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Publications

HiDDEN: a machine learning method for detection of disease-relevant populations in case-control single-cell transcriptomics data.

Goeva A, Dolan MJ, Luu J, et al. HiDDEN: a machine learning method for detection of disease-relevant populations in case-control single-cell transcriptomics data. Nature communications. 2024;15(1):9468. doi:10.1038/s41467-024-53666-8

Plasma protein-based organ-specific aging and mortality models unveil diseases as accelerated aging of organismal systems.

Goeminne LJE, Vladimirova A, Eames A, et al. Plasma protein-based organ-specific aging and mortality models unveil diseases as accelerated aging of organismal systems. Cell metabolism. 2024. doi:10.1016/j.cmet.2024.10.005

Clinical and Genomic Features of Classical and Basal Transcriptional Subtypes in Pancreatic Cancer.

Singh H, Xiu J, Kapner KS, et al. Clinical and Genomic Features of Classical and Basal Transcriptional Subtypes in Pancreatic Cancer. Clinical cancer research : an official journal of the American Association for Cancer Research. 2024;30(21):4932-4942. doi:10.1158/1078-0432.CCR-24-1164

Proteogenomic analysis integrated with electronic health records data reveals disease-associated variants in Black Americans.

Tahir UA, Barber JL, Cruz DE, et al. Proteogenomic analysis integrated with electronic health records data reveals disease-associated variants in Black Americans. The Journal of clinical investigation. 2024;134(21). doi:10.1172/JCI181802

Tumor-suppressive activities for pogo transposable element derived with KRAB domain via ribosome biogenesis restriction.

Tu Z, Bassal MA, Bell GW, et al. Tumor-suppressive activities for pogo transposable element derived with KRAB domain via ribosome biogenesis restriction. Molecular cell. 2024. doi:10.1016/j.molcel.2024.09.025

One-year employment outcome prediction after traumatic brain injury: A CENTER-TBI study.

Van Deynse H, Cools W, De Deken VJ, et al. One-year employment outcome prediction after traumatic brain injury: A CENTER-TBI study. Disability and health journal. 2024:101716. doi:10.1016/j.dhjo.2024.101716

Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations.

Lederer AR, Leonardi M, Talamanca L, et al. Statistical inference with a manifold-constrained RNA velocity model uncovers cell cycle speed modulations. Nature methods. 2024. doi:10.1038/s41592-024-02471-8

Dynamic evolution of fibroblasts revealed by single cell RNA sequencing of human pancreatic cancer.

Dimitrieva S, Harrison JM, Chang J, et al. Dynamic evolution of fibroblasts revealed by single cell RNA sequencing of human pancreatic cancer. Cancer research communications. 2024. doi:10.1158/2767-9764.CRC-23-0489

One-year employment outcome prediction after traumatic brain injury: A CENTER-TBI study.

Van Deynse H, Cools W, De Deken VJ, et al. One-year employment outcome prediction after traumatic brain injury: A CENTER-TBI study. Disability and health journal. 2024:101716. doi:10.1016/j.dhjo.2024.101716

A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features.

Klughammer J, Abravanel DL, Segerstolpe Åsa, et al. A multi-modal single-cell and spatial expression map of metastatic breast cancer biopsies across clinicopathological features. Nature medicine. 2024. doi:10.1038/s41591-024-03215-z