Carlos Ronchi
@chronchi
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Mathematician. Computational Biologist. Newsletter: https://t.co/q3u5xgysOa
Joined October 2015
New blog article challenging medical researchers who are drawn to clustering patients to create so-called "phenotypes" to think again: https://t.co/50fqPRSLLl
@MaartenvSmeden @statsepi0 #Statistics #PrecisionMedicine @vandy_biostat
fharrell.com
Patient clustering, often described as the finding of new phenotypes, is being used with increasing frequency in the medical literature. Most of the applications of clustering of observations are not...
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I defended my PhD thesis at EPFL! Thank you everyone that joined and contributed in every aspect of my PhD. I'm looking forward to what comes next in Chicago!
Hearty congratulations, @chronchi on outstanding and engaging public thesis defense! Best of luck, and we look forward to seeing all the amazing things you will accomplish! @epflSV @nature_npj Learn more about EMBER: https://t.co/oaEzrRWaEC
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Phenomenal work, tumor agnostic pipeline for oncology and precision medicine! ⬇️⬇️⬇️⬇️⬇️ @chronchi 's baby called #EMBER provides a calibration and reference tool that paves the way for using #RNAseq as a standard diagnostic and predictive tool for #ERpos breast cancer @CBrisken
I’m very happy to announce that our manuscript has been published at npj breast cancer, together with @CBrisken and Syed Haider! We propose a new algorithm to do single sample integration into a common reference space. (1/n) https://t.co/YYUhR0GkPY
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The analysis can be found online too ( https://t.co/hwpg3GRNy9) with all the figures and a chapter specific for the analysis done during the revision process. (6/6)
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It was very important for us to make the study as reproducible as possible. I created a docker image in which everyone should be able to reproduce all the figures from the paper ( https://t.co/oEbyjfHXfw). (5/n)
github.com
Scripts and prose for the molecular landscape paper - chronchi/molecular_landscape
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If you want to try our algorithm on your own data we provide an R package ( https://t.co/24ZJSfS1y4), with a website illustrating how to use it: https://t.co/0KypULWgGY (4/n)
github.com
Universal framework for molecular subtype and pathway scoring in breast cancer - chronchi/ember
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We conclude showing how important it is to use transcriptomics by further stratifying patients with high ER IHC (>= 90%) based on functional ER signaling. (3/n)
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We also show how the molecular subtypes are continuous and not discrete, and that they depend on varying levels of ER signaling, proliferation, EMT and DNA repair. (2/n)
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I’m very happy to announce that our manuscript has been published at npj breast cancer, together with @CBrisken and Syed Haider! We propose a new algorithm to do single sample integration into a common reference space. (1/n) https://t.co/YYUhR0GkPY
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Don't like p-values? We're presenting a completely new interpretation in the context of clinical trials. With Andrew Gelman, Sander Greenland, @guido_imbens Simon Schwab and Steve Goodman. @Lester_Domes @goodmanmetrics @NEJMEvidence
https://t.co/iIu46aY3mZ
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Fantastic talk by @jcheng at #positconf2023 on using #shiny with #quartopub. I've made an #rstats Quarto book demo with a wasm-embedded shiny app to demonstrate how class boundaries change with the complexity of natural splines. Sources: https://t.co/xMvr2uCID7
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It's amazing to see our work so beautifully represented, thank you @sciencebrush!
Polarons and bipolarons in crystalline and amrophous polymer domains. Excited to share this design 🎨 that I did for Prof. Natalie Banerji, first author Priscila Cavassin @CavassinP and colleagues from @DCBPunibern! The work was published in Advanced Materials @AdvSciNews and
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In new work, @LambdaMoses et al. introduce the Voyager platform for spatial and non-spatial 'omics analysis: 🚴♀️ Builds on the geospatial statistics tradition 🚴♀️ Addresses discordance between Seurat & Scanpy 🚴♀️ Engineered in R (@Bioconductor) & Python https://t.co/LR9hZdNRxK 1/🧵
biorxiv.org
Exploratory spatial data analysis (ESDA) can be a powerful approach to understanding single-cell genomics datasets, but it is not yet part of standard data analysis workflows. In particular, geospa...
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Had a great time in Gent, both presenting and learning from the other ESRs and PIs!
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I am very happy to share our recently published work on the impact of morphology on the electrochemical doping of organic mixed ionic-electronic conductors. It’s part of my PhD journey and I am proud of it 🥳⬇️ https://t.co/HyyNVdoPmq
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My book is done. I need to write a conclusion to the last chapter and will likely rewrite some paragraphs, but I won't make major changes anymore. So if you're interested in building reproducible analytical pipelines with #RStats, take a look it's free: https://t.co/Vx8LGpddwR
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Carlos Ronchi @chronchi gave a fantastic presentation on “Computational biology in cancer prevention”, public outreach initiative @ICPInews Olympic Museum @olympicmuseum for the occasion of World Cancer Day, a universally recognized day to raise awareness of cancer.
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Check out this insightful preview by @chronchi @CBrisken on targeting the #progesterone receptor in #ERpositive #breastcancer: mind the short form! @CANCERPREV1 @BreastCancerNow @ICR_London @epflSV #mifepristone #PRB #PRA
https://t.co/yF3V8GUqMY
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Please RT: ER/E2/breast cancer. We are seeking #crowdsourced datasets and opinions. We curated 136 published datasets, processed with one pipeline and made a browser to visualize E2-induced expression and ER binding. Feel free to try it out https://t.co/lOpu0vpm8H 🧵
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