Ava Khamseh
@avakhamseh.bsky.social
Reader (Associate Professor) in Biomedical AI at University of Edinburgh |Quantitative Biomedicine #causalinference #ML #AI - views are my own
Reposted by Ava Khamseh
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...
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...
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 ...
doi.org
November 16, 2025 at 10:33 AM
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...
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...
Reposted by Ava Khamseh
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.
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.
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
www.findaphd.com
October 28, 2025 at 8:27 PM
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.
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.
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)
October 1, 2025 at 11:36 AM
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!
Very much looking forward to teaching and discussing!
New course announced!
We're thrilled to be hosting the @embo.org Practical Course 'Causality in biomedicine: going beyond associations' from 4 – 9 October 2026.
Register your interest and be the first to hear when the course opens for applications: www.ebi.ac.uk/training/eve...
We're thrilled to be hosting the @embo.org Practical Course 'Causality in biomedicine: going beyond associations' from 4 – 9 October 2026.
Register your interest and be the first to hear when the course opens for applications: www.ebi.ac.uk/training/eve...
August 12, 2025 at 2:03 PM
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!
Very much looking forward to teaching and discussing!
Reposted by Ava Khamseh
📢 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...
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...
June 20, 2025 at 5:44 AM
📢 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...
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...
Reposted by Ava Khamseh
📢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....
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....
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...
www.embopress.org
January 3, 2025 at 9:45 AM
📢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....
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....
Reposted by Ava Khamseh
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!
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
shorturl.at
December 13, 2024 at 1:31 PM
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!