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.

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...

Comparing chromatin contact maps at scale: methods and insights www.nature.com/articles/s41...

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

#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!

Multiscale footprints reveal the organization of cis-regulatory elements www.nature.com/articles/s41...

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/...

Happy to share "super admixture", a new framework for modeling the human population structure! www.biorxiv.org/content/10.1...

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

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

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...

Happy to share HiC2Self, a self-supervised tool for denoising bulk and single-cell Hi-C contact maps! www.biorxiv.org/content/10.1...

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!

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.