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Publications

Explainable modeling of single-cell perturbation data using attention and sparse dictionary learning.

Xu Y, Fleming S, Tegtmeyer M, McCarroll SA, Babadi M. Explainable modeling of single-cell perturbation data using attention and sparse dictionary learning. Cell systems. 2025:101245. doi:10.1016/j.cels.2025.101245

A short and sickly life. Multi-indicator analysis of an infant from a late antique Italian burial site (Piano della Civita, Artena, 3rd-5th cent CE).

Cecconi V, Nava A, Lugli F, et al. A short and sickly life. Multi-indicator analysis of an infant from a late antique Italian burial site (Piano della Civita, Artena, 3rd-5th cent CE). International journal of paleopathology. 2025;49:93-103. doi:10.1016/j.ijpp.2025.03.004

Variant-to-function approaches for adipose tissue: Insights into cardiometabolic disorders.

Metz S, Belanich JR, Claussnitzer M, Kilpeläinen TO. Variant-to-function approaches for adipose tissue: Insights into cardiometabolic disorders. Cell genomics. 2025:100844. doi:10.1016/j.xgen.2025.100844

K-mer analysis of long-read alignment pileups for structural variant genotyping.

English AC, Cunial F, Metcalf GA, Gibbs RA, Sedlazeck FJ. K-mer analysis of long-read alignment pileups for structural variant genotyping. Nature communications. 2025;16(1):3218. doi:10.1038/s41467-025-58577-w

Precision Omics Initiative Sweden (PROMISE) will integrate research with healthcare.

Kämpe A, Gudmundsson S, Walsh CP, et al. Precision Omics Initiative Sweden (PROMISE) will integrate research with healthcare. Nature medicine. 2025. doi:10.1038/s41591-025-03631-9

Convergent and clonotype-enriched mutations in the light chain drive affinity maturation of a public antibody.

Rao V, Sapse I, Cohn H, et al. Convergent and clonotype-enriched mutations in the light chain drive affinity maturation of a public antibody. bioRxiv : the preprint server for biology. 2025. doi:10.1101/2025.03.07.642041

Convergent and clonotype-enriched mutations in the light chain drive affinity maturation of a public antibody.

Rao V, Sapse I, Cohn H, et al. Convergent and clonotype-enriched mutations in the light chain drive affinity maturation of a public antibody. bioRxiv : the preprint server for biology. 2025. doi:10.1101/2025.03.07.642041

Inverted Alu repeats in loop-out exon skipping across hominoid evolution.

Denisko D, Kim J, Ku J, Zhao B, Lee EA. Inverted Alu repeats in loop-out exon skipping across hominoid evolution. bioRxiv : the preprint server for biology. 2025. doi:10.1101/2025.03.07.642063

Inverted Alu repeats in loop-out exon skipping across hominoid evolution.

Denisko D, Kim J, Ku J, Zhao B, Lee EA. Inverted Alu repeats in loop-out exon skipping across hominoid evolution. bioRxiv : the preprint server for biology. 2025. doi:10.1101/2025.03.07.642063

Sex and Depot Specific Adipocyte Proteome Profiling In Vivo via Intracellular Proximity Labeling.

Simonian TL, Meyer AS, Guo J, et al. Sex and Depot Specific Adipocyte Proteome Profiling In Vivo via Intracellular Proximity Labeling. Comprehensive Physiology. 2025;15(2):e70007. doi:10.1002/cph4.70007