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Julien Roux

@julienroux.bsky.social
1.6K followers 826 following 143 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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Reposted by Julien Roux
Dr. Katja Thieme (she/they) @katjathieme.bsky.social · 28/09/2026
What do the researchers who work for Anthropic think about (1) having directed a machine to plagiarize other researchers' work, (2) posting a paper attaching their own names to these machine results, and (3) allowing the company to issue hype that goes far beyond the capacity of their results?
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c0nc0rdance @c0nc0rdance.bsky.social · 27/09/2026
I'll save you the click-through: A lab at University of Copenhagen had been feeding draft manuscripts & data into "Claude Science" & then Anthropic announces a discovery that this lab made a year ago but hasn't published yet. It's plausible that Claude found the same signatures independently...
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Marc Robinson-Rechavi @marcrr.bsky.social · 28/09/2026
I'm not writing in the NYT and I won't word it carefully: it's clear that AI companies are stealing researchers' work (and why wouldn't they? they steal artists' and journalists' work with no consequences), and I warned my group about it this morning.
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Alessandro Crimi @alecrimi.bsky.social · 24/09/2026
For #genomics #datasets, I often use these 4 portals: 🧬TCGA - www.cancer.gov/ccg/research... 🧬DepMap - depmap.org/portal/ 🧬1000 Genomes - www.internationalgenome.org 🧬recount3 - rna.recount.bio Are there better resources you use for genomics datasets? What am I missing?
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MwahahahahahadScientist @mads100tist.bsky.social · 18/09/2026
AI slop wins the Nikon competition? 🫠
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Jeremy Reiter @reitergroup.bsky.social · 18/09/2026
What in the world am I looking at here? @Nikon? www.nikonsmallworld.com/galleries/20...
nikonsmallworld.com
Abnormal beating of airway cilia from a child with Primary Ciliary Dyskinesia (PCD) | 2026 Small World in Motion Competition
Ning Xu - Abnormal beating of airway cilia from a child with Primary Ciliary Dyskinesia (PCD), a genetic disorder affecting respiratory function.
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Julien Roux @julienroux.bsky.social · 11/09/2026
Very good start of the #BaselSpatialOmicsSymposium today, with full auditorium and interesting talks! www.linkedin.com/posts/micros...
linkedin.com
#spatial | Microscopy Network Basel
Wow! It's amazing to see how the Basel Spatial Omics Symposium has grown in recent years. This year, we are holding the third edition. It initially started as a local Microscopy Network Basel event to...
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Arnaud Krebs @arnaudkr.bsky.social · 10/09/2026
EMBL QBMM is back this year with an outstanding line-up! Plenty of talks will be selected from submitted abstracts, with emphasis on junior scientists and representation across diverse fields. The abstract deadline is the end of this week, so don’t miss out! www.embl.org/about/info/c...
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Department of Biomedicine🔬🧪 @biomedizin.unibas.ch · 10/09/2026
🎉 Congrats to Hailey Kim and Mika Schneider, winner of the 2026 DBM Paper Prize for their study on EBV and autoreactive B cells in MS. And our Best Presentation Award goes to Dorssa Akbari! Read more: biomedizin.unibas.ch/en/newsdetai... #ResearchExcellence #DBMPaperPrize #BestPresentationAward
biomedizin.unibas.ch
Congratulations to this year’s DBM Paper Prize winners!
As every year, we celebrated the DBM Best Publication Award during our annual Summer Symposium today. This year, the award has a new name – the DBM Paper Prize – but its purpose remains the same: the ...
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Pierre-Luc Germain @plger.bsky.social · 26/08/2026
Sharing a new preprint about technical variation in (bulk/ #SingleCell ) #ATACseq and motif accessibility analyses, and methods to correct for them www.biorxiv.org/content/10.6...
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Department of Biomedicine🔬🧪 @biomedizin.unibas.ch · 03/09/2026
🏆 Two ERC Starting Grants for DBM researchers! Congratulations to Petya Apostolova and @dixon-lab.bsky.social, whose projects LIFE and NeuroCAN will explore new ways to understand and overcome cancer immune evasion. 🔗 Read more: biomedizin.unibas.ch/en/newsdetai... @erc.europa.eu @unibas.ch
biomedizin.unibas.ch
ERC Starting Grants Awarded to Two DBM Researchers
Each year, the European Research Council (ERC) awards Starting Grants to support outstanding early-career researchers in establishing ambitious and innovative research programs. We are delighted to an...
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Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · 02/09/2026
Hamed Najafabadi: GHT-Selex: in vitro profiling of TF binding, on genomic fragments instead of synthetic DNA -> allow analysis of genomic information. Results very similar to ChIPseq, with extra info on binding affinity from enrichment cycles. #ECCB2026 doi.org/10.1038/s41592-026-03177-9
nature.com
GHT-SELEX demonstrates unexpectedly high intrinsic sequence specificity and complex DNA binding of many human transcription factors - Nature Methods
GHT-SELEX—high-throughput SELEX with fragmented genomic DNA—shows that transcription factors can be rather particular about which genomic loci they bind, and that C2H2 zinc finger proteins often engage different fingers at different sites.
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Bgee database @bgee.org · 01/09/2026
If you're at #ECCB2026 and have questions about curated bulk and single-cell RNA-seq, members of the Bgee team (Frédéric Bastian, Anne Niknejad, Sébastien Moretti, @marcrr.bsky.social) and other scFAIR (sc-fair.org) participants are here and happy to speak with you. Don't hesitate to reach out!
sc-fair.org
scFAIR
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Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · 01/09/2026
Malaspinas: most ancient T. pallidum genomes are from dates around Colombian contact. One was isolated from 5500 yr old remains of a person with no disease symptoms. It turned out to be a new subspecies, outgroup to all known subspecies. #ECCB2026
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Riccardo Percudani @percud.bsky.social · 31/08/2026
“We not only have to share data, but also share the benefits of sharing data.” Powerful opening keynote by Jeremy Farrar at #ECCB2026 in Geneva — with no slides.
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Torsten Schwede @torstenschwede.bsky.social · 31/08/2026
Looking forward to three days full of exciting science and inspiring conversations. #ECCB2026
ECCB 2026 is hosted by SIB in Geneva
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Rob Waterhouse @rmwaterhouse.bsky.social · 31/08/2026
A grand opening to #ECCB2026 in #Geneva today with president Guy Parmelin @sib.swiss #GenevaLovesData
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Katja @jaggakatja.bsky.social · 31/08/2026
Excited that #ECCB26 is about to start! Looking forward to three days filled with exciting talks and poster presentations, interesting discussions and encounters, and, of course, catching up with colleagues from across the community.
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Kelvin Lau @klausenhauser on 🙅‍♂️🐘🪡 @klausenhauser.bsky.social · 26/08/2026
And I wake up to my friend sending me this. I think this is the highlight of the probe. It’s just a cut and paste world doing WB…
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Reese Richardson @reeserichardson.bsky.social · 25/08/2026
A massive update: At least ~15 companies~ are selling scientists antibodies using faked validation data. We've documented 18,000+ manipulated images on 17,000+ products sold by leading laboratory suppliers including Thermo Fisher, Abcam, Santa Cruz Biotechnology, Millipore Sigma and Bio-Techne. 1/🧵
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Bioconductor @bioconductor.bsky.social · 25/08/2026
📢 We’re running a developer survey to better understand the needs and priorities of the community and help shape the future of Bioconductor. The survey is open until September 30 and takes approximately 15-30 minutes to complete. 📝 Survey link: bit.ly/4zPf6h4 We look forward to hearing from you!
forms.gle
Bioconductor developer survey
Thank you for taking the time to complete this Bioconductor developer survey. For the purposes of this survey, "developer" includes package developers as well as contributors involved in…
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Andrea Musacchio @andrea-musacchio.bsky.social · 23/08/2026
www.science.org/doi/10.1126/... “MPIs operate on the Harnack principle: build an institute around a small group of exceptional scientists granted near-absolute autonomy. On paper, scientific paradise; in practice, junior scientists live entirely at the director’s pleasure.” Tranchant…
science.org
In (qualified) defense of the research project grant
In a debate that has been building for years, a growing coalition of reformers has concluded that the research project grant (RPG) approach used by many science funders in the United States and based ...
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Itai Yanai @itaiyanai.bsky.social · 24/08/2026
How to do science in the age of AI.
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Erik van Nimwegen @erikvannimwegen.bsky.social · 21/08/2026
Remember this? bsky.app/profile/did:... Rigorous visualization of the structure in your high-dimensional data. Fantastic work by @dhdegroot.bsky.social With help of the reviewers of Nat Biotech it is now updated, extended an officially published here: www.nature.com/articles/s41... 1/n
nature.com
Bonsai reconstructs tree representations for distortion-free visualization and exploration of high-dimensional data - Nature Biotechnology
High-dimensional data are visualized through representation on tree structures.
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Marc Robinson-Rechavi @marcrr.bsky.social · 06/08/2026
Yes! I hate that we've had to put it up on our database websites. But the AI bots are impossible to manage otherwise, at least for a small team.
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Rob Waterhouse @rmwaterhouse.bsky.social · 19/08/2026
Tomorrow the exhibition moves from Parc des Bastions to Rotonde du Mont-Blanc, in #GenevaLovesData #Datarium #biodiversity @bmd-project.eu
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Julien Roux @julienroux.bsky.social · 20/08/2026
Very happy to see this now published! www.nature.com/articles/s41...
nature.com
Rapid and long-lasting remodelling of the blood transcriptome following bariatric surgery - International Journal of Obesity
International Journal of Obesity - Rapid and long-lasting remodelling of the blood transcriptome following bariatric surgery
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Lucas Waltzer @lucaswaltzer.bsky.social · 17/08/2026
Appalling string of misconducts at Marseille IHU . 64 publications retracted & 270 with expression of concern... What a glorious success Dr Raoult!
link.springer.com
Follow-up investigation of ethics approvals and regulatory compliance in publications from the IHU-Mi - Research Integrity and Peer Review
Background Following our previous investigation of 456 articles published by the IHU-Méditerranée Infection (IHU-Mi) institute in Marseille, France, subsequent editorial actions, institutional reviews...
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Sholto David @sholtodavid.bsky.social · 06/08/2026
A tool used to rephrase plagiarised text changed "final solution" to "mass killing of an ethnic group" in a chemistry paper. Now retracted thanks to a PubPeer user who spotted this. pubpeer.com/publications...
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Olivia Guest · Ολίβια Γκεστ @olivia.science · 31/07/2026
🤠 youtu.be/BuiEVOSTbN4
youtu.be
Google kills AlphaFold. So much for AI curing cancer
YouTube video by Pivot to AI
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Itai Yanai @itaiyanai.bsky.social · 31/07/2026
Science funding has still not reached gender equality: "Projects led by male PIs received roughly twice the mean funding compared to female PIs." www.sciencedirect.com/science/arti...
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Benoit Bruneau @benoitbruneau.bsky.social · 21/07/2026
flying UMAPs
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The Night Science Podcast @nightsciencepod.bsky.social · 22/06/2026
🔥 New Night Science Podcast episode! What can comedy teach us about scientific discovery? With stand-up comedian and former research scientist Sarah Adelman, we discuss the surprising parallels between jokes and discoveries! open.spotify.com/episode/0zG2... podcasts.apple.com/us/podcast/n...
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Itai Yanai @itaiyanai.bsky.social · 16/06/2026
Fantastic idea Julien! @redpenblackpen.bsky.social, would you like to come on as a guest on the night science podcast? podcasts.apple.com/us/podcast/n...
podcasts.apple.com
Night Science
Natural Sciences Podcast · Updated Weekly · Where do ideas come from? In each episode, scientists Itai Yanai and Martin Lercher explore science's creative side with a leading colleague. New episodes c...
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Denny Carter @dennycarter.bsky.social · 17/06/2026
I guess one difference between Jim Crow then and Jim Crow now is that we have cool graphics to show how it's done.
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Marc Robinson-Rechavi @marcrr.bsky.social · 16/06/2026
Super happy to see this out. 😎
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BioHackrXiv @biohackrxiv.fediscience.org.ap.brid.gy · 15/06/2026
"Bioconductor Spatial Data and Image Analysis Hackathon" doi.org/10.37044/osf.io/9ej32_v1 "We report the outcomes of the Bioconductor Spatial Data and Image Analysis Hackathon, held in Venice, Italy in April 2026. Twenty-seven researchers and […] [Original post on fediscience.org]
One of the figures from the preprint. It shows a 2d image of tissue, colored with a red stain, showing the red and white image that we see. At the top there is the text "Overlay: Terra Image and Segmentation".
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Wolfgang Huber @wkhuber.bsky.social · 16/06/2026
Many results, new or improved packages, and future directions in this report on the Bioconductor Spatial Data and Image Analysis Hackathon that took place in Venice in April 2026. osf.io/preprints/bi...
Participants of the Bioconductor Spatial Data and Image Analysis Hackathon in Venice, April 2026.Participants of the Bioconductor Spatial Data and Image Analysis Hackathon in Venice, San Servolo, April 2026.
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Marc Robinson-Rechavi @marcrr.bsky.social · 14/06/2026
When the location of a conference is announced, can we take the habit of first highlighting accessibility by train rather than starting by highlighting airports?
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Reese Richardson @reeserichardson.bsky.social · 06/06/2026
Thermo Fisher now has a page up in response to our observations. They flatly deny that images were manipulated or fabricated while repeating that images were "optimized for presentation and clarity on the website", no lie, six times. www.thermofisher.com/us/en/home/l...
thermofisher.com
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Alejandro Montenegro @aemonten.bsky.social · 03/06/2026
No, they were not
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Tuomas Borman @tuomasborman.bsky.social · 03/06/2026
We are live!!! The program starts at 9 in Finnish time. Watch European Bioconductor Conference for free: utu.zoom.us/j/62224935664 #EuroBioC2026 #Bioconductor
lnkd.in
LinkedIn
This link will take you to a page that’s not on LinkedIn
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Tschopp Lab @tschopplab.bsky.social · 19/05/2026
Now accompanied by a lovely write-up from our communications office @unibas.ch - thanks @angelikajacobs.bsky.social 🙏 ! : www.unibas.ch/en/News-Even...
unibas.ch
You are what you eat: how diet drives evolution
A University of Basel study shows how different diets shape the evolution of intestinal cells in cichlid fishes.
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Marc Robinson-Rechavi @marcrr.bsky.social · 01/06/2026
Did I submit 3 papers or revisions in the last hour? Maybe. When projects end, it's sad to see people go, but great to see results come out. Find all of our work at @biorxiv-evobio.bsky.social @biorxiv-genomic.bsky.social
tinyurl.com
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Reese Richardson @reeserichardson.bsky.social · 28/05/2026
TL;DR: We've identified more than 100 cases of apparent manipulation in Thermo Fisher Scientific's antibody verification data. @sholtodavid.bsky.social @johanduchene.bsky.social reeserichardson.blog/2026/05/28/h...
reeserichardson.blog
How much of Thermo Fisher’s antibody data has been manipulated?
We’ve documented more than 100 instances of apparent data manipulation in Thermo’s catalog
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Yoav Gilad @ygilad.bsky.social · 04/04/2026
Beyond the mean: genetic control of gene expression fidelity and dispersion www.biorxiv.org/content/10.6...
biorxiv.org
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Julien Roux @julienroux.bsky.social · 12/05/2026
Finally found time to try mapping/demultiplexing a 10X Flex dataset (v1) using STARsolo github.com/alexdobin/ST... It's quite a versatile tool and we've been using for Chromium 10X 3'/5', w/ and w/o ADT/HTOs, PARSE-seq, BD Rhapsody, even for bulk RNA-seq with BRB-seq, so I wanted to give it a try!
github.com
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Stevie Ped @smped.bsky.social · 12/05/2026
Very pleased to be hosting this today. Two great speakers & a chance for the Bioconductor community throughout the Asia-Pacific to come together. Registrations are still open if you're interested in #rstats package development and bioinformatics 🧬 🖥️ 4pm AEST with relevant time zones on the site
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Rob Patro @robp.bsky.social · 11/05/2026
Just grab the latest: * simpleaf (github.com/COMBINE-lab/...; also available via bioconda) or * cyto (github.com/arcinstitute...; preprint here: www.biorxiv.org/content/10.6..., not my work, but the tool seems great and the devs are very solid) And you're off to the (much faster) races! 2/2
github.com
GitHub - COMBINE-lab/simpleaf: A rust framework to make using alevin-fry even simpler
A rust framework to make using alevin-fry even simpler - COMBINE-lab/simpleaf
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Rob Patro @robp.bsky.social · 11/05/2026
This is a very cool demonstration of the possibilities of 10x Flex link.springer.com/article/10.1...! But did you know that you can get near identical results MANY TIMES faster than CellRanger by processing flex data with piscem/alevin-fry or cyto? Both highly efficient & fully, truly open source?/2
link.springer.com
10 × Genomics Flex Gene Expression is a powerful tool for single-cell transcriptomics of xenografts models - Genome Biology
The 10 × Genomics Flex Gene Expression protocol is a probe-based method that profiles fixed or frozen material, simplifying sample handling before scRNA-seq. Although probes exist only for human and m...
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