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Zepeng (Phoenix) Mu

@ZepengMu

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(牟泽鹏) Postdoc @soumya_boston @BrighamWomens @broadinstitute | PhD @yang_i_li @UChicago | BS @UCAS1978 | Twin @charlie_z_mu

Boston, MA
Joined August 2016
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@ZepengMu
Zepeng (Phoenix) Mu
1 month
RT @YuriyBaglaenko: I am very excited to share our publication, out now in Nature, detailing our developed CRAFTseq methodology for capturi….
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nature.com
Nature - A plate-based assay called CRAFTseq has been developed that uses ‘multi-omic’ single-cell RNA sequencing and direct genotyping of CRISPR edits to test the functional effects of...
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@ZepengMu
Zepeng (Phoenix) Mu
1 month
RT @soumya_boston: Join me for this lecture to find out how we use genomics to decipher #autoimmunity and #rheumatoid arthritis.
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@ZepengMu
Zepeng (Phoenix) Mu
6 months
RT @saorisakaue: 📣Excited to share my last postdoc paper with.@soumya_boston on eQTL mechanisms depending on where the RNA is in the cell!….
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@ZepengMu
Zepeng (Phoenix) Mu
7 months
RT @Y_Gilad: My book, An Intuitive Primer on Effective Functional Genomics Study Design, is published! I’d really appreciate it if you coul….
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@ZepengMu
Zepeng (Phoenix) Mu
9 months
Huge thanks to my PhD advisor @yang_i_li and all collaborators especially @LB_Barreiro for their help and support!!! Huge thanks to all the donors! This data is a subset of a larger scRNA/scATAC data, read more about the cool discoveries in threads from @he_randolph!.
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@ZepengMu
Zepeng (Phoenix) Mu
9 months
To conclude, we believe it is crucial to continue studying the genetic regulation of molecular phenotypes in more disease-relevant contexts. Furthermore, we emphasize the necessity of integrating various functional assays to elucidate causal mechanisms at GWAS loci.
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@ZepengMu
Zepeng (Phoenix) Mu
9 months
Indeed, GWAS loci-gene links from COLOC with eQTL+caQTL in the same context are significantly enriched in the putative causal S2G (cS2G) data. Whereas eQTL-only and closest genes to caQTL-only GWAS loci are not enriched.
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@ZepengMu
Zepeng (Phoenix) Mu
9 months
caQTL COLOC with ~50% MORE GWAS loci than eQTL alone! But again, as most colocalized caQTL don’t influence gene expression in the same context, these caQTL-only GWAS loci may causally mediate disease risks in still other unprofiled cell types/states.
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@ZepengMu
Zepeng (Phoenix) Mu
9 months
This is consistent with the notion that open chromatin and caQTLs are more shared than eQTLs across contexts, but they do not necessarily regulate gene expression in all contexts.
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@ZepengMu
Zepeng (Phoenix) Mu
9 months
and that's what we did! We performed COLOC with DICE eQTL. Although most caQTLs are shared (~80%), they do not influence gene expression in all cell-types. However, cell-type specific E2G links and TF activity score are important predictors of caQTL effect on gene expression.
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@ZepengMu
Zepeng (Phoenix) Mu
9 months
We used pseudo-bulk allele-specific model and single-cell Poisson model (for the 1st time in scATAC) to map ~37,000 caQTLs in 5 cell types. Single-cell Poisson model allowed us to obtain full summary stats for caQTL and perform in-depth analysis on not possible before.
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@ZepengMu
Zepeng (Phoenix) Mu
9 months
To this end, we built a harmonized scATAC atlas from 3 studies containing 280,000 peripheral immune cells from 48 donors (with 25 new donors) with imputed genotype info, among the largest to date!
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@ZepengMu
Zepeng (Phoenix) Mu
9 months
Excited to share the final chapter my PhD research on @medrxivpreprint! eQTLs only explain 30% of GWAS loci and 11% of trait heritability. Here we investigate if epigenetic QTL can provide new insights at the remaining GWAS loci.
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medrxiv.org
Only a third of immune-associated loci from genome-wide association studies (GWAS) colocalize with expression quantitative trait loci (eQTLs). To learn about causal genes and mechanisms at the...
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@ZepengMu
Zepeng (Phoenix) Mu
9 months
RT @XuanyaoLiu: Our work is out in AJHG! I wholeheartedly thank all the co-authors @marie_saitou @andywdahl @qbw_128 for their time and eff….
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@ZepengMu
Zepeng (Phoenix) Mu
11 months
RT @JinghuiLi14637: Our work on trans regulation of proteome and how protein-protein interactions play a role in it🧬.
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@ZepengMu
Zepeng (Phoenix) Mu
1 year
RT @XuanyaoLiu: Our work led by @liliw_wang on identifying trans genetic effects of gene networks is out in @CellGenomics today!.
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@ZepengMu
Zepeng (Phoenix) Mu
1 year
RT @YuriyBaglaenko: CRISPR editing is hard. Editing in primary human cells is even harder. Editing non-coding variants in human cells is d….
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biorxiv.org
Genetic studies have identified thousands of individual disease-associated non-coding alleles, but identification of the causal alleles and their functions remain critical bottlenecks. Even though...
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@ZepengMu
Zepeng (Phoenix) Mu
1 year
Very interesting and impressive work! Congrats to my friend Wenhe!.
@Wenhe_Lin_
Wenhe Lin
1 year
Our paper is out in @CellGenomics! Huge thanks to all the collaborators for making it possible!.
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