A prestigious journal for omics and bioinformatics areas. 20 years of excellence since 2003.
Beijing
Joined January 2020
- Tweets1.4K
- Following2.7K
- Followers555
- Likes652
Genomics Proteomics Bioinformatics retweeted
Also, MACS3 paper is out, updating our 18yrs old reference paper after years of maintenance and development. Many thanks to the community for the continuous contributions and to CZI @cziscience EOSS program for the support. doi.org/10.1093/gpbjnl/qzag0… 2/2
Genomics Proteomics Bioinformatics retweeted
MACS 3.1.0 is released with a jaw-dropping 40-60x improvement in speed, thanks to @jmschreiber91's auto-optimize work! AI achieved in one weekend what I've been hoping for years! Now peak calling that once took minutes can be completed in seconds! github.com/macs3-project/MAC… 1/2
Genomics Proteomics Bioinformatics retweeted
Thrilled to share our new study in @Nature! 🎉
We uncover Lsp2 as a nutrient-responsive link between mTORC1, translation and lifespan in Drosophila.
Huge thanks to our wonderful collaborators Zongzhao Zhai and Jiongming Lu, and to everyone! (1/3)
Genomics Proteomics Bioinformatics retweeted
Our “Little Red Cat”, has finally been formally adopted by Nature Methods!
—UCSD's SRS metabolic imaging + Yale's spatial omics cell typing: one slide that nails identity, location, and metabolism, all while being extendable to transcriptomics, epigenomics, in live cells&tissues
Genomics Proteomics Bioinformatics retweeted
Very excited to see Spatial-ATAC-Hi-C published in @NatureMethods! Thanks to @yuefeng_1 for leading this effort. It jointly maps 3D genome organization and chromatin accessibility in tissues, revealing spatial epigenetic heterogeneity, CNV, and structural variations in tumor! 🥳
Excited to share Spatial-ATAC-Hi-C @naturemethods, spatial profiling of 3D genome organization + chromatin accessibility in tissue. Excitingly, it detects CNVs and SVs in tumors and reveals spatial heterogeneity.
Great collaboration with @RongFan8.
nature.com/articles/s41592-0…
Genomics Proteomics Bioinformatics retweeted
Raman Enhanced Delineation of Cell Atlases in Tissues (REDCAT) integrates stimulated Raman scattering microscopy and high-plex immunofluorescence to profile proteins, lipids, nuclear metabolites and redox metabolism in tissue.
nature.com/articles/s41592-0…
Genomics Proteomics Bioinformatics retweeted
Simultaneous single-cell profiling of chromatin, transcriptome and surface markers with OneCell CUT&Tag captures epigenomic reprogramming nature.com/articles/s41587-0…
Genomics Proteomics Bioinformatics retweeted
Today in @NatureBiotech we report OptiPrime, a mechanism-based machine learning model for predicting prime editing (PE) efficiencies and suggesting pegRNAs to achieve a user-specified edit. OptiPrime incorporates biochemical knowledge about PE into its mathematical structure, enabling training on ~300,000 PE efficiencies collected using 40 experimental conditions in multiple labs, and outcome predictions of PE variants such as twin prime editing not used in its training. OptiPrime enabled the rapid identification of efficient PE strategies across a variety of applications in vitro and in vivo, and could outperform months or years of manual experimental optimization.
Try out OptiPrime here: optipri.me
PDF: drive.google.com/file/d/13JZ…
1/15
Genomics Proteomics Bioinformatics retweeted
Virtual cells cannot be built on RNA alone.
A new Nature Methods Perspective maps how AI is transforming proteomics—from peptide identification and protein quantification to spatial and perturbation proteomics, multi-omics integration, and ultimately AI virtual cells.
Proteins execute cellular function. Without measuring their abundance, interactions, modifications and spatial organization, virtual cells remain incomplete.
nature.com/articles/s41592-0…
🤖 Made with AI
Genomics Proteomics Bioinformatics retweeted
🚀 DeepSeek-V4-Flash Official API is now LIVE in public beta!
🔷 We’ve massively upgraded its Agent capabilities—benchmark scores are now far surpassing the V4-Pro-Preview. Check out the massive performance leap below! 👇
🔷 The official V4-Flash now natively supports the Responses API format and is fully adapted for Codex!
Check out the configuration details in our official API docs: api-docs.deepseek.com/quick_…
Genomics Proteomics Bioinformatics retweeted
Nature research paper: AI-redesigned starting points and outcomes enhance protein evolution
go.nature.com/4wiD95H
Genomics Proteomics Bioinformatics retweeted
Coupling AI-guided binder design with GRAPE, our platform for in planta directed evolution published in @ScienceMagazine last year, we further enhance immune activation — yielding receptors that are specific, stackable, and confer superior resistance.
science.org/doi/10.1126/scie…
Genomics Proteomics Bioinformatics retweeted
Huge congratulations to PKU alumni Wang Hong and Deng Yu, recipients of the 2026 Fields Medal — mathematics’ highest honor! 🧮
Announced at the 2026 International Congress of Mathematicians (ICM) in Philadelphia, the pair are among four mathematicians worldwide to claim this prestigious prize, awarded every four years to outstanding scholars under 40.
The awards are historic on several levels.
—First time two mathematicians who completed undergraduate studies in mainland China win the Fields Medal in the same year.
—Both joined Peking University as undergraduates in 2007.
—Wang Hong becomes only the third female Fields Medalist ever, the first Chinese woman, and the first recipient with a bachelor’s degree from a mainland Chinese university.
We are immensely proud of their extraordinary breakthroughs and lasting contributions to global mathematics.
Genomics Proteomics Bioinformatics retweeted
Glad to see this joint work on nasopharyngeal microbiota culturomics officially published in @ScienceTM, featured as a cover story! By building this local bacterial catalog, we characterized a Fusobacterium-Prevotella mutualism in nasopharyngeal tumors.
science.org/doi/10.1126/scit…
Genomics Proteomics Bioinformatics retweeted
Excited to see our new paper out in @naturemethods. Spatio-DARLIN enables robust and efficient in situ lineage tracing in mice at single-cell resolution (nature.com/articles/s41592-0…). Big shoutout to my talented trainee @GauJarning, Zhanhao Zhang, and amazing collaborator @ShouwenW.
Genomics Proteomics Bioinformatics retweeted
Want to do spatial lineage tracing at single-cell resolution in mice at your favorite tissues? In a close collaboration with @Li_Li_666, we developed Spatio-DARLIN, now out at @naturemethods. rdcu.be/fq0WQ
Genomics Proteomics Bioinformatics retweeted
HiCFoundation: a foundation model trained on Hi-C data for comprehensive 3D genome and epigenomics analysis.
nature.com/articles/s41592-0…
Genomics Proteomics Bioinformatics retweeted
OrthoFinder v3: a tool for phylogenetic orthology inference with boosted accuracy and scalability for massive datasets. @Steve__Kelly @dr_belcher @David__Emms
nature.com/articles/s41592-0…
Genomics Proteomics Bioinformatics retweeted
Excited to share our paper now published in GigaScience: “4D single-cell spatial transcriptomics reveals dynamic morphogenetic gradients and regenerative domains in planarians” We study how planarians rebuild body structure after injury. academic.oup.com/gigascience…
Genomics Proteomics Bioinformatics retweeted
Nature research paper: Whole-genome duplication shaped cell-type evolution in the vertebrate brain
go.nature.com/4uwfDAB
