The emergence of multiscale connectomics-based approaches in stroke recovery💪
cell.com/trends/neurosc…

Astrocytes in selective vulnerability to neurodegenerative disease🫶
cell.com/trends/neurosc…

Innate immune activation in neurodegenerative diseases🧠 cell.com/immunity/abstr…

Beautiful Work! Congrats👏👏👏

Comparison of spatial transcriptomics technologies used for tumor cryosections 🧐biorxiv.org/content/10.110…

Single-cell RNA sequencing of human tissue supports successful drug targets👌 medrxiv.org/content/10.110…

The choice of whether to use Seurat or Scanpy for single-cell RNA-seq analysis typically comes down to a preference of R vs. Python. But do they produce the same results? In biorxiv.org/content/10.110… w/ Joseph Rich et al. we take a close look. The results are 👀 1/🧵

In their Specious Art paper, Chari & Lior Pachter claim that tSNE/UMAP are as arbitrary as a random elephant shape. But are they?

We show in our comment that this is false and throws the tSNE/UMAP baby out with the bathwater!

Details in 🧵& paper:

biorxiv.org/content/10.110…

1/8

Just finished teaching another semester of genomic #datavisualization 🥳

Discover the awesome #dataviz made by students in the class for various #singlecell #spatialtranscriptomics data

Check out the course notes + #Rstats code to explore for yourself: jef.works/genomic-data-v…

PAPER ALERT!! Our latest work is out in Nature Neuroscience! We used humanised models to characterise in-depth the complex response of human microglia to Alzheimer's pathology, and we delved into the mechanisms and impact of genetics. nature.com/articles/s4159…

Molecular and cellular mechanisms of selective vulnerability in neurodegenerative diseases nature.com/articles/s4158…

Repetitive head impacts induce neuronal loss and neuroinflammation in young athletes biorxiv.org/content/10.110…

Don't miss our next #Bioinformatics seminar held by
Matematicko-fyzikální fakulta Univerzity Karlovy and Faculty of Science of Charles University. 'Revolutionizing Modern Biomedical Research with Single-Cell and Spatial Transcriptomics' by Lukas Valihrach from Institute of Biotechnology
📅 Wed 3. 4.
⏲️17:20
🏦Malostranske nam. 25
bioinformatics.cuni.cz/seminar

Seq-Scope Protocol: Repurposing Illumina Sequencing Flow Cells for High-Resolution Spatial Transcriptomics

'a detailed step-by-step protocol to implement Seq-Scope with an Illumina NovaSeq 6000 sequencing flow'

biorxiv.org/content/10.110…

📢 How can we identify cell lineages from any scRNA-seq dataset ? Check our paper: nature.com/articles/s4146…. Very proud of massive amount of beautiful work by Almut Eisele, A. Dormann + fantastic collaboration with Marcel Tarbier and Pelechano lab. A 🧵

Wanna do standard 3’, 5’ etc ⁦⁦10x Genomics⁩ applications-seq without stress? No worries! FixNCut it baby!

Laura Jiménez Gracia YOU are the best! Holger Heyn Dr. Jasmine Plummer 👩🏻‍🔬🧬🇨🇦🇺🇸 CNAG ⁦Omniscope⁩ genomebiology.biomedcentral.com/articles/10.11…

In a pair of bioRxiv preprints just posted w/ Sina Booeshaghi and Angel Galvez Merchan, we describe algorithms for an open data Commons Cell Atlas and demonstrate how a Human Commons Cell Atlas can be used for discovery.
biorxiv.org/content/10.110…
biorxiv.org/content/10.110…
1/🧵

STCellbin

Use Nuclei+Cell Membrane/Wall stains to improve #CellSegmentation & single-cell-resolved #SpatialTranscriptomics

Tailored for #StereoSeq , but likely implementable for other ST methods

Susanne Brix & Xun Xu labs GigaByteJournal 2024
gigabytejournal.com/articles/110

DART-FISH
#SpatialTranscriptomics

Pad-lock probe
Rolony
RiboSoma for cell segmentation
Detect <1kb short RNA (able to probe pri-microRNAs?😁)

Very nice reading if interested in how to design/optimize imaging-based ST methods👍

121 genes for human Cortex
300 genes for human…

What a PERFFect day to share our new preprint!

With Tsion Abay #BobStickels Meril Takizawa Ronan Chaligne (He/Him) and Ansu Satpathy, we introduce PERFF-seq, a new experimental approach to studying rare cells with scRNA-seq via transcript-specific enrichment. biorxiv.org/content/10.110… 1/n