#spatialtranscriptomics search results

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🚨New #SpatialTranscriptomics #Bioinformatics data resource out in @naturemethods. SODB, a platform with >2,400 manually curated spatial experiments from >25 spatial omics technologies & interactive analytical modules. This🧵will walk you through all the features of SODB [1/33]

simocristea's tweet image. 🚨New #SpatialTranscriptomics #Bioinformatics data resource out in @naturemethods.

SODB, a platform with >2,400 manually curated spatial experiments from >25 spatial omics technologies & interactive analytical modules.

This🧵will walk you through all the features of SODB [1/33]

Ruochen Dong, @linheng_li lab, gave an outstanding presentation on using #SpatialTranscriptomics to interrogate HSC-niche interaction in the mouse fetal liver at #ISSCR2023. He also received merit and travel awards. Congratulations! @ISSCR

ScienceStowers's tweet image. Ruochen Dong, @linheng_li lab, gave an outstanding presentation on using #SpatialTranscriptomics to interrogate HSC-niche interaction in the mouse fetal liver at #ISSCR2023. He also received merit and travel awards. Congratulations! @ISSCR

Excited to share our #SingleCell and #SpatialTranscriptomics analysis of #ExerciseTraining remodeling of #WhiteAdiposeTissue through innervation, vascularization, and #ExtracellularMatrix in mouse and human with #LaurieGoodyear #JanWillemMiddelbeek @PasqualeNigro9 @MVamvini

manoliskellis's tweet image. Excited to share our #SingleCell and #SpatialTranscriptomics analysis of #ExerciseTraining remodeling of #WhiteAdiposeTissue through innervation, vascularization, and #ExtracellularMatrix in mouse and human with #LaurieGoodyear #JanWillemMiddelbeek @PasqualeNigro9 @MVamvini…
manoliskellis's tweet image. Excited to share our #SingleCell and #SpatialTranscriptomics analysis of #ExerciseTraining remodeling of #WhiteAdiposeTissue through innervation, vascularization, and #ExtracellularMatrix in mouse and human with #LaurieGoodyear #JanWillemMiddelbeek @PasqualeNigro9 @MVamvini…
manoliskellis's tweet image. Excited to share our #SingleCell and #SpatialTranscriptomics analysis of #ExerciseTraining remodeling of #WhiteAdiposeTissue through innervation, vascularization, and #ExtracellularMatrix in mouse and human with #LaurieGoodyear #JanWillemMiddelbeek @PasqualeNigro9 @MVamvini…
manoliskellis's tweet image. Excited to share our #SingleCell and #SpatialTranscriptomics analysis of #ExerciseTraining remodeling of #WhiteAdiposeTissue through innervation, vascularization, and #ExtracellularMatrix in mouse and human with #LaurieGoodyear #JanWillemMiddelbeek @PasqualeNigro9 @MVamvini…

Systematic comparisons among 4 subcellular-resolution #SpatialTranscriptomics methods Stereo-seq v1.3 Visium HD FFPE CosMx 6k Xenium 5k Human Tumors Ground truth CODEX, +scRNAseq Gene detection sensitivity (CosMx performance...🙁) (Spatial) false positives Transcript-protein…

HaoYin20's tweet image. Systematic comparisons among 4 subcellular-resolution #SpatialTranscriptomics methods

Stereo-seq v1.3
Visium HD FFPE
CosMx 6k
Xenium 5k

Human Tumors
Ground truth CODEX, +scRNAseq

Gene detection sensitivity (CosMx performance...🙁)
(Spatial) false positives
Transcript-protein…

How do we uncover cell-cell interactions from #SpatialTranscriptomics data? Excited to share Niche-DE (doi.org/10.1186/s13059…). Niche-DE asks how does a cell’s transcriptome depend on its spatial neighbors, by identifying Niche-Differentially Expressed genes. 1/9

NancyZh60672287's tweet image. How do we uncover cell-cell interactions from #SpatialTranscriptomics data? Excited to share Niche-DE (doi.org/10.1186/s13059…). Niche-DE asks how does a cell’s transcriptome depend on its spatial neighbors, by identifying Niche-Differentially Expressed genes. 1/9

CoCo-ST detects global and local biological structures in spatial transcriptomics datasets. #SpatialTranscriptomics #VarianceIdentification @NatureCellBio nature.com/articles/s4155…

jsantoyo's tweet image. CoCo-ST detects global and local biological structures in spatial transcriptomics datasets. #SpatialTranscriptomics #VarianceIdentification @NatureCellBio 
nature.com/articles/s4155…

#WernerSyndrome hiPSC-derived engineered vessel #SpatialTranscriptomics #Visium @10xGenomics + #Metabolomics▶️ #BranchedChainKetoAcid⬇️ #MonohydroxyFattyAcid⬆️ in Werner vessels with traits of #PrematureAging Aligned #SmoothMuscleCell in Collagen hydrogel➡️ Roll-up around φ…

HaoYin20's tweet image. #WernerSyndrome
hiPSC-derived engineered vessel

#SpatialTranscriptomics #Visium @10xGenomics + #Metabolomics▶️
#BranchedChainKetoAcid⬇️
 #MonohydroxyFattyAcid⬆️
in Werner vessels with traits of #PrematureAging

Aligned #SmoothMuscleCell in Collagen hydrogel➡️
Roll-up around φ…

Comparing single-cell #SpatialTranscriptomics methods on FFPE human tumor #TissueMicroArray CosMx 1k vs MERFISH 500 vs Xenium-UM/-MM 339 93 common genes lung adenocarcinoma pleural mesothelioma Corr. Bulk RNAseq, GeoMx "better F1-scores with Xenium-MM (median, > 75%) than…

HaoYin20's tweet image. Comparing single-cell #SpatialTranscriptomics methods on FFPE human tumor #TissueMicroArray

CosMx 1k vs MERFISH 500 vs Xenium-UM/-MM 339
93 common genes

lung adenocarcinoma
pleural mesothelioma

Corr. Bulk RNAseq, GeoMx

"better F1-scores with Xenium-MM (median, > 75%) than…

Excellent talk from @Sandy_Figiel in @Uroweb #EAUlab session at #EAU25 presenting our cool data (I'm bias!) on #SpatialTranscriptomics & #ClonalAnalysis to detect unique features of metastasing clones in #ProstateCancer. @OxPCaBiol #SPACE_Study #3DLightsheet

LambAlastair's tweet image. Excellent talk from @Sandy_Figiel in @Uroweb #EAUlab session at #EAU25 presenting our cool data (I'm bias!) on #SpatialTranscriptomics & #ClonalAnalysis to detect unique features of metastasing clones in #ProstateCancer. 

@OxPCaBiol #SPACE_Study #3DLightsheet
LambAlastair's tweet image. Excellent talk from @Sandy_Figiel in @Uroweb #EAUlab session at #EAU25 presenting our cool data (I'm bias!) on #SpatialTranscriptomics & #ClonalAnalysis to detect unique features of metastasing clones in #ProstateCancer. 

@OxPCaBiol #SPACE_Study #3DLightsheet
LambAlastair's tweet image. Excellent talk from @Sandy_Figiel in @Uroweb #EAUlab session at #EAU25 presenting our cool data (I'm bias!) on #SpatialTranscriptomics & #ClonalAnalysis to detect unique features of metastasing clones in #ProstateCancer. 

@OxPCaBiol #SPACE_Study #3DLightsheet
LambAlastair's tweet image. Excellent talk from @Sandy_Figiel in @Uroweb #EAUlab session at #EAU25 presenting our cool data (I'm bias!) on #SpatialTranscriptomics & #ClonalAnalysis to detect unique features of metastasing clones in #ProstateCancer. 

@OxPCaBiol #SPACE_Study #3DLightsheet

OmiCLIP #Visualomics github.com/GuangyuWangLab… An amazing Histology (HE) - #SpatialTranscriptomics foundation model Contrastive Learning: Image encoder + Gene/Text encoder Not Generative yet Building an ST-bank of 2.2 M image-Visium pairs in 1007 tissue samples, 32 organs Work…

HaoYin20's tweet image. OmiCLIP #Visualomics
github.com/GuangyuWangLab…

An amazing Histology (HE) - #SpatialTranscriptomics foundation model
Contrastive Learning: Image encoder + Gene/Text encoder
Not Generative yet

Building an ST-bank of 2.2 M image-Visium pairs in 1007 tissue samples, 32 organs

Work…

STORIES SpatioTemporal Omics eneRgIES Learning Waddington epigenetic (+regulon) landscape from multi-time-point Stereo-seq #SpatialTranscriptomics Potential-based Fused Gromov-Wasserstein #OptimalTransport Linear▶️gene expression error Quadratic▶️spatial consistency @gjhuizing

HaoYin20's tweet image. STORIES
SpatioTemporal Omics eneRgIES

Learning Waddington epigenetic (+regulon) landscape from multi-time-point Stereo-seq #SpatialTranscriptomics

Potential-based
Fused Gromov-Wasserstein #OptimalTransport
Linear▶️gene expression error
Quadratic▶️spatial consistency

@gjhuizing…

🔬 A new computational approach pioneered by researchers at the @broadinstitute eliminates time-intensive imaging, enabling high-resolution spatial mapping of gene expression in tissue. See how they're making #SpatialTranscriptomics easier for everyone: bit.ly/3G9Hrau

ScienceinBoston's tweet image. 🔬 A new computational approach pioneered by researchers at the @broadinstitute eliminates time-intensive imaging, enabling high-resolution spatial mapping of gene expression in tissue.

See how they're making #SpatialTranscriptomics easier for everyone: bit.ly/3G9Hrau

CODA integrative CrOss-sample alignment and spatially Differential gene Analysis for #SpatialTranscriptomics Global rigid alignment➡️ Shared coordinate grid embedding➡️ 3-channel image representation➡️ LightGlue common domain identification➡️ Local nonlinear alignment Work with…

HaoYin20's tweet image. CODA
integrative CrOss-sample alignment and spatially Differential gene Analysis for #SpatialTranscriptomics

Global rigid alignment➡️
Shared coordinate grid embedding➡️
3-channel image representation➡️
LightGlue common domain identification➡️
Local nonlinear alignment

Work with…

Myocilin marks the glia limitans superficialis Astrocyte Re-analysis of brain-wide #SpatialTranscriptomics & sc-/sn-RNAseq data➡️ Myoc+ 2% of total astrocytes that cover brain/spinal cord surface and extend processes into parenchyma Any marker for glia limitans perivascularis…

HaoYin20's tweet image. Myocilin marks the glia limitans superficialis Astrocyte

Re-analysis of brain-wide #SpatialTranscriptomics & sc-/sn-RNAseq data➡️
Myoc+ 2% of total astrocytes that cover brain/spinal cord surface and extend processes into parenchyma

Any marker for glia limitans perivascularis…

We’re all wondering what the future of #spatialtranscriptomics (ST) has in store. Well, I think the near future will look a lot like the new 6000-plex dataset reviewed here (link to the original source at the end of this post). SAMPLE An entire 100 mm² intact 5 µm FFPE section…

BrantBassamPhD's tweet image. We’re all wondering what the future of #spatialtranscriptomics (ST) has in store. Well, I think the near future will look a lot like the new 6000-plex  dataset reviewed here (link to the original source at the end of this post).

SAMPLE
An entire 100 mm² intact 5 µm FFPE section…
BrantBassamPhD's tweet image. We’re all wondering what the future of #spatialtranscriptomics (ST) has in store. Well, I think the near future will look a lot like the new 6000-plex  dataset reviewed here (link to the original source at the end of this post).

SAMPLE
An entire 100 mm² intact 5 µm FFPE section…
BrantBassamPhD's tweet image. We’re all wondering what the future of #spatialtranscriptomics (ST) has in store. Well, I think the near future will look a lot like the new 6000-plex  dataset reviewed here (link to the original source at the end of this post).

SAMPLE
An entire 100 mm² intact 5 µm FFPE section…
BrantBassamPhD's tweet image. We’re all wondering what the future of #spatialtranscriptomics (ST) has in store. Well, I think the near future will look a lot like the new 6000-plex  dataset reviewed here (link to the original source at the end of this post).

SAMPLE
An entire 100 mm² intact 5 µm FFPE section…

Pleased to share our latest #SpatialTranscriptomics output now on @biorxivpreprint We show marked variation in gene expr relating to @Decipher_VCYT, #Oncotype_DX & #ProstaDiag genomic scores Being presented by @Sandy_Figiel this afternoon #EAU23!! biorxiv.org/content/10.110…

LambAlastair's tweet image. Pleased to share our latest #SpatialTranscriptomics output now on @biorxivpreprint

We show marked variation in gene expr relating to @Decipher_VCYT, #Oncotype_DX & #ProstaDiag genomic scores

Being presented by @Sandy_Figiel this afternoon #EAU23!!

biorxiv.org/content/10.110…
LambAlastair's tweet image. Pleased to share our latest #SpatialTranscriptomics output now on @biorxivpreprint

We show marked variation in gene expr relating to @Decipher_VCYT, #Oncotype_DX & #ProstaDiag genomic scores

Being presented by @Sandy_Figiel this afternoon #EAU23!!

biorxiv.org/content/10.110…
LambAlastair's tweet image. Pleased to share our latest #SpatialTranscriptomics output now on @biorxivpreprint

We show marked variation in gene expr relating to @Decipher_VCYT, #Oncotype_DX & #ProstaDiag genomic scores

Being presented by @Sandy_Figiel this afternoon #EAU23!!

biorxiv.org/content/10.110…
LambAlastair's tweet image. Pleased to share our latest #SpatialTranscriptomics output now on @biorxivpreprint

We show marked variation in gene expr relating to @Decipher_VCYT, #Oncotype_DX & #ProstaDiag genomic scores

Being presented by @Sandy_Figiel this afternoon #EAU23!!

biorxiv.org/content/10.110…

"We all love the pretty pictures we get from #SpatialTranscriptomics but the real value lies in the ability to precisely determine the cellular composition & cell-cell relationships - not possible with bulk RNA or even scRNA approaches" 💯% well said @bayraktar_lab! 👏 #FoG2025

LambAlastair's tweet image. "We all love the pretty pictures we get from #SpatialTranscriptomics but the real value lies in the ability to precisely determine the cellular composition & cell-cell relationships - not possible with bulk RNA or even scRNA approaches"

💯% well said @bayraktar_lab!
👏
#FoG2025
LambAlastair's tweet image. "We all love the pretty pictures we get from #SpatialTranscriptomics but the real value lies in the ability to precisely determine the cellular composition & cell-cell relationships - not possible with bulk RNA or even scRNA approaches"

💯% well said @bayraktar_lab!
👏
#FoG2025
LambAlastair's tweet image. "We all love the pretty pictures we get from #SpatialTranscriptomics but the real value lies in the ability to precisely determine the cellular composition & cell-cell relationships - not possible with bulk RNA or even scRNA approaches"

💯% well said @bayraktar_lab!
👏
#FoG2025
LambAlastair's tweet image. "We all love the pretty pictures we get from #SpatialTranscriptomics but the real value lies in the ability to precisely determine the cellular composition & cell-cell relationships - not possible with bulk RNA or even scRNA approaches"

💯% well said @bayraktar_lab!
👏
#FoG2025

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