alforrest.bsky.social
Head of the Systems Biology and Genomics Lab at the Harry Perkins Institute of Medical Research, University of Western Australia
#FANTOM5 #transcriptomics #spatial #cellcommunication #ovariancancer #bioinformatics #singlecell
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1,299 following
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Link to job advert:
external.jobs.uwa.edu.au/en/job/51959...
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MagLOV!
MagLOV is a fluorescent protein you can "turn off" with a handheld magnet, engineered by @mariaingaramo.bsky.social.
We think/hope we can use it to turn arbitrary proteins (including drugs!) on and off in opaque creatures (including humans!).
bsky.app/profile/addg...
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It's just rate. 1 out of 3 submitted. For NT and TAS the %funded can be quite spiky year to year. This year TAS got none out of 20.
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Next time you are reviewing an Ideas grant and consider ROPE. Consider this inherent bias in funding rates. Less funds = less preliminary data, less continuity of research careers, less job opportunities for young scientists in WA. This is compounded over decades.
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That's a good sign!
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Awesome, looking good!
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Lucky you. My last visit was on the way back from Rome in cattle class. The previous experience was in the lounge upstairs. Chalk and cheese. Did find some good coffee downstairs at S34 cafe.
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Not very convinced, only paired with spatial data it "starts" to make sense but it's still a long shot. In this work doi.org/10.1038/s415... we filtered inferred communications based on spatial proximity and could validate some novel interactions in multiple sclerosis (Figure 4).
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We just started looking into how adipocyte secreted factors stimulate lipogenesis in epithelial breast cancer cells. We haven’t identified the specific signaling molecules yet, but the cell response is fascinating! khayneslab.wordpress.com/2024/10/21/r...
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We functionally tested putative L-R pairs in this paper: www.cell.com/cell/fulltex...
Bottom line: mRNA L-R pairs give a good experimental shortlist but aren’t always biologically functional. You still need to do the experiment!
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This is absolutely cool, but its low throughput. Experimental testing of cell-ligand-receptor-cell quads en masse is going to be a challenge as there are hundred (or thousands of predicted edges that scales with the number of cell types present).
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The last requires experimental testing and could be simple (ligand + 1 cell type), or 2 cell types + receptor KO, or in tissue slice or in animal model..
Recently Julio Aguirre-Ghiso's lab validated predictions from our NATMI tool in vivo.
www.cell.com/cell/abstrac...
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3. Do these ligand-receptor pairs exist in nature (depends on database, we use only manually curated with primary literature support in connectomeDB2020, others have used inferred interactions and high throughput PPI which just adds noise). $. Does this cell pair communicate via this LR pair (HARD).
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It depends on what the question is. 1. Do these cells have the potential to communicate? (I'd say yes to all potential pairs). 2. Do these pair of cells communicate more (or more specifically) with each other than another pair? (yes we can see this using multiple methods. 3..cont..