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Homeobox oncogene activation by pan-cancer DNA hypermethylation genomebiology.biomedcentral.com/articles/10.11…

Congratulations Ping

Nice work

Congratulations Xiaole Shirley Liu !!! Well deserved and long overdue!!

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. Fanglue Peng Eric J Wagner Wei Li biorxiv.org/content/10.110…

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

Our cancer driver gene prediction paper is finally online. advances.sciencemag.org/content/6/46/e…

Excited to share our new paper: Cellular Heterogeneity–Adjusted cLonal Methylation (CHALM) improves prediction of gene expression nature.com/articles/s4146…

💥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 👇Nature Genetics go.nature.com/2SF8aCU

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 Eric J Wagner Lei Li nature.com/articles/s4158…

Congratulations to Li Song on the great improvement on the TRUST algorithm! github.com/liulab-dfci/TR…

Our new scDaPars tool for single-cell alternative polyadenylation is published Genome Research genome.cshlp.org/content/early/…

Population-scale genetic control of alternative polyadenylation and its association with human diseases journal.hep.com.cn/qb/EN/10.15302…

Study of false positives when calling differentially expressed genes, from Yumei Li, Xinzhou Ge, Fanglue Peng, Wei Li & Jingyi Jessica Li (李婧翌). With population-scale sample sizes, common methods have inflated FDR. The authors suggest using Wilcoxon rank-sum test genomebiology.biomedcentral.com/articles/10.11…

Boris Hejblum (Boris Hejblum (@borishej.bsky.social).bsky.social) Michael Love @KasperDHansen Tim Triche, Jr. (@timtriche.bsky) Andrew Jaffe Lior Pachter Thiebaut Rodolphe 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.

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.

Our new paper Nature Communications 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…

Now online! A genome-wide spectrum of tandem repeat expansions in 338,963 humans dlvr.it/T576KX