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Have you used spatial genomics to map cell types in your favorite tissue? Are you interested in finding patterns in your results? We’ve developed a method just for you. The first paper from our lab is now on bioRxiv! biorxiv.org/content/10.110…

Happy New Year! Our Twigstats paper is now out! nature.com/articles/s4158…

when i joined #twitter in 2013, i wrote in my profile “.. trying to find out if twitter can improve life”. 12 years later i am appalled by what it has become- murderous insults & hate everywhere, & given all the lies & fakes a disinformation machine of grotesque size & power.

The first preprint of 2025! Together with @khorms, Vanja (Ivan Kulakovskiy), & our amazing team, we are excited to share PARADE: an AI framework for designing mRNA UTRs with enhanced cell-type specificity & stability. biorxiv.org/content/10.110…

Impact of Segmentation Errors in Analysis of Spatial Transcriptomics Data. biorxiv.org/cgi/content/sh… #biorxiv_bioinfo

Although it still misses some essential points, it is a good preprint. Highly recommended for anyone who is analyzing ST data.

Introducing constellation mapped read technology. This new tech simplifies the NGS workflow with on-flow-cell library prep while unlocking long-range genomic insights from existing NovaSeq™ X systems. Enhanced mapping. Ultra-long phasing. Better SV detection.

Molecular and spatial analysis of tertiary lymphoid structures in Sjogren’s syndrome nature.com/articles/s4146… Nature Communications Francesca Barone

I have read few papers as immediately useful and important as this one on Cacio e Pepe phase behavior. Tl;dr: the starchy pasta water is absolutely critical to avoiding “mozzarella phase”

A preprint that is truly essential in our lab

Today, Illumina and @NVIDIA join forces to expand the availability of AI tools for multiomic analysis. This partnership paves the way for the next frontier of biological discovery, in which data and AI will play a crucial role. bit.ly/4jg5TG0 #JPM25

Microsoft researchers introduce MatterGen, a model that can discover new materials tailored to specific needs—like efficient solar cells or CO2 recycling—advancing progress beyond trial-and-error experiments. msft.it/6012U8zX8

mRNA2vec: mRNA Embedding with Language Model in the 5'UTR-CDS for mRNA Design arxiv.org/abs/2408.09048

Bye, Twitter.