Lefteris Zormpas

🔍 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…)

**Please Retweet (Re-X?)** 🔥Postdoc #jobs in Spatial / Single Cell Omics Looking to become a #leader in #SpatialBiology? Love NGS & #MachineLearning? #Positions @harvardmed @broadinstitute linkedin.com/jobs/view/4038… #hiring #lab #boston #research #aiml #biotech #Science

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

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/articl…

Olympiacos. History makers 👏 The first Greek side to win a UEFA club competition 💫 @johnsportraits x #UECLfinal

WE ARE THE @europacnfleague WINNERS! WE ARE THE CHAMPIONS! 🔴⚪🏆🇬🇷 #Olympiacos #UECL #Champion #Winners #Europe #Greece #WeKeepOnDreaming

ΝΑΙ ΡΕ ΘΡΥΛΕ!!! 🔴⚪🏆🇬🇷

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/gga… @JesperMaag @F1000Research 2018 f1000research.com/articles/7-157…

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!

STT: Spatial transition tensor of single cells nature.com/articles/s4159…

#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

Olympiakos in the final!!! 💪💪

@DalalSci Because someone did this with me when I was an undergrad helping me to become a scientist and eventually reach where I am now. Science is getting from the previous and giving back to the next generation of scientists so that amazing things can happen in the future! 😁

It is always great to share knowledge with fellow researchers and gather important feedback! Thank you for hosting me! #SpatialTranscriptomics

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/110

SpatialData spatialdata.scverse.org/en/latest/ 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/s4159…

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/25… If you are a #SpatialOmics learner like me, this is a particularly useful, timely piece of reading 😀

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/CI…

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

@NimwegenLab UMAP is useful for drawing beautiful 2D paintings of your data, not for interpreting the painting's layout in an attempt to extract biological meaning.

This is not how one does serious science. One cannot show a picture, claim it shows the 'structure in the data' and then be completely unable to explain what this 'structure' supposedly represents. It's a joke, frankly. n/n