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GENCODE: massively expanding the lncRNA catalog through capture long-read RNA sequencing | bioRxiv biorxiv.org/content/10.110…

Some thoughts and practical tips on how to develop better coding practices in academia in this paper—relevant well beyond bioinformatics. It even comes with a climbing analogy 🧗 Paper: academic.oup.com/bioinformatics…

Our new Nature Aging paper: We built 14 "biological clocks" representing the biological age and rate of aging of 14 major body systems using data from 13,000 people of the Human Phenotype Project Key findings: 1. Biological clocks are clinically meaningful: People with higher

New experiments in @SciSignal delineate how the enzyme Adssl1, which helps synthesize the metabolite inosine, supports the repair of heart tissue in mice and could be a potential therapeutic target after heart attack. bit.ly/4frG7Mv

Transcriptome-wide splicing network reveals specialized regulatory functions of the core spliceosome | Science science.org/doi/10.1126/sc…

Scalable test of statistical significance for protein-DNA binding changes with insertion and deletion of bases in the genome projecteuclid.org/journals/annal…

Benchmarking and building DNA binding affinity models using allele-specific and allele-agnostic transcription factor binding data genomebiology.biomedcentral.com/articles/10.11…

GEEES: Inferring Cell-specific Gene-#Enhancer Interactions from #Multimodal Single Cell Data doi.org/10.1093/bioinf…

Excited to share our latest preprint, as part of ENCODE4, on a consensus variant-to-function (cV2F) score for functionally prioritizing variants for complex disease - led by Tabassum Fabiha and co-mentored with Alkes Price. biorxiv.org/content/10.110…

We are thrilled to share that our first paper from my new lab, Spateo (github.com/aristoteleo/sp…) for spatiotemporal modeling of molecular holograms, is now online in Cell: cell.com/cell/fulltext/…. Spateo is a comprehensive analytical framework for 3D whole-embryo spatiotemporal

Check out our new work led by Ashton Omdahl discussing matrix factorization across GWAS, accounting for sample overlap. Factors with varying polygenicity, enrichment for cell type / developmental stage... Ashton is speaking at #biodata24 today! biorxiv.org/content/10.110…

The Evo model made the cover of Science this month. Perspective: Learning the language of DNA science.org/doi/10.1126/sc… Research paper: Sequence modeling and design from molecular to genome scale with Evo science.org/doi/10.1126/sc… Code (Apache) github.com/evo-design/evo

It is finally out! My first Science Magazine paper is online and it does not seem real😃. I am Incredibly happy! Really thanks to all my coauthors and special mention to my incredible supervisor Ivan Đikić for all the support and trust ! 🫶. Science science.org/doi/10.1126/sc…

check out our new preprint led by Yichao (Charles) Zhou and supervised by Mengjie Chen and me doi.org/10.1101/2024.1… where we present scPrediXcan which integrates deep learning and single cell expression data into a powerful cell type specific TWAS framework

Excited to share our study on spatio-temporal reconstruction of cardiac scar formation led by Andy Chan. We combine scRNA-seq with spatial transcriptomics to resolve the fibrotic niche and the niche of dedifferentiating cardiomyocytes. biorxiv.org/content/10.110…

Wow nature.com/articles/s4158…

It really does nothing of the sort. It’s so well researched and understood that in 2010 when it was published in that obscure science journal Nature, I commissioned a Lego version and made a film about it. youtu.be/RLPVCJjTNgk?si…

rdcu.be/d7rux Mapping the topography of spatial gene expression with interpretable deep learning

🚀 What do genomic Transformers actually learn about biology? •What knowledge do they hold at random init, after pre‑training, and following fine‑tuning? •We dove deep into every attention head to find out. 📄 Preprint live now “Interpreting Attention Mechanisms in Genomic

The human transcription factor occupancy landscape viewed using high-resolution in situ base-conversion strand-specific ... biorxiv.org/content/10.110… #biorxiv_genomic