Yu Zhao
129 posts
Yu Zhao
@yu48693
Postdoctoral Research Fellow, Bioinformatics, Systems Immunology @BrighamWomens @broadinstitute
Boston Katılım Mayıs 2019
627 Takip Edilen224 Takipçiler
Yu Zhao retweetledi
Paper from me @michecurtis @soumya_boston and co out now in @naturemethods! We now call the tool starCAT instead of *CAT but the strategy is the same: Build a catalog of ~50 interpretable T cell gene expression programs + use them to interpret new data nature.com/articles/s4159…
Dylan Kotliar@DKotliar
@michecurtis and I are thrilled to share our preprint "Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions" from the @soumya_boston lab @BrighamResearch and @broadinstitute! biorxiv.org/content/10.110… 1/12
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Our latest work on T cell annotation pipeline TCAT is now online! Feel free to try out and discuss. Happy to be involved. nature.com/articles/s4159…
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Yu Zhao retweetledi
So excited to share our latest with Betty Diamond and many colleagues from the AMP RA/SLE consortium, @NIH_NIAMS , and @NIAIDNews ! A large-scale blood and tissue atlas of Lupus Nephritis! biorxiv.org/content/10.110…
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Yu Zhao retweetledi
Thrilled to announce the publication of our latest manuscript on CD4 Trm cells in Nature Immunology! @NatImmunol
A huge thank you to our amazing team and collaborators for their incredible work!
nature.com/articles/s4159…
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Yu Zhao retweetledi
📣Excited to share my last postdoc paper with
@soumya_boston on eQTL mechanisms depending on where the RNA is in the cell! @BrighamResearch @broadinstitute
TL;DR:Early RNA eQTL variants in the nucleus and late RNA eQTL variants in the cytosol have distinct molecular mechanism🧵👇
bioRxiv Genomics@biorxiv_genomic
Early and late RNA eQTL are driven by different genetic mechanisms biorxiv.org/content/10.110… #biorxiv_genomic
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Yu Zhao retweetledi
Excited to tell you about VIMA (Variational Inference-based Microniche Analysis), our deep learning + stats hybrid for case-control analysis of multi-sample spatial molecular datasets. 🧵👇biorxiv.org/content/10.110…. @soumya_boston , @broadinstitute , @BrighamResearch
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Yu Zhao retweetledi
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. medrxiv.org/content/10.110…
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Yu Zhao retweetledi
Tidyplots makes it easy to generate publication-ready plots for scientific papers 🚀
tidyplots.org
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Yu Zhao retweetledi
Hi friends! Genotype-Neighborhood Associations (GeNA) by @LaurieRumker et al is now published! @broadinstitute @BrighamResearch nature.com/articles/s4158…
Laurie Rumker@LaurieRumker
We are excited to share Genotype-Neighborhood Associations, GeNA, a new tool adapting our CNA framework to detect cell states associated in abundance with genetic variants at genome-wide scale in high-dimensional single-cell data w/ @soumya_boston doi.org/10.1101/2023.1… 🧵
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We are happy to announce that scLinaX paper is finally published in @CellGenomics 🐧!! If you are interested in escape from X chromosome inactivation, a mechanism contributing to sex difference of transcriptome, please check our paper!
cell.com/cell-genomics/…
Tweetorial↓
YoshihikoTomofuji@YoshiTomofuji
We are happy to announce that our new preprint regarding the scLinaX, software to quantify escape from X chromosome inactivation from 10X scRNA-seq data, was released from bioRxiv 🎉🎉🎉!! biorxiv.org/content/10.110… (1/N)
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Yu Zhao retweetledi
Science Immunology has just published our pooled in vivo CRISPR-screen (iCROP-seq). In this study we also address T cell plasticity in the kidney of ANCA-GN patients. Thanks to everybody involved in this study!
science.org/doi/10.1126/sc…
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Yu Zhao retweetledi
SCENT defines non-coding disease mechanisms using single-cell multi-omics go.nature.com/3R8yu3X #ToolsoftheTrade by @saorisakaue @harvardmed @broadinstitute #NRGToT
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Yu Zhao retweetledi
AMP-RA study defining chromatin states in inflammatory #RheumatoidArthritis tissue is out! We argue: single cells can be grouped into chromatin classes, encompassing multiple transcriptional cells states. @NIH_NIAMS @broadinstitute @BrighamResearch
link.springer.com/article/10.103…
Soumya Raychaudhuri সৌম্য রায়চৌধুরী@soumya_boston
So excited to share our #RheumatoidArthritis tissue chromatin atlas of 87K cells from 30 individuals! With, @soumya_boston, @saorisakaue, @aparnanathan, @Donlinlab, Kevin Wei and #AMP-RA! @NIH_NIAMS. biorxiv.org/content/10.110… (Tweeting on behalf of the talented Kathryn Weinand)
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Yu Zhao retweetledi
Excited to share our preprint proposing pgBoost, an eQTL-informed gradient boosting model that integrates scores from single-cell enhancer-gene linking methods and genomic distance to predict regulatory SNP-gene links (a key step in interpreting GWAS discoveries)!🧬
1/4
medRxiv@medrxivpreprint
Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance medrxiv.org/cgi/content/sh… #medRxiv
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Yu Zhao retweetledi
@michecurtis and I are thrilled to share our preprint "Reproducible single cell annotation of programs underlying T-cell subsets, activation states, and functions" from the @soumya_boston lab @BrighamResearch and @broadinstitute!
biorxiv.org/content/10.110…
1/12
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