Wei Li retweetledi
Now online! A genome-wide spectrum of tandem repeat expansions in 338,963 humans dlvr.it/T576KX
English
Wei Li
27 posts
Wei Li
@superweili
Professor of Bioinformatics at University of California, Irvine
Irvine, CA Katılım Temmuz 2010
55 Takip Edilen820 Takipçiler
Thrilled to share our UCI TR-gnomAD published in Cell today: cell.com/cell/fulltext/…. UCI TR-gnomAD is the first biobank-scale genetic reference for ~1.0M Tandem Repeat (TR) expansions across 340K humans, facilitating TR-based disease association studies and clinical diagnostics
English
@Goodell_Lab Congratulations Peggy @Goodell_Lab! I enjoyed our collaborations very much.
English
The lab recently passed its 25th b-day! They surprised me today w/ a party including alumni videos, lab swag, and more. So fortunate to have wonderful current and former trainees and staff. Deeply grateful to them all!
Houston, TX 🇺🇸 English
Our new paper @NatureComms performed the first Alternative polyadenylation transcriptome-wide association study for 11 brain disorders with 17,300 RNA-seq samples. We identified 354 novel APA-linked risk genes including ATXN3 for ALS.
nature.com/articles/s4146…
Irvine, CA 🇺🇸 English
Wei Li retweetledi
Ultimately, adjusting hidden covariates or not examines different DE effects (conditional vs marginal). But regardless of this difference, I still think no DE genes are expected be found (in the average sense) from permuted samples where conditional labels are randomly shuffled.
Michael Love@mikelove
@jsb_ucla @JunyanLu1118 @borishej @KasperDHansen @timtriche @andrewejaffe @lpachter @RodThiebaut @denis_agniel I always look at PCA plot. With 20+ samples, I expect batch effects. We have always used RUV factors when we see structure in the PCA, common with n > 50. There are pkgs in Bioc for partitioning variance by latent factors. This is not specific to us, but common practice I think.
English
Wei Li retweetledi
@borishej @mikelove @KasperDHansen @timtriche @andrewejaffe @lpachter @RodThiebaut @denis_agniel We thank @borishej et al for sending us the draft of their correspondence on May 3. Here is a threshold of key points in our reply sent on that day. 1/ The main message of our article is that using popular methods without a sanity check may lead to inflated FDR.
English
Wei Li retweetledi
Study of false positives when calling differentially expressed genes, from @YM123411, @ge_xinzhou, @FanglueP, @superweili & @jsb_ucla. With population-scale sample sizes, common methods have inflated FDR. The authors suggest using Wilcoxon rank-sum test genomebiology.biomedcentral.com/articles/10.11…
English
Wei Li retweetledi
Population-scale genetic control of alternative polyadenylation and its association with human diseases
journal.hep.com.cn/qb/EN/10.15302…
English
Our new scDaPars tool for single-cell alternative polyadenylation is published
@genomeresearch
genome.cshlp.org/content/early/…
English
@YongshengShi @NeugebauerKarla @TheTracyLab @cshlmeetings looks like a very exciting meeting. Any chance to be in person?
English
Alberto Kornblihtt, @NeugebauerKarla , @TheTracyLab , and I are co-organizing the upcoming @cshlmeetings on RNA Processing (Aug 24). Please submit your abstracts by June 25!
meetings.cshl.edu/meetings.aspx?…
English
Wei Li retweetledi
💥An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and disease heritability | by Eric J. Wagner & Wei Li and colleagues
Find it here 👇@NatureGenet
go.nature.com/2SF8aCU
English
@kauralasoo @anshulkundaje @Wagnerlab_RNA @LeiLi_bioinfo @eQTLCatalogue Hi Kaur, Thank you for the comments. It would be great if you could run Dapars on all of your eQTL Catalogue datasets.
English
@superweili @anshulkundaje @Wagnerlab_RNA @LeiLi_bioinfo @eQTLCatalogue I'm truly curious what the differences are between txrevise and DaPars and if it would be worth for us to run DaPars on all of the eQTL Catalogue datasets.
English
Super excited to share our recent work on 3′UTR alternative polyadenylation (APA) quantitative trait loci (3′aQTLs), which can explain ~16.1% GWAS SNPs and are largely distinct from eQTLs. Wonderful collaborations with @Wagnerlab_RNA @LeiLi_bioinfo
nature.com/articles/s4158…
English
Wei Li retweetledi
Congratulations to @mourisl on the great improvement on the TRUST algorithm! github.com/liulab-dfci/TR…
Li Song@mourisl
1/6 Our lab has developed the TRUST method to recover T/B-cell receptors from RNA-seq data. We present its new version TRUST4 in the @naturemethods paper, with features of better CDR3 accuracy, full-length assembly, and supporting single-cell data. nature.com/articles/s4159…
English
New paper from our lab!
#PLOSGenetics: Mechanism and consequences of herpes simplex virus 1-mediated regulation of host mRNA alternat ... dx.plos.org/10.1371/journa…
English
Excited to share our new paper: Cellular Heterogeneity–Adjusted cLonal Methylation (CHALM) improves prediction of gene expression
nature.com/articles/s4146…
English
English
Our work on zebrafish epigneome/3D genome/sex chromosome is available @nature. Transcriptome, methylome, ATAC-Seq, candidate enhancer/silencer across 11 tissues. Great collaboration with @twang5,@rosshardison,Topczewski/Kai Wang/Glenn Gerhard/Keith Cheng. rdcu.be/cbjkT
English
Our cancer driver gene prediction paper is finally online. advances.sciencemag.org/content/6/46/e…
English
Wei Li retweetledi
Twenty years of Genome Biology. Quite honored that our MACS is one of the top papers published in the last two decades, together with Bowtie, DESeq, TopHat2, SCANPY, DAVID, and BioConductor!
genomebiology.biomedcentral.com/20years
English