Julien Roux
@julienroux.bsky.social
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 🧬 🖥️
Interested in bulk and single-cell omics, data analysis, experimental design, data visualization, R/Bioc, open science, EDI, etc 🧬 🖥️
Reposted by Julien Roux
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.
November 28, 2025 at 10:46 AM
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.
Reposted by Julien Roux
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.
November 28, 2025 at 10:46 AM
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.
Reposted by Julien Roux
Orchestrating Spatial Transcriptomics Analysis with Bioconductor
(including interoperability with Python)
Paper: www.biorxiv.org/content/10.1...
Book: bioconductor.org/books/OSTA/
#Rstats
(including interoperability with Python)
Paper: www.biorxiv.org/content/10.1...
Book: bioconductor.org/books/OSTA/
#Rstats
November 21, 2025 at 5:39 PM
Orchestrating Spatial Transcriptomics Analysis with Bioconductor
(including interoperability with Python)
Paper: www.biorxiv.org/content/10.1...
Book: bioconductor.org/books/OSTA/
#Rstats
(including interoperability with Python)
Paper: www.biorxiv.org/content/10.1...
Book: bioconductor.org/books/OSTA/
#Rstats
Reposted by Julien Roux
We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor”!
Many people hours, calls and messages later: OSTA is now “in (pre)print”, though the real thing lives at bioconductor.org/books/OSTA.
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
Check it out, get in touch. We welcome any feedback, suggestions, wishes (& contributions).
It’s been a joy working with you @estellayixingdong.bsky.social!
November 22, 2025 at 12:38 PM
We are excited to share our online book and preprint on “Orchestrating Spatial Transcriptomics Analysis with Bioconductor”!
Reposted by Julien Roux
Not sure why @lpachter.bsky.social did not post this here. But it is brilliant. Single cell genomics finally makes it to the clinic.
November 18, 2025 at 2:19 AM
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...
November 14, 2025 at 7:59 AM
Spatial omics images? bsky.app/profile/lape...
Reposted by Julien Roux
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. 😅📚🎬
steven spielberg is sitting in a chair with his hands folded
ALT: steven spielberg is sitting in a chair with his hands folded
media.tenor.com
November 11, 2025 at 6:10 AM
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. 😅📚🎬
Reposted by Julien Roux
Unbelievable! How can this crap still be published?
Reverse Image Forensics Challenge: Try to find a unique area in Figure 9 of this recent Scientific Reports paper: 10.1038/s41598-025-17456-6 [Aug 2025] - Annotated by ImageTwin.ai
November 11, 2025 at 4:22 AM
Unbelievable! How can this crap still be published?
Reposted by Julien Roux
I like this obit better...
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.
www.statnews.com
November 9, 2025 at 7:50 AM
I like this obit better...
Reposted by Julien Roux
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.
November 9, 2025 at 9:41 PM
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.
Reposted by Julien Roux
#ECCB2026 European Conference on Computational Biology, Geneva🇨🇭:
Call for tutorials & workshops.
⬇️⬇️⬇️
Call for tutorials & workshops.
⬇️⬇️⬇️
📣 The call for tutorials & workshops at #ECCB2026 is now open! Share your tools, methods or expertise with the community.
🗓️ Deadline: 5 January 2026
👉 Submit: tinyurl.com/tw-eccb26
💡 ECCB will take place on 31 Aug–4 Sept in Geneva, gathering 1,000+ scientists from academia, industry, & healthcare.
🗓️ Deadline: 5 January 2026
👉 Submit: tinyurl.com/tw-eccb26
💡 ECCB will take place on 31 Aug–4 Sept in Geneva, gathering 1,000+ scientists from academia, industry, & healthcare.
November 5, 2025 at 3:31 PM
#ECCB2026 European Conference on Computational Biology, Geneva🇨🇭:
Call for tutorials & workshops.
⬇️⬇️⬇️
Call for tutorials & workshops.
⬇️⬇️⬇️
Reposted by Julien Roux
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
Editorial_Board
Editorial Team
Editor-in-Chief
Xun Xu, PhD; BGI Research, Shenzhen, China
Executive Editor
Hongling Zhou; GigaScience Press, BGI Shenzhen, China
Edito
academic.oup.com
October 29, 2025 at 4:03 PM
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
Reposted by Julien Roux
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...
deseq2 — InMoose 0.8.0 documentation
inmoose.readthedocs.io
August 2, 2025 at 8:36 AM
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...
Reposted by Julien Roux
Sigh. We're gonna need a bigger story...
October 26, 2025 at 7:15 AM
Sigh. We're gonna need a bigger story...
Reposted by Julien Roux
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
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
November 17, 2023 at 8:46 PM
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
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
Reposted by Julien Roux
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
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
October 23, 2025 at 7:27 AM
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
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
It's happening next Monday, all-day (CEST), and it's online so you can attend from anywhere
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!
💡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
October 20, 2025 at 6:21 AM
📣 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
It's happening next Monday, all-day (CEST), and it's online so you can attend from anywhere
Reposted by Julien Roux
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
"'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...
www.nature.com
August 7, 2025 at 10:38 PM
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
"'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
Reposted by Julien Roux
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...
A must read for trainees!
www.nature.com/articles/s41...
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...
www.nature.com
August 8, 2025 at 7:34 PM
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...
A must read for trainees!
www.nature.com/articles/s41...
Reposted by Julien Roux
The article has also a table with more in depth resources on various aspects of experimental design for more advance design needs.
August 7, 2025 at 7:44 PM
The article has also a table with more in depth resources on various aspects of experimental design for more advance design needs.
Reposted by Julien Roux
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...
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...
www.nature.com
August 7, 2025 at 7:43 PM
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...
Our course will actually be taught online, to make it easier for people abroad to attend!
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!
💡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
September 18, 2025 at 2:55 PM
Our course will actually be taught online, to make it easier for people abroad to attend!
Reposted by Julien Roux
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
September 10, 2025 at 7:31 AM
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
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!
💡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
September 8, 2025 at 9:43 AM
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!
💡Why attend? More and more policies require attention to sex and gender in research projects, but incorporating this variable is challenging!
Reposted by Julien Roux
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
September 8, 2025 at 9:18 AM
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