Jin Gu

Machine Learning & Precision Oncology

[Jin Gu @GLab_Bioinfo]

Our latest work for GBC by @NatureGenet : Multi-omic analysis of gallbladder cancer identifies distinct tumor microenvironments associated with disease progression https://t.co/hjaLqTJGWH with News & Views https://t.co/vgJLsaueAi

[ISCB News @iscb]

In case you missed the feature in our February newsletter: ISCB is happy to share this year’s ISCB 2025 award recipients!

Please join us in congratulating each of our 2025 awardees!

[DeepSeek @deepseek_ai]

🚀 Introducing NSA: A Hardware-Aligned and Natively Trainable Sparse Attention mechanism for ultra-fast long-context training & inference!

Core components of NSA:
• Dynamic hierarchical sparse strategy
• Coarse-grained token compression
• Fine-grained token selection

💡 With optimized design for modern hardware, NSA speeds up inference while reducing pre-training costs—without compromising performance. It matches or outperforms Full Attention models on general benchmarks, long-context tasks, and instruction-based reasoning.

�� For more details, check out our paper here: https://t.co/HJiqzwnUV7

[Jin Gu @GLab_Bioinfo]

The inference of candidate drivers is important for understanding and regulating the cell fate transitions. Congs to Prof. Zhang and Dr. Xi!🤠

[Xuegong @XuegongZ]

Happy Chinese New Year! I'm glad to share our new work on using biological knowledge to guide the design of interpretable AI models, for prioritizing potential driving regulators for cell state transitions. https://t.co/LnqY5HgQdN

[Jin Gu @GLab_Bioinfo]

According to our lab's experiences, edgeR is the most "stable" method for gene differential expression analysis for real biological datasets. Highly recommend.

[Xueyi Dong 董雪漪 @DongXueyi]

edgeR v4: powerful differential analysis of sequencing data with expanded functionality and improved support for small counts and larger datasets https://t.co/IPiHI5IPAg

[Jin Gu @GLab_Bioinfo]

@jsb_ucla It is still hard to draw a conclusion which one is the best, but we can avoid the poor ones😂

[ISCB News @iscb]

🚨 Submissions are open for #ISMBECCB2025 Proceedings!

Submit your full paper by January 23, 2025 and share your research with the global community.

🌐 Details: https://t.co/rUNL4FzFII

[Jin Gu @GLab_Bioinfo]

Dechipher the tumor cell dynamics after the drug treatment by aligning the unpaired cells https://t.co/fKa1bqitDD @GenomeBiology Dynamics is crucial for advancing "cybernetics" to biological systems🤔

[Human Cell Atlas @humancellatlas]

We are thrilled to share an HCA Collection of 40+ peer-reviewed papers in @NaturePortfolio shedding light on human development, healthy and disease biology and vital analytical tools. #HCA2024NatureCollection #HumanCellAtlas https://t.co/TKWn8CjXRd

[Jin Gu @GLab_Bioinfo]

Cellular atlases are unlocking the mysteries of the human body https://t.co/pDupiiMmUj We arew working on cell atlas techniques for atlas building & mapping

[Jin Gu @GLab_Bioinfo]

scTrace+: enhance the cell fate inference by integrating the lineage-tracing and multi-faceted transcriptomic similarity information https://t.co/3YATByk5vU Information integration for better inference!

[Jin Gu @GLab_Bioinfo]

A great resource for building a foundation model of cancer cells🤡

[bioRxiv Cancer Bio @biorxiv_cancer]

The Curated Cancer Cell Atlas: comprehensive characterisation of tumours at single-cell resolution https://t.co/1HmUt6vRJb #biorxiv_cancer

[Jin Gu @GLab_Bioinfo]

@RiyueSunnyBao Our scCancer/scCancer2 package may do it by only keeping the anchors in non-epithelial cells

[ISCB News @iscb]

📅 #RECOMB2025 is accepting submissions!

Key deadlines:
🔹 Abstract registration: Oct 16, 2024
🔹 Full paper submission: Oct 25, 2024

Submit soon to be a part of this great conference!

📌More info: https://t.co/WZugcuhH5T

[Jin Gu @GLab_Bioinfo]

Repost an updated resource for hepatocellular carcinoma (5573 bulk transcriptomes, 182,832 cells, and 69,352 spatial spots): HCCDB v2.0: Decompose Expression Variations by Single-cell RNA-seq and Spatial Transcriptomics in HCC https://t.co/mRmJgItHNJ

[Katherine Benjamin @kfbenjamin]

1/5 Very happy to share our work on flexible, multiscale cell type assignment for subcellular spatial transcriptomics, now in @Nature

https://t.co/ycqRLMpo9R

[Jin Gu @GLab_Bioinfo]

@jmuiuc I think microenvironment & niche have no obvious difference.... But, "cool" is very important for publishment🤠

[Xuegong @XuegongZ]

Our scFoundation has been finally published. It is currently one of the largest cellular models, pretrained on the transcriptomes of 50M single cells. Check out its performance on all the downstream tasks. https://t.co/6p8xXZkmGX

[Genomics Proteomics Bioinformatics @GPBees]

Special Issue "New Era of Large Cohort Studies" organized by @AniruddhPatelMD @wallacemwang @ZhaoDylan --publish your large cohort studies in GPB! https://t.co/QsSxRwUS19

[Jin Gu @GLab_Bioinfo]

Personalized cancer assembloid models for precision medicine @NatureComms . The mini-bulk and single cell omics joint analyses provide important information for the model evaluation and further optimization. https://t.co/I833jy0Y6a