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The Wild West of spike-in normalization go.nature.com/3XLUMw3

Optimal transport + variational inference sampling and generative modelling centred around divergences on path space a score-based annealing technique that crucially adapts both forward and backward dynamics in a diffusion model arxiv.org/abs/2307.01050

I'm so delighted that I shared our work with Mehdijoodaki and Costa Lab - @costalab.bsky.social at ISCB News #RSGDREAM 2024 in Madison this October on the disease trajectory detection using PILOT check out our paper embopress.org/doi/full/10.10… #SystemsBiology #singlecell #pathomics

Thrilled to share PHLOWER, which uses Hodge Laplacians to build trajectory-level embedding for inferring complex cellular differentiation trees from multimodal (RNA+ATAC) single-cell data by Mingbo Jitske Jansen with Rafael Kramann, MD PhD Christoph Kuppe tinyurl.com/yvu48j6k 1/7

Polars is between 10 and 100 times as fast as pandas for common operations and is actually one of the fastest DataFrame libraries overall. blog.jetbrains.com/pycharm/2024/0… via PyCharm, a JetBrains IDE?

Really nice to contribute to this study by Kleger Lab with Mina Shaigan - @minashaigan.bsky.social showing that a composite mutation (gene truncation in one locus and a enhancer deletion in the other locus) of the transcription factor Onecut1 causes early onset diabetes. cell.com/cell-reports/f…

Kleger Lab Mina Shaigan - @minashaigan.bsky.social This also builds up on previous work where we observed several GWAS hits affecting TF binding sites in enhancers of ONECUT1 nature.com/articles/s4159…

Transplantation of chemically induced pluripotent stem-cell-derived islets under abdominal anterior rectus sheath in a type 1 diabetes patient: Cell cell.com/cell/fulltext/…

Analyzing whole genome DNA methylation data? Our new method MethyLasso is out in NAR! It can help you identify regions with low or partial methylation (LMR, UMR, DMV, PMD, PMD) or differentially methylated regions (DMR) and was benchmarked against others doi.org/10.1093/nar/gk…

Keeping weight off may be stymied by fat cells’ ‘memory’ of obesity sciencenews.org/article/weight…

Look what I learned on Duolingo in 2024! #Duolingo365

Biological aging may not be driven by what we thought livescience.com/health/ageing/…

NetworkVI: Biologically Guided Variational Inference for Interpretable Multimodal Single-Cell Integration and Mechanistic Discovery biorxiv.org/content/10.110…

📢 Attending #ISMBECCB2025 in #Liverpool ? Don’t miss our #tutorial:"Computational approaches for cell-cell communication from #singlecell & #spatialtranscriptomics" in collaboration with CostaLab Costa Lab - @costalab.bsky.social 🗓 July 15 | 🕘 09:00 BST | 💻 Virtual 🔗 iscb.org/ismbeccb2025/r…

[1/5] Data often has inherent geometric and topological properties that can be exploited by machine learning algorithms. Below are four areas of machine learning that explore this important aspect.

Nature, Published online: 18 July 2025; doi:10.1038/s41586-025-09225-2Pathology-oriented multiplexing (PathoPlex) represents a framework for widespread access to multiplexed imaging and computational image analysis of clinical specimens at a relatively hig nature.com/articles/s4158…

🔬 Ever wonder how your immune system ages? 📊 We used single-cell multi-omics (RNA + ATAC) + bulk ATAC on PBMCs to build a cell-by-cell map of aging. 🧠 Find out which genes fade, which chromatin gates close and why some immune systems age slower. 👉 Poster C-482 #ISMBECCB2025