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Publications

DNA methylation-environment interactions in the human genome.

Johnston RA, Aracena KA, Barreiro LB, Lea AJ, Tung J. DNA methylation-environment interactions in the human genome. eLife. 2024;12. doi:10.7554/eLife.89371

DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements.

DaSilva LF, Senan S, Patel ZM, et al. DNA-Diffusion: Leveraging Generative Models for Controlling Chromatin Accessibility and Gene Expression via Synthetic Regulatory Elements. bioRxiv : the preprint server for biology. 2024. doi:10.1101/2024.02.01.578352

Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Household Transmission during the Omicron Era in Massachusetts: A Prospective, Case-Ascertained Study using Genomic Epidemiology.

Banga J, Brock-Fisher T, Petros BA, et al. Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Household Transmission during the Omicron Era in Massachusetts: A Prospective, Case-Ascertained Study using Genomic Epidemiology. medRxiv : the preprint server for health sciences. 2024. doi:10.1101/2024.02.05.24302348

Associations of a multidimensional polygenic sleep health score and a sleep lifestyle index on health outcomes and their interaction in a clinical biobank.

Paz V, Wilcox H, Goodman M, et al. Associations of a multidimensional polygenic sleep health score and a sleep lifestyle index on health outcomes and their interaction in a clinical biobank. medRxiv : the preprint server for health sciences. 2024. doi:10.1101/2024.02.06.24302416

affinity maturation of the HIV-1 Env-binding domain of CD4.

Pan A, Bailey CC, Ou T, et al. affinity maturation of the HIV-1 Env-binding domain of CD4. bioRxiv : the preprint server for biology. 2024. doi:10.1101/2024.02.03.578630

Considerations for reporting variants in novel candidate genes identified during clinical genomic testing.

Chong JX, Berger SI, Baxter S, et al. Considerations for reporting variants in novel candidate genes identified during clinical genomic testing. bioRxiv : the preprint server for biology. 2024. doi:10.1101/2024.02.05.579012

An evolutionary learning-based method for identifying a circulating miRNA signature for breast cancer diagnosis prediction.

Sathipati SY, Tsai MJ, Aimalla N, et al. An evolutionary learning-based method for identifying a circulating miRNA signature for breast cancer diagnosis prediction. NAR genomics and bioinformatics. 2024;6(1):lqae022. doi:10.1093/nargab/lqae022

An evolutionary learning-based method for identifying a circulating miRNA signature for breast cancer diagnosis prediction.

Sathipati SY, Tsai MJ, Aimalla N, et al. An evolutionary learning-based method for identifying a circulating miRNA signature for breast cancer diagnosis prediction. NAR genomics and bioinformatics. 2024;6(1):lqae022. doi:10.1093/nargab/lqae022

Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer.

Tong X, Patel AS, Kim E, et al. Adeno-to-squamous transition drives resistance to KRAS inhibition in LKB1 mutant lung cancer. Cancer cell. 2024. doi:10.1016/j.ccell.2024.01.012

Phage-assisted evolution of highly active cytosine base editors with enhanced selectivity and minimal sequence context preference.

Zhang E, Neugebauer ME, Krasnow NA, Liu DR. Phage-assisted evolution of highly active cytosine base editors with enhanced selectivity and minimal sequence context preference. Nature communications. 2024;15(1):1697. doi:10.1038/s41467-024-45969-7