boxiangliu.bsky.social
Presidential Young Professor @ National University of Singapore. Stanford PhD, ex-Baidu Research Lead. Functional Genomics, Data Science, AI/ML. www.boxiangliulab.com
23 posts
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Regular Contributor
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This is the third collaborative paper between the two labs. Looking forward to many projects to come!
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And here is the Nature Genetics Cover!
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In summary, we established a robust single-cell splicing analysis pipeline and uncovered functional regulatory pathways and novel disease mechanisms.
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We also identified and validated a putative causal mechanism.
A genetic variant influencing the TCHP exon 4 inclusion, which putatively affects Graves' disease risk. We validated the variant-to-splicing relationship using a minigene assay.
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We identified a pathway from genetic variants -> cis-eQTL (of a splicing factor) -> trans-sQTL (of a key T-cell differentiation marker) -> T-cell proportions (of naive vs. memory T cells). All of these are inferred using a single population-scale single-cell dataset.
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Dynamic AS and dynamic sQTLs are widespread along the B-cell development trajectory, some of which may be implicated in disease. For example, PAX5 dynamic isoforms are key determinants of B cell differentiation, and CLEC2D dynamic sQTL is colocalized with autoimmune disease.
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We observed significant improvement in exon coverage compared to 3' short-read data (4-6 fold!).
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We established a robust pipeline to analyze alternative splicing using 10x 5' single-cell data. Because of "exon painting" effect, ~90% of exons are covered by 5' short-read, despite 5' bias. ~86% of short-read ss are replicated by long-read, likely more with more long-read samples.
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Dear Su-In, I’m an assistant professor at the National University of Singapore. I would love to be included on your list. Thank you!!