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Publications

Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements.

Hu Y, Ma S, Kartha VK, et al. Single-cell multi-scale footprinting reveals the modular organization of DNA regulatory elements. bioRxiv : the preprint server for biology. 2023. doi:10.1101/2023.03.28.533945

Self-delivering CRISPR RNAs for AAV Co-delivery and Genome Editing .

Zhang H, Kelly K, Lee J, et al. Self-delivering CRISPR RNAs for AAV Co-delivery and Genome Editing . bioRxiv : the preprint server for biology. 2023. doi:10.1101/2023.03.20.533459

Integrative metabolomics differentiate coronary artery disease, peripheral artery disease, and venous thromboembolism risks.

Lee J, Gilliland T, Koyama S, et al. Integrative metabolomics differentiate coronary artery disease, peripheral artery disease, and venous thromboembolism risks. medRxiv : the preprint server for health sciences. 2023. doi:10.1101/2023.06.21.23291103

S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness.

Yurkovetskiy L, Egri S, Kurhade C, et al. S:D614G and S:H655Y are gateway mutations that act epistatically to promote SARS-CoV-2 variant fitness. bioRxiv : the preprint server for biology. 2023. doi:10.1101/2023.03.30.535005

Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial transcriptomics and optimal transport analysis.

Shiau C, Cao J, Gregory MT, et al. Therapy-associated remodeling of pancreatic cancer revealed by single-cell spatial transcriptomics and optimal transport analysis. bioRxiv : the preprint server for biology. 2023. doi:10.1101/2023.06.28.546848

Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation.

Mitchell W, Goeminne LJE, Tyshkovskiy A, et al. Multi-omics characterization of partial chemical reprogramming reveals evidence of cell rejuvenation. bioRxiv : the preprint server for biology. 2023. doi:10.1101/2023.06.30.546730

CHARR efficiently estimates contamination from DNA sequencing data.

Lu W, Gauthier LD, Poterba T, et al. CHARR efficiently estimates contamination from DNA sequencing data. bioRxiv : the preprint server for biology. 2023. doi:10.1101/2023.06.28.545801

Cross-kingdom anti-inflammatory effects of fungal melanin on airway epithelium by post-translational blockade of chemokine secretion.

Reedy JL, Crossen AJ, Ward RA, et al. Cross-kingdom anti-inflammatory effects of fungal melanin on airway epithelium by post-translational blockade of chemokine secretion. bioRxiv : the preprint server for biology. 2023. doi:10.1101/2023.03.28.534632

Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops.

Harada T, Kalfon J, Perez MW, et al. Leukemia core transcriptional circuitry is a sparsely interconnected hierarchy stabilized by incoherent feed-forward loops. bioRxiv : the preprint server for biology. 2023. doi:10.1101/2023.03.13.532438

MAPS: Pathologist-level cell type annotation from tissue images through machine learning.

Shaban M, Bai Y, Qiu H, et al. MAPS: Pathologist-level cell type annotation from tissue images through machine learning. bioRxiv : the preprint server for biology. 2023. doi:10.1101/2023.06.25.546474