Danilo Dubocanin

Genetics PhD Student in the Altemose Lab @Stanford

[Danilo Dubocanin @DubocDan]

I’m excited to share the first manuscript out of my PhD work with @NAltemose, in which we describe FiberFold: a deep learning tool that predicts cell-type-specific and haplotype-specific 3D genome organization from a single experiment!
https://t.co/FwJldYnCGe 1/

[Danilo Dubocanin @DubocDan]

Check out some of our most recent work!

[Stergachis Lab @stergachislab]

Mapping cancer somatic variants T2T. 16% of mutations occur in sequences missing from GRCh38. Satellites are UV-damage hotspots. Centromeres undergo extensive genetic and epigenetic remodeling. Somatic epimutations remodel cancer epigenomes. @SMaHTnetwork
https://t.co/vlkQKQnXNI

[bioRxiv Genomics @biorxiv_genomic]

A telomere-to-telomere map of somatic mutation burden and functional impact in cancer https://t.co/xNsV0RTdf5 #biorxiv_genomic

[Stergachis Lab @stergachislab]

Plasmid-based reporter assays are the bedrock of regulatory genomics. But a basic question has gone unanswered for decades: Do chromatin architectures form on plasmids transfected into mammalian cells—and does it matter? We finally have answers.
https://t.co/34hcyRPN0z

[The Dark Matter Project @DarkMatterDNA]

https://t.co/EG1veZPbv3

[Anders Sejr Hansen @Anders_S_Hansen]

(1/n) New preprint from @claricehongky Fan Fang @VarshiniRam23 in collab w Jie Liu

Q: How do we get ultra-high-res 3D genome maps?

A: New deep learning model, Cleopatra.

Cleo trains on Micro-C, fine-tunes on RCMC, and predicts genome-wide 3D maps
https://t.co/Wf7tppUk2p

[Betty Liu @bettieliu]

Delighted to share our latest work deciphering the landscape of chromatin accessibility and modeling the DNA sequence syntax rules underlying gene regulation during human development! https://t.co/zIUjPy6ZLz. Read on for more 🧵 [1/16]

[Danilo Dubocanin @DubocDan]

We would like to thank @stergachislab including @mrvollger for all of their contributions to this project, as well as @AnyaKalygina, @matt_franklin_, @CyChittenden, and the rest of the Altemose Lab. Thanks as well to @anshulkundaje for very helpful feedback. 17/17

[Danilo Dubocanin @DubocDan]

I’m excited to share the first manuscript out of my PhD work with @NAltemose, in which we describe FiberFold: a deep learning tool that predicts cell-type-specific and haplotype-specific 3D genome organization from a single experiment!
https://t.co/FwJldYnCGe 1/

[Danilo Dubocanin @DubocDan]

FiberFold represents a major advance in genomic analysis: haplotype-specific 3D genome prediction from a single, accessible assay. By bridging single-molecule epigenomics and 3D genome modeling, we've created a powerful tool for both basic research and clinical applications. 16/