bramble projects spliced genomic alignments into transcriptomic space. Any spliced genome alignments go in (tested with several, happy to add more if you find an incompatibility), a transcriptomic BAM comes out, salmon / oarfish / TranSigner carry on as normal. 📄 www.biorxiv.org/content/10.6...

Bramble: projection of spliced genomic alignments into transcriptomic space for improved transcript quantification

Accurate transcript abundance estimation is central to many transcriptomic studies. Many current quantification methods rely on reads mapped directly to the transcriptome, but transcriptome alignment ...

biorxiv.org

Very happy to share our pre-print co-led with Nathan Andrews where we reveal splicing and isoform changes in a single-cell CRISPRi screen. For example, GEMIN5 knockdown produced minimal gene expression changes yet extensively reshaped the isoform landscape.

Tuuli Lappalainen@tuuliel.bsky.social · 3mo ago

With my postdocs Nathan Andrews and @josiegleeson.bsky.social , we demonstrate the importance and analyze methods for isoform-level resolution in single cell-CRISPR perturbations. TL;DR: Long reads are the way. 3/3 www.biorxiv.org/content/10.6...

Congratulations to @tuuliel.bsky.social PhD, Senior Associate Faculty Member at the New York Genome Center, on receiving a prestigious award from the @eshg.bsky.social! Read more about this well-deserved recognition: www.nygenome.org/news-events/...

Tuuli Lappalainen, PhD Receives Prestigious European Society of Human Genetics Award - March 25, 2026

Read about Tuuli Lappalainen, PhD Receives Prestigious European Society of Human Genetics Award at the New York Genome Center on March 25, 2026

nygenome.org

If you're studying #RNA transcript isoforms, check out IsoVis (the Isoform Visualiser webserver). isomix.org/isovis/ Recent updates now also allow visualisation of: 1. RNA modification sites and levels 2. Peptides mapping to open reading frames in isoforms and their abundances. 🧪

Our call for 27 PULSE #postdocs is OPEN! PhD within the last 3 years looking to grow your life science career? SciLifeLab PULSE (MSCA Cofund) offers 3-year postdoc fellowships at Swedish universities with academic & industry secondments 🧪 🖥️ 🧬 📅 Apply Dec 15, 2025-Mar 16, 2026 👉 bit.ly/3MD7Pwz

We're hiring! My team at @nygenome.org is looking for a statistical genetics postdoc to decipher functional architecture of complex diseases from cutting-edge CRISPR+scRNA-seq data, with @nevillesanjana.bsky.social lab. Happy to meet at #ASHG25, apply here jobs.silkroad.com/NYGenome/Car...

Congratulations Ric and @michaelbclark.bsky.social!

Mike Clark@michaelbclark.bsky.social · last yr.

🧪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....

Great work Yupei!

Yupei You@youyupei.bsky.social · last yr.

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...

Very excited to see our latest paper published!

Mike Clark@michaelbclark.bsky.social · last yr.

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/...

New preprint! My (now former) postdoc @kvastad.bsky.social led this integration of GWAS and spatial transcriptomics (ST) data to identify tissue structures with enrichment of disease-implicated genes = likely causal drivers of disease biology. www.biorxiv.org/content/10.1...

Spatial transcriptomics and genetically implicated genes identify putative causal tissue structures for complex traits

Spatially resolved transcriptomics is transforming our understanding of cellular and molecular diversity of tissues. Here, to identify tissue structures that are enriched for putatively causal disease...

biorxiv.org