PhD candidate, researcher, citizen - reading, thinking, creating. 🇬🇷
Joined June 2022
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🔍 Exciting News! Our latest publication in Cell (@CellCellPress) is here! 🎉 We explore the challenges and opportunities in analysing transcriptome data with a spatial dimension. (doi.org/10.1016/j.cell.2023.…)
Lefteris Zormpas retweeted
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🔥Postdoc #jobs in Spatial / Single Cell Omics
Looking to become a #leader in #SpatialBiology?
Love NGS & #MachineLearning? #Positions @harvardmed @broadinstitute
linkedin.com/jobs/view/40389…
#hiring #lab #boston #research #aiml #biotech #Science
Lefteris Zormpas retweeted
𝗦𝗧𝗔𝗠𝗣: single cell (spatial?)
Being asked what I think about it (NOT involved).
1) What is STAMP? Should I care about it?
STAMP is a clever way of using 𝘀𝗽𝗮𝘁𝗶𝗮𝗹 𝗮𝘀𝘀𝗮𝘆𝘀 to get 𝗶𝗻𝘀𝗮𝗻𝗲𝗹𝘆 𝗹𝗼𝘄 𝗰𝗼𝘀𝘁 𝘀𝗶𝗻𝗴𝗹𝗲 𝗰𝗲𝗹𝗹 𝗱𝗮𝘁𝗮
tinyurl.com/nwetc3te
Lefteris Zormpas retweeted
What is a cell type and how to define it?
#DevoEvo
Linking morphologic, geographic & functional attributes with Transcriptomic/Epigenomic taxonomy
Connectomics
Path-seq
Retro-seq
......
How many neuron omic techniques have been/can be adapted for microvasculature?😆
@HongkuiZeng @CellCellPress 2022
sciencedirect.com/science/ar…
Lefteris Zormpas retweeted
Olympiacos. History makers 👏
The first Greek side to win a UEFA club competition 💫
@johnsportraits x #UECLfinal
Lefteris Zormpas retweeted
WE ARE THE @europacnfleague WINNERS! WE ARE THE CHAMPIONS! 🔴⚪🏆🇬🇷
#Olympiacos #UECL #Champion #Winners #Europe #Greece #WeKeepOnDreaming
Lefteris Zormpas retweeted
gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2
Draw Animal/Plant organs or some cell organelles in R
github.com/jespermaag/gganat…
@JesperMaag @F1000Research 2018
f1000research.com/articles/7…
Lefteris Zormpas retweeted
Pleased to share our new Research highlights article, which summarizes some of the core features and applications of the BANKSY spatial omics algo. Viewable via: rdcu.be/dH1mz !
Thanks @NigelChouS @NatureRevGenet @shyam_lab @khchenlab @astar_gis!
Lefteris Zormpas retweeted
STT: Spatial transition tensor of single cells nature.com/articles/s41592-0…
Lefteris Zormpas retweeted
#BGI-Research's cutting-edge liver studies have been selected as the cover story for @NatureGenet . These two studies integrate scRNA-seq and Stereo-seq data to characterize molecular signatures and interactions of liver cell types across different states including homeostasis, damage, repair, and regeneration. bit.ly/3vKGd0D
It is always great to share knowledge with fellow researchers and gather important feedback!
Thank you for hosting me!
#SpatialTranscriptomics
The first seminar after the Easter break was a great talk from @LZormpas on mapping the transcriptome🗺Join us again next week! 🍕
Lefteris Zormpas retweeted
STCellbin
Use Nuclei+Cell Membrane/Wall stains to improve #CellSegmentation & single-cell-resolved #SpatialTranscriptomics
Tailored for #StereoSeq, but likely implementable for other ST methods
Susanne Brix & Xun Xu labs @GigaByteJournal 2024
gigabytejournal.com/articles…
Lefteris Zormpas retweeted
SpatialData
spatialdata.scverse.org/en/l…
Establish a global common coordinate framework->
Multi-modal #SpatialOmics integration
Align multislice for 3D #SpatialOmics
napari-spatialdata
Work with
(RNA) Visium Xenium CosMx MEFISH
(protein) CycIF MIBI-TOF #ImagingMassCytometry
+HE histology image
Now Python, will be R
will support #Vitessce
will incorporate time component
@LucaMarconato2 @notjustmoore @fabian_theis @OliverStegle @naturemethods 2024
nature.com/articles/s41592-0…
Lefteris Zormpas retweeted
TransformerST
#SpatialTranscriptomics
Vision transformer
Adaptive graph transformer
Cross-scale internal graph network
Image-gene co-representation:
Gene expression+Spatial coordinates+Histologic images
"could achieve super-resolved resolution of a single cell per subspot" w/o scRNAseq reference
Note for Lung Microvascular researchers with #VISIUM
✅stLearn SpaGCN TransformerST
@BriefingBioinfo 2024
academic.oup.com/bib/article…
If you are a #SpatialOmics learner like me, this is a particularly useful, timely piece of reading 😀
Lefteris Zormpas retweeted
Molecular & Spatial Signatures of🐭Embryonic Endothelial Cells at Single-Cell Resolution
e9.5/12.5/15.5
#ArterioVenousHierarchy & #Organotypicity of Embryonic #EndothelialCell
scRNAseq
#MERFISH #SpatialTranscriptomics
#SciArt
William Pu lab @CircRes 2024
ahajournals.org/doi/10.1161/…
Lefteris Zormpas retweeted
I see we are getting to the stage of the discussion where people are starting to defend UMAP saying it can 'reveal patterns' or 'structure' in the data. Without ever specifying what precisely these patterns/structures represent. This is not surprising because hardly anybody 1/n
Lefteris Zormpas retweeted
SpaRx
Predict (Spatial) drug responses of tumors using single-cell-resolved #SpatialTranscriptomics #CosMx Lung cancer #MERSCOPE
Trained on GDSC CCLE cell line (>1k) drug screening database
Graph-based Adversarial adaptation
@BriefingBioinfo 2023
academic.oup.com/bib/article…
The amount of papers being published every week in spatial trascriptomics is disproportionate to the amount I can read in a week... However, one can find real gems in "lower level" journals. You just have to find the time to really dig through the pile of publications...
