We're out in @CellCellPress! Cells in our body are continuously forming and subsequently dying. But dead cell contents can be inflammatory and too much build up can trigger auto-immune diseases. An imaging, scRNA-seq, and math modelling study...

@OxfordJournals @LabPhan @UNSWScience @UNSWMedicine @CellularFutures ENTRAIN is compatible with a range of methods, from pseudotime to RNA velocity to paired single-cell and spatial data. Check out the github: https://t.co/5z1BdPxcUf https://t.co/r3MbsWwkTJ

@OxfordJournals @LabPhan @UNSWScience @UNSWMedicine @CellularFutures ENTRAIN quantifies this influence by querying NicheNet for LR-gene network edges and fitting a random forest to the observed RNA velocity (or pseudotime) genes. We validate by recovering known drivers of differentiation - such as IL7 for B cells and Bdnf for neurons. 4/5

@OxfordJournals @LabPhan @UNSWScience @UNSWMedicine @CellularFutures Therefore, if a large number of dynamical genes are known to be regulated by ligand-receptor binding, it suggests that the cell's differentiation trajectory is highly influenced by environmental signaling. 3/5

@OxfordJournals @LabPhan @UNSWScience @UNSWMedicine @CellularFutures We initially observed that the results of trajectory analysis occasionally "agree" with the results of ligand-receptor analysis: some dynamical genes (e.g. with big RNA velocity likelihoods) are also genes that are known to be regulated by extracellular ligands. 2/5

We noticed that cell-cell communication analysis and cellular trajectories are almost always performed in isolation - so we developed ENTRAIN to change that! Out in @OxfordJournals Bioinformatics @LabPhan @UNSWScience @UNSWMedicine @CellularFutures 1/5 https://t.co/VgYlUgXRCa

Still vibing after a cracker day 1 at #AIMS2023 @GarvanInstitute. Australian intravital microscopy is THRIVING & it's awesome to be part of such a vibrant diverse community. Deep thoughtful science grounded in biology. Asking the hard questions. Can't wait for day 2 bring it on!

Finally dad's memoir will be out just in time for summer holiday reading with proceeds to go to @UNSWMedicine. Many thx to Interim Dean @DrAdiTorda for hosting book launch December 14 VIPs incl mum, dad (& @ThomasKeneally). Special pre-launch offer here: https://t.co/s72Y67U2DR

🔬 New imaging technique published @NatureProtocols, developed by @DrNayanB, allows longitudinal imaging of🐁bones for 12 hr sessions over multiple days. We've used this to monitor bone remodeling, dormant cancer cells, osteoclast fission/fusion, and more https://t.co/dYuB5ipWpQ

Ever wanted to do intravital imaging of intact long bone? Now you can! @DrNayanB & @wunniess takes you step-by-step @NatureProtocols. Super effort by whole team @GarvanInstitute @INCITeCentre incl @Timpson_Lab @anuobig. Inspired by Peter Croucher... 1/5 https://t.co/JwLuIILSwR

Cytocipher: Scanpy/Scverse compatible cluster significance analysis for scRNA-seq data, that scales to atlas level data with high accuracy. https://t.co/rmArNZpcSW

@UNSWMedicine @GarvanInstitute If you have a dataset of differentiating cells, and want to understand the cell-cell interactions that are driving that differentiation, have a try: https://t.co/ZvYZQjmIRh… @LabPhan @nhmrc

@UNSWMedicine Validated on both bone marrow & spatially resolved neurogenesis datasets, ENTRAIN uncovered known & novel environmental drivers of differentiation whilst ignoring ligand-receptor pairs that did not contribute specifically to differentiation. @GarvanInstitute

This integration of two previously separate streams of single-cell analysis, trajectories and cell-cell communication, enables ENTRAIN to identify those extracellular signals that contribute to cell differentiation. @UNSWMedicine

We've just released ENTRAIN on @biorxivpreprint. ENTRAIN is a tool designed to reveal the cell-cell interactions shaping cellular differentiation. It goes beyond expression similarity and RNA velocity by incorporating ligand regulatory networks as well.

And that's a wrap #CSMyeloidCells23 #CMYE2023. Thanks for the insightful conference and for my first ever international talk. 🎉🎉

So happy to see this out @JExpMed - epic effort led by @ElissaDeenick #Scientia A/Prof @UNSWMedicine & @GarvanInstitute. PIK3R1 LOF & PIKCD GOF - same but diff't! Amazing collab with @Tangye_Lab et al. Big congrats to 1st authors Nguyen, Lau & @bier_julia! https://t.co/phlUI8NpPL

Great synthesis @BajenoffL & Elisa! Love the chameleon metaphor to describe TBMs especially because we used the @CoherentLaser Chameleon II to generate the movies in the paper @LabPhan. @AbigailGroot129

Tingible body macrophages: Gargantuan chameleons of the germinal center. Elisa Baudon & Marc Bajenoff ( https://t.co/sbyUnc2CxO) discuss recent reports from @NGurwicz, @zivshulman et al. https://t.co/fAZJSs9p2h & Grootveld et al. https://t.co/orO6iNqLoW

1/ So proud of this work from the lab, out today in @ScienceAdvances. Huge amount of work by Jordan Hastings, @sharissa_latham and the team at @GarvanInstitute and @CancerEcoGarvan. Big thankyou to collaborators @KidsCancerInst and @sysbioire as well! https://t.co/6pz39xtOSA

Now online! Apoptotic cell fragments locally activate tingible body macrophages in the germinal center