@Spatial_Cell_ID profile picture
Spatial-Cell-ID @Spatial_Cell_ID
Joined January 2022
  • Tweets 38
  • Following 98
  • Followers 127
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Spatial-Cell-ID@Spatial_Cell_ID
19 Dec 2023
📢We are recruiting!! Spatial-Cell-ID is looking for a postdoctoral fellow or research engineer in image analysis applied to spatial transcriptomics. Come join us in Lyon to analyze our beautiful MERFISH data! shorturl.at/eijC0
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Yad Ghavi-Helm 🐾@yad_ghavi
4 Oct 2024
🚨Preprint alert! tinyurl.com/2zkmynsd Did you ever dream of generating spatial maps of #enhancer activity at #singlecell resolution in a multicellular organism using massively parallel enhancer-reporter assays? Then spatial-scERA is the method for you!

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Join us on June 12th for a workshop on scRNA-seq Registration (limited to 50 people) is free but mandatory spatial-cell-id.ens-lyon.fr/…
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Looking for an internship in #SpatialOMICs #scOMICs? Look no further! 👇
Sergio Sarnataro@SarnataroSergio
17 Apr 2023
At @Spatial_Cell_ID we are looking for a motivated M2 student for an internship in Bioinformatics. Find more information here: drive.google.com/file/d/1_jc… Contact me if you have any questions! #SpatialTranscriptomics #Job #WeAreHiring #SingleCell #bioinformatics #ENSLyon
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Yad Ghavi-Helm 🐾@yad_ghavi
28 Mar 2023
It's tomorrow!! We're expecting a full room for an exciting day of science and spatialOMICs discussions 🤩
Spatial-Cell-ID@Spatial_Cell_ID
2 Mar 2023
Join us in Lyon for the annual Spatial-Cell-ID day! We will welcome @DenisSchapiro (@UniHeidelberg) and Marco Grillo (@MatsNilssonLab @scilifelab) as keynote speakers. Full program available here: spatial-cell-id.ens-lyon.fr/…
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Join us in Lyon for the annual Spatial-Cell-ID day! We will welcome @DenisSchapiro (@UniHeidelberg) and Marco Grillo (@MatsNilssonLab @scilifelab) as keynote speakers. Full program available here: spatial-cell-id.ens-lyon.fr/…
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Yad Ghavi-Helm 🐾@yad_ghavi
30 Aug 2022
🔔Proud and excited to share our latest preprint! We asked this simple question: do TADs really act as strong boundaries or can functional enhancer-promoter interactions be established across TAD boundaries? biorxiv.org/content/10.1101/… A 🧵on our main conclusions: (1/n)

Enhancer-promoter interactions form independently of genomic distance and are functional across TAD...

Developmental enhancers are essential regulatory elements that drive precise spatio-temporal gene expression patterns. They do so by interacting with the promoter of their target genes, often across...

biorxiv.org
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Do you love #imaging, #spatialOMICs, and tech development? Come join the @Spatial_Cell_ID team @ENSdeLyon !
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Nature Methods@naturemethods
16 May 2022
Using transcriptomic similarity and spatial coordinates, PASTE allows aligning and integrating spatial transcriptomics data generated from adjacent tissue slices. @RonZeira @benjraphael nature.com/articles/s41592-0…
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s.@mssanjavickovic
10 Feb 2022
I’m so happy to present our spatial multi-omics work out today! nature.com/articles/s41467-0… #spatial #transcriptomics #citeseq #smomics

SM-Omics is an automated platform for high-throughput spatial multi-omics

Nature Communications - The spatial organisation of cells and molecules plays a key role in tissue function. Here the authors report Spatial MultiOmics (SM-Omics) as a fully automated,...

nature.com
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Spatial-Cell-ID retweeted
Rong Fan@RongFan8
10 Feb 2022
Spatial-CUT&Tag! @ScienceMagazine, unfolding a new chapter of #spatialomics 🤗 . From my phenomenal postdoc @DengYanxiang of @YaleSEAS @YaleBME, @yalepathology @YaleMed @YaleCancer Thanks to awesome collaborators @GoCasteloBranco @marekbartosovic @PKukanja science.org/doi/10.1126/scie…

Spatial-CUT&Tag: Spatially resolved chromatin modification profiling at the cellular level

Spatial-CUT&Tag enables genome-wide tissue mapping of chromatin modification states at a cellular level.

science.org
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Spatial-Cell-ID retweeted
Danila
@gtcaa
7 Feb 2022
It's great to see our article about the multimodal omics analysis framework muon out! Many thanks to everyone who provided feedback along the way. 🙌 See a few highlights in the thread below.
Genome Biology@GenomeBiology
2 Feb 2022
MUON, from @gtcaa, Kats & @OliverStegle, a package for organizing, analyzing, visualizing & exchanging multi-omics data. It is based around MuData, an open data structure for multimodal data. An example given is ATAC-seq and RNA-seq from single cells genomebiology.biomedcentral.…
Alternative example workflows for integrating multiple omics for latent space inference and clustering

ALT Alternative example workflows for integrating multiple omics for latent space inference and clustering

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Developmental Cell@Dev_Cell
7 Feb 2022
New Resource online now at Dev Cell: A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell identity mutants - zpr.io/6nU8Z95mJ8qS

A single-cell Arabidopsis root atlas reveals developmental trajectories in wild-type and cell...

How do transcriptional networks regulate organ development? Using scRNA-seq, Shahan and Hsu et al. produced an Arabidopsis root atlas, revealing gradual gene expression changes underlying different...

cell.com
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Giovanni Palla@g_palla1
7 Feb 2022
"Spatial components of molecular tissue biology", review wrote with @davidsebfischer @fabian_theis and Aviv Regev is out in @NatureBiotech. We outline biological questions and computational challenges in spatial analysis of tissues. 1/N nature.com/articles/s41587-0…

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Nikos Karaiskos@nu_karaiskos
9 Nov 2021
How to efficiently analyse & process large-scale spatial transcriptomics data from different techs? We've developed Spacemake that does this and much more biorxiv.org/content/10.1101/…
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Spatial-Cell-ID retweeted
Luciano Martelotto 🛠🧬💻🇦🇺@LGMartelotto
7 Feb 2022
Power analysis for spatial omics | bioRxiv biorxiv.org/content/10.1101/…

Power analysis for spatial omics

As spatially-resolved multiplex profiling of RNA and proteins becomes more prominent, it is increasingly important to understand the statistical power available to test specific hypotheses when...

biorxiv.org
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Spatial-Cell-ID retweeted
Min Dai
@artofbiology
4 Feb 2022
Spatially resolved transcriptomics and its applications | Nice review from Prof. Mingyao Li's group @DrMingyaoLi Statistical and machine learning methods for spatially resolved transcriptomics with histology sciencedirect.com/science/ar…
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Spatial-Cell-ID retweeted
Eduard Chelebian@EChelebian
5 Feb 2022
How cool is it to be able to visualize multiresolution #InSituSequencing and #SpatialTranscriptomics images with millions of overlaying points from your phone browser!? 🔬📱 TissUUmaps 3 allows it: visit our gallery for more examples tissuumaps.github.io/gallery…
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Nikos Karaiskos@nu_karaiskos
7 Feb 2022
Optocoder: a computational tool that decodes spatially indexed bead arrays. Optocoder processes spatial transcriptomics microscopy images to extract bead locations and their barcodes (led by fantastic PhD student @nssenel at @N_Rajewsky lab) (1/4) biorxiv.org/content/10.1101/…
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📢The Spatial-Cell-ID facility is looking for a bioinformatician! Do you love #singlecell and #spatialtranscriptomics? Want to be part of an exciting project with state-of-the-art equipment? Come join us @ENSdeLyon @UniversiteLyon @IGFLyon shorturl.at/ituN6
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