@superweili

Professor of Bioinformatics at University of California, Irvine

 Irvine, CA
openwetware.org/wiki/Li_Lab
Joined July 2010
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Now online! A genome-wide spectrum of tandem repeat expansions in 338,963 humans dlvr.it/T576KX

A genome-wide spectrum of tandem repeat expansions in 338,963 humans

The Tandem Repeat Aggregation Atlas (TR-Atlas) is a biobank-scale reference of 0.86 million TRs derived from 338,963 whole-genome sequencing (WGS) samples of diverse ancestries.

cell.com
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Thrilled to share our UCI TR-gnomAD published in Cell today: cell.com/cell/fulltext/S0092…. 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
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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/s41467-0… – at Irvine, CA
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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@mikelove17 May 2022
Replying to @jsb_ucla @JunyanLu1118 @borishej @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.
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Replying to @borishej @mikelove @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.
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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.…
Graphs of number of identified DEGs versus number of datasets where a gene is wrongly identified as a DEG for six different methods

ALT Graphs of number of identified DEGs versus number of datasets where a gene is wrongly identified as a DEG for six different methods

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Population-scale genetic control of alternative polyadenylation and its association with human diseases journal.hep.com.cn/qb/EN/10.…
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Our new scDaPars tool for single-cell alternative polyadenylation is published @genomeresearch genome.cshlp.org/content/ear…
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💥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

An atlas of alternative polyadenylation quantitative trait loci contributing to complex trait and...

Nature Genetics - A multi-tissue atlas of alternative polyadenylation (APA) quantitative trait loci (3′aQTLs) identifies approximately 0.4 million common genetic variants associated with the...

nature.com
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Congratulations to @mourisl on the great improvement on the TRUST algorithm! github.com/liulab-dfci/TRUST…

GitHub - liulab-dfci/TRUST4: TCR and BCR assembly from RNA-seq data

TCR and BCR assembly from RNA-seq data. Contribute to liulab-dfci/TRUST4 development by creating an account on GitHub.

github.com
Li Song@mourisl13 May 2021
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/s41592-0…
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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/s41588-0…
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Excited to share our new paper: Cellular Heterogeneity–Adjusted cLonal Methylation (CHALM) improves prediction of gene expression nature.com/articles/s41467-0…

Cellular Heterogeneity–Adjusted cLonal Methylation (CHALM) improves prediction of gene expression

Nature Communications - Here, the authors introduce Cell Heterogeneity–Adjusted cLonal Methylation (CHALM) as a methylation quantification method that considers the heterogeneity of sequenced...

nature.com
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Our cancer driver gene prediction paper is finally online. advances.sciencemag.org/cont…
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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.…

Genome Biology

Genome Biology is a leading open access journal in biology and biomedicine research, with 9.4 Impact Factor and 14 days to first decision. As the ...

link.springer.com
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Super Excited to share our new pre-print describing the first atlas of human 3'QTLs, i.e. ~0.4 million genetic variants associated with APA of target genes across 46 #GTEx tissues. @FanglueP @Wagnerlab_RNA @superweili biorxiv.org/content/10.1101/…

Genetic Basis of Alternative Polyadenylation is an Emerging Molecular Phenotype for Human Traits...

Genome-wide association studies have identified thousands of non-coding variants that are statistically associated with human traits and diseases. However, functional interpretation of these variants...

biorxiv.org
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Congratulations @XShirleyLiu !!! Well deserved and long overdue!!
ISCB News
@iscb25 Feb 2019
February 25, 2019: ISCB Congratulates and Introduces the 2019 Class of Fellows! iscb.org/iscb-news-items/390…
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Nice work – at Pearland, TX
Christine Mayr@Mayr_Christine27 Aug 2018
Our new paper is online at Nature! Tumor-suppressor genes are often inactivated through changes in mRNA processing that enable expression of truncated proteins. This mechanism of inactivation does not require DNA mutations in the affected genes. rdcu.be/5iTD
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Congratulations Ping
UTMB Provost's Office@UTMBProvost26 Jun 2018
Dr. Ping Ji has received a new two-year award from @theNCI to study factors in the development and progression of glioblastoma multiforme, the most common and aggressive brain tumor. Dr. Ji is an Assistant Professor in @bmb_utmb. We congratulate him on this research opportunity!
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Homeobox oncogene activation by pan-cancer DNA hypermethylation genomebiology.biomedcentral.…

Homeobox oncogene activation by pan-cancer DNA hypermethylation

Genome Biology - Cancers have long been recognized to be not only genetically but also epigenetically distinct from their tissues of origin. Although genetic alterations underlying oncogene...

link.springer.com
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