Jingjing Zhai

Postdoc in Cornell University

[Anshul Kundaje @anshulkundaje]

Just want to give a shout-out to David Kelley @drklly who I think often does not get the credit he deserves (outside our core community).

I want to highlight why I think he is such a fantastic scientist and leader in regulatory genomics. 1/

[bioRxiv Bioinfo @biorxiv_bioinfo]

PlantCAD2: A Long-Context DNA Language Model for Cross-Species Functional Annotation in Angiosperms https://t.co/neiv4U4Jnb #biorxiv_bioinfo

[Jingjing Zhai @jingjing19941]

@szintri Thank you James!

[Alex Rives @alexrives]

Introducing ESM Cambrian.

Unsupervised learning can invert biology at scale to reveal the hidden structure of the natural world.

We’ve scaled up compute and data to train a new generation of protein language models. ESM C defines a new state of the art for protein representation learning.

[Ed Buckler @EdBuckler]

What’s remarkable about PlantCaduceus is its ability to be fine-tuned in Arabidopsis and still retain accuracy in distant species like major grass crops, such as corn. 🌱→ 🌽🌾

This class of models are a game changer for plant genomics! https://t.co/jKRzFRBvQZ

[Ed Buckler @EdBuckler]

Over two decades ago, we mapped the variant making sweet corn sweet—after tremendous effort. PlantCaduceus easily identifies this single base pair causal variant. 🌽

Give it a try—this model paves the way for treating all plants as a single molecular system!

[Ed Buckler @EdBuckler]

PlantCaduceus - Cross-species modeling of plant genomes
Led by Jingjing Zhai and Aaron Gokaslan, with the Kuleshov lab, we’re having our “ChatGPT moment” with DNA Large Models. PlantCaduceus predicts functional DNA sequences with single base resolution across flowering plants.

[Pushmeet Kohli @pushmeet]

We love the excitement & results from the community on AlphaFold 3 and are doubling the AF Server daily job limit to 20. Happy to also share that we're working on releasing the AF3 model (incl weights) for academic use, which doesn’t depend on our research infra, within 6 months.

[Anshul Kundaje @anshulkundaje]

To all budding compbio & ML folks interested in bio: Don't just only run behind the latest ML model hype train. The greatest long run impact will come by really assimilating prior bio/compbio literature with the goal of really understanding strategies for how to model biology. 1/

[Bob Schmitz @Schmitz_Lab]

Great work @Pabster212! Investigating the cis-Regulatory Basis of C3 and C4 Photosynthesis in Grasses at Single-Cell Resolution https://t.co/4YABwHGi0g

[Fei Lu (鲁非) @fei_genetics]

It is time to do wheat population genomics using long reads :)

[bioRxiv @biorxivpreprint]

bioRxiv has launched a pilot to provide AI-generated summaries for all preprints thanks to @Science_Cast. We hope this will increase a preprint’s reach.
Feedback welcome below.
Full announcement: https://t.co/ZDDOnjRZk2

[Andrew Carroll @acarroll_ATG]

Initial release of DeepSomatic, which identifies subclonal variants when given tumor and normal BAM files. Pre-trained models and case studies available for Illumina and PacBio. Development led by @kishwarshafin which built off a framework by @pichuan

https://t.co/YpB46RlhiB

[Ming "Tommy" Tang @tangming2005]

Copilot in Rstudio https://t.co/3TdvPhNogC

[Zuguang Gu | 顾祖光 @jokergoo_gu]

New blog post: simplified simplifyEnrichment plot

https://t.co/hke1VkzqZX

[Ed Buckler @EdBuckler]

New whole-genome alignment tools are needed for tapping into plant div... https://t.co/GaSusQIqBH

[Jingjing Zhai @jingjing19941]

@Ax_cordoba @McGillHaricots @mcgillu @PlantMcGill Congrats Henry!!

[Dr. Aimee Schulz @aimeejschulz]

The first chapter of my dissertation is now available on BioRxiv as a preprint! In collaboration with @ShengKaiHsu , @jingjing19941, and Brandon Monier, we developed a machine learning pipeline, reelGene, to leverage evolution for evaluating gene model annotations. A 🧵:

[Zhikai Liang @shanwai1234]

🪘 🪘 I am hiring one graduate student and one postdoc. Please RT!! E-mail me at [email protected] if you are interested.

[Dr. Merritt Khaipho-Burch @MerKhaiBurch]

My article is now out in @Nature!

It’s been ~1 year since my post about the flaws within 2 high-profile articles that claimed 33-68% increases in crop yield. Our paper describes common issues & suggests yield-testing criteria for future pubs. A thread🧵

https://t.co/gxmNkLc2ai