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Alex Monell

@amonell.bsky.social
30 followers 31 following 6 posts

Bioinformatics PhD Student at UC San Diego @GoldrathLab @yeo_lab

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Alex Monell @amonell.bsky.social · 09/02/2025
In that case the cell size is the biologically meaningful part. We could pay more attention to size before making interpretations. I like the idea of looking at relative upregulation of transcripts since it fits well with gene signatures and cell annotations derived from scRNA seq
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Alex Monell @amonell.bsky.social · 08/02/2025
Seems like mrna abundance is generally correlated with cell size, but some genes have a higher correlation than others. pmc.ncbi.nlm.nih.gov/articles/PMC... I’m leaning towards not normalizing transcript expression to cell volume.
pmc.ncbi.nlm.nih.gov
Differential scaling of gene expression with cell size may explain size control in budding yeast
Yeast cells must grow to a critical size before committing to division. It is unknown how size is measured. We find that as cells grow, mRNAs for some cell cycle activators scale faster than size, inc...
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Reposted by Alex Monell
Maximilian Heeg @maximilian.heeg.io · 31/01/2025
📢 Join our team at @alleninstitute.bsky.social! We're hiring a Bioinformatics Scientist II for spatial transcriptomics in immunology. Our latest work in Nature shows how tissue architecture shapes immune cell diversity. Now we're expanding our team! Learn more: alleninstitute.org/careers/jobs...
alleninstitute.org
Jobs
We are working to solve the biggest mysteries in bioscience.
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Reposted by Alex Monell
Di Jiang @dijiang319.bsky.social · 24/01/2025
This week @science.org Sarfatis, Moffitt et al. from @bostonchildrens.bsky.social @harvardmed.bsky.social @broadinstitute.org Highly multiplexed spatial transcriptomics in bacteria | Science www.science.org/doi/10.1126/... #microsky #microbial #microbiology #genomics #transcriptomic 🦠🧫
science.org
Highly multiplexed spatial transcriptomics in bacteria
Single-cell decisions made in complex environments underlie many bacterial phenomena. Image-based transcriptomics approaches offer an avenue to study such behaviors, yet these approaches have been hin...
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Reposted by Alex Monell
Journal of Experimental Medicine @jem.org · 22/01/2025
New: Amir Ferry, Ananda Goldrath and colleagues @ucsdhealthsci.bsky.social show that differentiation of tissue-resident memory T cells (TRM) is accompanied by the upregulation of the conventional DC1 (cDC1) chemoattractant, Xcl1. buff.ly/4hrKCYe #MucosalImmunology #TumorImmunology
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Alex Monell @amonell.bsky.social · 24/01/2025
Waiting for your synthetic cis regulatory element phase
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Alex Monell @amonell.bsky.social · 24/01/2025
Congrats!!
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Reposted by Alex Monell
dominik1klein.bsky.social @dominik1klein.bsky.social · 23/01/2025
Good to see moscot-tools.org published in @nature.com ! We made existing Optimal Transport (OT) applications in single-cell genomics scalable and multimodal, added a novel spatiotemporal trajectory inference method and found exciting new biology in the pancreas! tinyurl.com/33zuwsep
tinyurl.com
Mapping cells through time and space with moscot - Nature
Moscot is an optimal transport approach that overcomes current limitations of similar methods to enable multimodal, scalable and consistent single-cell analyses of datasets across spatial and temporal...
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Reposted by Alex Monell
Miguel Reina-Campos @reinacampos.bsky.social · 22/01/2025
How do T cells find the proper instructions to navigate tissues? In the Goldrath Lab @ucsdhealthsci.bsky.social, Amir Ferry mapped it out play-by-play. Potentiating these interactions strengthens the immunity cycle and enhances tumor control 1/n
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Reposted by Alex Monell
Miguel Reina-Campos @reinacampos.bsky.social · 22/01/2025
It turns out the immune system is playing 4D chess while we thought it was just playing checkers. Using #spatialtranscriptomics from @10xgenomics.bsky.social and @vizgen.bsky.social we were able to peek into the secret lives of tissue resident T cells in the gut as they form after infection 1/n
nature.com
Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted - Nature
Profiling of the location and transcriptome of tissue-resident memory CD8 T cell formation at single-transcript resolution finds regionalized signalling as the basis of immune diversity in t...
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Alex Monell @amonell.bsky.social · 22/01/2025
Beautiful
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Alex Monell @amonell.bsky.social · 22/01/2025
Excited that our work went public, Take a look at Max’s thread outlining our research 🧪 @reinacampos.bsky.social @heeg.io www.nature.com/articles/s41...
nature.com
Tissue-resident memory CD8 T cell diversity is spatiotemporally imprinted - Nature
Profiling of the location and transcriptome of tissue-resident memory CD8 T cell formation at single-transcript resolution finds regionalized signalling as the basis of immune diversity in t...
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