Yupei You

Postdoctoral researcher at the Walter and Eliza Hall Institute in Matt Ritchie’s lab.

Research topic: Genomics | Transcriptomics | Long-read sequencing | Singl

[Yupei You @youyupei]

Excited to share our latest preprint!

[bioRxiv Genomics @biorxiv_genomic]

Benchmarking long-read RNA-sequencing technologies with LongBench: a cross-platform reference dataset profiling cancer cell lines ... https://t.co/QndofWdaXJ #biorxiv_genomic

[bioRxiv Bioinfo @biorxiv_bioinfo]

Igniting full-length isoform analysis in single-cell and spatial RNA-seq data with FLAMESv2 https://t.co/zyHdHA99bF #biorxiv_bioinfo

[Millennium Science @mscienceaustnz]

Benchmark long-read analysis with 10x Genomics + LongBench.
The LongBench resource from @mritchieau's lab, led by @youyupei showcases how @10xGenomics single-cell and single-nucleus workflows reveal full-length transcripts and uncover isoform diversity.

[Yupei You @youyupei]

@WEHI_research @AAHMS_health No thanks

[WEHI (Walter and Eliza Hall Institute) @WEHI_research]

Interested in Honours, Masters, or PhD studies in medical research?

We have over 70 student research projects starting in 2025, across the breadth of research areas at WEHI.

Explore the opportunities here: https://t.co/KKvDhaKxex

#WEHIStudents #StudyInMelbourne #UniMelb

[James Ferguson @Psy_Fer_]

We have just released v0.4.0 of buttery-eel, a slow5 guppy/dorado basecaller.

It can now do barcode demultiplexing and works with the dorado server/client while maintaining compatibility with guppy.

https://t.co/68E07NoGPm

[Simona Cristea @simocristea]

Amazing week for #DeepLearning in #spatial #singlecell biology, with 2🔥new Graph Neural Networks methods!

1.STELLAR🇺🇸 @jure: a cell type annotation & discovery atlas-type framework
2.NCEM🇪🇺 @fabian_theis: an approach to infer cellular communication patterns

Deep dive below🧵

[Mike Clark @ClarksysCorner]

We're hiring!

If you want to work with a great bunch of people on long-read scRNA-seq analysis to better understand brain development, please apply.

https://t.co/BsvW7DwoRa

#RNA #scRNA #Bioinformatics

[Mike Clark @ClarksysCorner]

Our tool BLAZE for identifying cell barcodes from @nanopore scRNA-seq is now published in @GenomeBiology https://t.co/dkXd0fbTsy

Lots of improvements from preprint
-faster
-high sensitivity mode
-output to run empty drops to save/discard cells
-robust to different read depths

[James Ferguson @Psy_Fer_]

Want to basecall faster? Want to scale your basecalling with hardware? Use our new tool: buttery-eel, to basecall SLOW5 files with the latest guppy basecaller and models, including methylation with remora -> uSAM.

https://t.co/atoX9QvWs4

[Computational Transcriptomics @goekelab]

We are happy to announce the preprint for Bambu - “Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu” https://t.co/0IVtfNaRna. Available now from BioConductor https://t.co/haQlu0vZ3n and Github https://t.co/mbrItbzxLC 1/7

[Yupei You @youyupei]

10pm on a public holiday. Still love it!

[Genome Biology @GenomeBiology]

@youyupei Now @youyupei is taking questions on line, presumably from Melbourne where it's well past 10 pm. Good effort. #gi2022

[Mike Clark @ClarksysCorner]

Long-read scRNA-seq is awesome for studying RNA isoforms. But @nanopore has relied on matched short-reads to identify cell barcodes and assign reads to cells.
Pleased to share BLAZE, a new tool to identify cell barcodes from nanopore scRNA-seq. Short-reads not required. 1/4

[Yupei You @youyupei]

Many thanks to my supervisors @heejungshim @ClarksysCorner for all your help to get this paper published!

[Yupei You @youyupei]

Excited to share our paper "NanoSplicer: Accurate identification of splice junctions using Oxford Nanopore sequencing" @nanopore
https://t.co/bwnphDtv7W

[Yupei You @youyupei]

When annotations are available, NanoSplicer provides higher accuracy than FLAIR when there are multiple annotated junctions nearby, or the true junction utilised unannotated splice site. (3/3)

[Yupei You @youyupei]

@goekelab I am very happy that you found it interesting. We are currently working on moving from the "corrected junctions" to "corrected reads/isoforms", so we can output in .bam files.

[MRC Biostatistics Unit @MRC_BSU]

Thanks again to @heejungshim for giving a virtual seminar on 'NanoSplicer: Accurate identification of splice junctions using Oxford Nanopore sequencing'. If you missed it, you can watch here: https://t.co/dGqro8zmVV