Our latest preprint and software "NanoSplicer: Accurate identification of splice junctions using Oxford Nanopore sequencing" led by Yupei You in collaboration with Mike Clark biorxiv.org/content/10.110… github.com/shimlab/NanoSp… Oxford Nanopore 1/3

We're hiring! Position available for an RA to join our lab to help us investigate brain development. Looking for an enthusiastic individual with cell culture and molecular biology experience. jobs.unimelb.edu.au/en/job/907050/…

Thanks again to Heejung Shim for giving a virtual seminar on 'NanoSplicer: Accurate identification of splice junctions using Oxford Nanopore sequencing'. If you missed it, you can watch here: youtube.com/watch?v=3YNGnn…

Long-read scRNA-seq is awesome for studying RNA isoforms. But Oxford 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

10pm on a public holiday. Still love it!

Amazing week for #DeepLearning in #spatial #singlecell biology, with 2🔥new Graph Neural Networks methods! 1.STELLAR🇺🇸 Jure Leskovec: a cell type annotation & discovery atlas-type framework 2.NCEM🇪🇺 Fabian Theis: an approach to infer cellular communication patterns Deep dive below🧵

We are happy to announce the preprint for Bambu - “Context-Aware Transcript Quantification from Long Read RNA-Seq data with Bambu” biorxiv.org/content/10.110…. Available now from BioConductor bioconductor.org/packages/bambu/ and Github github.com/GoekeLab/bambu 1/7

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. biorxiv.org/content/10.110…

Our tool BLAZE for identifying cell barcodes from Oxford Nanopore scRNA-seq is now published in Genome Biology genomebiology.biomedcentral.com/articles/10.11… Lots of improvements from preprint -faster -high sensitivity mode -output to run empty drops to save/discard cells -robust to different read depths

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. jobs.unimelb.edu.au/en/job/912934/… #RNA #scRNA #Bioinformatics

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. github.com/Psy-Fer/butter…

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: wehi.edu.au/education/stud… #WEHIStudents #StudyInMelbourne #UniMelb

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

Igniting full-length isoform analysis in single-cell and spatial RNA-seq data with FLAMESv2 biorxiv.org/content/10.110… #biorxiv_bioinfo