Jasmine Plummer

Join us to the last #GESTALT seminar the year!

Free for all GESTALT member. If you are interested in anything #spatialbiology come be part of our growing community

GESTALT Seminar Series globalspatial.org/seminar-seri...

December 19 10am EST @ioavlachos.bsky.social @lgmartelotto.bsky.social

Thanks @natbiotech.nature.com for the shoutout and supporting our work at attempting QC in this emerging field of #spatial #transcriptomics @lgmartelotto.bsky.social @christophermason.bsky.social

Spatial Touchstone brings quality control to spatial transcriptomics Explore Spatial Touchstone’s open-source tools and data for standardized spatial transcriptomics, enabling reliable, cross-institutional gene expression analysis.

Spatial Touchstone brings quality control to spatial transcriptomics #NBTintheNews via @stjuderesearch.bsky.social www.stjude.org/media-resour...

The Spatial Touchstone resource provides a robust, open-source repository for the field and enables researchers to assess the quality of their own spatial transcriptomics datasets and compare results across institutions.

@jasmineplummer.bsky.social, PhD, said: “The project started because I was frustrated with the field lacking quality metrics. Other technologies have established baseline expectations using set cell lines to tell if variation is due to the sample, machine or technician.”

Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets - Nature Biotechnology A multi-institute, multi-platform initiative generates standard metrics and best practices for spatial transcriptomics analysis.

Standardized metrics for assessment and reproducibility of imaging-based spatial transcriptomics datasets - @jasmineplummer.bsky.social @lgmartelotto.bsky.social go.nature.com/4rBC1Z0

Goliath effort to help with standards in spatial trancriptomics-can only be more amazing when done with @lgmartelotto.bsky.social @christophermason.bsky.social 🚀

Paper: nature.com/articles/s4158…
Touchstone portal: spatialtouchstone.org
Spatial touchstone protocols: protocols.io/view/spatial-t���

Our 2025 Workshop, “Leveraging the Power of Artificial Intelligence to Foster Progress in Immuno-oncology..." educated the IO community to develop new cancer immunotherapies and improve patient care with AI. @jasmineplummer.bsky.social @aruthak.bsky.social @fertiglab.bsky.social @dinler.bsky.social

Counting my lucky stars⭐️that not only do I get to work with these amazing scientists Jiwoon Park @christophermason.bsky.social but also give fun @cshlnews.bsky.social lectures together💪.Big thank you to @lgmartelotto.bsky.social Nicholas Navin Julea Vlassakis for uniting this #singlecell #dreamteam

STAMP:Single cell Transcriptomics Analysis & Multimodal Profiling-cheap scprofiling-MILLIONS of cells, multimodal, pertubation expts & tissue atlas'ing at scale.Thx to brilliant colleagues @lgmartelotto.bsky.social Holger Heyn & our amazing teams. @cellpress.bsky.social www.cell.com/cell/abstrac...

“STAMP allows us to profile a million cells simultaneously, compared to tens of thousands typical of current methods, making it far more scalable,” said @jasmineplummer.bsky.social, PhD, St. Jude Center for Spatial Omics director.

👩‍🔬The lead authors of the study are Dr. @pascual-reguant.bsky.social & Emanuele Pitino (CNAG) with Felipe Segato Dezem (@stjuderesearch.bsky.social)

Corresponding authors: Dr. @hoheyn.bsky.social (CNAG), Dr. @jasmineplummer.bsky.social (St. Jude) & Dr. @lgmartelotto.bsky.social (Univ. of Adelaide)

Webinar (June 3, 8am PDT) on using single-cell to better understand complex biology. If you're new to the field or already an expert, there’ll be a little of something for everyone. Free registration link: www.technologynetworks.com/tn/webinars/...

#singlecell #analysis #transcriptomic #omics

Beyond cell atlases: spatial biology reveals mechanisms behind disease - Nature Biotechnology As the next generation of spatial transcriptomics tools hits the market, researchers are uncovering previously unknown interactions that could transform clinical research.

Latest news feature in @natbiotech.nature.com on recent developments in spatial biology to unravel disease mechanisms, with insights from experts in field. @aruthak.bsky.social @nebanovich.bsky.social @ai4pathology.bsky.social @jasmineplummer.bsky.social www.nature.com/articles/s41...

Are you interested in learning about the intersection of #AI and molecular #biology? Come to our @keystonesymposia.bsky.social this September in beautiful Santa Fe! keysym.us/KSAIBio26 #KSAIBio26

Scholarship + short talk deadline May 20 so apply soon! Look forward to seeing you there!

#AcademicSky

Single-cell profiling of the human endometrium in polycystic ovary syndrome - Nature Medicine A transcriptomic atlas of the endometrium of women with polycystic ovary syndrome uncovers both disease signatures and potential therapeutic targets.

Single-cell profiling of the human endometrium in polycystic ovary syndrome. #NatureMedicine

This study presents a comprehensive cellular atlas of the endometrium during the proliferative phase, comparing women with PCOS to healthy controls.

www.nature.com/articles/s41...

Deconvoluting single-cell transcriptomics reveals cellular programs regulated by cell-cell communication in colorectal cancer https://www.biorxiv.org/content/10.1101/2025.04.09.648030v1

Spatial transcriptomics AI agent charts hPSC-pancreas maturation in vivo https://www.biorxiv.org/content/10.1101/2025.04.01.646731v1

Single-Cell Multiomics Reveals Regulatory Mechanisms of CAR T Cell Persistence and Dysfunction in Multiple Myeloma https://www.biorxiv.org/content/10.1101/2025.04.01.646378v1

Integrated single-cell and spatial multiomic analysis reveals widespread reactivation of developmental programs in diseased human hearts https://www.biorxiv.org/content/10.1101/2025.04.01.646460v1

scContrast: A contrastive learning based approach for encoding single-cell gene expression data https://www.biorxiv.org/content/10.1101/2025.04.07.647292v1

🔥New Night Science paper!!
Discovery happens when your initial plans fall apart but it requires you to have a particular mindset: it's not extraverted, orderly, neurotic or agreeable that's the most important – discovery requires an OPENNESS to new ideas and unexpected insights.

CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data Nature Protocols - CellPhoneDB combines a curated database of receptor–ligand interactions with methods to infer cell–cell communication from single-cell expression data. This protocol...

CellPhoneDB v5: inferring cell–cell communication from single-cell multiomics data www.nature.com/articles/s4...

Leveraging real-world data to advance biomarker discovery and precision oncology www.cell.com/cancer-cell...

Best day of the yearfor all single cell lovers and it’s free!!! satijalab.org/scgd25/ hosted by the Satija lab -Single Cell Genomics Day on Friday, April 25, 2025.

Single-cell transcriptomic and functional studies identify glial state changes and a role for inflammatory RIPK1 signaling in ALS pathogenesis: @cp-immunity.bsky.social www.cell.com/immunity/ful...

Identification of clinically relevant T cell receptors for personalized T cell therapy using combinatorial algorithms - Nature Biotechnology Tumor-reactive T cell receptors are predicted based on single-cell RNA sequencing and single-cell T cell receptor sequencing.

Tumor-reactive T cell receptors are predicted based on single-cell RNA sequencing and single-cell T cell receptor sequencing go.nature.com/4b8aN3p
rdcu.be/efeUq

Yes please

Identification and characterization of cell niches in tissue from spatial omics data at single-cell resolution | Nature Communications Deciphering the features, structure, and functions of the cell niche in tissues remains a major challenge. Here, we present scNiche, a computational framework to identify and characterize cell niches from spatial omics data at single-cell resolution. We benchmark scNiche with both simulated and biological datasets, and demonstrate that scNiche can effectively and robustly identify cell niches while outperforming other existing methods. In spatial proteomics data from human triple-negative breast cancer, scNiche reveals the influence of the microenvironment on cellular phenotypes, and further dissects patient-specific niches with distinct cellular compositions or phenotypic characteristics. By analyzing mouse liver spatial transcriptomics data across normal and early-onset liver failure donors, scNiche uncovers disease-specific liver injury niches, and further delineates the niche remodeling from normal liver to liver failure. Overall, scNiche enables decoding the cellular microenvironm

🔬 Exciting breakthrough! The scNiche framework identifies cell niches from spatial omics at single-cell level with unmatched accuracy! #scNiche #BiotechRevolution PMID:39956823, Nat Commun 2025, @NatureComms https://doi.org/10.1038/s41467-025-57029-9 #Medsky 🧪

ISCO - ISCO

🚀 Join the #ISCO2025 community at @mdc-berlin.bsky.social on May 12-13! 🚀
Don't miss this incredible opportunity to connect with top #singlecell & #spatial omics experts and participate in a special Workshop led by @itaiyanai.bsky.social.
⏳Abstract submissions: March 21)
www.isco-conference.eu