Jasmine Plummer

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

spatial Omics in R/Bioconductor 19-21 May 2025 To foster international participation, this course will be held online

🚀 Interested Spatial Omics with R/Bioconductor?
🧨Do you want to learn how to analyse these data in R with the #tidyverse?

Join us in May for this course with @stemang.bsky.social & @lgmartelotto.bsky.social

🔗 www.physalia-courses.org/courses-work...

#SpatialOmics #Bioinformatics #RStats

If you work with Xenium data segmentation, you may want to check out Segger!

Segger provides accurate and scalable segmentation for IIS and FISH-based spatial omics datasets, using a novel heterogenous GNN approach.

Authors: elihei.bsky.social and Andrew Moorman.

Bioinformatics Tip: Why Wet Biologists Should Involve Bioinformaticians Early in Experiment Design 🧵

🧵 Bioinformatics: Keeping Up with Rapidly Advancing Technologies
1/ Bioinformatics evolves fast. Just as we catch up with single-cell RNA-seq (scRNA-seq), spatial transcriptomics arrives with new challenges.

🧵 Bioinformatics Tip: Stop Struggling with Large Files—Master sed for Fast Text Processing

Eric Green is out as head of National Human Genome Research Institute The longtime director of the National Human Genome Research Institute is stepping down, as the larger NIH braces for more changes.

Still processing what this means. www.statnews.com/2025/03/17/t...

MUUMI: an R package for statistical and network-based meta-analysis for MUlti-omics data Integration www.biorxiv.org/content/10....

spVelo: RNA velocity inference for multi-batch spatial transcriptomics data www.biorxiv.org/content/10....