Sean S. So
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sean-so.bsky.social
Sean S. So
@sean-so.bsky.social
32 followers 73 following 0 posts
Postdoctoral researcher @ Monash University (Stone Lab).
Multiomics (CRISPR, proteomics), GPCR signalling networks, leukocyte chemotaxis, and bioinformatics.
Reposting anything I find cool!
Posts Replies Media Videos
Reposted by Sean S. So
haoyin.bsky.social
Systematic comparisons among 4 subcellular-resolution #SpatialTranscriptomics methods

Stereo-seq v1.3
Visium HD FFPE
CosMx 6k
Xenium 5k

Human Tumors
Ground truth CODEX, +scRNAseq

#NatComm 2025
www.nature.com/articles/s41...
October 24, 2025 at 10:45 AM
Reposted by Sean S. So
chembl.bsky.social
ChEMBL 36 is out!

chembl.blogspot.com/2025/09/chem...
ChEMBL 36 is out!
📊 Database Scale 🆕 New Data Sources Src_ID 72 – Chemical Probe data from Scientific Literature NLP and manual extraction from probe-r...
chembl.blogspot.com
September 23, 2025 at 2:42 PM
Reposted by Sean S. So
mbeisen.bsky.social
Finally, someone has solved a real problem with AI! No more having to take a paper in the format for a journal that rejected you, and reformat it for a new journal. Well done!! formatmypaper.com
October 15, 2025 at 6:33 AM
Reposted by Sean S. So
erin-rod.bsky.social
Today, I would like to honor the memory of Roger Y. Tsien, who died on August 24, 2016. His legacy lives with all who use his technologies, including calcium sensors, fluorescent proteins, the acetoxymethyl (AM) ester, & many more! #FluorescenceFriday
www.nature.com/articles/nme...
August 22, 2025 at 1:17 PM
Reposted by Sean S. So
laurakwhite.bsky.social
Sure, we all know it depends on the protein. But why some proteins can be pushed to 40%(!) of total protein like here and others are a pain to get adequately expressed probably involves some real fun unsolved mysteries in RNA biology.
dereklowe.bsky.social Derek Lowe @dereklowe.bsky.social · Aug 21
Just how hard can you push cells to make proteins that they don’t need to make?
Cranking Up Protein Expression to the Limit
www.science.org
August 23, 2025 at 4:03 AM
Reposted by Sean S. So
embl.org
EMBL-EBI ARISE fellow @melanieschneider.bsky.social & EMBL Grenoble’s Marquez team developed EnsembleFlex 🖥️! It can analyse flexibility, identify protein states, and show drug binding, providing new insights into protein dynamics!
doi.org/10.1016/j.st...
August 14, 2025 at 8:44 AM
Reposted by Sean S. So
emblaustralia.org
🔬 To decode the universe, sometimes you need to see what’s never been seen.

Dr Senthil Arumugam is building advanced custom light-sheet microscopes to see biology in stunning new detail.

🔗 More in our Impact Report: bit.ly/3EVhwD8

#ScienceWeek #DecodingTheUniverse
August 14, 2025 at 11:56 PM
Reposted by Sean S. So
emblaustralia.org
🌏 Inside every cell is a world in motion.

Dr Vaishnavi Ananthanarayanan @vaishananth.bsky.social uses advanced live-cell microscopy to decode the choreography of motor proteins and the cytoskeleton - molecular systems that power everything.🔬

🔗More: bit.ly/3EVhwD8
#ScienceWeek #DecodingTheUniverse
August 15, 2025 at 12:08 AM
Reposted by Sean S. So
mariabernabeu.bsky.social
We are happy to show one ourt first exciting papers. We have developed a blood-brain barrier model to study the disruptive effects caused by the malaria parasite, Plasmodium falciparum.

First, congratulations to the fearless @liviapiatti.bsky.social and @alinabatzi.bsky.social

rdcu.be/ezBl7
Plasmodium falciparum egress disrupts endothelial junctions and activates JAK-STAT signaling in a microvascular 3D blood-brain barrier model
Nature Communications - Here the authors show that Plasmodium falciparum egress products disrupt endothelial barrier and activate JAK-STAT and interferon type response in a 3D blood-brain barrier...
rdcu.be
August 7, 2025 at 7:27 AM
Reposted by Sean S. So
grosselab.bsky.social
Hi all, check out our new preprint where we uncover:"Regulation of YAP activity by nuclear G-actin binding", www.biorxiv.org/cgi/content/...
#actin #YAP/TAZ #transcription #nucleus with help from Sonja-Verena Albers
‪@archaellum.bsky.social‬
Regulation of YAP activity by nuclear G-actin binding
The Yes-associated protein YAP belongs to the TEAD (TEA/ATTS domain) transcriptional co-activators that shuttle between cytoplasm and nuclear compartment. YAP and its paralog TAZ (transcriptional co-a...
www.biorxiv.org
July 31, 2025 at 6:34 AM
Reposted by Sean S. So
stanislauy.bsky.social
Happy to share our latest work on the structure and assembly of holocentric kinetochores! Huge thanks to Ines for a very fruitful collaboration, Claudio for all the support, and congratulations to Christine and all co-authors!

www.biorxiv.org/content/10.1...
July 15, 2025 at 4:36 PM
Reposted by Sean S. So
malloryfreeberg.bsky.social
🧬 New @emblebi.bsky.social service beta launched:
Perturbation Catalogue

🔎 Browse genetic perturbation datasets
🧠 Train models
🧬 Interpret variant function
🧭 Explore gene dependencies

Search, test APIs, suggest datasets, send feedback!
🔗 www.ebi.ac.uk/perturbation...

Funded by @opentargets.org
July 23, 2025 at 10:06 AM
Reposted by Sean S. So
rupress.org
In new @jcb.org study from Muziyue Wu et al. @oweinerlab.bsky.social, in vivo biochemistry sheds new light on how the WAVE complex templates the characteristic shape of lamellipodial protrusions. rupress.org/jcb/article/...

#Cytoskeleton #Actin #Migration #Motility #Biophysics
July 16, 2025 at 6:45 PM
Reposted by Sean S. So
saezlab.bsky.social
🎉 The revised version of CORNETO, our unified Python framework for knowledge-driven network inference from omics data, is published in peer reviewed form
🔗 Paper: www.nature.com/articles/s42...
📖 News & Views: www.nature.com/articles/s42...
💻 Code: corneto.org
🧵 Thread 👇
July 22, 2025 at 3:23 PM
Reposted by Sean S. So
abbybuch.bsky.social
Another paper bluetorial! Today: how does the spatial location of genes influence their function? (1/n) www.nature.com/articles/s41...
The nuclear periphery confers repression on H3K9me2-marked genes and transposons to shape cell fate - Nature Cell Biology
Marin et al. report the role of lamin proteins and the lamin B receptor (LBR) in chromatin positioning at the nuclear periphery. Knockout of all lamins and LBR in mouse embryonic stem cells leads to h...
www.nature.com
July 22, 2025 at 5:10 PM
Reposted by Sean S. So
johannaivaska.bsky.social
Excited to share our most recent study on #integrintraffic #cancer #migration #focaladhesion by @ivaskalab.bsky.social @drpaulinamoreno.bsky.social Niklas Jäntti et al www.sciencedirect.com/science/arti...
EPLINα controls integrin recycling from Rab21 endosomes to drive breast cancer cell migration
Epithelial protein lost in neoplasm (EPLIN), an actin-binding protein, has been described as both a tumor promoter and tumor suppressor in different c…
www.sciencedirect.com
July 16, 2025 at 7:26 AM
Reposted by Sean S. So
clauswilke.com
AlphaFold is great, but contrary to public opinion it has not completely solved the protein folding problem. Much work remains to be done.
clauswilke.substack.com/p/no-alphafo...
No, AlphaFold has not completely solved protein folding
Biology is hard. Yes, even for AI.
clauswilke.substack.com
July 12, 2025 at 6:19 PM
Reposted by Sean S. So
mdibl.org
"Squid creatures" by Marko Pende, 2023

This Hawaiian bobtail squid and longfin inshore squid tissue was cleared with the DeepClear method, captured via #lightsheet microscope and 3D rendered using AMIRA.

#microscopymonday #standwithscience #researchmatters #fluorescentproteins 🧪 🤝 🔬
July 7, 2025 at 12:40 PM
Reposted by Sean S. So
anshulkundaje.bsky.social
Social media has truly warped science consumption. On one hand it has massively democratized it. On the other hand, it's become extremely easy to use hype to simply amplify things that are simply not true. 1/
July 10, 2025 at 11:20 PM
Reposted by Sean S. So
focalplane.bsky.social
Check out our latest #preprint list on FocalPlane. This week we focus on bioimage analysis tools and their application to biological images.
focalplane.biologists.com/2025/07/11/m...
Microscopy preprints - bioimage analysis - FocalPlane
Microscopy preprints - bioimage analysis - News
focalplane.biologists.com
July 11, 2025 at 2:43 PM
Reposted by Sean S. So
franbottanelli.bsky.social
For #TcellThursday I am going to repost our recent work where we use CRISPR and imaging to highlight the role of protrusions in early T cell signaling. I think Carmen’s work beautifully shows how one can extract quant info by imaging processes as they happen in cells! www.biorxiv.org/content/10.1...
T cell protrusions enable fast, localised initiation of CAR signalling
Actin-rich protrusions densely cover the surface of T cells and are well characterised for their role in cell migration. However, recent studies have uncovered their role in antigen surveillance and i...
www.biorxiv.org
July 10, 2025 at 1:27 PM
Reposted by Sean S. So
anhhle2702.bsky.social
OMG, this is such a cool paper from Patrick Caswell's lab. They express Rab25-mCherry-GFP-nanobody in cells, microinject GFP-magnetic particles, then use a magnet to pull Rab25 to the plasma membrane to show that it can trigger actin protrusions! I want this system.
www.science.org/doi/10.1126/...
Live-cell magnetic manipulation of recycling endosomes reveals their direct effect on actin protrusions to promote invasive migration
Repositioning of Rab25 vesicles containing formin and integrin cargos to the cell periphery promotes protrusion formation.
www.science.org
July 8, 2025 at 9:21 PM
Reposted by Sean S. So
laurakwhite.bsky.social
Built a thing to solve my annoyance setting up Python + Quarto projects in Positron (& teaching others to do the same)

For anyone moving from .Rmd to .qmd who wants a cleaner on-ramp: meet Quoncierge.

🔗 github.com/lkwhite/Quoncierge

#positron #quarto #rstats #datascience #reproducibility #jupyter
GitHub - lkwhite/Quoncierge: Automate initializing reproducible Quarto + Jupyter + GitHub projects
Automate initializing reproducible Quarto + Jupyter + GitHub projects - lkwhite/Quoncierge
github.com
July 8, 2025 at 6:01 PM
Reposted by Sean S. So
haoyin.bsky.social
STORIES
SpatioTemporal Omics eneRgIES

Learning Waddington epigenetic (+regulon) landscape from multi-time-point Stereo-seq #SpatialTranscriptomics

Fused Gromov-Wasserstein #OptimalTransport
Linear▶️gene expression error
Quadratic▶️spatial consistency

bioRxiv 2025
www.biorxiv.org/content/10.1...
July 6, 2025 at 11:28 AM
Reposted by Sean S. So
johanduchene.bsky.social
A comparison of mouse vs human tumor microenvironments shows a major difference.

Mouse TMEs have more macrophages, while human TMEs have more T cells.

Chemokine expression patterns are also different.

Learn more: www.biorxiv.org/content/10.1...
July 7, 2025 at 5:16 AM