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Julien Roux

@julienroux.bsky.social
1.6K followers 834 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
P(aul) Frazee @pfrazee.com · 13/10/2026
Meanwhile, at every home office in the world
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Jonathan Pritchard @jkpritch.bsky.social · 09/10/2026
Another possible topic is that I am looking to hire: -- a senior scientist and --1-2 postdocs Looking for a strong publication record in at least one of: functional genomics/single cell work/computational methods/statgen/popgen.
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Marc Robinson-Rechavi @marcrr.ecoevo.social.ap.brid.gy · 07/10/2026
Day 3 of Nobel week: ♂♂♂♂♂♂
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Nick Stroustrup @nstroustrup.bsky.social · 05/09/2026
Did you know that the cells of old animals contain much less mRNA than the cells of young ones? Let me share with you some results from an ongoing project in the lab, where we are finding that a progressive depletion of total mRNA abundance is a crucial part of aging 1/22
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David Grimm @david-grimm.bsky.social · 06/10/2026
"Franklin knew the earlier photo had revealed a helix—the epiphany Watson claimed for himself—and that is precisely why she made a second, more refined version, photograph 51." @science.org
science.org
How did Rosalind Franklin miss the helix in her iconic DNA image? She didn’t
New analysis refutes James Watson’s claim he was first to recognize significance of famed photograph 51
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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
Last talk! Enes Ugur from @priscaliberali.bsky.social @fmiscience.bsky.social Single-cell transcriptomics and MS-based proteomics in the same cells: www.biorxiv.org/content/10.6... Now extending this to the spatial dimension in the aging intestine!
biorxiv.org
In the same cell, the proteome defines cellular state and the transcriptome marks transitions
Bulk transcriptome and proteome correlate only modestly, but this has not been investigated in the same cell or across cell-state changes. Here we introduce a scalable technology that quantifies thous...
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Julien Roux @julienroux.bsky.social · 11/09/2026
Benjamin Hershey from the lab of @andreasmoor.bsky.social @bsse.ethz.ch presents an organoid model of liver metastasis from colorectal cancer. #BaselSpatialOmicsSymposium
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Julien Roux @julienroux.bsky.social · 11/09/2026
Jonas Zierer from @novartis.bsky.social, studying Sjögren's disease with Xenium. This autoimmune disease is characterized by expansion of B cells in salivary glands. #BaselSpatialOmicsSymposium
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Julien Roux @julienroux.bsky.social · 11/09/2026
Mariana Ribeiro from @iobswiss.bsky.social presents the FLIGHT-seq method = spatial transcriptomics + long reads 🤯🚀 #BaselSpatialOmicsSymposium
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Julien Roux @julienroux.bsky.social · 11/09/2026
@lguerard.bsky.social from the @biozentrum.unibas.ch presents the Sopa pipeline for analyses of image-based spatial omics: www.nature.com/articles/s41..., and their improvements to it. #opensource FTW! #BaselSpatialOmicsSymposium
nature.com
Sopa: a technology-invariant pipeline for analyses of image-based spatial omics - Nature Communications
The complexity of spatial omics data presents analytical challenges and demands substantial computing resources. Here, the authors introduce Sopa, a technology-invariant, memory-efficient pipeline wit...
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Julien Roux @julienroux.bsky.social · 11/09/2026
Next up: Sarp Uzun from University Hospital Basel talking about adverse effects of immunotherapies in the liver
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Julien Roux @julienroux.bsky.social · 11/09/2026
Curdin Franziscus from @spanglab.bsky.social @biozentrum.unibas.ch Presents the SPEx method allowing to do proteomics at the subcellular scale, used to measure proteome of Golgi, nucleus and nucleoli organelles. Paper available here: elifesciences.org/reviewed-pre... #BaselSpatialOmicsSymposium
elifesciences.org
SPEx: Compartment-Resolved Proteomics via Expansion Microscopy–Guided Microdissection
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Julien Roux @julienroux.bsky.social · 11/09/2026
Kristy Ou from @biomedizin.unibas.ch: Follicular lymphoma originate in the lymph nodes and can transform into an aggressive lymphoma. Generated a dataset including many spatial omics modalities on a cohort of 6 patients to characterize this process. #BaselSpatialOmicsSymposium
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Julien Roux @julienroux.bsky.social · 11/09/2026
Benedek Pesti from Roche on a mouse model of Alzheimer disease, to see the spatial effects of treatment targeting amyloid plaques #BaselSpatialOmicsSymposium
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Julien Roux @julienroux.bsky.social · 11/09/2026
Next up: @yinanwan.bsky.social from the @biozentrum.unibas.ch (soon starting her lab at @unil.bsky.social) She presents a whole-embryo spatial transcriptomics atlas in zebrafish www.science.org/doi/10.1126/...
science.org
Whole-embryo spatial transcriptomics at subcellular resolution from gastrulation to organogenesis
Gene expression patterns underlie development, but their systematic detection in whole embryos has remained elusive. We introduce a whole-embryo imaging platform using multiplexed error-robust fluores...
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Julien Roux @julienroux.bsky.social · 11/09/2026
Also some recent work on inferring copy number variation from imaging-based spatial transcriptomics data: www.biorxiv.org/content/10.1... @nilssonlab.org #BaselSpatialOmicsSymposium
biorxiv.org
In Situ Inference of Copy Number Variations in Image-Based Spatial Transcriptomics
Copy number variations (CNVs) drive cancer progression. So far, spatial CNV inference has relied on whole transcriptome-based sequencing technologies. However, advances in image-based spatial transcri...
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Julien Roux @julienroux.bsky.social · 11/09/2026
He presents the COSTE method (cell-GPS package) to reveal the spatial organization of tissues: www.biorxiv.org/content/10.6... @nilssonlab.org #BaselSpatialOmicsSymposium
biorxiv.org
Cophenetic Spatial Topology Embedding reveals multiscale tissue architecture in spatial omics
The spatial organization of tissues emerges from cell interactions across multiple scales, yet current spatial omics analysis tools often emphasize local neighborhoods and may not summarize broader ti...
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Julien Roux @julienroux.bsky.social · 11/09/2026
Keynote Mats Nillson presents a historical perspective on the development of padlock probes behind the Xenium technology #BaselSpatialOmicsSymposium
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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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Julien Roux @julienroux.bsky.social · 31/07/2026
Was there not long ago! 👌
A view of Corrie Fee National Nature Reserve at Glen Clova
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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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