Day 1 of our #SummerSchool : @carolinamonzo.bsky.social , Satrio Wibowo, Mahmud Sami Aydin and @tianyuanliu.bsky.social introducing participants to #LongReads sequencing technologies, how to design #lrRNAseq experiments, library preparation strategies for #lrRNAseq, mapping, QC and more!

And we are not alone!!! Our project on LrRNASeq benchmarking gathered an amazing team of hackers here in Berlin and in Australia!! @conesalab.bsky.social @bcbhubcsic.bsky.social

🎉 New paper from our lab in Nature Comms!
We compare 2 strategies—Join & Call vs Call & Join—across PacBio and ONT data, tissues, and 6 lrRNAseq transcript reconstruction tools. Take away:
👉Join & Call 4 novel isoforms
👉Call & Join 4 2 obtain highly replicated signals.
www.nature.com/articles/s41...

Next at #VALT2026: Juan Francisco Cervilla on evaluating gene fusion expression in B-ALL at single-cell resolution, using long reads to resolve fusion transcripts cell by cell. #LongTREC #lrRNAseq #FusionGenes

The brilliant Angela Brooks kicks off our keynotes at #VALT2026: multi-omic long-read sequencing and the contribution of chromatin to RNA transcription and processing. Tying chromatin state to isoform regulation at single-molecule resolution. #LongTREC #lrRNAseq

Now at #VALT2026: the Oxford Nanopore workshop. Aino Järvelin kicks off, then Jonathan Göke on the cDNA beta test and library prep for long-read RNA-seq, and Christoph Dieterich on RNA modification co-occurrence from direct RNA-seq. #LongTReC #lrRNAseq

To join, or not to join? 🎭

That's the question Fabian Jetzinger is putting to us next, on handling biological replicates in lrRNA-seq data.

#VALT2026 #LongReads #lrRNAseq #CallOrJoin

⚡ Flash talks at #VALT2026 ⚡: four quickfire takes on building and annotating transcriptomes with long reads: transcript-end detection in FLAIR4, the non-coding transcriptome, structural gene prediction, and tissue-specific isoform atlases. #LongTREC #lrRNAseq

Next at #VALT2026: Anastasiya Grinko on expanding the known transcriptome at the single-cell level, using long reads to surface novel isoforms in macrophages and monocytes from diseased tissues. #LongTREC #lrRNAseq #SingleCellLongRead

Next at #VALT2026: Maximillian Gabriel Marin on personalized transcriptome annotation, exposing reference-biased isoforms and how structural variation shapes human transcript diversity. #LongTREC #lrRNAseq

ext at #VALT2026: Fairlie Reese on long-read transcriptomics across a genetically diverse human cohort, revealing ancestry bias in gene annotation. Non-European transcripts are underrepresented in current references. #LongTREC #lrRNAseq

Next at #VALT2026: Mahmud Sami Aydin on de novo transcript construction and isoform clustering from gene clusters. Reference-free assembly of paralogous regions, where reference-guided methods tend to struggle. #LongTREC #lrRNAseq #DeNovoTranscriptReconstruction

Next at #VALT2026: Pablo Angulo on long-read sequencing, uncovering transcriptional allele-specific dosage compensation in aneuploidy. Phasing expression to its allele of origin to see how cells buffer altered chromosome dosage. #LongTREC #lrRNAseq #Aneuploidy #AlleleSpecificExspression

Continuing the epigenome theme at #VALT2026: Tianyuan Liu on SQANTI-Epi, integrating Fiber-seq with long-read RNA-seq to link chromatin state to isoform regulation.
#LongTREC #VALT2026 #lrRNAseq #transcriptomics