Adam He retweetet
Monthly median Received to Accepted time (days) at Nature Genetics
English
Adam He
214 posts
Adam He
@missing_a_rib
Machine learning, RNA transcription, genomics, statistical genetics. Postdoc @ Stanford Genetics
Palo Alto, CA Beigetreten Temmuz 2013
529 Folgt172 Follower
Adam He retweetet
🧩 Just out in Bioinformatics Advances: "Deciphering cis-regulatory elements using REgulamentary"
Read the full paper here: doi.org/10.1093/bioadv…
English
Adam He retweetet
@missing_a_rib Wait didn't I tell you. No more CNS for you in return for pay raise.
English
@anshulkundaje Will we be able to afford such excess after paying for all the fancy PDF branding?
English
@anshulkundaje @aedwards02 @jmschreiber91 @garrytan Also they use Malinois to generate MPRA activity predictions for their designed CREs. The paper describing Malinois is literally titled "Machine-guided design of cell-type-targeting cis-regulatory elements" 🤦nature.com/articles/s4158…
English
@aedwards02 @jmschreiber91 @garrytan This is a much harder and realistic problem than designing enhancers for extremely different random cell lines.
English
Jacob is being very kind here.
@garrytan (who has blocked me) & YC seem to be astonishingly uncalibrated & unaware to be funding startups like these. It's just embarrassing at this point.
Jacob Schreiber@jmschreiber91
@garrytan It's always nice to see more people in this space, but "barely touched territory" seems exaggerated. To design these enhancers, they use a model from a paper that also does AI-based enhancer design! And they provided wetlab validation of their sequences.
English
Adam He retweetet
New OpenFold3 preview out! (OF3p2)
It closes the gap to AlphaFold3 for most modalities.
Most critically, we're releasing everything, including training sets & configs, making OF3p2 the only current AF3-based model that is functionally trainable & reproducible from scratch🧵1/9
English
Adam He retweetet
Thrilled to announce alphagenome-pytorch, an accurate, readable, and careful port of AlphaGenome's architecture and weights to PyTorch. Work with @gtcaa @m_kjellberg @chriswzou @tuxinming as part of the GenomicsxAI initiative between @anshulkundaje and @pkoo562 labs.
English
Adam He retweetet
The Programmable Genomics Lab at @UMassGCB
just officially launched our site!
We have a "simple" goal: to develop synthetic regulatory elements that target every cell type in every tissue, and control payload dosage/duration
Check it out!
programmable-genomics.github.io
English
Adam He retweetet
GPU-accelerated single-cell analysis at scale with rapids-singlecell arxiv.org/abs/2603.02402
English
Adam He retweetet
1/n New preprint! varTFBridge combines statistical association and fine-mapping with functional predictive models (VAR2TFBS, ABC-FP-Max, AlphaGenome) to trace common AND rare noncoding variants to the TFs and genes they affect. (1/) 📄 biorxiv.org/content/10.648…
English
Adam He retweetet
There are SO MANY dead scientific repos out there because basic research funders never figured out a model that could pay for support
They can all just work again now
Greg Medlock@MedlockGreg
My favorite one-shot Claude Code process for scientific computing is quickly becoming: “clone this repo that hasn’t been touched in 5 years, update to run with uv, update to a modern Python and package version, verify versioning works by comparing output” Works in one-shot for 99% of analysis projects that are small enough to run locally. Nirvana.
English
Adam He retweetet
Just posted a preprint on a huge new single-cell study of Parkinson’s and its application to understanding noncoding variation. 🧵below. Led by Shreya Menon and Adam Turner and in collab w/ GP2 (@ASAP_Research), @BelloyMichael, @ZihHuaFang and others. doi.org/10.64898/2026.…
English
Adam He retweetet
Rewiring of 3D Enhancer-Promoter Interactome Underlies Diabetic Endothelial Dysfunction biorxiv.org/content/10.648… #biorxiv_genomic
English
Adam He retweetet
〈プレスリリース〉DNA言語に対する生成AI基盤モデルを開発 オーソログ進化パターンに基づく遺伝子配列再設計で異種生物での高発現を可能に～バクテリアのプラスチック分解能力を最大約10倍向上～
jst.go.jp/pr/announce/20…
導入先の生物に適したDNA配列を生成する深層学習モデルを開発しました。
#JST
日本語
Adam He retweetet
PerturBERT: Learning Gene Co-Variation Embeddings from Perturbation Signatures openreview.net/forum?id=ZsDeY…
English
Adam He retweetet
Happy 30th birthday, Pokémon! Since 1996, the Japanese media sensation has inspired generations of researchers in fields as diverse as evolution, biodiversity and research integrity. go.nature.com/4tZOzKY
English
Adam He retweetet
We’ve been working with AlphaGenome for a while — today we’re sharing two updates:
• alphagenome-ft: a lightweight structured fine-tuning wrapper
• MPRA fine-tuning results with SOTA performance
Adapting AlphaGenome's JAX/Haiku stack to new assays isn’t trivial. 1/8
English
Adam He retweetet
Excited to share new finetuning scripts for AlphaGenome in JAX! This was in collaboration with @anshulkundaje group.
As part of the initial release, we provide lightweight wrapper to finetune AlphaGenome on functional genomics (i.e. bigwig) tracks.
English