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Publications

ralphi: a deep reinforcement learning framework for haplotype assembly.

Battistella E, Maheshwari A, Ekim B, Berger B, Popic V. ralphi: a deep reinforcement learning framework for haplotype assembly. bioRxiv : the preprint server for biology. 2025. doi:10.1101/2025.02.17.638151

Single-cell analyses reveal increased gene expression variability in human neurodevelopmental conditions.

Upadhya S, Klein JA, Nathanson A, Holton KM, Barrett LE. Single-cell analyses reveal increased gene expression variability in human neurodevelopmental conditions. American journal of human genetics. 2025. doi:10.1016/j.ajhg.2025.02.011

Functional diversification of dietary plant small molecules by the gut microbiome.

Kuziel GA, Lozano GL, Simian C, et al. Functional diversification of dietary plant small molecules by the gut microbiome. Cell. 2025. doi:10.1016/j.cell.2025.01.045

Cross-Ancestry Comparison of Aptamer and Antibody Proteomics Measures.

Nicholas JC, Katz DH, Tahir UA, et al. Cross-Ancestry Comparison of Aptamer and Antibody Proteomics Measures. Research square. 2025. doi:10.21203/rs.3.rs-5968391/v1

Dietary cysteine enhances intestinal stemness via CD8 T cell-derived IL-22.

Chi F, Zhang Q, Shay JES, et al. Dietary cysteine enhances intestinal stemness via CD8 T cell-derived IL-22. bioRxiv : the preprint server for biology. 2025. doi:10.1101/2025.02.15.638423

Hematologic dynamics during pregnancy and their association with obstetric complications: a retrospective cohort study.

Tozzo V, Petherbridge R, James K, et al. Hematologic dynamics during pregnancy and their association with obstetric complications: a retrospective cohort study. medRxiv : the preprint server for health sciences. 2025. doi:10.1101/2025.02.13.25322250

Deep Learning Derived Adipocyte Size Reveals Adipocyte Hypertrophy is under Genetic Control.

Jørsboe E, Kubitz P, Honecker J, et al. Deep Learning Derived Adipocyte Size Reveals Adipocyte Hypertrophy is under Genetic Control. medRxiv : the preprint server for health sciences. 2025. doi:10.1101/2025.02.11.25322053

KCTD20 suppression mitigates excitotoxicity in tauopathy patient organoids.

Berlind JE, Lai JD, Lie C, et al. KCTD20 suppression mitigates excitotoxicity in tauopathy patient organoids. Neuron. 2025. doi:10.1016/j.neuron.2025.02.001

Germline variants and mosaic chromosomal alterations affect COVID-19 vaccine immunogenicity.

Sonehara K, Uwamino Y, Saiki R, et al. Germline variants and mosaic chromosomal alterations affect COVID-19 vaccine immunogenicity. Cell genomics. 2025:100783. doi:10.1016/j.xgen.2025.100783

SplitFusion enables ultrasensitive gene fusion detection and reveals fusion variant-associated tumor heterogeneity.

Bian W, Zhang B, Song Z, et al. SplitFusion enables ultrasensitive gene fusion detection and reveals fusion variant-associated tumor heterogeneity. Patterns (New York, N.Y.). 2025;6(2):101174. doi:10.1016/j.patter.2025.101174