𝐟𝐟𝐞𝐫𝐞𝐧𝐜𝐞𝐬 𝐛𝐲 𝐁𝐢𝐨𝐥𝐨𝐠𝐢𝐜𝐚𝐥 𝐒𝐞𝐱 www.sib.swiss/training/cou...

💡Why attend? More and more policies require attention to sex and gender in research projects, but incorporating this variable is challenging!
Best Practices for Investigating Gene Expression Differences by Biological Sex
Overview Sex and gender have been historically ignored as explanatory variables in transcriptomics studies, in particular because of the fear that add
www.sib.swiss
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · 24d
Half-half, but we'll plan backup options for the hands-on part for people with limited R knowledge!
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · Sep 10
Newcomers are more than welcome of course! A bit of background on the analysis of genomics and transcriptomics data would be useful however
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Reposted by Julien Roux
sib.swiss
SIB Swiss Institute of Bioinformatics @sib.swiss · Sep 10
Our invited speakers for the parallel session on ‘Computational methods for single-cell and spatial omics’ is @stephaniehicks.bsky.social from Johns Hopkins Bloomberg School of Public Health, USA. Session is chaired by @marianna-raps.bsky.social and @julienroux.bsky.social. #bc2basel‬‬‬‬‬‬‬
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · Sep 8
🗓️📍Date and location: 27 October 2025, Bern, Switzerland

Contact us if you need more info!
@sib.swiss
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · Sep 8
Ideally, data analysts should be involved even before data is generated, so you need to be ready to take on this role! 🧑‍🔬
During the day we'll guide you through the steps of designing robust genomics experiments, and rigorously analysing them to draw valid conclusions. 🖥️ 🧬
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · Sep 8
Registrations now open for our course 𝐁𝐞𝐬𝐭 𝐏𝐫𝐚𝐜𝐭𝐢𝐜𝐞𝐬 𝐟𝐨𝐫 𝐈𝐧𝐯𝐞𝐬𝐭𝐢𝐠𝐚𝐭𝐢𝐧𝐠 𝐆𝐞𝐧𝐞 𝐄𝐱𝐩𝐫𝐞𝐬𝐬𝐢𝐨𝐧 𝐃𝐢𝐟𝐟𝐞𝐫𝐞𝐧𝐜𝐞𝐬 𝐛𝐲 𝐁𝐢𝐨𝐥𝐨𝐠𝐢𝐜𝐚𝐥 𝐒𝐞𝐱 www.sib.swiss/training/cou...

💡Why attend? More and more policies require attention to sex and gender in research projects, but incorporating this variable is challenging!
Best Practices for Investigating Gene Expression Differences by Biological Sex
Overview Sex and gender have been historically ignored as explanatory variables in transcriptomics studies, in particular because of the fear that add
www.sib.swiss
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Reposted by Julien Roux
sib.swiss
SIB Swiss Institute of Bioinformatics @sib.swiss · Sep 8
Welcome everyone to the 2025 [BC]² Basel Computational Biology Conference. Speakers and attendees from all over the world gather for 3 exciting days of discussion to shape the future of data-driven biology where #Bioinformatics meets #AI. #bc2basel
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Reposted by Julien Roux
martinroosli.bsky.social
Martin Röösli @martinroosli.bsky.social · Aug 22
Just released by @swisstph.ch: new figures of the heat-related mortality monitoring in Switzerland: In summer 2024 (6th warmest in CH), around 326 deaths were attributed to heat, less than in summers 2022 and 2023. South was mostly affected.
www.nccs.admin.ch/nccs/en/home...
The figure shows how summer temperature has increased in CH since 1980 and how heat related mortality developed during that period.
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Reposted by Julien Roux
marcrr.bsky.social
Marc Robinson-Rechavi @marcrr.bsky.social · Aug 19
I'm told that @eseb2025.bsky.social is communicating on X/Twitter. I call on the organisers to leave it now. Being there reinforces the network, we don't have to do that. Pin a message sending to Bluesky (even Mastodon? @eseb.bsky.social is there) and people will follow. #ESEB2025
marcrr.ecoevo.social.ap.brid.gy
Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · Aug 19
Friends don’t let friends use X/Twitter. If you know people live-posting #eseb2025 on the cursed network, kindly point them towards Mastodon or Bluesky. (I think there are good reasons to prefer Mastodon, but Bluesky is infinitely better than continuing to promote X by posting scientific content […]
Original post on ecoevo.social
ecoevo.social
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Reposted by Julien Roux
bioconductor.bsky.social
Bioconductor @bioconductor.bsky.social · Aug 21
⏳ One week left to register!
Join us at EuroBioC2025 in Barcelona and the Bioconductor Carpentry Workshops for hands-on learning, community building, and cutting-edge bioinformatics.

🗓️ Registration closes August 28 — don’t miss out!
🔗 eurobioc2025.bioconductor.org

#EuroBioC2025 #RStats
European Bioconductor Conference 2025 – EuroBioC2025
The European Bioconductor Conference (EuroBioC2025) will take place on September 17th to 19th, 2025, in Barcelona, Spain. EuroBioC2025 will bring together the Bioconductor community to showcase the…
eurobioc2025.bioconductor.org
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · Jun 26
Congrats! What are you going to do with all these genomes? 🤯
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Reposted by Julien Roux
ygilad.bsky.social
Yoav Gilad @ygilad.bsky.social · Jun 7
We developed CrossFilt, a read-level, cross-species filtering approach that avoids these errors without sacrificing usable data. It outperforms all existing strategies and exposes just how much signal in comparative genomics has been misread.

doi.org/10.1101/2025...
CrossFilt: A Cross-species Filtering Tool that Eliminates Alignment Bias in Comparative Genomics Studies
Comparative functional genomic studies are often affected by biased read mapping across species due to inter-species differences in genome structure, sequence composition, and annotation quality. We d...
doi.org
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Reposted by Julien Roux
riderius.bsky.social
W. Dow Rieder @riderius.bsky.social · Dec 9
"IN MICE" is back! Now with bonus yelling! He actually had a noticeable effect on medical reporting with the Old Blue Site "justsaysInMice" account through encouraged ridicule.

Worth a follow if you care about basic accuracy in medical reporting 8-)
inmice.bsky.social
IN MICE @inmice.bsky.social · Dec 9
PS I DON'T "JUST" SAY IN MICE ANY MORE BECAUSE IT'S MY GODDAMN IDEA AND TODAY I HAVE DECIDED IT IS BETTER WITH YELLING
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · Jun 23
But sometimes…
<begin rant>
... You realize that the authors have no intention to share anything with the community ("data available upon reasonable request").

This slows science down so much! We simply can’t build on previous work without the data behind results shown in papers! 💩😡
</end rant>
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · Jun 23
(So I've uploaded pre-processed data to GEO — GSE273902 — and the code to reproduce all figures from there is on Github: github.com/julien-roux/...)
GitHub - julien-roux/Roux_et_al_bariatric_surgery_paper: Code, necessary data and settings for a conda environment allowing to reproduce the analyses presented in Roux et al., 2025, Rapid and long-las...
Code, necessary data and settings for a conda environment allowing to reproduce the analyses presented in Roux et al., 2025, Rapid and long-lasting remodelling of the blood transcriptome following ...
github.com
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · Jun 23
Sometimes human data (e.g., raw sequencing reads) cannot be shared due to patient privacy. Still, it’s super helpful to share aggregated data such as read count tables! We’re actually in this exact situation as the patients in our cohort did not sign up a consent allowing data sharing 🙃
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Julien Roux @julienroux.bsky.social · Jun 23
📊 A word about the comparative analysis:
A big part of this study was to compare our results to other transcriptomics datasets, in the context of obesity, type 2 diabetes, bariatric surgery, etc.

Some datasets were a dream to work with: raw data was public, clean, well-annotated.
Others, less so…
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · Jun 23
At some point, I thought that this deserved to be out as a paper, so I decided to take it as a “side project” — on top of all routine work on the table (if there is such thing as routine in this job 😆)
Having this out now feels really rewarding! 🎉
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · Jun 23
A PI in my department brought in this dataset in 2021, originally generated by collaborators even before. I did the analysis as usual, but with noone was a clear lead on the project so things stalled...
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julienroux.bsky.social
Julien Roux @julienroux.bsky.social · Jun 23
A bit of backstory on this paper:

As a bioinformatician in a core facility, it’s rare to be first author on a paper, so this project is special!
julienroux.bsky.social
Julien Roux @julienroux.bsky.social · Jun 23
🚨Pre-print alert! 🧬🖥️🧪
For the first time we looked at what happens in the blood transcriptome just after bariatric surgery. A lot happens and it happens fast!

So happy to push this “side project” to the finish line! A thread 👇🧵
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medrxivpreprint.bsky.social
medRxivpreprint @medrxivpreprint.bsky.social · Jun 22
Rapid and long-lasting remodelling of the blood transcriptome following bariatric surgery https://www.medrxiv.org/content/10.1101/2025.06.20.25329990v1
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