Happy to be on the student/postdoc organizing committee for the 4DN Hackathon. Please check the website here: hack4dnucleome.github.io

1/6 🍍🍕🧬 What do a photo of Italians savoring pineapple pizza and a synthetic DNA sequence have in common? Both can be intricately crafted by generative AI! Introducing DNA-Diffusion, our AI model set to advance #SyntheticBiology and #GeneRegulation: biorxiv.org/content/10.110…

Pleased to share the conclusion of the first 4DN Hackathon! It was an incredible experience with a dedicated team consisting of Anupama Jha , Katie Gjoni , sean , Shu Zhang, and Akanksha Sachan.

I understand imitation is the sincerest form of flattery, but as junior faculty it is frustrating when Oxford Nanopore copies the figures of your work verbatim without any credit. youtube.com/watch?v=1NkBr3… Figure 1: biorxiv.org/content/10.110… Figure 4: biorxiv.org/content/10.110…

🌟 NEW! We are super excited to announce our collaboration with Tinkle Magazine to bring you an inspiring series of comics featuring brilliant women scientists from our institute! 👩‍🔬 The first comic features Dr. Deepti Trivedi, who heads the Drosophila facility at NCBS.

UW Genome Sciences Hackathon Leads to New Long-Read Sequencing Technology brotmanbaty.org/news/uw-genome…

Fibertools is published in Genome Research! Ultra-fast m6A calling for PacBio #Fiberseq. Seamless processing of any long-read epigenetic or genetic data. Wonderful collaboration (tinyurl.com/3t3zz29f) led by Mitchell R. Vollger Anupama Jha and Dr. Bohaczuk. genome.cshlp.org/content/early/…

Made it to ISMB 2024 in Montreal. Visa was dicey for a minute, but glad to be here! #ISMB2024

Are you attending #ISMB2024 in person or virtually? Come to my talk on Monday at 4:40 PM in the MLCSB COSI. I will discuss TwinC, our tool for predicting interchromosomal Hi-C contacts from DNA sequences.

Congratulations to Anupama Jha and Ran Zhang on receiving NHGRI K99 awards!

I've been looking forward to this release for a while: tangermeme v0.4.0 is out and asks "so... what did my model actually learn?" v0.4.0 moves past the individual components I've been building and shows how using them together can be very powerful. 1/ github.com/jmschrei/tange…

Our new paper HiCFoundation is online: biorxiv.org/content/10.110… HiCFoundation is a generalizable Hi-C foundation model for chromatin architecture, single-cell and multi-omics analysis across species.

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.

Our Archetypal Analysis Network (AAnet) methodology stars on Australian TV starting around 6:40! Based on our paper with Christine Chaffer applying the method to understanding heterogeneity in triple negative breast cancer. abc.net.au/news/2025-08-0…

Glad to share our latest publication in Nature Genetics Nature Genetics: Tracing the evolution of single-cell 3D genomes in Kras-driven cancers. In this work, we generated the first single-cell 3D genome atlases of any cancer using any technique.

💡 Cancer cells don’t just mutate—they reorganize their DNA in 3D space. Our new study shows how the genome’s folding pattern shifts as tumors progress, cell by cell 🧩🧬. It’s the first 3D genome atlas of cancer progression. Thread 👇

Agents for computational biology are advancing rapidly, but evals are lagging. Current benchmarks can be overly prescriptive. Full analysis vignettes are hard to verify. We introduce CompBioBench: 100 diverse, challenging, verifiable tasks + benchmark general-purpose agents. 1/9

Jha Lab at Yale Genetics is looking for postgraduate associates! If curious about AI/ML, gene regulation and 3G genome architecture, please apply! Postgraduate Associate-Jha Lab @ Yale Genetics, AI/ML, Gene Regulation Anupama Jha Yale University See the full job description

Please apply jhalab.org/join/