researcher at CRCT (Toulouse, France). immunogenetics, compbio, biostats, pun lover.

Great to see this out and participate in this effort
🎉🧹 The #tidyomics ecosystem is official! Into #omic data analysis? Spanning #Seurat @Bioconductor #SCE, #SE, #GRanges, #Citometry? Now, just use #tidyverse ! Co-led with @mikelove and @TonyPapenfuss @WEHI_research #singlecell The preprint biorxiv.org/cgi/content/shor…
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Pierre-Paul Axisa retweeted
Replying to @mikelove
Late to the party but I also have some codes to share for the blue place, happy to connect with interested people by DM. There is also an invite pool here from @micahgallen forms.gle/ZyYhpa5MHT66mBS59
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Pierre-Paul Axisa retweeted
I am thrilled to announce the release of my first R/Bioconductor package, "easylift." This library simplifies the genomic liftover process, interfaces seamlessly with GRanges and UCSC chain files, and integrates with BiocFileCache. bioconductor.org/packages/ea…
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It amazes me that "Statistical analysis" are single subsection of "Methods" appendices in #microbiome papers. Y'all have separate sections for "Sample storage" (with careful justification), "DNA extraction" (w/ careful justification), "qPCR" (w/ careful justification)... 1/6
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Anyone else want invite codes for MLSky / ImmunoSky / MedSky / GeneSky? (genomics & immunology pretty active over there, could use some cliques of machine learning / deep learning folks to busy up that feed)

ALT I Belive I Can Fly Blue Sky GIF

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Publication pressure ‘trickles down’ to academics, residents, med. students, HS . High pressure, hi volume/hi speed ‘academic’ environs grooming bad methods habits, ‘research’ becomes devalued & hollow word. How do we break the vicious circle of hype, noise and research waste?
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Maybe someone’s playing among us with academic colleagues and they all have imposter syndrome.

ALT Liar Trolling GIF by Partiful

If sitting in a seminar with an open laptop is considered polite then you should be able to bring a playstation to talks
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every time I look for an illustration of my work in #Bioinformatics #rstats, I stumble on the mighty *laptop with double helix on screen*. Do people usually visualize all their NGS data as a double helix DNA, am I doing something wrong?
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#crowdresearch is awesome! Do you love #tidyverse and #omic' research? There are 20+ open challenges still waiting for a champion. Join our effort, solve one (or many), and become part of our upcoming #publication! github.com/orgs/tidyomics/pr… #tidyomics @Bioconductor
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Hats off to EMBL for rethinking the assessment of researchers. Judging a paper by its content above the journal name is as revolutionary as it is obvious. But I'm wary of asking candidates to write a narrative about their research. 1/3 embl.org/news/lab-matters/re…
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It's honestly tragic that there is a structural incentive for dishonesty in academia... We really really really need to change the incentive structures. 2 major changes we need: 1) Create equal incentive for replication/refutation studies 2) Grade on content rather than prestige
A culture that "reward[s] 'winners' (postdocs who generate favorable results) and marginalizes 'losers' (postdocs who struggle to generate such data)” leads to 20 years of "fudging of results [in] labs at three separate institutions". stanforddaily.com/2023/07/19…
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TCR-independent CD137 (4-1BB) signaling promotes CD8+-exhausted T cell proliferation and terminal differentiation sciencedirect.com/science/ar…
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Pierre-Paul Axisa retweeted
Genetics can predict the toxicity of cancer #immunotherapy, via a mechanism shared with #autoimmune diseases. In their News and Views, Caroline Robert & colleagues discuss the implications for biomarker and treatment strategies. @GustaveRoussy @Inserm nature.com/articles/s41591-0…
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Thrilled to see our study out in @ScienceTM with @tomomimyoshida @LaLilli11 @lucasite_lab @EricVerdin @SumidaTomokazu @DavidHaflerMD during my time @YaleMed. We took a deep dive into the role of HDAC7 in Tregs in the context of #MultipleSclerosis risk.🧵science.org/doi/pdf/10.1126/…
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When I started at @YaleMed, I had freedom to learn everything from human immunology and genetics, to genomics and #Bioinformatics. I found my happy place doing computational work and learning about complex traits #Genetics. Grateful to all colleagues who helped in the process🙏🫂
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Link to original association study:doi.org/10.1016/j.cell.2018.… Link to sequencing data: ncbi.nlm.nih.gov/geo/query/a… Link to code for RNAseq analysis:github.com/ImmuneAxisa/HDAC7… Link to code + intermediate analysis files for RNAseq analysis: doi.org/10.6084/m9.figshare.…
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