Rui Yang
@ruiyang.bsky.social
Postdoc in Computational Biology @Buenrostro Lab | 3D Genome & Epigenomics | PhD @Leslie Lab
Reposted by Rui Yang
Free in-person registration is open for #MLCB2025! Sept 10-11 at @nygenome.org and online at youtube.com/@mlcbconf. Paper/abstract deadline is June 1, more deets including our fantastic invited speaker lineup at mlcb.org! Please RP.
Machine Learning in Computational Biology
Youtube channel for the Machine Learning in Computational Biology conference: https://mlcb.github.io/
youtube.com
May 15, 2025 at 12:24 AM
Free in-person registration is open for #MLCB2025! Sept 10-11 at @nygenome.org and online at youtube.com/@mlcbconf. Paper/abstract deadline is June 1, more deets including our fantastic invited speaker lineup at mlcb.org! Please RP.
Reposted by Rui Yang
Our preprint on designing and editing cis-regulatory elements using Ledidi is out! Ledidi turns *any* ML model (or set of models) into a designer of edits to DNA sequences that induce desired characteristics.
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Programmatic design and editing of cis-regulatory elements
The development of modern genome editing tools has enabled researchers to make such edits with high precision but has left unsolved the problem of designing these edits. As a solution, we propose Ledi...
www.biorxiv.org
April 24, 2025 at 12:59 PM
Our preprint on designing and editing cis-regulatory elements using Ledidi is out! Ledidi turns *any* ML model (or set of models) into a designer of edits to DNA sequences that induce desired characteristics.
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Preprint: www.biorxiv.org/content/10.1...
GitHub: github.com/jmschrei/led...
Reposted by Rui Yang
Excited to share our newest preprint! Glad to see how this evolved from a serendipitous finding from a rotation project. Led by the brilliant graduate student
@ycz23.bsky.social
@ycz23.bsky.social
Excited to share our new work, “Inverse Flow and Consistency Models”! We tackle inverse generation problems—like denoising in scenarios where you only have noisy measurements and no access to clean data, which is often the case in biological data and beyond.
arxiv.org/abs/2502.11333
(1/9)
arxiv.org/abs/2502.11333
(1/9)
Inverse Flow and Consistency Models
Inverse generation problems, such as denoising without ground truth observations, is a critical challenge in many scientific inquiries and real-world applications. While recent advances in generative ...
arxiv.org
February 19, 2025 at 4:23 PM
Excited to share our newest preprint! Glad to see how this evolved from a serendipitous finding from a rotation project. Led by the brilliant graduate student
@ycz23.bsky.social
@ycz23.bsky.social
Reposted by Rui Yang
#MLCB2025 will be Sept 10-11 at @nygenome.org in NYC! Paper deadline June 1st & in-person registration will open in May. Please sign up for our mailing list groups.google.com/g/mlcb/ for future announcements. More details at mlcb.github.io. Please RP!
January 27, 2025 at 6:40 PM
#MLCB2025 will be Sept 10-11 at @nygenome.org in NYC! Paper deadline June 1st & in-person registration will open in May. Please sign up for our mailing list groups.google.com/g/mlcb/ for future announcements. More details at mlcb.github.io. Please RP!
Reposted by Rui Yang
Multiscale footprints reveal the organization of cis-regulatory elements
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Multiscale footprints reveal the organization of cis-regulatory elements - Nature
We developed PRINT, a computational method that identifies footprints of DNA–protein interactions from bulk and single-cell chromatin accessibility data across multiple scales of protein size.
www.nature.com
January 22, 2025 at 8:21 PM
Multiscale footprints reveal the organization of cis-regulatory elements
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Rui Yang
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
www.encodeproject.org/single-cell/...
Single cell – ENCODEHomo sapiens clickable body map
www.encodeproject.org
January 7, 2025 at 9:29 PM
Very excited to announce that the single cell/nuc. RNA/ATAC/multi-ome resource from ENCODE4 is now officially public. This includes raw data, processed data, annotations and pseudobulk products. Covers many human & mouse tissues. 1/
www.encodeproject.org/single-cell/...
www.encodeproject.org/single-cell/...
Reposted by Rui Yang
Happy to share "super admixture", a new framework for modeling the human population structure!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Coancestry superposed on admixed populations yields measures of relatedness at individual-level resolution
The admixture model is widely applied to estimate and interpret population structure among individuals. Here we consider a "standard admixture" model that assumes the admixed populations are unrelated...
www.biorxiv.org
January 6, 2025 at 3:29 PM
Happy to share "super admixture", a new framework for modeling the human population structure!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Rui Yang
www.nature.com/articles/s41...
(1/n) Ever wonder how transcription factors locate, "invade," and activate their enhancers during cell fate acquisition? 🧬🚀 Check out our latest collaborative work with the Soufi lab, now published in @Nature
(1/n) Ever wonder how transcription factors locate, "invade," and activate their enhancers during cell fate acquisition? 🧬🚀 Check out our latest collaborative work with the Soufi lab, now published in @Nature
Nucleosome fibre topology guides transcription factor binding to enhancers - Nature
Motif grammar on nucleosome fibres acts as signpost elements, directing TF combinatorial binding to enhancers.
www.nature.com
December 18, 2024 at 5:34 PM
www.nature.com/articles/s41...
(1/n) Ever wonder how transcription factors locate, "invade," and activate their enhancers during cell fate acquisition? 🧬🚀 Check out our latest collaborative work with the Soufi lab, now published in @Nature
(1/n) Ever wonder how transcription factors locate, "invade," and activate their enhancers during cell fate acquisition? 🧬🚀 Check out our latest collaborative work with the Soufi lab, now published in @Nature
Reposted by Rui Yang
www.nature.com/articles/s41...
Single-molecule states link transcription factor binding to gene expression
Deep insights into multiple facets of TF binding, accessibility & expression with biophysical models of single molecule data by Ben Doughty, Michaela Hinks, Bintu & Greenleaf labs
Single-molecule states link transcription factor binding to gene expression
Deep insights into multiple facets of TF binding, accessibility & expression with biophysical models of single molecule data by Ben Doughty, Michaela Hinks, Bintu & Greenleaf labs
Single-molecule states link transcription factor binding to gene expression - Nature
A study uses single-molecule footprinting to measure protein occupancy at regulatory elements on individual molecules in human cells and describes how different properties of transcription factor bind...
www.nature.com
November 21, 2024 at 4:15 PM
www.nature.com/articles/s41...
Single-molecule states link transcription factor binding to gene expression
Deep insights into multiple facets of TF binding, accessibility & expression with biophysical models of single molecule data by Ben Doughty, Michaela Hinks, Bintu & Greenleaf labs
Single-molecule states link transcription factor binding to gene expression
Deep insights into multiple facets of TF binding, accessibility & expression with biophysical models of single molecule data by Ben Doughty, Michaela Hinks, Bintu & Greenleaf labs
Reposted by Rui Yang
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
ChIP-DIP maps binding of hundreds of proteins to DNA simultaneously and identifies diverse gene regulatory elements - Nature Genetics
ChIP-DIP (ChIP done in parallel) is a highly multiplex assay for protein–DNA binding, scalable to hundreds of proteins including modified histones, chromatin regulators and transcription factors, offe...
www.nature.com
November 27, 2024 at 4:13 AM
Gene regulation involves thousands of proteins that bind DNA, yet comprehensively mapping these is challenging. Our paper in Nature Genetics describes ChIP-DIP, a method for genome-wide mapping of hundreds of DNA-protein interactions in a single experiment.
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Happy to share HiC2Self, a self-supervised tool for denoising bulk and single-cell Hi-C contact maps!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
HiC2Self: self-supervised denoising for bulk and single-cell Hi-C contact maps
Hi-C is a chromosome conformation capture assay used to study 3D genome organization. The recent development of single-cell Hi-C technologies has further enabled the examination of 3D chromatin organi...
www.biorxiv.org
November 26, 2024 at 12:39 PM
Happy to share HiC2Self, a self-supervised tool for denoising bulk and single-cell Hi-C contact maps!
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by Rui Yang
Here is a #compbio starter kit! go.bsky.app/QVPoZXp To all the #Bioinformatics #Genomics #MachineLearning folks: please RP and let’s build this together!
November 23, 2024 at 4:17 AM
Here is a #compbio starter kit! go.bsky.app/QVPoZXp To all the #Bioinformatics #Genomics #MachineLearning folks: please RP and let’s build this together!
Reposted by Rui Yang
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 at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
November 18, 2024 at 6:22 PM
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 at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.
If you are interested in doing a Ph.D. with me at UMass Chan Medical (Genomics and Comp Bio Department), see the links below. Deadline is Dec 1st.