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Exchange at #SingleCell genomics symposium with researchers from EPFL Université de Lausanne FMI science

Nb Peaks called by MACS2 on ATAC-seq data vs depth of sample (from 100k reads to 100M). Does it make any sense? Is there an euclidean division/modulo in the model?

A new paper in eLife - the journal by David Suter shows how by #pluripotency transcription factors dynamically regulate #chromatin accessibility across the cell cycle doi.org/10.7554/eLife.…

We’re excited to release a Seurat update with support for Spatial Transcriptomics data! Includes clustering, interactive visualization, and integration with scRNA-seq references. Check out our vignette on 10x Genomics Visium data: satijalab.org/seurat/v3.1/sp…

Our exciting work together with Ronald Dijkman shows that we can reliably detect #HCoV2 viral transcripts in infected human cells using BRB-seq (tinyurl.com/y3l5hut8) even at the early stage. Affordable #transcriptomics opens a great perspective for mass #COVID19 diagnostics

Proud of this huge collaborative effort by @PhilipVkovski, Mitra Silvio Steiner, Dr. Jenna Kelly 👩🏻‍🔬👩🏻‍💻🦠🧬🇨🇦🇨🇭 Volker Thiel Daniel Alpern, and all other coauthors. Inspired by earlier work by Prof. Akiko Iwasaki. Universität Bern HONOURs-ITN #virology #COVID19 disq.us/t/3o8cdvi

EPFL Professor Andrea Ablasser from EPFL Life Sciences shares the Leenaards Foundation 2020 Science Prize with Professor Michel Gilliet from the CHUV / Centre hospitalier universitaire vaudois. Their project aims to gain insight into the causes and effects of an overactive innate immune system. actu.epfl.ch/news/andrea-ab…

mRNA Vaccine xkcd.com/2425/ m.xkcd.com/2425/

Genes that dance to the circadian rhythm bit.ly/2ZaScAz via EPFL #Swisstech #VDtech

Fly Cell Atlas is out!! check BioRxiv and flycellatlas.org; thanks everyone #FCAconsortium. biorxiv.org/content/10.110…

C’est avec tristesse et émotion que la Ligue contre le cancer vient d’apprendre le décès d’Axel Kahn.

Any questions?

No time to get bored. Half-time retreat Day#3 with Vincent Gardeux Vincent Gardeux EPFL Maira Ihsan EMBL-EBI and Judith Zaugg Judith Zaugg EMBL Marie Skłodowska-Curie Actions

Half-time retreat Day#3 (students' perspective) with Vincent Gardeux EPFL "Hands-on session on analyzing single-cell data" Marie Skłodowska-Curie Actions

The reasons are simple: PhDs don't want to move to a random city for 1-2 years for a job that pays only $50K.

Ladies and gentlemen: the Python ecosystem

Among the new SIB Resources, ASAP, the Automated #Singlecell Analysis Portal, is now presented at the SAB meeting, with SIB's Vincent Gardeux from @BartDeplancke's group EPFL. Looking to analyze single-cell #omics data? Check the resource out: asap.epfl.ch

Happy to finally share this work. It started as a side project during the lockdown, but then took on a life of its own. doi.org/10.1101/2023.0… A thread 🧵 :

A few days left to register with early bird rate to our [BC]2 SIB workshop "Standardization of single-cell metadata: an Open Research Data initiative" with Jason Hilton of cellxgene & David Osumi-Sutherland EMBL-EBI #SingleCell #FAIRdata bc2.ch/tutorials-work…

I am often invited to review papers on deep learning for medical images. Unfortunately many papers do the same mistake; they split data into training/validation/test on the slice/image/patch level instead of on the patient level. This will lead to inflated test scores, as images