The radial positioning of genomic loci, i.e. how far they are from the nuclear lamina has been associated with genome structure and function for several decades. But in genomics everything is correlated, e.g. radial positioning with genomic compartments with gene activity etc

One of the X chromosomes in females is silenced with a microscopically distinct chromatin configuration. Happy to share our latest work on deciphering how the X chromosome folds during its inactivation for the first time in mouse female embryos! nature.com/articles/s4158…

I have a YouTube playlist for molecular biology for my undergrad interns in the lab. I might as well share it here. youtube.com/playlist?list=…

The Wild West of spike-in normalization go.nature.com/3XLUMw3

Genes2Genes is a Bayesian framework developed by @Teichlab for aligning single cell pseudotime trajectories at the per gene level. nature.com/articles/s4159…

📢 We are thrilled to announce our new manuscript out on BioRxiv: "Chromatin folding motifs define the basic grammar of TAD architecture in single alleles" 🔬🧬 Read the full paper on bioRxiv: 🔗 biorxiv.org/content/10.110… 🔗 Check out our key findings below! 👇

Congratulation Gabriel da Silva Pescador Danielson Baia Amaral @jmvarberg Ying Yan Hao and Laurence Florens Stowers Institute Stowers Grad School Protein profiling of zebrafish embryos unmasks regulatory layers during early embryogenesis: Cell Reports cell.com/cell-reports/f…

Okay, now successfully submitted to bioicons.com under CC0, with the name "singlecell_droplet_overloading" 😀

Published in 2009, bwa-aln is one of the oldest short-read aligners. It remains a popular choice for aligning ancient DNA reads. The following blog post explains the algorithmic reasons. lh3.github.io/2024/09/28/why…

Thrilled to report Patho-DBiT, just published in Cell 😊. It allows us to directly “see” all kinds of RNA species on the same clinical FFPE tissue slide, including mRNA, miRNA, snRNA, snoRNA, tRNA, etc, and splicing isoforms, genetic alterations (SNV, CNV, etc). Really a fun,

STAMP: Single-Cell Transcriptomics Analysis and Multimodal Profiling through Imaging | bioRxiv ⁦Dr. Jasmine Plummer 👩🏻‍🔬🧬🇨🇦🇺🇸⁩ ⁦Holger Heyn⁩ ⁦@pascual_reguant⁩ ⁦@eliseinsing⁩ ⁦CNAG⁩ ⁦Adelaide Centre for Epigenetics⁩ ⁦St. Jude Research⁩ biorxiv.org/content/10.110…

Semi-supervised Omics Factor Analysis (SOFA) disentangles known sources of variation from latent factors in multi-omics data | bioRxiv biorxiv.org/content/10.110…

A great collaboration with the ML team here at Genentech. Happy to see this pre-print out: biorxiv.org/content/10.110… (@lal_avantika gokcen Surag Nair and many others)

🚀 Thrilled to announce #inTRACKtive: a web-based tool for exploring massive cell-tracking datasets, no software installation required! Just open your browser and dive into terabytes of developmental biology data. We used it to build the virtual embryozoo.org of

Thrilled to share our paper published in nature, where we uncover a new process of tumor initiation through a polyclonal-to-monoclonal transition at the @precancerous stage. So proud of my fantastic team (led by Zhaolian Lu ) and incredible collaborators! nature.com/articles/s4158…

Glad to share the first results from the ongoing user survey on BioIcons. Really appreciate that it's used around the globe! You can read more about the results here: blog.bioicons.com/post/user_surv…

It's well known that the success of #AlphaFold comes from the Protein Data Bank (Protein Data Bank). But did you know that the PDB called for machine-readable data deposition since its inception in 1971? #Genomics ought to take note...

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

Pleased to share my thesis work developing MultiPerturb-seq (high-throughput CRISPR + ATAC + RNA screens) to explore cancer reprogramming therapies for the rare pediatric brain tumor AT/RT. See thread below! Excited to see where future applications may go!

I'm delighted to present our nationwide effort to identify genetic determinants of child health and development in Japan. medrxiv.org/cgi/content/sh…