Yan Gao

If you have HiFi or Nanopore R10 metagenomic data, try myloasm from Jim Shaw. You will probably find more complete circular contigs to higher resolution especially for R10 or environmental samples. Scalable to >500GB data. Written in Rust. Published in @NatureBiotech

Myloasm, our long-read metagenome assembler, is now published! w/ Max Marin & @lh3lh3 Very rewarding after > a year of development and countless hours thinking about assembly. Thanks to beta testers, Li lab, and reviewers for helpful feedback. Link: rdcu.be/famFj

@csuhuangneng Thank you Neng!

Congrats @Ryan07GY, super cool work!

Long reads carry multiple small vars and SVs and their phasing. LongcallD is the only caller that tightly integrates germline/mosaic small/structural vars/MEIs and their phasing in a single C program. One command line to get competitive small variant calls and better SVs.

New preprint on longcallD: a unified framework for joint calling and phasing of small, structural and mosaic variants from long reads. Improved SV calling and competitive small variant calling. Supervised by @lh3lh3 , co-work with @QianAlvinQin1, @wwliao88 and @irahall9.

@Zhiliang_Bai @MIT @MITdeptofBE @kochinstitute Congrats Zhiliang!!! And welcome to Boston!!!

I’m beyond thrilled to share that I will be joining the @MIT Department of Biological Engineering @MITdeptofBE as an Assistant Professor in January 2026! I will also be an intramural member of the legendary Koch Institute for Integrative Cancer Research at MIT @kochinstitute

Exicted to share our recent work, longcallD, for long-read variant calling. More features are coming! Many thanks to my supervisor Dr. Heng Li @lh3lh3!!!

longcallD is a new variant caller for genomic long reads. It jointly calls phased small and structural variants. Single binary, one command line for the whole process. Comparable accuracy to mainstream callers. Great work by Yan Gao. github.com/yangao07/longc…

Check out our new paper, "isoCirc catalogs full-length circular RNA isoforms in human transcriptomes". We report a nanopore long-read sequencing strategy and companion computational pipeline to characterize circular RNA isoforms of human genes. nature.com/articles/s4146…

@si_hardwick @martinalexsmith @sequ_in @hagentilgner Thanks for the kind notification! I found the quantification result file for those 4 ONT datasets. Are the raw long-reads gonna be released?

@martinalexsmith @Ryan07GY @sequ_in @hagentilgner The nanopore data is now available on GEO :)

My first preprint is now available online! We used nanopore long-read sequencing to identify hundreds of unannotated non-coding RNAs overlapping GWAS SNPs associated with neuropsychiatric traits. Collab with @martinalexsmith @sequ_in @hagentilgner et al. biorxiv.org/content/10.110…

@hashirkhalid123 @BleacherReport How about Durant's performance in 16' WCF against the warriors, btw, which is his current team.

@BleacherReport Where was his "REPEAT MVP" performance in WCF last year ?

James Harden calling his repeat MVP right after the game ✌️ twitter.com/BleacherReport…