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Publications

Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species.

Marin MG, Quinones-Olvera N, Wippel C, et al. Pitfalls of bacterial pan-genome analysis approaches: a case study of Mycobacterium tuberculosis and two less clonal bacterial species. Bioinformatics (Oxford, England). 2025;41(5). doi:10.1093/bioinformatics/btaf219

Patient agency and large language models in worldwide encoding of equity.

Armoundas AA, Loscalzo J. Patient agency and large language models in worldwide encoding of equity. NPJ digital medicine. 2025;8(1):258. doi:10.1038/s41746-025-01598-y

Celeste: A cloud-based genomics infrastructure with variant-calling pipeline suited for population-scale sequencing projects.

Siddiqui N, Lee B, Yi V, et al. Celeste: A cloud-based genomics infrastructure with variant-calling pipeline suited for population-scale sequencing projects. medRxiv : the preprint server for health sciences. 2025. doi:10.1101/2025.04.29.25326690

The multilayered transcriptional architecture of glioblastoma ecosystems.

Nomura M, Spitzer A, Johnson KC, et al. The multilayered transcriptional architecture of glioblastoma ecosystems. Nature genetics. 2025;57(5):1155-1167. doi:10.1038/s41588-025-02167-5

Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics.

Spitzer A, Johnson KC, Nomura M, et al. Deciphering the longitudinal trajectories of glioblastoma ecosystems by integrative single-cell genomics. Nature genetics. 2025;57(5):1168-1178. doi:10.1038/s41588-025-02168-4

Eclipse: a Python package for alignment of two or more nontargeted LC-MS metabolomics datasets.

Hitchcock DS, Krejci JN, Sturgeon CE, et al. Eclipse: a Python package for alignment of two or more nontargeted LC-MS metabolomics datasets. Bioinformatics (Oxford, England). 2025;41(6). doi:10.1093/bioinformatics/btaf290

Cross-sectional study of plasma phosphorylated tau 217 in persons without dementia.

Saari TT, Palviainen T, Hiltunen M, et al. Cross-sectional study of plasma phosphorylated tau 217 in persons without dementia. Alzheimer’s & dementia (Amsterdam, Netherlands). 2025;17(2):e70107. doi:10.1002/dad2.70107

Generation of a Biliary Tract Cancer Cell Line Atlas Identifies Molecular Subtypes and Therapeutic Targets.

Vijay V, Karisani N, Shi L, et al. Generation of a Biliary Tract Cancer Cell Line Atlas Identifies Molecular Subtypes and Therapeutic Targets. Cancer discovery. 2025;15(9):1858-1882. doi:10.1158/2159-8290.CD-24-1383

Three-dimensional genome landscape of primary human cancers.

Yost KE, Zhao Y, Hung KL, et al. Three-dimensional genome landscape of primary human cancers. Nature genetics. 2025;57(5):1189-1200. doi:10.1038/s41588-025-02188-0

X-linked competition - implications for human development and disease.

Boone PM, Buenaventura T, King JWD, Merkenschlager M. X-linked competition - implications for human development and disease. Nature reviews. Genetics. 2025;26(8):571-580. doi:10.1038/s41576-025-00840-3