Ava Khamseh

Norwich Single-Cell and Spatial Symposium 2026 Bringing together the international single-cell and spatial community for a two-day discussion across model and non-model systems.

📣 In case you missed it - we've opened expressions of interest for our Norwich #SingleCell and #Spatial symposium this summer, including speakers @tatsuyanobori.bsky.social, @arnausebe.bsky.social, and @avakhamseh.bsky.social! 👏

Find out more below 👇

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Systematic morphological profiling of human and mouse miRNAs in 24M single cells MicroRNAs (miRNAs) are post-transcriptional regulators of gene expression whose contributions to cell biology remain underexplored. Here, we used Cell Painting to quantify the morphological effect of ...

New📢
Between molecular and human traits is a yawning gap: What do molecules do to single cells?
We tested *all* human or mouse miRNA mimics for their cell morphological effects on 5 cell lines.
To do so, we applied Cell Painting at the *single cell* level (100,000+ images).
doi.org/10.1101/2025...

Personalised blood-based biomarkers for Myalgic Encephalomyelitis / Chronic Fatigue Syndrome (ME/CFS) symptom severity at University of Edinburgh on FindAPhD.com PhD Project - Personalised blood-based biomarkers for Myalgic Encephalomyelitis / Chronic Fatigue Syndrome (ME/CFS) symptom severity at University of Edinburgh, listed on FindAPhD.com

Interested in ME/CFS research?
Want to do a PhD with @aryback.bsky.social, @avakhamseh.bsky.social, @sjoerdvbeentjes.bsky.social & @cgatist.bsky.social?
Then apply for a *funded* Future Medicine PhD Fellowship.
See: www.findaphd.com/phds/project...
Please contact us to discuss before applying.

Great cross-disciplinary work with @cgatist.bsky.social @sjoerdvbeentjes.bsky.social @breesheyrh.bsky.social Olivier Labayle, Kelsey Tetley-Campbell, Mark van der laan @berkeleyctml.bsky.social (n/n)

Now published: TarGene stat/ML engine doi.org/10.1093/bios...
TarGene pipeline: targene.github.io/targene-pipe...
General purpose TMLE Julia package: doi.org/10.21105/jos... (3/n)

DNA variants modulate each other’s effects, but finding interactions in population cohorts is hard due to tiny effect sizes + massive testing burden. Using TarGene on 9 nuclear hormone receptor mechanisms we uncovered 535 2-point & 185 3-point interactions, revealing sex-biased genetic risk. (2/n)

We integrate population genetics, functional genomics & targeted ML to uncover 100s of TF-linked epistatic interactions across 768 traits in UK Biobank. Epistasis, informed by mechanism, empowered by robust stat/ML, is detectable & widespread. doi.org/10.1101/2025... (1/n)

New course “EMBO Causality in Biomedicine”: We have organised the first EMBO course in *causal* stats/ML methods for quantitative biomedicine. @sjoerdvbeentjes.bsky.social @nimahejazi.org @pablormier.bsky.social @DariaSokolova @CarolineUhler

Very much looking forward to teaching and discussing!

📢 Now published:
www.embopress.org/doi/full/10.....
Since the preprint, we replicated 9 of 14 traits in All of Us & showed that #pwME with PEM-like symptoms have stronger biomarker differences.
bsky.app/profile/cgat...

High order expression dependencies finely resolve cryptic states and subtypes in single cell data | Molecular Systems Biology imageimageStator assigns multiple states and (sub)types to a single cell using coordinated gene expression and/or non-expression in a data-driven manner. Its application of structure learning has incr...

📢Now published!
Know that clustering cells in reduced dimensions is problematic?
Want to identify cell subtypes or states *without* clustering?
Then check out Stator which finely resolves states & subtypes even among apparently homogeneous cells Thread
www.embopress.org/doi/full/10....

EASTBIO: Mapping DNA variants to cell states in health and disease at University of Aberdeen on FindAPhD.com PhD Project - EASTBIO: Mapping DNA variants to cell states in health and disease at University of Aberdeen , listed on FindAPhD.com

I am STOKED that myself and @avakhamseh.bsky.social are looking for a joint EastBIO PhD candidate across @uniofaberdeen.bsky.social and @uoe-sps.bsky.social to develop cutting-edge statistical models at the interface of single cell genomics and quantitative genetics: shorturl.at/vQo0P pls reskeet!