LongTREC

A microscopic image of Volvox, a spherical green colonial alga composed of many small cells arranged in a hollow globe, glowing against a dark background. “Beyond Humans: The Eukaryotic Frontier”

A collage grid showing diverse eukaryotic life — including fungi, a seahorse, insects, deer, protists, bees, trees, birds, mammals, plants, and marine invertebrates — representing the breadth of species across Earth. “A moonshot for LIFE on Earth: deliver reference genomes for all known eukaryotic species — 1.8 million — in the next decade.”

A stylized image of Earth encircled by a glowing DNA double helix, surrounded by animals, plants, fungi, and marine life, symbolizing the genetic unity and diversity of life on the planet. “What secrets are hidden in the DNA of life on Earth?” image generated by AI

Beyond humans lies the eukaryotic frontier. 🧬🌍
Sequencing the human genome showed us how powerful a single reference can be.
Now the challenge is scaling that insight across all eukaryotic life — plants, animals, fungi, and the vast unknown diversity of the Tree of Life.

A Visual Guide to DNA Sequencing.

Learn how different DNA sequencing technologies work, from Sanger sequencing to Illumina to nanopores. (Complete with illustrations!)

Written by Evan DeTurk. Illustrated by Ella Watkins-Dulaney.

#VALT symposium website is active again! Do you want to know who's coming? 👉 longtrec.eu/valt/
📨Accepting abstracts for oral and poster presentation!

Accurate strand-specific long-read transcript isoform discovery and quantification at bulk, single-cell, and single-nucleus resolution https://www.biorxiv.org/content/10.64898/2026.02.12.705617v1

On International Day of Women and Girls in Science, we celebrate the brilliant women across LongTREC — from PhD researchers to supervisors, project managers, counsellors, trainers and partners. Your work drives our science forward every day. #WomenInScience #LongTREC #STEM

LongPolyASE: An end-to-end framework for allele-specific gene and isoform analysis in polyploids using long-read RNA-seq https://www.biorxiv.org/content/10.64898/2026.02.03.703480v1

We can't wait to see you in Valencia this summer at VALT! Check out our exciting Line up of speakers below. Interested in sharing your work on #LongReadTranscriptomics ? Abstract submission deadline 📅 March 31st.
#LongTREC #LongReadSequencing #Nanopore #Pacbio

Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM - Nature Biotechnology Differential isoform usage is identified with high statistical power from spatial transcriptomics data.

Mapping isoforms and regulatory mechanisms from spatial transcriptomics data with SPLISOSM - @columbiasysbio.bsky.social @davidaknowles.bsky.social go.nature.com/3NaXw31

We can't wait to see you in Valencia this summer at VALT! Abstract submission deadline 📅 March 31st.
#LongReadsTranscriptomics

The registration to the #VALT symposium is open! longtrec.eu/valt/ Sign up to receive updates!

Abstract submission deadline 📅 March 31st.

We can't wait to see you in Valencia this summer for the most exciting Long Read Transcriptomics conference this year.

Transcriptomics in the era of long-read sequencing Nature Reviews Genetics - Advances in long-read sequencing are driving the implementation of these technologies for transcriptome profiling. The authors provide a comprehensive guide to long-read...

Transcriptomics in the era of long-read sequencing
#Review by @carolinamonzo.bsky.social, Tianyuan Liu & @anaconesa.bsky.social @conesalab.bsky.social @csic.es
Free to read here: rdcu.be/efBjP

To join or not to join: handling biological replicates in long-read RNA sequencing data Long-read RNA sequencing (lrRNA-seq) has revolutionized transcriptomics facilitating the study of alternative splicing and resulting in identification of thousands of novel transcripts. While isoform ...

New preprint on #LongReadTranscriptomics from @fabianjetzinger.bsky.social #LongTREC. How you combine replicates in long-read experiments matters more than you think — it shapes detection of both known and novel transcripts! A must read for Long read RNA-seq users!
www.biorxiv.org/content/10.6...

📣 Yesterday our study uncovering the ancestry bias in gene annotations was finally published in @natcomms.nature.com!
www.nature.com/articles/s41...

If you work in human genetics or transcriptomics, do not miss our tweetorial!👇

@guigolab.bsky.social @bsc-cns.bsky.social @crg.eu

This is a very exciting opportunity to connect researchers working on RNA data analysis issues. I can´t wait to see this community growing!!! @bcbhubcsic.bsky.social @i2sysbio.es @hitseq.bsky.social @conesalab.bsky.social

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

The #LongTREC consortium is well represented at #BioHackathon Europe in Berlin! Advancing open-source tools to accelerate innovation — perfectly aligned with our own goals more specifically in #LongReadTranscriptomics. Congratulations to all who took part! @anaconesa.bsky.social

We’re thrilled to announce the first symposium dedicated to #LongReadsTranscriptomics, taking place in Valencia, Spain!

More information available at: 👉 longtrec.eu/VALT/

Meet the #LongReadsTranscriptomics community, connect with experts, and explore the latest advances in this research area.

The Most Efficient Traveler Isn’t a Bird or a Fish—It’s You on a Bike A famous graphic, now updated, compares locomotion in the animal kingdom

A famous graphic, now updated, compares locomotion in the animal kingdom

Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods Nature Reviews Molecular Cell Biology, Published online: 06 October 2025; doi:10.1038/s41580-025-00895-4Co-transcriptional mRNA maturation is a complex, multistep process. This Review focuses on how the development of long-read sequencing methods enabled investigating the timing, coordination and outcomes of alternative uses of transcription start sites, splice sites and polyadenylation sites and their disease implications.

ICYMI: New Online! Elucidating the coordination of RNA processing using short-read and long-read RNA-sequencing methods

Long-read sequencing reveals the RNA isoform repertoire of neuropsychiatric risk genes in human brain - Genome Biology Background Neuropsychiatric disorders are highly complex conditions and the risk of developing a disorder has been tied to hundreds of genomic variants that alter the expression and/or RNA isoforms made by risk genes. However, how these genes contribute to disease risk and onset through altered expression and RNA splicing is not well understood. Results Combining our new bioinformatic pipeline IsoLamp with nanopore long-read amplicon sequencing, we deeply profile the RNA isoform repertoire of 31 high-confidence neuropsychiatric disorder risk genes in Human brain. We show most risk genes are more complex than previously reported, identifying 363 novel isoforms and 28 novel exons, including isoforms which alter protein domains, and genes such as ATG13 and GATAD2A where most expression was from previously undiscovered isoforms. The greatest isoform diversity is detected in the schizophrenia risk gene ITIH4. Mass spectrometry of brain protein isolates confirms translation of a novel exon skipping event in ITIH4, suggesting a new regulatory mechanism for this gene in the brain. Conclusions Our results emphasize the widespread presence of previously undetected RNA and protein isoforms in the human brain and provide an effective approach to address this knowledge gap. Uncovering the isoform repertoire of candidate neuropsychiatric risk genes will underpin future analyses of the functional impact these isoforms have on neuropsychiatric disorders, enabling the translation of genomic findings into a pathophysiological understanding of disease.

🧪Happy to share our latest paper in Genome Biology.

We profiled #RNA isoforms from 31 neuropsychiatric risk genes in the human brain using long-read sequencing. Unannotated isoforms commonly made up a significant proportion of a gene's expression.

genomebiology.biomedcentral.com/articles/10....

Detecting Foldback Artifacts in Long-reads. #LongReads #ReadsArtifacts #QC #Bioinformatics #Genomics @biorxivpreprint.bsky.social 🧬 🖥️
www.biorxiv.org/content/10.1...

Advances in haplotype phasing and genotype imputation Nature Reviews Genetics, Published online: 24 September 2025; doi:10.1038/s41576-025-00895-2Haplotype phasing and genotype imputation improve genomic analyses by determining which variants occur together on a chromosome and inferring unobserved varants, respectively. In this Review, Sun and Li describe how tools for haplotype phasing and genotype imputation have evolved to accommodate increasingly larger genomic datasets and new sequencing technologies.

New online! Advances in haplotype phasing and genotype imputation

Benchmarking long-read RNA-sequencing technologies with LongBench: a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches Long-read RNA sequencing enables full-length transcript profiling and improved isoform resolution, but variable platforms and evolving chemistries demand careful benchmarking for reliable application....

Excited to share our latest preprint: LongBench—a cross-platform reference dataset profiling cancer cell lines with bulk and single-cell approaches.
www.biorxiv.org/content/10.1...

A spatial long-read approach at near-single-cell resolution reveals developmental regulation of splicing and polyadenylation sites in distinct cortical layers and cell types. #LongReads #SingleCell #Spatialtranscriptomics #IsoSeq #PolyA @natcomms.nature.com
www.nature.com/articles/s41...

Isoform-level profiling of m6A epitranscriptomic signatures in human brain Direct RNA-seq in brain reveals RNA isoform and region-specific m6A modifications, highlighting their role in gene regulation.

Our paper using Oxford #Nanopore direct RNA sequencing to identify m6A modifications on RNA isoforms in human brain is now out in Science Advances. 🧪
www.science.org/doi/10.1126/...

The July blog-post of the @conesalab.bsky.social is out! Intense activities right before the break: visits, conferences, @longtrec.bsky.social summer school, and biking for sustainable science @i2sysbio.es @hitseq.bsky.social @bcbhubcsic.bsky.social @iscb.bsky.social
conesalab.uv.es/july-from-va...

One week on, and we're still processing an amazing week at #ISMBECCB2025. We have learned so much and have been inspired by others to have some great ideas. One thing is undeniable - the future of computational biology is very bright!

🚀 Our new preprint is now live on bioRxiv!
“A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long-read data”
🔗 Read here: www.biorxiv.org/content/10.1...

🔬 About the study
We present the first comprehensive benchmark of bioinformatics tools 👇

A systematic benchmark of bioinformatics methods for single-cell and spatial RNA-seq Nanopore long-read data https://www.biorxiv.org/content/10.1101/2025.07.21.665920v1

Dont miss your second chance to catch all our #LongTREC posters on day 4 of #ISMBECCB2025 ! Also, dont miss an exciting talk by
@tianyuanliu.bsky.social - "Transcriptome Universal Single-isoform Control (TUSCO) A framework for evaluating transcriptome quality." 15:40–15:50 Track iRNA · Room 02N