#SpatialTranscriptomics

Decoding cell–cell communication using spatial transcriptomics

#spatialtranscriptomics #omics #ccc
https://www.nature.com/articles/s41576-025-00824-3

Spatiotemporal single-cell roadmap of human skin wound healing
#scRNA-seq

#spatialtranscriptomics

#visium

#RNAScope
https://www.cell.com/cell-stem-cell/fulltext/S1934-5909(24)00412-0?dgcid=raven_jbs_aip_email

#job alert: junior/mid-career PI opportunities in cancer research @ Oxford university: https://www.ludwig.ox.ac.uk/news/vacancies-assistant-or-associate-professor-level-cancer-researchers

Areas we're looking for:
#epigenetics #chromatin #epitranscriptomics #RNA #myeloidCells #spatialTranscriptomics

Please boost for visibility! @academicchatter #hiring

"Uncovering Plaque-Glia Niches in Human Alzheimer’s Disease Brains Using #SpatialTranscriptomics" . https://www.biorxiv.org/content/10.1101/2024.09.05.611566v1

Tools (#preprint from 10x Genomics).
'Here, we introduce Visium HD Spatial Gene Expression (“Visium HD”) and demonstrate its use as a discovery platform for profiling CRC in multiple patients using FFPE tissue blocks. Visium HD slides provide a dramatically increased oligonucleotide barcode density over the Visium v2 slides (11,000,000 continuous features in a 6.5 mm Visium HD capture area, compared to 5,000 features with gaps between them in a 6.5 mm Visium v2 capture area). The single cell scale resolution of Visium HD allowed us to map distinct populations of immune cells, specifically macrophages and T cells, and evaluate differential gene expression at the tumor boundary to explore the potential contribution of these immune cell populations in the TME.'
#Immunology #Immunotherapy #SpatialTranscriptomics
https://www.biorxiv.org/content/10.1101/2024.06.04.597233v1

Some really great talks and discussions today on advances in virus-livestock omics at the #Turing institute, who kindly supported the event. Talks include those by Ge Wu and Marie Di Placido (pictures) from the #Pirbright Institute.

Great to have input from the #BBSRC and #SFTC #Harttree Centre too.

Looking forward to new adventures in this area...

#livestock #virus #genomics #antibody #genome #mutation #pangenome #omics #transcriptomics #spatialtranscriptomics #fmdv​

Last chance to register for our meeting "Advancing virus-livestock omics" on Thurs 28th Sept at the Alan Turing Institute.

Registration closes end of Mon 25th.

See https://www.turing.ac.uk/events/advancing-virus-livestock-omics

Register here: https://t.ly/wYA7d

Schedule below

Zoom stream possible for those from further afield

#livestock #virus #genomics #antibody #genome #mutation #pangenome #omics #transcriptomics #spatialtranscriptomics #fmdv

Marius Lange #BC2basel: increasing complexity of #SingleCell data leads to problems of temporal, spatial and spatio-temporal mapping. The solution proposed is optimal transport applications, implemented in Moscot:
https://moscot.readthedocs.io/en/latest/
https://www.biorxiv.org/content/10.1101/2023.05.11.540374v2 #SpatialTranscriptomics #scRNAseq

Excellent conclusions of Jean Fan #BC2basel on #machinelearning applied to #scRNAseq #SpatialTranscriptomics

Impressive work by Jean Fan's lab #BC2basel: aligning different spatial transcriptomics results, not only from different experiments but different protocols, e.g. MERFISH - Visium. Combining with #scRNAseq clustering and her lab's spot deconvolution allows to compare directly gene expression between these different experiments, https://www.biorxiv.org/content/10.1101/2023.04.11.534630v2.abstract #SpatialTranscriptomics

There is Minecraft. And then there is the #Visium manual fiducial alignment

#SpatialTranscriptomics #BioInformatics

Excited for participating in this #spatialtranscriptomics #Visium platform study with an expert team from @NICHD_NIH, in the first step of studying the spatial biology of #pituitary corticotroph tumors, revealing their heterogeneity.

https://www.medrxiv.org/content/10.1101/2023.08.04.23293576v1

I might as well have make a pinned post.

We published Vesalius a tool that uses Image analysis methods to analyze spatial-omics data.

A new version will be coming soon that will include multimodal analysis and alignment!

GitHub: https://patrickcnmartin.github.io/Vesalius/

MSB: https://www.embopress.org/doi/full/10.15252/msb.202211080

#SpatialTranscriptomics #ImageAnalysis

Computational Scientist

Icahn School of Medicine at Mount Sinai

Come join our team as a #computationalScientist: #multiOmics modeling of #myeloma, including #singleCell, #spatialTranscriptomics and #flowCytometry

See the full job description on jobRxiv: https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-computational-scientist-5/?feed_id=47998

#ScienceJobs #hi...
https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-computational-scientist-5/?feed_id=47998

Postdoctoral Researcher

Icahn School of Medicine at Mount Sinai

Come join our team as a #bioinformatics postdoc: #multiOmics modeling of #myeloma, including #singleCell, #spatialTranscriptomics and #flowCytometry

See the full job description on jobRxiv: https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-postdoctoral-researcher-4/?feed_id=47893

#ScienceJobs #hi...
https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-postdoctoral-researcher-4/?feed_id=47893

O Psoriasis, a troubling foe,
We seek to know what causes your woes.
Your lesions so hard to manage
What makes them range?
Our search will make your secrets known.

#psoriasis #genetics #spatialtranscriptomics #research #ode #poetry

http://www.medicalnewstoday.com/articles/researchers-investigate-what-causes-psoriasis-and-how-it-spreads

Computational Scientist

Icahn School of Medicine at Mount Sinai

Come join our team as a #computationalScientist: #multiOmics modeling of #myeloma, including #singleCell, #spatialTranscriptomics and #flowCytometry

See the full job description on jobRxiv: https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-computational-scientist-5/?feed_id=45913

#ScienceJobs #hi...
https://jobrxiv.org/job/icahn-school-of-medicine-at-mount-sinai-27778-computational-scientist-5/?feed_id=45913

Beautiful multiomic analysis of retina organoid during differentiation.
https://www.nature.com/articles/s41587-023-01747-2
#spatialtranscriptomics #multiome #organoid

Alignment of spatial transcriptomics data from different platforms by Jean Fan group
https://www.biorxiv.org/content/10.1101/2023.04.11.534630v1
#spatialtranscriptomics #xenium #visium #bioinformatics

Use visium to predict missing genes in xenium #spatialtranscriptomics #geneimputation #bioinformatics #xenium #visium
https://www.biorxiv.org/content/10.1101/2023.02.07.527488v1