Yiran Meng

Excited to share that my postdoctoral work is finally out @NatureCellBio, thanks to all the great people @Simona66274422 @SThongjuea I've been working with @UniofOxford @MRC_WIMM. What a journey! nature.com/articles/s4155…

Equips Claude with skills for scientific research workflows github.com/K-Dense-AI/cla…

Teaching a new course @Stanford this quarter on explainable AI, motivated by neuroscience. I have curated a paper list 4 pages long (link in comment). What are your favorite papers on explainable AI/mechanistic interpretability that I am missing? Please comment or DM. thanks!

On arXiv, there’s a 200+ page overview book on AI and LLMs available. Covers pretty much all the fundamentals.

We are excited to announce the release of the @enGenome_srl VarChat track for hg38 and hg19. This track uses AI to search papers for variants, providing information such as its gene, HGVS nomenclature, and dbSNP rsID. Learn more at #022425" target="_blank" rel="nofollow noopener">genome.ucsc.edu/goldenPath/new….

1/🧵Excited to re-introduce Memento in (cell.com/cell/fulltext/…), a scalable method for differential analysis of scRNA-seq data. It provides first-in-class performance in statistical power and calibration for comparing differences in mean, variability, and gene correlation.👇

💡Thinking of using scRNA-seq to design antibody panels for spatial or single-cell profiling? Happy to launch Cytomarker, an interactive web-app and new antibody screening strategy to design and validate custom panels 1/6

📣Excited to share our new study in @NatureMedicine that @KexinHuang5 , @marinkazitnik, and I have been working on for the last four years! TxGNN is a graph-based foundation model for zero- shot drug repurposing that can find therapies for diseases with zero treatment options.

The integration of #cancer #biomarkers has revolutionized cancer treatment, allowing remarkable advancements in cancer therapeutics & the prognosis of cancer patients. This review paints the road ahead. sciencedirect.com/science/articl…

Neoantigen immunogenicity landscapes and evolution of tumor ecosystems during immunotherapy with nivolumab @NatureMedicine @GeneCollector @xrtGenomics nature.com/articles/s4159…

Coordinated, multicellular patterns of transcriptional variation that stratify patient cohorts are revealed by tensor decomposition go.nature.com/47ARizC

CellChat for systematic analysis of cell–cell communication from single-cell transcriptomics nature.com/articles/s4159…

The first and last review written in my postdoc days. I may have left academia, but it's always fun to talk about HSCs.🥸🥸

Long-read sequencing for 29 immune cell subsets (Transcriptomic Resource of Immune Cells using Long-read Sequencing, TRAILS) reveals disease-linked isoforms nature.com/articles/s4146…

Single-cell multi-ome regression models identify functional and disease-associated enhancers and enable chromatin potential analysis | Nature Genetics nature.com/articles/s4158… #Bioinformatics

Accurate and sensitive mutational signature analysis with MuSiCal | Nature Genetics nature.com/articles/s4158… #Bioinformatics

A neoadjuvant treatment regimen of anti-PD-L1 #immunotherapy followed by anti-PD-L1 + chemotherapy was well tolerated and led to pathologic response rate of 70% in patients with resectable #GastricCancer or GEJ adenocarcinoma @MyriamChalabi @NKI_nl nature.com/articles/s4159…

Mosaic integration and knowledge transfer of single-cell multimodal data with MIDAS nature.com/articles/s4158… #journals #feedly

CAR-T cell manufacturing: Major process parameters and next-generation strategies. A new review by Melanie Ayala Ceja, Yvonne Y. Chen and colleagues @UCLA hubs.la/Q02gDYfy0 #Immunotherapy #CancerFocus #leukemia #lymphoma

The word "cure" hasn't been associated with treating autoimmune diseases. Until now, from advances in understanding the immune system and building tolerance to specific antigens, it's in the realm of the possible nature.com/articles/d4158… new feature @Nature

Super-duper resolution it is! nature.com/articles/d4158…