NIH finally allocates funding for improving and maintaining software. - R03, budget $300k over 2 yrs - Due 12/4/24; 6/4/25 - RFA-OD-24-010 - Building Sustainable Software Tools for Open Science grants.nih.gov/grants/guide/r…

SVbyEye: A visual tool to characterize structural variation among whole genome assemblies biorxiv.org/content/10.110…

Two new chapters from my free online book in human genetics out this weekend! These complete Part 3 of the book, on human population structure and history: 3.3: Inferring human prehistory from genetic data [this thread] 3.4: Ancient DNA [next thread] web.stanford.edu/group/pritchar…

It’s disappointing to see Tsinghua acknowledging this list. First, it’s not officially announced or recognized by Stanford University, and second, it contains several flaws.

Fantastic initiative—crucial for building sustainable research software beyond bioinformatics! 🙌

Beautiful work, Zheng!! Congrats to you and team!! 👏

ecDNA are rogue genetic material that amplify genes, contribute to treatment resistance and drive genomic heterogeneity. We report on the Origins and impact of extrachromosomal DNA today in nature nature.com/articles/s4158…

Exploring public cancer gene expression signatures across bulk, single-cell and spatial transcriptomics data with signifinder Bioconductor package academic.oup.com/nargab/article…

Thrilled to share my latest project out in nature—fully open for $600, not $11,000! Interested in reproducing it? A bioinformatician and maybe some lumber available upon reasonable request. 😂

I’m super excited to share what I’ve been working on for the last (many) years: a spatial + genomic + transcriptomic characterization of how the breast cancer microenvironment evolves through immunotherapy! (1/x) biorxiv.org/content/10.110…

Gentle reminder that deceptive hyping in scientific publications is actually antithetical to the core mission of the scientific process. Revealing caveats, pitfalls & limitations speeds up progress. We can stay grounded, truthful, humble while being ambitious.

I shared my thoughts in a Nature Medicine comment on the urgent need for more standardized benchmarks in #AI for biomedicine. nature.com/articles/s4159…

How do you make sense of single cell multi-modal data beyond clustering? We need better methods that incorporate biological principles! Check out our latest method MIDAA, deep learning for single-cell multiomics with evolutionary principles: genomebiology.biomedcentral.com/articles/10.11…

Here is how NOT to respond when science is under existential threat

Excited to share some updates on lineage tracing from my lab: 1. A comprehensive evaluation on mtDNA lineage tracing by combining simulations and real data analysis doi.org/10.1186/s13059… 2. A novel phylodynamic inference framework for cell lineage trees doi.org/10.1016/j.cels…

What's heritable and what's plastic in cancer drug resistance? The two are linked! (Epi)genetic molecular memory is under Darwinian selection but encodes multiple plastic phenotypes. We found this with organoid experimental evolution + ML for multiomics. aacrjournals.org/cancerres/arti…

Enhancers, how do they work (in vivo)? To find out, we mutagenized 7 human enhancers comprehensively in 12bp blocks and scored for activity in developing mouse embryos. rdcu.be/erD22 nature #mutagenesis #noncoding #enhancers

Excited to share #AlphaGenome, a start of our AlphaGenome named journey to decipher the regulatory genome! The model matches or exceeds top-performing external models on 24 out of 26 variant evaluations, across a wide range of biological modalities.1/6

We’ll be hosting the Bioinformatics Summer Workshop from August 11–15. The workshop is completely free and held 100% online. If you are interested, please go ahead and register: sites.google.com/view/bioinfowo…