Interested in LLMs for genomic research but don't know where to start? looking for a review/survey to get started in this field? 👇👇😀 I am very excited to share that our review paper titled "To Transformers and Beyond: Large Language Models for the Genome" is now available as a preprint (arxiv.org/abs/2311.07621)! Our review unveils a revolution in genomics analysis with Genome LLMs. 🧬 🔍 What's Inside: ✅ The power & challenges of transformers in genomics. ✅ Cutting-edge models like HeynaDNA and scGPT & their impact. ✅ Deep dives into Enformer, DNABERT, and other Genome LLMs. 🌍 Why it Matters: 1. GPT-4's influence reshapes AI in genomics. Unmatched insights into transformers' role in genomics. 2. Critical analysis of new models, addressing interpretability, privacy, & computational needs. 3. Essential for computational biologists & computer scientists to navigate the future of genomic data analysis. This is a work led by the amazing PhD student, Mica Consens, in the lab! Also, a huge collaborative work with lots of field leaders @fabian_theis @genophoria @MKarimzade @michaelwainberg and Alan Moses! @UofT @VectorInst @UofTCompSci @UofT_LMP @UHN @pmcc_ai @UHNAIHUB

Did @10xGenomics just make newer versions of Cell Ranger open source? github.com/10XGenomics/cellr… (cc @sjackman, @luizirber). This is a huge win for open, transparent, and reproducible science if it’s the case!

Computational immunogenomic approaches to predict response to cancer immunotherapies nature.com/articles/s41571-0…

We are happy to announce release of FinnGen-UKBB meta-analysis results for 679 phenotypes at: public-metaresults-fg-ukbb.f… - enjoy browsing and downloading! #genomics #OpenScience

pyCirclize: a Python implementation of circlize github.com/moshi4/pyCirclize

veloVI enhances RNA velocity analysis with uncertainty quantification and extensibility by deep generative modeling of gene-specific transcriptional dynamics. @adamgayoso @PhilippWeiler7 @fabian_theis @YosefLab OA paper: nature.com/articles/s41592-0…

Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis | Nature Communications nature.com/articles/s41467-0… #Bioinformatics

Systematic transcriptional analysis of human cell lines for gene expression landscape and tumor representation🧬 nature.com/articles/s41467-0…

We're still learning about cancer immunotherapy —When more mutations don't lead to a better response nature.com/articles/s41588-0… @NatureGenet @PeterMKWestcott @LabJacks @isidrolauscher —Outstanding review of targeting innate pathways cell.com/immunity/fulltext/S… @ImmunityCP @jkagan1

Cellatlas: Universal preprocessing of single-cell genomics data biorxiv.org/content/10.1101/…

Automated Bioinformatics Analysis via AutoBA biorxiv.org/content/10.1101/…

Announcing Python in Excel techcommunity.microsoft.com/…

Do you want to build a hierarchy of cell types using a single-cell reference Atlases? and the.use that to map a new query and detect novel cell-types/states, or harmonize cell-types across multiple datasets ? Then check treeArches academic.oup.com/nargab/arti……

SCROAM: Highly accurate estimation of cell type abundance in bulk tissues based on single-cell reference and domain adaptive matching biorxiv.org/content/10.1101/…

New #JITC article: Efficacy of PD-(L)1 blockade monotherapy compared with PD-(L)1 blockade plus chemotherapy in first-line PD-L1-positive advanced lung adenocarcinomas: a cohort study jitc.bmj.com/content/11/7/e0… @ArielleElkrief @alessi_joao @XinAnnWang @charlesrudin @DrMarkAwad @AdamJSchoenfeld

In case it is of help. With tidyHeatmap (uses ComplexHM as engine): tbl |> heatmap( sample, symbol, count, scale = "row" ) |> layer_point( pvalue<0.05 ) |> layer_square(...) |> layer_arrow_up(...) github.com/stemangiola/tidyH…

Want to join a global consortium using #singlecell technologies to understand human diversity? Are #AI and #MachineLearning your #s? Come to Singapore! We're looking for leaders to drive v1 of the Human Diversity Atlas within the #HumanCellAtlas. tinyurl.com/5ccsfffz

EGFRm+ NSCLC treatment landscape Key assets, trials and companies segmented by treatment line and mutation type Some takeaways from this competitive space:

Clustering algorithms report clusters even when none exist. In single-cell RNA-Seq pipelines, novel cell types are often identified by clustering algorithms. Expanding on Kimes et al.'s work, we introduce significance analysis for single-cell RNA-Seq data: nature.com/articles/s41592-0…

This Fall I'll be teaching "quick data visualization" as part of a 1st year grad student seminar again for PBGG at UGA. The graphical abstract has 7 sections, but an 8th section on figure assembly has been added as well. Contents available on GitHub: github.com/cxli233/Online_R_…