Han Yuan
@HY3952
Computational biologist @Calico. Previously Ph.D in Leslie lab at @MSKCC. Study system biology and regulatory genomics.
1/ DNA sequence models like Borzoi predict gene expression and variant effects across 1000s of tissues — but what if your data comes from a custom experiment? @drklly @jjohlin and I propose a lightweight solution: parameter-efficient fine-tuning (PEFT). biorxiv.org/content/10.110…
check out our groups latest preprint using Borzoi to inform fine-mapping of GWAS variants!
I'm excited to share work on a research direction my team has been advancing: connecting machine learning derived genetic variant embeddings to downstream tasks in human genetics. This work was led by the amazing @divyanshi91! biorxiv.org/content/10.110…
Last week I shared tomtom-lite, a super fast re-implementation of Tomtom for annotating short genomic spans with the motifs they most resemble. Now, there's a convenient command line tool `ttl` that comes with the installation. You can get it with `pip instal memelite`
I wrote a quick application note on Tomtom-lite, a Python implementation of the Tomtom algorithm for comparing PWMs against each other. This implementation can be 10-1000x faster and, as a Python function, can be integrated into your workflows easier. biorxiv.org/content/10.110…
Checkout this lastest work from Anya et al. to improve variant effect prediction of DNA sequence model on indels and structural variants!
⚡️ Our latest preprint is on bioRxiv! Shift augmentation improves DNA convolutional neural network indel effect predictions biorxiv.org/content/10.110…
[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!
Borzoi paper is finally out! It takes DNA sequence as input, trains directly on RNA-seq profiles, and can be used to study gene regulation and variant effects on transcription, splicing as well as polyadenylation! Congrats to Johannes and the team!
The Borzoi manuscript is now out in Nature Genetics: doi.org/10.1038/s41588… Borzoi predicts RNA-seq profiles in many tissues & cell types from DNA sequence as its only input. With it, we can score the impact of genetic variants on a number of gene-regulatory functions. 1/
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…
#MLCB2024 kicks off in 22h (9am PST) with keynote from @zhou_jian on DL for transcriptional initiation! Full schedule at mlcb.github.io and public livestream at youtube.com/live/reqWvNOKl…. Please RT!
We’re opening a researcher position in my group for a machine learning-focused computational biologist! calicolabs.com/careers/?gh_ji…
Come join us!
We have a machine learning scientist opening in my group to tackle problems in gene regulation and single cell genomics! Apply here calicolabs.com/careers?gh_jid…
Check our new paper “Predicting RNA-seq coverage from DNA sequence as a unifying model of gene regulation”. biorxiv.org/content/10.110…
Delighted to share that our Epiphany model is now published in #GenomeBiology: genomebiology.biomedcentral.com/articles/10.11…. By using a customized set of epigenomic signals, we can accurately predict cell-type specific Hi-C contact maps. Dive into the details and explore the potentials of Epiphany!
Come join us!
Excited to highlight @Calico’s 2023 summer internship program, which my group will be participating in! If you’re interested in gaining experience with deep learning models in regulatory genomics, consider applying to join us here: calicolabs.com/careers?gh_jid…