Rui Yang

Thrilled to announce our paper in @Nature introducing MUSIC! For the first time, MUSIC enables simultaneous mapping of multiplexed chromatin interactions, RNA-chromatin interactions, RNA-RNA interactions & gene transcription at single-cell resolution. doi.org/10.1038/s41586…

Comp bio postdoc positions available! Come work with us @Princeton on computational method development and applications in regulatory genomics, genome editing, immunology and cancer, in mouse and human: pritykinlab.github.io/#jobs Please share among all those who may be interested!

Tokenization has been the final barrier to truly end-to-end language models. We developed the H-Net: a hierarchical network that replaces tokenization with a dynamic chunking process directly inside the model, automatically discovering and operating over meaningful units of data

Our preprint on designing and editing cis-regulatory elements using Ledidi is out! Ledidi turns *any* ML model (or set of models) into edit designers! Now, you can easily find minimal sets of edits to DNA sequences that induce desired characteristics.

I’m excited to share my work over the last few years with @JD_Buenrostro! Chronic inflammation creates an epigenetic memory in colonic stem cells, priming them for tumor growth: tinyurl.com/ColitisNagaraj…. Here’s a walkthrough of what we found (🧵)

[SAVE THE DATE] MLCB 2025 is happening Sep 10-11 at the NY Genome Center—NYC! Attend the premier conference at the intersection of ML & Bio, share your research and make lasting connections! Submission deadline: Jun 1 Details: mlcb.github.io Spread the word—please RT!

Super excited to share our new study from the @JD_Buenrostro Lab in @Nature! We developed a computational method for tracking transcription factor and nucleosome binding using single-cell ATAC-seq and deep learning. Paper: nature.com/articles/s4158…

Our work just got accepted at AISTATS'25 🦾. In this work, we present an algorithm that estimates the eigenvalues (more precisely, the spectral moments) of a large matrix from its random submatrix: arxiv.org/pdf/2410.17998.

Incredibly excited that our paper linking single molecule states of TF binding to gene expression using quantitative thermodynamic models is out in Nature today. An amazing collaboration with the Bintu Lab. Congrats to Ben, Michaela, and Julia! nature.com/articles/s4158…

My goal is to understand the regulatory role of every nucleotide in the genome, and how this changes across every cell in the human body. If you are interested in doing a Ph.D. with me @UMassGCB, see the links below. Deadline is Dec 1st.

Out in @NatureComms ! ChromaFold predicts 3D contact maps using single-cell ATAC-seq alone. nature.com/articles/s4146…

Hi all, I am currently on the academic job market. I am a postdoctoral researcher in Dr. Christina Leslie's lab at the Computational and Systems Biology Program at Memorial Sloan Kettering Cancer Center. My research focuses on deciphering causal and dynamic gene regulation…

Excited to share new work on “Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion.” We extend Score Entropy Discrete Diffusion to regulatory DNA! Work led by @ani_itsme. paper: biorxiv.org/cgi/content/sh…

Happy to share the final version of our #GAGEseq published today @NatureGenet! The single-cell co-assay for #scHiC and #scRNA reveals 3D genome & gene expression interplay in mouse cortex (also integration w/ #MERFISH) and during human hematopoiesis. 1/3 nature.com/articles/s4158…

By learning to embed DNA k-mers and cells into a joint space, CellSpace improves single-cell ATAC-seq analysis in multiple tasks such as latent structure discovery, transcription factor activity inference, and batch effect mitigation. nature.com/articles/s4159…