#Spatialtranscriptomics
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10xgenomics.bsky.social
Stop wondering, start analyzing. Our new Xenium Analysis Guides help you start faster and master downstream workflows immediately. Explore the guides: https://bit.ly/3KWNAJw

#spatialtranscriptomics #dataanalysis
October 21, 2025 at 10:00 PM
cancerdynamics.bsky.social
Big news: The Vicković Lab’s study on colon aging has been accepted by @natbiotech.nature.com! The team built a detailed atlas of aging colon tissue, using spatial transcriptomics + a new tool (cSplotch) to profile ~1,500 samples & 400k nuclei.
🔗 Read more: bit.ly/4hj3ry7
#SpatialTranscriptomics
cSplotch Summary Schematic
October 22, 2025 at 12:53 PM
imetascience.bsky.social
🧬 Benchmarking 14 spatial clustering methods across ~600 #SpatialTranscriptomics datasets
🧫 10 technologies, 8 organs — consistent insights
⚙️ Clear guidance for method choice & preprocessing
🔗 doi.org/10.1002/imt2...
#Bioinformatics #SpatialOmics #scRNA
A comprehensive benchmarking for spatially resolved transcriptomics clustering methods across variable technologies, organs, and replicates
Spatial clustering is a critical step in spatially resolved transcriptomics. Here, we conducted a comprehensive benchmarking analysis of 14 spatial clustering methods using ~600 datasets, including b...
doi.org
October 19, 2025 at 3:14 PM
positron96.bsky.social
#SpatialTranscriptomics #SpatialOmics #SpatialBiology #Transcriptomics #SingleCell #IBD #Crohns #UlcerativeColitis #Healthcare #PrecisionMedicine #SystemsBiology #MachineLearning #ArtificialIntelligence #AIinHealthcare #ComputationalPathology #AI
September 19, 2025 at 6:37 PM
haoyin.bsky.social
#SpatialTranscriptomics #BrainOrganoid #Glioblastoma

Striatal implant of Brain organoids
+TERT p.C228T TP53 R248Q➡️SOX11+ Proneural GBM
+TERT p.C228T PTENΔ NF1Δ➡️ERBB3+ Mesenchymal GBM

Single-cell spatial transcriptional+CNV landscape

#AdvSci 2025
advanced.onlinelibrary.wiley.com/doi/10.1002/...
September 15, 2025 at 11:44 AM
biolidia.bsky.social
En el "Cancer Immunotherapy (CIT) Lab" buscamos un candidato #predoctoral para solicitar una beca #PFIS asociada a un proyecto destinado al estudio del microambiente tumoral mediante #SpatialTranscriptomics y testaje de fármacos que mejoren la inmunoterapia en cáncer de próstata.
January 11, 2025 at 4:26 PM
loicaroyer.bsky.social
🧬🔬🧪 We are seeking a Scientist to push the limits of spatial transcriptomics in zebrafish! Come join us!
#MolBio #SpatialTranscriptomics #DevelopmentalBiology #ScienceJobs 🧫🐟🔍

job-boards.greenhouse.io/chanzuckerbe...
Scientist, Spatial Molecular Cartography (Jacobo/Royer Group - Biohub SF)
San Francisco, California, United States
job-boards.greenhouse.io
April 15, 2025 at 6:27 PM
kaminskimed.bsky.social
Just added this 👇🏼 to my #SpatialTranscriptomics and #CureIPF weekend reading lists - so should you
December 14, 2024 at 9:17 PM
cellima-science.bsky.social
🔗 Read the full reveiw here: cellima.notion.site/Comparative-...

#SpatialTranscriptomics #Oncology #Research #DeepLearning #immunooncolgy
#SpatialBiology

www.cellima.com
February 5, 2025 at 1:51 PM
haoyin.bsky.social
#SpatialTranscriptomics Visium
Human embryonic heart valves
Carnegie stage 16 & 19 female

Novel aortic valve markers
LINC00632 PDLIM3 FLRT2 MXRA8 RBP1

Defects of aortic valvulogenesis in RBP1 (Retinol Binding Protein 1) KO🐭

#PLOSGenetics 2023
journals.plos.org/plosgenetics...
October 31, 2024 at 12:05 PM
lcolladotor.bsky.social
Next we have Gregory Schwartz presenting new computational approaches to understand cancer heterogeneity and non uniform response to treatment across cancer evolution

Greg started to work cell to cell communication using #SpatialTranscriptomics data with his colleagues

#SpatialBiology
December 5, 2024 at 11:26 PM
drjimmylee.bsky.social
Thrilled to share our new @naturecomms.bsky.social study with @sam-n-barnett.bsky.social on early vs late #COVID19 lung damage 🫁.
Using single-cell & histopathology-informed #SpatialTranscriptomics, we uncovered key biomarkers & immune patterns. Thanks to collaborators, UKCIC & @humancellatlas.org
sangerinstitute.bsky.social Wellcome Sanger Institute @sangerinstitute.bsky.social · Mar 10
How lung damage worsens during COVID-19 has been mapped at a cellular level. 🦠

By understanding how our lungs respond to the virus over time, this new knowledge may help identify future therapies for COVID-19.

www.sanger.ac.uk/news_item/ce...
Cellular changes as lung damage worsens in COVID-19 revealed
Researchers uncover cellular changes as damage to alveoli in the lungs progresses during COVID-19.
www.sanger.ac.uk
March 12, 2025 at 6:35 AM
svanuytven.bsky.social
Weekly Reads 10/3/25

🔬 PDAC metastasis & the role of transcriptomic plasticity
🧠 NNNSF: Scalable modeling for spatial & temporal data
🦠 MYC ecDNA driving heterogeneity & therapy resistance

open.substack.com/pub/behindth...

#Bioinformatics #CancerResearch #SpatialTranscriptomics #SingleCell
Weekly reads 10/3/25
This week’s highlights include an exciting study on transcriptomic plasticity in metastatic pancreatic cancer, a new method (NNNSF) for handling large spatial and temporal transcriptomics datasets, an...
open.substack.com
March 17, 2025 at 11:57 AM
haoyin.bsky.social
#SpatialTranscriptomics Stereo-seq 👤Carotid #Atherosclerosis

IntraPlaque #TertiaryLymphoidOrgan😎
CD138+ Plasma cells +diverse B cells

❎ #GerminalCenter
✅ #Lymphangiogenesis ✅#HEV
Col5A1+ fibroblast-like #SmoothMuscleCell as #LymphoidTissueOrganizer

#NatCVR 2025
www.nature.com/articles/s44...
April 30, 2025 at 11:34 AM
tmpentimalli.bsky.social
#Spatialtranscriptomics is revolutionizing gene expression profiling at subcellular resolution!

🔬These 'molecular microscopes' can unlock disease mechanisms & guide therapies...but how to bring ST to the clinic?

Our thoughts w @N_Rajewsky & @nukappa.bsky.social out @annualreviews.bsky.social

🧵👇
February 18, 2025 at 1:02 PM
yuminzheng.bsky.social
(1/n) Excited to share our new work accepted at ICML 2025. SUICA, a novel method to enhance the quality of spatial transcriptomics from multiple ST platforms including Visium, stereo-seq, slide-seq-V2....
#SpatialTranscriptomics
Paper at: arxiv.org/abs/2412.01124
Code at: github.com/Szym29/SUICA
SUICA pipeline
May 19, 2025 at 4:31 PM
jendzjowsky.bsky.social
Recent publication from my lab. Using all the “omics” to map out the neuroimmune landscape in the lung in response to fungal asthma.

www.frontiersin.org/journals/imm...
#immunosky #spatialtranscriptomics
#medsky
#phdsky
Frontiers | Comprehensive sequencing of the lung neuroimmune landscape in response to asthmatic induction with Alternaria alternata in mice
Evidence demonstrates that sensory neurons respond to pathogenic/allergic infiltration and mediate immune responses, forming an integral part of host defense...
www.frontiersin.org
February 21, 2025 at 8:32 PM
haoyin.bsky.social
#SpatialTranscriptomics #GeoMx @nanostringtech #HypertrophicCardiomyopathy

4 Cases+2 Ctrls, 72 ROIs
1800 transcripts

Focal myocyte disarray showing IFN signaling & mito & ECM perturbations

CD99 signaling b/w cardiomyocytes!?🤪

Michael Chin lab #IJMSMDPI 2023
www.mdpi.com/1422-0067/24...
January 8, 2024 at 4:13 PM
haoyin.bsky.social
STmut
Inferring+Visualizing #SomaticMutation #CopyNumberVariation Germline SNP/#AllelicImbalance in Tumor #SpatialTranscriptomics

#SomaticMutation SNP CNV
sequencing-based ST needed

#GenomeBiology 2023
genomebiology.biomedcentral.com/articles/10....
February 4, 2024 at 1:02 PM
haoyin.bsky.social
GASTON
Gradient Analysis of #Spatialtranscriptomics Organization with Neural networks

"models gene expression as a Piecewise linear function of the Isodepth"

Work with Visium Xenium MERFISH Slide-seq V2 Stereo-seq

@uthsav.bsky.social @naturemethods.bsky.social 2025
www.nature.com/articles/s41...
March 6, 2025 at 12:23 PM
cancerdynamics.bsky.social
Dr. Bianca Dumitrascu (bimidu.bsky.social) led a new study published in naturemethods.bsky.social on a computational pipeline linking spatial transcriptomics + mechanical forces in tissue development. Read more: bit.ly/4kCgT1q #CancerResearch #Mechanobiology #SpatialTranscriptomics #IICDColumbia
Bridging Biology and Biomechanics: The Dumitrascu Lab’s New Computational Framework Illuminates Tissue Development | Columbia University
bit.ly
March 18, 2025 at 4:52 PM
dingyao-zhang.bsky.social
🔬 Join me for my talk on spatial profiling of the whole transcriptome. #SpatialTranscriptomics #Bioinformatics #RNASeq #RNA25
May 26, 2025 at 4:17 PM
jef.works
To supplement my students' learning, I made this brief explanation + demo on how to analyze #spatialtranscriptomics data to identify spatially variable genes using Moran's I #dataanalysis #Rstats

Code along: www.youtube.com/watch?v=aaAN...

#AcademicSky #codetutorials #Bioinformatics
May 12, 2025 at 4:15 PM
glb-lab.bsky.social
New preprint on bioRxiv! #singlecell #multiomics, #spatialtranscriptomics, #lineagetracing reveal 2 glutamatergic lineages arising from distinct progenitors; Sp9 regulates visual #thalamus fate! By Puche-Aroca et al. @guillelbendito.bsky.social @jplopez-atalaya.bsky.social @neuroalc.bsky.social
Early lineage divergence segregates sensory and non-sensory thalamic circuits
The thalamus integrates sensory, motor, and associative functions via distinct nuclei, yet the developmental principles driving their specification remain unclear. Here, we generate a spatiotemporal s...
www.biorxiv.org
July 23, 2025 at 4:47 PM
fanzhangphd.bsky.social
Thrilled 🎉 to shared I received my R01 NoA today @NIH_NIAMS! We will continue pushing the frontiers of autoimmune research by developing novel #AI #MachineLearning for #SingleCell #SpatialTranscriptomics 🧬💻💊! @cuanschutz.bsky.social @cudeptofmedicine.bsky.social @cubiomedinfo.bsky.social
August 12, 2025 at 6:30 PM