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Boxiang Liu

@boxiangliu.bsky.social
426 followers 44 following 38 posts

Presidential Young Professor @ National University of Singapore. Stanford PhD, ex-Baidu Research Lead. Functional Genomics, Data Science, AI/ML. www.boxiangliulab.com

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Boxiang Liu @boxiangliu.bsky.social · 19/07/2026
Also, locuscompare2 (locuscompare2.com) allows cloud-based colocalization analysis. Give it a try and let us know your feedback!
locuscompare2.com
LocusCompare v2
Web site created using create-react-app
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Boxiang Liu @boxiangliu.bsky.social · 19/07/2026
After a period of downtime and maintenance, I am excited to announce that locuscompare.com is back with a more enriched feature set. The new locuscompare suite includes: 1) The locuscomparer R package 2) The locuscomparepy Python module 3) The locuscompare website (locuscompare.com)
locuscompare.com
LocusCompare
A suite of tools for visualizing and interpreting the colocalization of genetic association summary statistics.
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Boxiang Liu @boxiangliu.bsky.social · 24/05/2026
If you are interested in single-cell splicing QTL analysis, it will worth trying ISSAC. My talk at the Biology of Genomes 2026: youtu.be/ObWtjpYBie4 ISSAC Preprint: www.medrxiv.org/content/10.6...
medrxiv.org
Single-cell splicing analysis with ISSAC links cell type-specific and cell state-dependent sQTLs to neurological disorders
Single-cell RNA sequencing enables comprehensive profiling of gene expression and splicing at cellular resolution, revealing cell type-specific and cell state-dependent regulation (variation within ce...
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Boxiang Liu @boxiangliu.bsky.social · 09/05/2026
My summary slide from #BOG2026
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Boxiang Liu @boxiangliu.bsky.social · 09/05/2026
Preprint: www.medrxiv.org/content/10.6...
medrxiv.org
Single-cell splicing analysis with ISSAC links cell type specific and cell state-dependent sQTLs to neurological disorders
Single-cell RNA sequencing enables comprehensive profiling of gene expression and splicing at cellular resolution, revealing cell type-specific and cell state-dependent regulation (variation within ce...
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Boxiang Liu @boxiangliu.bsky.social · 09/05/2026
In addition, my lab is recruiting PhD students and postdoctoral fellows with competitive salaries. Wetlab experience is a plus. Reach out by emailing boxiangliu@nus.edu.sg.
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Boxiang Liu @boxiangliu.bsky.social · 09/05/2026
3) Applied to 3 million DLPFC single-nuc data, we identified more than 33,000 cell-type-specific sQTLs, as well as cell-state-dependent and G x disease sQTLs. 4) We validated the genetic mechanism of TRPT1 sQTL which also underlies neuroticism risk
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Boxiang Liu @boxiangliu.bsky.social · 09/05/2026
Sharing our exciting single-cell splicing method ISSAC. Key features include: 1) ISSAC is 1.4 to 2.5-fold power increase over LeafCutter on single-cell sQTL discovery, and scalable to millions of cells 2) ISSAC is able to map cell-state-dependent sQTLs and intron-retention sQTLs.
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Boxiang Liu @boxiangliu.bsky.social · 19/07/2025
HUGE shoutout to our amazing team: Wang Wenjing, Liew Wei Lin, Liu Mei Hui, Xueling Sim, and Tai E Shyong!
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Boxiang Liu @boxiangliu.bsky.social · 19/07/2025
Colocalization with 12 Asian GWAS traits pinpoints 16 metabolic risk genes, revealing how lifestyle modulates genetic risk at loci like DHRS4L2 and YBX3.
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Boxiang Liu @boxiangliu.bsky.social · 19/07/2025
Splicing QTLs (sQTLs) also respond to intervention, with attenuated regulation at T2D risk gene ANK1 and dynamic changes in mitochondrial genes.
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Boxiang Liu @boxiangliu.bsky.social · 19/07/2025
We identify hundreds of lifestyle-responsive eQTLs, including context-specific regulation of ACTN3, NEB, and ATP2A1.
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Boxiang Liu @boxiangliu.bsky.social · 19/07/2025
Muscle transcriptome rewiring reveals activation of insulin signaling and mitochondrial genes—plus significant shifts in alternative splicing.
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Boxiang Liu @boxiangliu.bsky.social · 19/07/2025
We conducted a 16-week lifestyle intervention, which led to ~10% weight loss and improved insulin sensitivity, reshaping body composition and lipid metabolism.
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Boxiang Liu @boxiangliu.bsky.social · 19/07/2025
Excited to share our new paper on Cell Genomics: We mapped how genetics shape the muscle transcriptome in response to exercise and diet intervention. 📄 www.cell.com/cell-genomic...
doi.org
Redirecting
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Boxiang Liu @boxiangliu.bsky.social · 25/01/2025
This is the third collaborative paper between the two labs. Looking forward to many projects to come!
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Boxiang Liu @boxiangliu.bsky.social · 25/01/2025
Collaborative work led by Zhihao and me finally online at Nature Communications! nature.com/articles/s41... Huge congratulations to Zhihao and his outstanding leadership. Also, to first author Foozhan Tahmasebinia, and key contributions from Yinglu Tang and Rushi Tang!
nature.com
The 40S ribosomal subunit recycling complex modulates mitochondrial dynamics and endoplasmic reticulum - mitochondria tethering at mitochondrial fission/fusion hotspots - Nature Communications
Coordinating protein translation with energy supply is a significant challenge faced by cells. Here, the authors found that the protein quality control network may provide a link between the two.
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Boxiang Liu @boxiangliu.bsky.social · 18/12/2024
And here is the Nature Genetics Cover!
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Boxiang Liu @boxiangliu.bsky.social · 11/12/2024
Exciting new benchmark for DNA language models!
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Boxiang Liu @boxiangliu.bsky.social · 09/12/2024
This study is truly amazing.
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Boxiang Liu @boxiangliu.bsky.social · 06/12/2024
The next Human Cell Atlas will be held in Singapore in June 2025. The early-bird registration is already open: 2025events.humancellatlas.org/2025GM I highly encourage single-cell folks to register. Many exciting talks ahead!
2025events.humancellatlas.org
2025 Human Cell Atlas General Meeting
The 2025 HCA General Meeting will convene our community to share updates on assembling HCA Atlases of specific tissues, and to plan for the release of the first draft Human Cell Atlas. We will discuss...
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Boxiang Liu @boxiangliu.bsky.social · 05/12/2024
In summary, we established a robust single-cell splicing analysis pipeline and uncovered functional regulatory pathways and novel disease mechanisms.
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Boxiang Liu @boxiangliu.bsky.social · 05/12/2024
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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Boxiang Liu @boxiangliu.bsky.social · 05/12/2024
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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Boxiang Liu @boxiangliu.bsky.social · 05/12/2024
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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Boxiang Liu @boxiangliu.bsky.social · 05/12/2024
We observed significant improvement in exon coverage compared to 3' short-read data (4-6 fold!).
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Boxiang Liu @boxiangliu.bsky.social · 05/12/2024
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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Boxiang Liu @boxiangliu.bsky.social · 05/12/2024
Our paper on single-cell splicing QTL is now published as a cover article in Nature Genetics. www.nature.com/articles/s41... Congratulations to co-first authors Chi Tian, Yihan Tong, and Yuntian Zhang! Huge thanks to AIDA leaders Shyam Prabhakar, @jayshin.bsky.social, Woong-Yang, and Kian Hong!
nature.com
Single-cell RNA sequencing of peripheral blood links cell-type-specific regulation of splicing to autoimmune and inflammatory diseases - Nature Genetics
This analysis of single-cell RNA sequencing data from peripheral blood mononuclear cells for 474 individuals of diverse Asian ancestries in the Asian Immune Diversity Atlas links cell-type-specific sp...
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Boxiang Liu @boxiangliu.bsky.social · 05/12/2024
Very exciting work for biology and drug discovery!
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Boxiang Liu @boxiangliu.bsky.social · 04/12/2024
QC is arguably the most important step in any single cell analysis. Low quality data can lead to incorrect conclusions.
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Boxiang Liu @boxiangliu.bsky.social · 03/12/2024
HCA Asia 2024 off to a great start!
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Boxiang Liu @boxiangliu.bsky.social · 02/12/2024
En route to HCA Hong Kong. Excited to reconnect with old friends and making new ones!
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Boxiang Liu @boxiangliu.bsky.social · 29/11/2024
Comprehensive knockdown of 305 splicing-related proteins and their effect on splicing. Such a tour de force!!
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Boxiang Liu @boxiangliu.bsky.social · 25/11/2024
Here is a starter pack for functional genomics on bluesky. Not sure if there is one already but do let me know if so. Let me know if you want to be added to the list. go.bsky.app/SvBtD4d
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Boxiang Liu @boxiangliu.bsky.social · 25/11/2024
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!!
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Boxiang Liu @boxiangliu.bsky.social · 21/11/2024
The SG Academies South-East Asia Fellowship Programme (2024 Round) application is now open and will close on 31 Jan 2025. snas.org.sg/saseaf.
snas.org.sg
Programme Details — Singapore National Academy of Science
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Boxiang Liu @boxiangliu.bsky.social · 21/11/2024
Is there a starter pack for functional genomics? Should I start one?
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Boxiang Liu @boxiangliu.bsky.social · 20/11/2024
Has anyone used Video Byte or Graphical Abstract service by Springer Nature? Is it worth it?
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