Lefteris Zormpas

PhD candidate, researcher, citizen - reading, thinking, creating.
🇬🇷

[Lefteris Zormpas @LZormpas]

🔍 Exciting News! Our latest publication in Cell (@CellCellPress) is here! 🎉 We explore the challenges and opportunities in analysing transcriptome data with a spatial dimension. (https://t.co/Z2rWecefHH)

[Ioannis Vlachos // @ioavlachos.bsky.social @ioavlachos]

**Please Retweet (Re-X?)**
🔥Postdoc #jobs in Spatial / Single Cell Omics
Looking to become a #leader in #SpatialBiology?
Love NGS & #MachineLearning? #Positions @harvardmed @broadinstitute
https://t.co/iDGqu2zj4P
#hiring #lab #boston #research #aiml #biotech #Science

[Ioannis Vlachos // @ioavlachos.bsky.social @ioavlachos]

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
https://t.co/v9nNsbJ5kx

[Hao Yin @HaoYin20]

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
https://t.co/pqmlxsB9hu

[UEFA Conference League @Conf_League]

Olympiacos. History makers 👏

The first Greek side to win a UEFA club competition 💫

@johnsportraits x #UECLfinal

[Olympiacos FC @olympiacosfc]

WE ARE THE @europacnfleague WINNERS! WE ARE THE CHAMPIONS! 🔴⚪🏆🇬🇷

#Olympiacos #UECL #Champion #Winners #Europe #Greece #WeKeepOnDreaming

[Olympiacos FC @olympiacosfc]

ΝΑΙ ΡΕ ΘΡΥΛΕ!!! 🔴⚪🏆🇬🇷

[Hao Yin @HaoYin20]

gganatogram: An R package for modular visualisation of anatograms and tissues based on ggplot2

Draw Animal/Plant organs or some cell organelles in R

https://t.co/PdpNJigkUj

@JesperMaag @F1000Research 2018
https://t.co/jWVOHLHzPk

[Vipul Singhal @vipul1891]

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: https://t.co/7mhwhrLKFl !

Thanks @NigelChouS @NatureRevGenet @shyam_lab @khchenlab @astar_gis!

[antisense. @razoralign]

STT: Spatial transition tensor of single cells https://t.co/9ReuwPZqRm

[BGI Group @TheBgiGroup]

#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. https://t.co/PKPpHdFKwf

[Lefteris Zormpas @LZormpas]

Olympiakos in the final!!! 💪💪

[el sombrero @sombrerogr]

Ένα παιχνίδι μακριά από μια ευρωπαϊκή κούπα!

[Lefteris Zormpas @LZormpas]

@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! 😁

[Lefteris Zormpas @LZormpas]

It is always great to share knowledge with fellow researchers and gather important feedback!

Thank you for hosting me!
#SpatialTranscriptomics

[Science talks @ CFL @SciencetalksCFL]

The first seminar after the Easter break was a great talk from @LZormpas on mapping the transcriptome🗺Join us again next week! 🍕

[Hao Yin @HaoYin20]

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
https://t.co/TmbhT17bAb

[Hao Yin @HaoYin20]

SpatialData
https://t.co/esVxkr9PLz

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
https://t.co/x8tYXQqFQN

[Hao Yin @HaoYin20]

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
https://t.co/9v87Mf5ZXp

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

[Hao Yin @HaoYin20]

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
https://t.co/GTvzSfAxcc

[NimwegenLab @NimwegenLab]

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 @LZormpas]

@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.