#spatialtranscriptomics 検索結果
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…
Systematic benchmarking of computational methods to identify spatially variable genes. #SpatialTranscriptomics #MethodsBenchmarking @GenomeBiology genomebiology.biomedcentral.com/articles/10.11…
#SpatialTranscriptomics Visium #CerebralMalaria 🐭+P.berghei ANKA -/+Artesunate Malaria infection▶️ ⏫🧠#EndothelialCell, immune cells SPATA spatial trajectory inference of EC-rich spots in infected🧠▶️ ⏫EC antigen processing/presentation + leukocyte adhesion ⏬BBB Partially…
"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
#SpatialTranscriptomics #BrainOrganoid #Glioblastoma Striatal implant of Brain organoids +Mutant TERT p.C228T TP53 R248Q➡️SOX11+ Proneural GBM subtype +Mutant TERT p.C228T PTENΔ NF1Δ➡️ERBB3+ Mesenchymal GBM subtype In-depth single-cell spatial transcriptional & CNV landscape…
🧬 14 spatial clustering methods benchmarked across ~600 #SpatialTranscriptomics datasets 💻 Covering 10 technologies & 8 organs 📊 Reveals how data traits & spatial patterns shape accuracy ⚙️ Recommends optimal preprocessing & method selection 🔗 doi.org/10.1002/imt2.7……
GOD IS GOOD! Today, I passed my #PhD Dissertation Defense!!! 🎉 Thank you to everyone who believed in me. Thank you to all my mentors, friends, and family. 🥰 I would not be where I am today without all of you. 🙏❤️ @SBS_UNTHSC #SpatialTranscriptomics #DoubleDocs @A_P_S_A
#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…
November's #DukeSCIRIP seminar will feature: 1. Xiaohui Jiang of @DukeBiostats on 'X-bridge' for #SingleCell and spatial panel analysis 2. Dr. Ru-Rong Ji of @DukeMedSchool on #SpatialTranscriptomics of #SensoryNeurons 11/5 12-1pm in MSRBIII or online dmpi.duke.edu/duke-single-ce…
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…
#SpatialTranscriptomics 🐭#Stroke #Visium @10xGenomics #Photothrombosis 3 dpi Stroke▶️ ⏫Microglia/Macrophage Galectin-1/3/9➡️ Astrocyte/Oligodendrocyte CD44 at peri-infarct zone▶️ ⏫remyelination ⏫neurobehavioral performance Post-stroke benefits of LGALS9-expressing…
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
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
⚡️Exciting Breakthrough in Progressive Multiple Sclerosis⚡️ Much humbled to contribute to this exciting project from @Pluchinolab . Analysing 200+ sections from 50+ patients, showcases the power of #spatialtranscriptomics in rare cell localization. 🧠 @IBT_CAS @LukasValihrach
Proud to see our work out in @NeuroCellPress ! cell.com/neuron/fulltex… With Bongsoo Park, Dimitris Tsitsipatis @DanielZucha @LukasValihrach @irina_mohorianu @Pluchinolab @BeermanHSCaging !
Accurate cell segmentation is integral to #spatialtranscriptomics—that's why we never stop improving ours. Large cells? Tissues with dense nuclei? We’ve got you covered. See how you can segment cells more accurately than ever before: bit.ly/4m1nEcz
Has @Tom_J_Mitchell finally come round to #SpatialTranscriptomics?! Lovely talk & scope of work presented at #ESUR23 from his @EarlyCancerCam group Using ST to define transition from benign to malignant #KidneyCancer & oppo for early detection/intervention @ChloePacyna @Uroweb
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
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…
I'm excited to present my first postdoctoral research project: FineST⭐[GitHub:github.com/StatBiomed/Fin…]. Welcome to join and discuss! Your valuable feedback would be greatly appreciated. 🤝 #SpatialTranscriptomics #TumorMicroenvironment #Bioinformatics #CellCommunication
![LingyuLi61's tweet image. I'm excited to present my first postdoctoral research project: FineST⭐[GitHub:github.com/StatBiomed/Fin…]. Welcome to join and discuss! Your valuable feedback would be greatly appreciated. 🤝
#SpatialTranscriptomics #TumorMicroenvironment #Bioinformatics #CellCommunication](https://pbs.twimg.com/media/G36U6HiWsAAt32C.jpg)
Visium HD or Xenium Prime 5K? Two paths to spatial insights—one for broad, unbiased discovery, the other for targeted, cell-level precision. Read how each fits discovery and validation workflows: signiosbio.com/blog/10x-visiu… #SpatialBiology #SingleCell #SpatialTranscriptomics
Excited to share the fresh STOmics Newsletter (Aug–Sep 2025)! 🎉 220+ Stereo-seq breakthroughs, Alzheimer’s atlas, event recaps & how-to videos—all in one click. Read & retweet! 👉bit.ly/4o0AdXt #STOmics #StereoSeq #SpatialTranscriptomics
🦠💩 #Microbiome 🧬🔬 #SpatialTranscriptomics 🤖🗣️🤖 #ArtificialIntelligence Agents for #PrecisionMedicine & #ColorectalCancer Research 💉 Proud of our #VelazquezVillarrealLab team for presenting TWO outstanding posters on 🎉 2025 @cityofhope Annual Poster Session @PECGSnetwork
November's #DukeSCIRIP seminar will feature: 1. Xiaohui Jiang of @DukeBiostats on 'X-bridge' for #SingleCell and spatial panel analysis 2. Dr. Ru-Rong Ji of @DukeMedSchool on #SpatialTranscriptomics of #SensoryNeurons 11/5 12-1pm in MSRBIII or online dmpi.duke.edu/duke-single-ce…
🧬 14 spatial clustering methods benchmarked across ~600 #SpatialTranscriptomics datasets 💻 Covering 10 technologies & 8 organs 📊 Reveals how data traits & spatial patterns shape accuracy ⚙️ Recommends optimal preprocessing & method selection 🔗 doi.org/10.1002/imt2.7……
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…
🚨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]](https://pbs.twimg.com/media/FpqfK6HaUAAQZAo.jpg)
"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
#SpatialTranscriptomics 🐭#Stroke #Visium @10xGenomics #Photothrombosis 3 dpi Stroke▶️ ⏫Microglia/Macrophage Galectin-1/3/9➡️ Astrocyte/Oligodendrocyte CD44 at peri-infarct zone▶️ ⏫remyelination ⏫neurobehavioral performance Post-stroke benefits of LGALS9-expressing…
A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types. #LongReads #SingleCell #Spatialtranscriptomics #IsoSeq #PolyA @NatureComms nature.com/articles/s4146…
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…
🧬 14 spatial clustering methods benchmarked across ~600 #SpatialTranscriptomics datasets 💻 Covering 10 technologies & 8 organs 📊 Reveals how data traits & spatial patterns shape accuracy ⚙️ Recommends optimal preprocessing & method selection 🔗 doi.org/10.1002/imt2.7……
Accurate cell segmentation is integral to #spatialtranscriptomics—that's why we never stop improving ours. Large cells? Tissues with dense nuclei? We’ve got you covered. See how you can segment cells more accurately than ever before: bit.ly/4m1nEcz
#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…
#SpatialTranscriptomics Visium #CerebralMalaria 🐭+P.berghei ANKA -/+Artesunate Malaria infection▶️ ⏫🧠#EndothelialCell, immune cells SPATA spatial trajectory inference of EC-rich spots in infected🧠▶️ ⏫EC antigen processing/presentation + leukocyte adhesion ⏬BBB Partially…
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…
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
#SpatialTranscriptomics #BrainOrganoid #Glioblastoma Striatal implant of Brain organoids +Mutant TERT p.C228T TP53 R248Q➡️SOX11+ Proneural GBM subtype +Mutant TERT p.C228T PTENΔ NF1Δ➡️ERBB3+ Mesenchymal GBM subtype In-depth single-cell spatial transcriptional & CNV landscape…
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
GOD IS GOOD! Today, I passed my #PhD Dissertation Defense!!! 🎉 Thank you to everyone who believed in me. Thank you to all my mentors, friends, and family. 🥰 I would not be where I am today without all of you. 🙏❤️ @SBS_UNTHSC #SpatialTranscriptomics #DoubleDocs @A_P_S_A
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…
We are very very VERY excited to be running #cosmx #singlecell #spatialtranscriptomics experiments in @UofGlasgow @UofGCancerSci @UofGMVLS Well done to the @LabSpatialNBJ team @nanostringtech
#SpatialOmics #ImagingMassSpec #SpatialTranscriptomics MISTy Multiview Intercellular SpaTial modeling framework bioconductor.org/packages/relea… View/spatial scale-specific feature interactions Intraview - same location (intra-to-multicellulat) Juxtaview - immediate neighborhood…
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
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